Microorganisms

23 pages, 3846 KiB

Open AccessArticle

Actinotignum schaalii: Relation to Concomitants and Connection to Patients’ Conditions in Polymicrobial Biofilms of Urinary Tract Catheters and Urines

by Iva Kotásková, Vít Syrovátka, Hana Obručová, Petra Vídeňská, Barbora Zwinsová, Veronika Holá, Eva Blaštíková, Filip Růžička and Tomáš Freiberger

Microorganisms 2021, 9(3), 669; https://doi.org/10.3390/microorganisms9030669 - 23 Mar 2021

Cited by 3 | Viewed by 4476

Abstract

Actinotignum schaalii is an emerging, opportunistic pathogen and its connection to non-infectious diseases and conditions, such as prostate or bladder cancer, or chronic inflammation has been proposed. Here, we analyzed 297 urine, ureteral and urinary catheter samples from 128 patients by Polymerase Chain [...] Read more.

Actinotignum schaalii is an emerging, opportunistic pathogen and its connection to non-infectious diseases and conditions, such as prostate or bladder cancer, or chronic inflammation has been proposed. Here, we analyzed 297 urine, ureteral and urinary catheter samples from 128 patients by Polymerase Chain Reaction followed by Denaturing Gradient Gel Electrophoresis and Sequencing (PCR-DGGE-S), and culture, and 29 of these samples also by 16S rRNA Illumina sequencing, to establish A. schaalii’s prevalence in urinary tract-related samples, its relation to other bacteria, and its potential association with patients’ conditions and samples’ characteristics. A. schaalii-positive samples were significantly more diverse than A. schaalii negative and between-group diversity was higher than intra-group. Propionimicrobium lymphophilum, Fusobacterium nucleatum, Veillonella sp., Morganella sp., and Aerococcus sp. were significantly more often present in A. schaalii-positive samples; thus, we suggest these species are A. schaalii’s concomitants, while Enterobacter and Staphylococcaceae were more often identified in A. schaalii-negative samples; therefore, we propose A. schaalii and these species are mutually exclusive. Additionally, a significantly higher A. schaalii prevalence in patients with ureter stricture associated hydronephrosis (p = 0.020) was noted. We suggest that A. schaalii could be an early polybacterial biofilm colonizer, together with concomitant species, known for pro-inflammatory features. Full article

(This article belongs to the Special Issue Clinical Implications of Microbial Biofilm)

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15 pages, 4272 KiB

Open AccessArticle

Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus

by Emilija Žukauskienė, Monika Šimoliūnienė, Lidija Truncaitė, Martynas Skapas, Algirdas Kaupinis, Mindaugas Valius, Rolandas Meškys and Eugenijus Šimoliūnas

Microorganisms 2021, 9(3), 668; https://doi.org/10.3390/microorganisms9030668 - 23 Mar 2021

Cited by 5 | Viewed by 2322

Abstract

A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed [...] Read more.

A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents. Full article

(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)

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16 pages, 5585 KiB

Open AccessArticle

Molecular Physiological Characterization of a High Heat Resistant Spore Forming Bacillus subtilis Food Isolate

by Zhiwei Tu, Peter Setlow, Stanley Brul and Gertjan Kramer

Microorganisms 2021, 9(3), 667; https://doi.org/10.3390/microorganisms9030667 - 23 Mar 2021

Cited by 14 | Viewed by 3506

Abstract

Bacterial endospores (spores) are among the most resistant living forms on earth. Spores of Bacillus subtilis A163 show extremely high resistance to wet heat compared to spores of laboratory strains. In this study, we found that spores of B. subtilis A163 were indeed [...] Read more.

Bacterial endospores (spores) are among the most resistant living forms on earth. Spores of Bacillus subtilis A163 show extremely high resistance to wet heat compared to spores of laboratory strains. In this study, we found that spores of B. subtilis A163 were indeed very wet heat resistant and released dipicolinic acid (DPA) very slowly during heat treatment. We also determined the proteome of vegetative cells and spores of B. subtilis A163 and the differences in these proteomes from those of the laboratory strain PY79, spores of which are much less heat resistant. This proteomic characterization identified 2011 proteins in spores and 1901 proteins in vegetative cells of B. subtilis A163. Surprisingly, spore morphogenic protein SpoVM had no homologs in B. subtilis A163. Comparing protein expression between these two strains uncovered 108 proteins that were differentially present in spores and 93 proteins differentially present in cells. In addition, five of the seven proteins on an operon in strain A163, which is thought to be primarily responsible for this strain’s spores high heat resistance, were also identified. These findings reveal proteomic differences of the two strains exhibiting different resistance to heat and form a basis for further mechanistic analysis of the high heat resistance of B. subtilis A163 spores. Full article

(This article belongs to the Special Issue Bacillus subtilis as a Model Organism to Study Basic Cell Processes)

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25 pages, 5860 KiB

Open AccessArticle

Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

by Niccolò Forin, Alfredo Vizzini, Federico Fainelli, Enrico Ercole and Barbara Baldan

Microorganisms 2021, 9(3), 666; https://doi.org/10.3390/microorganisms9030666 - 23 Mar 2021

Cited by 6 | Viewed by 3063

Abstract

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically [...] Read more.

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations. Full article

(This article belongs to the Special Issue Hotspots of Fungal Diversity)

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20 pages, 2669 KiB

Open AccessArticle

Transcriptomic Analysis Reveals Host miRNAs Correlated with Immune Gene Dysregulation during Fatal Disease Progression in the Ebola Virus Cynomolgus Macaque Disease Model

by Christopher P. Stefan, Catherine E. Arnold, Charles J. Shoemaker, Elizabeth E. Zumbrun, Louis A. Altamura, Christina E. Douglas, Cheryl L. Taylor-Howell, Amanda S. Graham, Korey L. Delp, Candace D. Blancett, Keersten M. Ricks, Scott P. Olschner, Joshua D. Shamblin, Suzanne E. Wollen, Justine M. Zelko, Holly A. Bloomfield, Thomas R. Sprague, Heather L. Esham and Timothy D. Minogue

Microorganisms 2021, 9(3), 665; https://doi.org/10.3390/microorganisms9030665 - 23 Mar 2021

Cited by 3 | Viewed by 2564

Abstract

Ebola virus is a continuing threat to human populations, causing a virulent hemorrhagic fever disease characterized by dysregulation of both the innate and adaptive host immune responses. Severe cases are distinguished by an early, elevated pro-inflammatory response followed by a pronounced lymphopenia with [...] Read more.

Ebola virus is a continuing threat to human populations, causing a virulent hemorrhagic fever disease characterized by dysregulation of both the innate and adaptive host immune responses. Severe cases are distinguished by an early, elevated pro-inflammatory response followed by a pronounced lymphopenia with B and T cells unable to mount an effective anti-viral response. The precise mechanisms underlying the dysregulation of the host immune system are poorly understood. In recent years, focus on host-derived miRNAs showed these molecules to play an important role in the host gene regulation arsenal. Here, we describe an investigation of RNA biomarkers in the fatal Ebola virus disease (EVD) cynomolgus macaque model. We monitored both host mRNA and miRNA responses in whole blood longitudinally over the disease course in these non-human primates (NHPs). Analysis of the interactions between these classes of RNAs revealed several miRNA markers significantly correlated with downregulation of genes; specifically, the analysis revealed those involved in dysregulated immune pathways associated with EVD. In particular, we noted strong interactions between the miRNAs hsa-miR-122-5p and hsa-miR-125b-5p with immunological genes regulating both B and T-cell activation. This promising set of biomarkers will be useful in future studies of severe EVD pathogenesis in both NHPs and humans and may serve as potential prognostic targets. Full article

(This article belongs to the Special Issue Hemorrhagic Fever Viruses: Pathogenesis and Countermeasures)

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11 pages, 456 KiB

Open AccessArticle

Are Faecal Microbiota Analyses on Species-Level Suitable Clinical Biomarkers? A Pilot Study in Subjects with Morbid Obesity

by Per G. Farup and Maria G. Maseng

Microorganisms 2021, 9(3), 664; https://doi.org/10.3390/microorganisms9030664 - 23 Mar 2021

Cited by 4 | Viewed by 2185

Abstract

Background: An abnormal faecal microbiota could be a causal factor for disease. This study evaluated a new method for faecal microbiota analysis in subjects with obesity and irritable bowel syndrome. Methods: The study had a matched case-control design. Forty-six subjects with morbid obesity [...] Read more.

Background: An abnormal faecal microbiota could be a causal factor for disease. This study evaluated a new method for faecal microbiota analysis in subjects with obesity and irritable bowel syndrome. Methods: The study had a matched case-control design. Forty-six subjects with morbid obesity (defined as BMI > 40 or >35 kg/m² with obesity-related complications) of whom 23 had irritable bowel syndrome (IBS), were compared with 46 healthy volunteers. The faecal microbiota was analysed with Precision Microbiome Profiling (PMP™) which quantified 104 bacteria species. The primary aim was comparisons between the cases and controls. Results: Two men and 44 women with a mean age of 43.6 years were included in each of the groups; BMI in the groups was (mean and SD) 41.9 (3.5) and 22.5 (1.5) kg/m², respectively. Seventeen bacterial species showed statistically significant differences between the groups after adjusting for multiple testing. In a post hoc analysis, the sensitivity and specificity were 78%. Alpha diversity was lower in the group with obesity. In subjects with morbid obesity, no clinically significant differences were seen between subjects with and without IBS or from before to six months after bariatric surgery. Conclusions: The results encourage further evaluation of the new microbiome profiling tool. Full article

(This article belongs to the Special Issue Gut Microbiota and Metabolism in Different Stages of Life and Health)

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11 pages, 1067 KiB

Open AccessReview

The Impact of Tick-Borne Diseases on the Bone

by Imran Farooq and Tara J. Moriarty

Microorganisms 2021, 9(3), 663; https://doi.org/10.3390/microorganisms9030663 - 23 Mar 2021

Cited by 4 | Viewed by 7622

Abstract

Tick-borne infectious diseases can affect many tissues and organs including bone, one of the most multifunctional structures in the human body. There is a scarcity of data regarding the impact of tick-borne pathogens on bone. The aim of this review was to survey [...] Read more.

Tick-borne infectious diseases can affect many tissues and organs including bone, one of the most multifunctional structures in the human body. There is a scarcity of data regarding the impact of tick-borne pathogens on bone. The aim of this review was to survey existing research literature on this topic. The search was performed using PubMed and Google Scholar search engines. From our search, we were able to find evidence of eight tick-borne diseases (Anaplasmosis, Ehrlichiosis, Babesiosis, Lyme disease, Bourbon virus disease, Colorado tick fever disease, Tick-borne encephalitis, and Crimean–Congo hemorrhagic fever) affecting the bone. Pathological bone effects most commonly associated with tick-borne infections were disruption of bone marrow function and bone loss. Most research to date on the effects of tick-borne pathogen infections on bone has been quite preliminary. Further investigation of this topic is warranted. Full article

(This article belongs to the Special Issue Advance in Tick-Borne Diseases Research)

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11 pages, 11848 KiB

Open AccessArticle

The Epithelial-to-Mesenchymal Transition-Like Process Induced by TGF-β1 Enhances Rubella Virus Binding and Infection in A549 Cells via the Smad Pathway

by Ngan Thi Kim Pham, Quang Duy Trinh, Kazuhide Takada, Chika Takano, Mari Sasano, Shoko Okitsu, Hiroshi Ushijima, Shihoko Komine-Aizawa and Satoshi Hayakawa

Microorganisms 2021, 9(3), 662; https://doi.org/10.3390/microorganisms9030662 - 23 Mar 2021

Cited by 6 | Viewed by 2338

Abstract

Virus–host cell interactions in rubella virus (RuV) are of great interest in current research in the field, as their mechanism is not yet well understood. By hypothesizing that the epithelial-to-mesenchymal transition (EMT) may play a role in RuV infection, this study aimed to [...] Read more.

Virus–host cell interactions in rubella virus (RuV) are of great interest in current research in the field, as their mechanism is not yet well understood. By hypothesizing that the epithelial-to-mesenchymal transition (EMT) may play a role in RuV infection, this study aimed to investigate the influence of TGF-β1-induced EMT of human lung epithelial A549 cells on the infectivity of RuV. A549 cells were cultured and treated with TGF-β1 for 1 to 2 days prior to virus infection (with a clinical strain). Viral infectivity was determined by flow cytometry analysis of cells harvested at 24 and 48 h post-infection (hpi) and by titration of supernatants collected at 48 hpi. The results showed that the percentages of the TGF-β1-treated A549 cells that were positive for RuV were at least twofold higher than those of the control, and the viral progeny titers in the supernatants collected at 48 hpi were significantly higher in the treatment group than in the control group. In addition, the virus binding assay showed a strong increase (more than threefold) in the percentages of RuV-positive cells, as determined by flow cytometry analysis and further confirmed by real-time PCR. Such an enhancement effect on RuV infectivity was abolished using LY364947 or SB431542, inhibitors of the TGF-β/Smad signaling pathway. The findings suggest that the TGF-β1-induced EMT-like process enhances RuV binding and infection in A549 cells via the Smad pathway. Further studies are necessary to identify possible proteins that facilitate viral binding and entry into treated cells. Full article

(This article belongs to the Special Issue Viral Infections Acquired in Pregnancy and through Breastfeeding: Novel Approaches to an Old Paradigm)

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12 pages, 2325 KiB

Open AccessArticle

Rapid Classification of Clostridioides difficile Strains Using MALDI-TOF MS Peak-Based Assay in Comparison with PCR-Ribotyping

by Adriana Calderaro, Mirko Buttrini, Monica Martinelli, Benedetta Farina, Tiziano Moro, Sara Montecchini, Maria Cristina Arcangeletti, Carlo Chezzi and Flora De Conto

Microorganisms 2021, 9(3), 661; https://doi.org/10.3390/microorganisms9030661 - 23 Mar 2021

Cited by 7 | Viewed by 2844

Abstract

Typing methods are needed for epidemiological tracking of new emerging and hypervirulent strains because of the growing incidence, severity and mortality of Clostridioides difficile infections (CDI). The aim of this study was the evaluation of a typing Matrix-Assisted Desorption/Ionization-Time of Flight Mass Spectrometry [...] Read more.

Typing methods are needed for epidemiological tracking of new emerging and hypervirulent strains because of the growing incidence, severity and mortality of Clostridioides difficile infections (CDI). The aim of this study was the evaluation of a typing Matrix-Assisted Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS (T-MALDI)) method for the rapid classification of the circulating C. difficile strains in comparison with polymerase chain reaction (PCR)-ribotyping results. Among 95 C. difficile strains, 10 ribotypes (PR1–PR10) were identified by PCR-ribotyping. In particular, 93.7% of the isolates (89/95) were grouped in five ribotypes (PR1–PR5). For T-MALDI, two classifying algorithm models (CAM) were tested: the first CAM involved all 10 ribotypes whereas the second one only the PR1–PR5 ribotypes. Better performance was obtained using the second CAM: recognition capability of 100%, cross-validation of 96.6% and agreement of 98.4% (60 correctly typed strains, limited to PR1–PR5 classification, out of 61 examined strains) with PCR-ribotyping results. T-MALDI seems to represent an alternative to PCR-ribotyping in terms of reproducibility, set up time and costs, as well as a useful tool in epidemiological investigation for the detection of C. difficile clusters (either among CAM included ribotypes or out-of-CAM ribotypes) involved in outbreaks. Full article

(This article belongs to the Special Issue Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogenic Microorganisms)

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12 pages, 1061 KiB

Open AccessArticle

Variability in Bacteriophage and Antibiotic Sensitivity in Serial Pseudomonas aeruginosa Isolates from Cystic Fibrosis Airway Cultures over 12 Months

by Isaac Martin, Dervla T. D. Kenna, Sandra Morales, Eric W. F. W. Alton and Jane C. Davies

Microorganisms 2021, 9(3), 660; https://doi.org/10.3390/microorganisms9030660 - 22 Mar 2021

Cited by 6 | Viewed by 2409

Abstract

Antibiotic treatment for Pseudomonas aeruginosa (Pa) in cystic fibrosis is limited in efficacy and may lead to multi-drug resistance (MDR). Alternatives such as bacteriophages are being explored but well designed, and controlled trials are crucial. The rational selection of patients with bacteriophage susceptible [...] Read more.

Antibiotic treatment for Pseudomonas aeruginosa (Pa) in cystic fibrosis is limited in efficacy and may lead to multi-drug resistance (MDR). Alternatives such as bacteriophages are being explored but well designed, and controlled trials are crucial. The rational selection of patients with bacteriophage susceptible infections is required for both safety and efficacy monitoring. We questioned whether bacteriophage susceptibility profiles were constant or variable over time, variability having been reported with antibiotics. Serial Pa isolates (n = 102) from 24 chronically infected cystic fibrosis (CF) patients over one year were investigated with plaque and antibiotic disc diffusion assays. Variable number tandem repeat (VNTR) analysis identified those patients with >1 isolate. A median (range) of 4 (3–6) isolates/patient were studied. Twenty-one (87.5%) individuals had a single VNTR type; three (12.5%) had two VNTR types at different times. Seventy-five percent of isolates were sensitive to bacteriophage at ≥ 1 concentration; 50% of isolates were antibiotic multidrug resistant. Serial isolates, even when representing a single VNTR type, varied in sensitivity to both bacteriophages and antibiotics. The rates of sensitivity to bacteriophage supports the development of this therapy; however, the variability in response has implications for the selection of patients in future trials which must be on the basis of current, not past, isolate testing. Full article

(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)

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17 pages, 10522 KiB

Open AccessArticle

New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

by Elias Asimakis, Panagiota Stathopoulou, Apostolis Sapounas, Kanjana Khaeso, Costas Batargias, Mahfuza Khan and George Tsiamis

Microorganisms 2021, 9(3), 659; https://doi.org/10.3390/microorganisms9030659 - 22 Mar 2021

Cited by 6 | Viewed by 2703

Abstract

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) [...] Read more.

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology. Full article

(This article belongs to the Special Issue Microbiota in Insects)

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15 pages, 8623 KiB

Open AccessArticle

First Detection of Bartonella spp. in Small Mammals from Rice Storage and Processing Facilities in Myanmar and Sri Lanka

by Inga Böge, Martin Pfeffer, Nyo M. Htwe, Pyai P. Maw, Siriwardana Rampalage Sarathchandra, Vincent Sluydts, Anna P. Piscitelli, Jens Jacob and Anna Obiegala

Microorganisms 2021, 9(3), 658; https://doi.org/10.3390/microorganisms9030658 - 22 Mar 2021

Cited by 13 | Viewed by 2473

Abstract

(1) Background: Bartonella spp. are zoonotic bacteria with small mammals as main reservoirs. Bartonella spp. prevalence in small mammals from Myanmar and Sri Lanka are yet unknown. (2) Methods: Small mammals were snap trapped in Sri Lanka and Myanmar in urban surroundings. Spleens-derived [...] Read more.

(1) Background: Bartonella spp. are zoonotic bacteria with small mammals as main reservoirs. Bartonella spp. prevalence in small mammals from Myanmar and Sri Lanka are yet unknown. (2) Methods: Small mammals were snap trapped in Sri Lanka and Myanmar in urban surroundings. Spleens-derived DNA was screened for Bartonella spp. using conventional PCR based on three target genes. Positive samples were sequenced. (3) Results: 994 small mammals were collected comprising 6 species: Bandicota bengalensis, Bandicota indica, Rattus exulans, Rattus rattus, Mus booduga, and Suncus murinus. In Myanmar, the Bartonella prevalence in Bandicoot rats (68.47%) was higher than in Rattus rattus (41.67%), Rattus exulans (21.33%), and Suncus murinus (3.64%). Furthermore the prevalence in Myanmar (34%, n = 495) was twice as high as in Sri Lanka (16%, n = 499). In Sri Lanka, Bartonella spp. occurred almost exclusively in R. rattus. In Myanmar, Bartonella kosoyi was mainly detected (56%), followed by Bartonella sp. KM2529 (15%), Bartonella sp. SE-Bart D (12%) and Bartonella henselae (1%). In Sri Lanka, B. phoceensis (60%) and Bartonella sp. KM2581 (33%) were predominant. (4) Conclusions: Bartonella spp. were detected in all investigated small mammal species from Myanmar and Sri Lanka for the first time. Bartonella kosoyi and B. henselae are zoonotic. As these small mammals originated from urban settlements, human bartonellosis seems likely to occur. Full article

(This article belongs to the Special Issue Bartonella Infections in Humans and Animals)

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22 pages, 2832 KiB

Open AccessArticle

Bacterial Dimethylsulfoniopropionate Biosynthesis in the East China Sea

by Ji Liu, Yunhui Zhang, Jingli Liu, Haohui Zhong, Beth T. Williams, Yanfen Zheng, Andrew R. J. Curson, Chuang Sun, Hao Sun, Delei Song, Brett Wagner Mackenzie, Ana Bermejo Martínez, Jonathan D. Todd and Xiao-Hua Zhang

Microorganisms 2021, 9(3), 657; https://doi.org/10.3390/microorganisms9030657 - 22 Mar 2021

Cited by 13 | Viewed by 3280

Abstract

Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules. Recently, many marine heterotrophic bacteria were shown to produce DMSP, but few studies have combined culture-dependent and independent techniques to study their abundance, distribution, diversity and activity in seawater or sediment environments. Here [...] Read more.

Dimethylsulfoniopropionate (DMSP) is one of Earth’s most abundant organosulfur molecules. Recently, many marine heterotrophic bacteria were shown to produce DMSP, but few studies have combined culture-dependent and independent techniques to study their abundance, distribution, diversity and activity in seawater or sediment environments. Here we investigate bacterial DMSP production potential in East China Sea (ECS) samples. Total DMSP (DMSPt) concentration in ECS seawater was highest in surface waters (SW) where phytoplankton were most abundant, and it decreased with depth to near bottom waters. However, the percentage of DMSPt mainly apportioned to bacteria increased from the surface to the near bottom water. The highest DMSP concentration was detected in ECS oxic surface sediment (OSS) where phytoplankton were not abundant. Bacteria with the genetic potential to produce DMSP and relevant biosynthesis gene transcripts were prominent in all ECS seawater and sediment samples. Their abundance also increased with depth and was highest in the OSS samples. Microbial enrichments for DMSP-producing bacteria from sediment and seawater identified many novel taxonomic groups of DMSP-producing bacteria. Different profiles of DMSP-producing bacteria existed between seawater and sediment samples and there are still novel DMSP-producing bacterial groups to be discovered in these environments. This study shows that heterotrophic bacteria significantly contribute to the marine DMSP pool and that their contribution increases with water depth and is highest in seabed surface sediment where DMSP catabolic potential is lowest. Furthermore, distinct bacterial groups likely produce DMSP in seawater and sediment samples, and many novel producing taxa exist, especially in the sediment. Full article

(This article belongs to the Section Environmental Microbiology)

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20 pages, 2599 KiB

Open AccessArticle

Cranberry Proanthocyanidins and Dietary Oligosaccharides Synergistically Modulate Lactobacillus plantarum Physiology

by Ezgi Özcan, Michelle R. Rozycki and David A. Sela

Microorganisms 2021, 9(3), 656; https://doi.org/10.3390/microorganisms9030656 - 22 Mar 2021

Cited by 11 | Viewed by 3084

Abstract

Plant-based foods contain bioactive compounds such as polyphenols that resist digestion and potentially benefit the host through interactions with their resident microbiota. Based on previous observations, we hypothesized that the probiotic Lactobacillus plantarum interacts with cranberry polyphenols and dietary oligosaccharides to synergistically impact [...] Read more.

Plant-based foods contain bioactive compounds such as polyphenols that resist digestion and potentially benefit the host through interactions with their resident microbiota. Based on previous observations, we hypothesized that the probiotic Lactobacillus plantarum interacts with cranberry polyphenols and dietary oligosaccharides to synergistically impact its physiology. In this study, L. plantarum ATCC BAA-793 was grown on dietary oligosaccharides, including cranberry xyloglucans, fructooligosaccharides, and human milk oligosaccharides, in conjunction with proanthocyanidins (PACs) extracted from cranberries. As a result, L. plantarum exhibits a differential physiological response to cranberry PACs dependent on the carbohydrate source and polyphenol fraction introduced. Of the two PAC extracts evaluated, the PAC1 fraction contains higher concentrations of PACs and increased growth regardless of the oligosaccharide, whereas PAC2 positively modulates its growth during xyloglucan metabolism. Interestingly, fructooligosaccharides (FOS) are efficiently utilized in the presence of PAC1, as this L. plantarum strain does not utilize this substrate typically. Relative to glucose, oligosaccharide metabolism increases the ratio of secreted acetic acid to lactic acid. The PAC2 fraction differentially increases this ratio during cranberry xyloglucan fermentation compared with PAC1. The global transcriptome links the expression of putative polyphenol degradation genes and networks and metabolic phenotypes. Full article

(This article belongs to the Special Issue An Update on Lactobacillus)

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16 pages, 1760 KiB

Open AccessArticle

Critical Role of 3′-Downstream Region of pmrB in Polymyxin Resistance in Escherichia coli BL21(DE3)

by Fuzhou Xu, Atsushi Hinenoya, Ximin Zeng, Xing-Ping Li, Ziqiang Guan and Jun Lin

Microorganisms 2021, 9(3), 655; https://doi.org/10.3390/microorganisms9030655 - 22 Mar 2021

Cited by 2 | Viewed by 2517

Abstract

Polymyxins, such as colistin and polymyxin B, are the drugs used as a last resort to treat multidrug-resistant Gram-negative bacterial infections in humans. Increasing colistin resistance has posed a serious threat to human health, warranting in-depth mechanistic research. In this study, using a [...] Read more.

Polymyxins, such as colistin and polymyxin B, are the drugs used as a last resort to treat multidrug-resistant Gram-negative bacterial infections in humans. Increasing colistin resistance has posed a serious threat to human health, warranting in-depth mechanistic research. In this study, using a functional cloning approach, we examined the molecular basis of colistin resistance in Escherichia coli BL21(DE3). Five transformants with inserts ranging from 3.8 to 10.7 kb displayed significantly increased colistin resistance, three of which containing pmrB locus and two containing pmrD locus. Stepwise subcloning indicated that both the pmrB with a single G361A mutation and at least a 103 bp downstream region of pmrB are essential for conferring colistin resistance. Analysis of the mRNA level and stability showed that the length of the downstream region drastically affected the pmrB mRNA level but not its half-life. Lipid A analysis, by mass spectrometry, revealed that the constructs containing pmrB with a longer downstream region (103 or 126 bp) have charge-altering l-4-aminoarabinose (Ara4N) and phosphoethanolamine (pEtN) modifications in lipid A, which were not observed in both vector control and the construct containing pmrB with an 86 bp downstream region. Together, the findings from this study indicate that the 3′-downstream region of pmrB is critical for the PmrB-mediated lipid A modifications and colistin resistance in E. coli BL21(DE3), suggesting a novel regulatory mechanism of PmrB-mediated colistin resistance in E. coli. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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12 pages, 878 KiB

Open AccessArticle

Adhesion Properties, Biofilm Forming Potential, and Susceptibility to Disinfectants of Contaminant Wine Yeasts

by Giorgia Perpetuini, Alessio Pio Rossetti, Noemi Battistelli, Giuseppe Arfelli and Rosanna Tofalo

Microorganisms 2021, 9(3), 654; https://doi.org/10.3390/microorganisms9030654 - 22 Mar 2021

Cited by 16 | Viewed by 2762

Abstract

In this study, yeasts isolated from filter membranes used for the quality control of bottled wines were identified and tested for their resistance to some cleaning agents and potassium metabisulphite, adhesion to polystyrene and stainless-steel surfaces, and formation of a thin round biofilm, [...] Read more.

In this study, yeasts isolated from filter membranes used for the quality control of bottled wines were identified and tested for their resistance to some cleaning agents and potassium metabisulphite, adhesion to polystyrene and stainless-steel surfaces, and formation of a thin round biofilm, referred to as a MAT. A total of 40 strains were identified by rRNA internal transcribed spacer (ITS) restriction analysis and sequence analysis of D1/D2 domain of 26S rRNA gene. Strains belong to Pichia manshurica (12), Pichia kudriavzevii (9), Pichia membranifaciens (1), Candida sojae (6), Candida parapsilosis (3), Candida sonorensis (1), Lodderomyces elongisporus (2), Sporopachydermia lactativora (3), and Clavispora lusitaniae (3) species. Regarding the adhesion properties, differences were observed among species. Yeasts preferred planktonic state when tested on polystyrene plates. On stainless-steel supports, adhered cells reached values of about 6 log CFU/mL. MAT structures were formed only by yeasts belonging to the Pichia genus. Yeast species showed different resistance to sanitizers, with peracetic acid being the most effective and active at low concentrations, with minimum inhibitory concentration (MIC) values ranging from 0.08% (v/v) to 1% (v/v). C. parapsilosis was the most sensible species. Data could be exploited to develop sustainable strategies to reduce wine contamination and establish tailored sanitizing procedures. Full article

(This article belongs to the Special Issue Microbial Dynamics in Wine Production)

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14 pages, 728 KiB

Open AccessArticle

Synergistic Effects of Nisin, Lysozyme, Lactic Acid, and Citricidal^TM for Enhancing Pressure-Based Inactivation of Bacillus amyloliquefaciens, Geobacillus stearothermophilus, and Bacillus atrophaeus Endospores

by Sadiye Aras, Niamul Kabir, Sabrina Wadood, Jyothi George, Shahid Chowdhury and Aliyar Cyrus Fouladkhah

Microorganisms 2021, 9(3), 653; https://doi.org/10.3390/microorganisms9030653 - 21 Mar 2021

Cited by 3 | Viewed by 2719

Abstract

The inactivation of bacterial endospores continues to be the main curtailment for further adoption of high-pressure processing in intrastate, interstate, and global food commerce. The current study investigated the effects of elevated hydrostatic pressure for the inactivation of endospore suspension of three indicator [...] Read more.

The inactivation of bacterial endospores continues to be the main curtailment for further adoption of high-pressure processing in intrastate, interstate, and global food commerce. The current study investigated the effects of elevated hydrostatic pressure for the inactivation of endospore suspension of three indicator spore-forming bacteria of concern to the food industry. Additionally, the effects of four bacteriocin/bactericidal compounds were studied for augmenting the decontamination efficacy of the treatment. Elevated hydrostatic pressure at 650 MPa and at 50 °C was applied for 0 min (untreated control) and for 3, 7, and 11 min with and without 50K IU of nisin, 224 mg/L lysozyme, 1% lactic acid, and 1% Citricidal^TM. The results were statistically analyzed using Tukey- and Dunnett’s-adjusted ANOVA. Under the condition of our experiments, we observed that a well-designed pressure treatment synergized with mild heat and bacteriocin/bactericidal compounds could reduce up to >4 logs CFU/mL (i.e., >99.99%) of bacterial endospores. Additions of nisin and lysozyme were able, to a great extent, to augment (p < 0.05) the decontamination efficacy of pressure-based treatments against Bacillus amyloliquefaciens and Bacillus atrophaeus, while exhibiting no added benefit (p ≥ 0.05) for reducing endospores of Geobacillus stearothermophilus. The addition of lactic acid, however, was efficacious for augmenting the pressure-based reduction of bacterial endospores of the three microorganisms. Full article

(This article belongs to the Special Issue Frontiers in Public Health Microbiology: Prevention of Foodborne and Waterborne Diseases in the Changing Climate)

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22 pages, 5054 KiB

Open AccessArticle

In-Situ Metatranscriptomic Analyses Reveal the Metabolic Flexibility of the Thermophilic Anoxygenic Photosynthetic Bacterium Chloroflexus aggregans in a Hot Spring Cyanobacteria-Dominated Microbial Mat

by Shigeru Kawai, Joval N. Martinez, Mads Lichtenberg, Erik Trampe, Michael Kühl, Marcus Tank, Shin Haruta, Arisa Nishihara, Satoshi Hanada and Vera Thiel

Microorganisms 2021, 9(3), 652; https://doi.org/10.3390/microorganisms9030652 - 21 Mar 2021

Cited by 12 | Viewed by 6585

Abstract

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the [...] Read more.

Chloroflexus aggregans is a metabolically versatile, thermophilic, anoxygenic phototrophic member of the phylum Chloroflexota (formerly Chloroflexi), which can grow photoheterotrophically, photoautotrophically, chemoheterotrophically, and chemoautotrophically. In hot spring-associated microbial mats, C. aggregans co-exists with oxygenic cyanobacteria under dynamic micro-environmental conditions. To elucidate the predominant growth modes of C. aggregans, relative transcription levels of energy metabolism- and CO₂ fixation-related genes were studied in Nakabusa Hot Springs microbial mats over a diel cycle and correlated with microscale in situ measurements of O₂ and light. Metatranscriptomic analyses indicated two periods with different modes of energy metabolism of C. aggregans: (1) phototrophy around midday and (2) chemotrophy in the early morning hours. During midday, C. aggregans mainly employed photoheterotrophy when the microbial mats were hyperoxic (400–800 µmol L⁻¹ O₂). In the early morning hours, relative transcription peaks of genes encoding uptake hydrogenase, key enzymes for carbon fixation, respiratory complexes as well as enzymes for TCA cycle and acetate uptake suggest an aerobic chemomixotrophic lifestyle. This is the first in situ study of the versatile energy metabolism of C. aggregans based on gene transcription patterns. The results provide novel insights into the metabolic flexibility of these filamentous anoxygenic phototrophs that thrive under dynamic environmental conditions. Full article

(This article belongs to the Special Issue Advances in the Biology of Phototrophic Bacteria)

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17 pages, 2580 KiB

Open AccessArticle

Genetic but No Phenotypic Associations between Biocide Tolerance and Antibiotic Resistance in Escherichia coli from German Broiler Fattening Farms

by Alice Roedel, Szilvia Vincze, Michaela Projahn, Uwe Roesler, Caroline Robé, Jens Andre Hammerl, Matthias Noll, Sascha Al Dahouk and Ralf Dieckmann

Microorganisms 2021, 9(3), 651; https://doi.org/10.3390/microorganisms9030651 - 21 Mar 2021

Cited by 21 | Viewed by 3559

Abstract

Biocides are frequently applied as disinfectants in animal husbandry to prevent the transmission of drug-resistant bacteria and to control zoonotic diseases. Concerns have been raised, that their use may contribute to the selection and persistence of antimicrobial-resistant bacteria. Especially, extended-spectrum β-lactamase- and AmpC [...] Read more.

Biocides are frequently applied as disinfectants in animal husbandry to prevent the transmission of drug-resistant bacteria and to control zoonotic diseases. Concerns have been raised, that their use may contribute to the selection and persistence of antimicrobial-resistant bacteria. Especially, extended-spectrum β-lactamase- and AmpC β-lactamase-producing Escherichia coli have become a global health threat. In our study, 29 ESBL-/AmpC-producing and 64 NON-ESBL-/AmpC-producing E.coli isolates from three German broiler fattening farms collected in 2016 following regular cleaning and disinfection were phylogenetically characterized by whole genome sequencing, analyzed for phylogenetic distribution of virulence-associated genes, and screened for determinants of and associations between biocide tolerance and antibiotic resistance. Of the 30 known and two unknown sequence types detected, ST117 and ST297 were the most common genotypes. These STs are recognized worldwide as pandemic lineages causing disease in humans and poultry. Virulence determinants associated with extraintestinal pathogenic E.coli showed variable phylogenetic distribution patterns. Isolates with reduced biocide susceptibility were rarely found on the tested farms. Nine isolates displayed elevated MICs and/or MBCs of formaldehyde, chlorocresol, peroxyacetic acid, or benzalkonium chloride. Antibiotic resistance to ampicillin, trimethoprim, and sulfamethoxazole was most prevalent. The majority of ESBL-/AmpC-producing isolates carried bla_CTX-M (55%) or bla_CMY-2 (24%) genes. Phenotypic biocide tolerance and antibiotic resistance were not interlinked. However, biocide and metal resistance determinants were found on mobile genetic elements together with antibiotic resistance genes raising concerns that biocides used in the food industry may lead to selection pressure for strains carrying acquired resistance determinants to different antimicrobials. Full article

(This article belongs to the Special Issue Antimicrobial Resistance and Molecular Tracing of Foodborne Pathogens)

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20 pages, 4202 KiB

Open AccessArticle

Isolation and Characterization of a Novel Lytic Bacteriophage against the K2 Capsule-Expressing Hypervirulent Klebsiella pneumoniae Strain 52145, and Identification of Its Functional Depolymerase

by Botond Zsombor Pertics, Alysia Cox, Adrienn Nyúl, Nóra Szamek, Tamás Kovács and György Schneider

Microorganisms 2021, 9(3), 650; https://doi.org/10.3390/microorganisms9030650 - 21 Mar 2021

Cited by 28 | Viewed by 3636

Abstract

Klebsiella pneumoniae is among the leading bacteria that cause nosocomial infections. The capsule of this Gram-negative bacterium is a dominant virulence factor, with a prominent role in defense and biofilm formation. Bacteriophages, which are specific for one bacterial strain and its capsule type, [...] Read more.

Klebsiella pneumoniae is among the leading bacteria that cause nosocomial infections. The capsule of this Gram-negative bacterium is a dominant virulence factor, with a prominent role in defense and biofilm formation. Bacteriophages, which are specific for one bacterial strain and its capsule type, can evoke the lysis of bacterial cells, aided by polysaccharide depolymerase enzymes. In this study, we isolated and characterized a bacteriophage against the nosocomial K. pneumoniae 52145 strain with K2 capsular serotype. The phage showed a narrow host range and stable lytic activity, even when exposed to different temperatures or detergents. Preventive effect of the phage in a nasal colonization model was investigated in vivo. Phlyogenetic analysis showed that the newly isolated Klebsiella phage B1 belongs to the Webervirus genus in Drexlerviridae family. We identified the location of the capsule depolymerase gene of the new phage, which was amplified, cloned, expressed, and purified. The efficacy of the recombinant B1dep depolymerase was tested by spotting on K. pneumoniae strains and it was confirmed that the extract lowers the thickness of the bacterium lawn as it degrades the protective capsule on bacterial cells. As K. pneumoniae strains possessing the K2 serotype have epidemiological importance, the B1 phage and its depolymerase are promising candidates for use as possible antimicrobial agents. Full article

(This article belongs to the Special Issue Bacteriophages and Their Components as Promising and Alternative Tools for the Control of Bacterial Pathogens)

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19 pages, 706 KiB

Open AccessReview

Epidemiological Aspects of Crimean-Congo Hemorrhagic Fever in Western Europe: What about the Future?

by Aránzazu Portillo, Ana M. Palomar, Paula Santibáñez and José A. Oteo

Microorganisms 2021, 9(3), 649; https://doi.org/10.3390/microorganisms9030649 - 21 Mar 2021

Cited by 44 | Viewed by 7150

Abstract

Crimean-Congo hemorrhagic fever virus (CCHFV) is an arthropod-borne virus (arbovirus), mainly transmitted by ticks, belonging to the genus Orthonairovirus (family Nairoviridae, order Bunyavirales). CCHFV causes a potentially severe, or even fatal, human disease, and it is widely distributed in Africa, Asia, [...] Read more.

Crimean-Congo hemorrhagic fever virus (CCHFV) is an arthropod-borne virus (arbovirus), mainly transmitted by ticks, belonging to the genus Orthonairovirus (family Nairoviridae, order Bunyavirales). CCHFV causes a potentially severe, or even fatal, human disease, and it is widely distributed in Africa, Asia, eastern Europe and, more recently, in South-western Europe. Until a few years ago, no cases of Crimean-Congo hemorrhagic fever (CCHF) had been reported in western Europe, with the exception of several travel-associated cases. In 2010, the CCHFV was reported for the first time in South-western Europe when viral RNA was obtained from Hyalomma lusitanicum ticks collected from deer in Cáceres (Spain). Migratory birds from Africa harboring CCHFV-infected ticks and flying to Spain appear to have contributed to the establishment of the virus (genotype III, Africa-3) in this country. In addition, the recent findings in a patient and in ticks from deer and wild boar of viral sequences similar to those from eastern Europe (genotype V, Europe-1), raise the possibility of the introduction of CCHFV into Spain through the animal trade, although the arrival by bird routes cannot be ruled out (Africa-4 has been also recently detected). The seropositive rates of animals detected in regions of South-western Spain suggest an established cycle of tick-host-tick in certain areas, and the segment reassortment detected in the sequenced virus from one patient evidences a high ability to adaptation of the virus. Different ixodid tick genera can be vectors and reservoirs of the virus, although Hyalomma spp. are particularly relevant for its maintenance. This tick genus is common in Mediterranean region but it is currently spreading to new areas, partly due to the climate change and movement of livestock or wild animals. Although to a lesser extent, travels with our pets (and their ticks) may be also a factor to be considered. As a consequence, the virus is expanding from the Balkan region to Central Europe and, more recently, to Western Europe where different genotypes are circulating. Thus, seven human cases confirmed by molecular methods have been reported in Spain from 2016 to August 2020, three of them with a fatal outcome. A One Health approach is essential for the surveillance of fauna and vector populations to assess the risk for humans and animals. We discuss the risk of CCHFV causing epidemic outbreaks in Western Europe. Full article

(This article belongs to the Special Issue Hemorrhagic Fever Viruses: Pathogenesis and Countermeasures)

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15 pages, 2988 KiB

Open AccessArticle

Genome Sequencing of five Lacticaseibacillus Strains and Analysis of Type I and II Toxin-Antitoxin System Distribution

by Alessia Levante, Camilla Lazzi, Giannis Vatsellas, Dimitris Chatzopoulos, Vasilis S. Dionellis, Periklis Makrythanasis, Erasmo Neviani and Claudia Folli

Microorganisms 2021, 9(3), 648; https://doi.org/10.3390/microorganisms9030648 - 21 Mar 2021

Cited by 8 | Viewed by 2193

Abstract

The analysis of bacterial genomes is a potent tool to investigate the distribution of specific traits related to the ability of surviving in particular environments. Among the traits associated with the adaptation to hostile conditions, toxin–antitoxin (TA) systems have recently gained attention in [...] Read more.

The analysis of bacterial genomes is a potent tool to investigate the distribution of specific traits related to the ability of surviving in particular environments. Among the traits associated with the adaptation to hostile conditions, toxin–antitoxin (TA) systems have recently gained attention in lactic acid bacteria. In this work, genome sequences of Lacticaseibacillus strains of dairy origin were compared, focusing on the distribution of type I TA systems homologous to Lpt/RNAII and of the most common type II TA systems. A high number of TA systems have been identified spread in all the analyzed strains, with type I TA systems mainly located on plasmid DNA. The type II TA systems identified in these strains highlight the diversity of encoded toxins and antitoxins and their organization. This study opens future perspectives on the use of genomic data as a resource for the study of TA systems distribution and prevalence in microorganisms of industrial relevance. Full article

(This article belongs to the Special Issue Toxin–Antitoxin Systems in Pathogenic and Non-Pathogenic Bacteria)

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12 pages, 3126 KiB

Open AccessCommunication

Dynamics of Gut Microbiota Recovery after Antibiotic Exposure in Young and Old Mice (A Pilot Study)

by Daniel Laubitz, Katri Typpo, Monica Midura-Kiela, Clairessa Brown, Albert Barberán, Fayez K. Ghishan and Pawel R. Kiela

Microorganisms 2021, 9(3), 647; https://doi.org/10.3390/microorganisms9030647 - 20 Mar 2021

Cited by 15 | Viewed by 3139

Abstract

Antibiotics have improved survival from previously deadly infectious diseases. Antibiotics alter the microbial composition of the gut microbiota, and these changes are associated with diminished innate immunity and decline in cognitive function in older adults. The composition of the human microbiota changes with [...] Read more.

Antibiotics have improved survival from previously deadly infectious diseases. Antibiotics alter the microbial composition of the gut microbiota, and these changes are associated with diminished innate immunity and decline in cognitive function in older adults. The composition of the human microbiota changes with age over the human lifespan. In this pilot study, we sought to identify if age is associated with differential recovery of the microbiota after antibiotic exposure. Using 16S rRNA gene sequencing, we compared recovery of the gut microbiota after the 10-day broad-spectrum antibiotic treatment in wild-type C57BL/six young and older mice. Immediately after antibiotic cessation, as expected, the number of ASVs, representing taxonomic richness, in both young and older mice significantly declined from the baseline. Mice were followed up to 6 months after cessation of the single 10-day antibiotic regimen. The Bray-Curtis index recovered within 20 days after antibiotic cessation in young mice, whereas in older mice the microbiota did not fully recover during the 6-months of follow-up. Bifidobacterium, Dubosiella, Lachnospiraceae_NK4A136_group became dominant in older mice, whereas in young mice, the bacteria were more evenly distributed, with only one dominant genus of Anaeroplasma. From 45 genera that became extinct after antibiotic treatment in young mice, 31 (68.9%) did not recover by the end of the study. In older mice, from 36 extinct genera, 27 (75%) did not recover. The majority of the genera that became extinct and never recovered belonged to Firmicutes phylum and Clostridiales family. In our study, age was a factor associated with the long-term recovery of the gut microbiota after the 10-day antibiotic treatment. Full article

(This article belongs to the Special Issue Gut Microbiome and Aging)

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18 pages, 2774 KiB

Open AccessArticle

In Silico Prediction and Analysis of Unusual Lantibiotic Resistance Operons in the Genus Corynebacterium

by Oliver Goldbeck, Dominik Weixler, Bernhard J. Eikmanns and Christian U. Riedel

Microorganisms 2021, 9(3), 646; https://doi.org/10.3390/microorganisms9030646 - 19 Mar 2021

Cited by 5 | Viewed by 2811

Abstract

Post-translationally modified, (methyl-)lanthionine-containing peptides are produced by several Gram-positive bacteria. These so-called lantibiotics have potent activity against various bacterial pathogens including multidrug-resistant strains and are thus discussed as alternatives to antibiotics. Several naturally occurring mechanisms of resistance against lantibiotics have been described for [...] Read more.

Post-translationally modified, (methyl-)lanthionine-containing peptides are produced by several Gram-positive bacteria. These so-called lantibiotics have potent activity against various bacterial pathogens including multidrug-resistant strains and are thus discussed as alternatives to antibiotics. Several naturally occurring mechanisms of resistance against lantibiotics have been described for bacteria, including cell envelope modifications, ABC-transporters, lipoproteins and peptidases. Corynebacterium species are widespread in nature and comprise important pathogens, commensals as well as environmentally and biotechnologically relevant species. Yet, little is known about lantibiotic biosynthesis and resistance in this genus. Here, we present a comprehensive in silico prediction of lantibiotic resistance traits in this important group of Gram-positive bacteria. Our analyses suggest that enzymes for cell envelope modification, peptidases as well as ABC-transporters involved in peptide resistance are widely distributed in the genus. Based on our predictions, we analyzed the susceptibility of six Corynebacterium species to nisin and found that those without dedicated resistance traits are more susceptible and unable to adapt to higher concentrations. In addition, we were able to identify lantibiotic resistance operons encoding for peptidases, ABC-transporters and two-component systems with an unusual predicted structure that are conserved in the genus Corynebacterium. Heterologous expression shows that these operons indeed confer resistance to the lantibiotic nisin. Full article

(This article belongs to the Special Issue Genetics and Physiology of Corynebacteria)

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14 pages, 1665 KiB

Open AccessArticle

Yield Losses Caused by Barley Yellow Dwarf Virus-PAV Infection in Wheat and Barley: A Three-Year Field Study in South-Eastern Australia

by Narelle Nancarrow, Mohammad Aftab, Grant Hollaway, Brendan Rodoni and Piotr Trębicki

Microorganisms 2021, 9(3), 645; https://doi.org/10.3390/microorganisms9030645 - 19 Mar 2021

Cited by 23 | Viewed by 4513

Abstract

Barley yellow dwarf virus (BYDV) is transmitted by aphids and significantly reduces the yield and quality of cereals worldwide. Four experiments investigating the effects of barley yellow dwarf virus-PAV (BYDV-PAV) infection on either wheat or barley were conducted over three years (2015, 2017, [...] Read more.

Barley yellow dwarf virus (BYDV) is transmitted by aphids and significantly reduces the yield and quality of cereals worldwide. Four experiments investigating the effects of barley yellow dwarf virus-PAV (BYDV-PAV) infection on either wheat or barley were conducted over three years (2015, 2017, and 2018) under typical field conditions in South-Eastern Australia. Plants inoculated with BYDV-PAV using viruliferous aphids (Rhopalosiphum padi) were harvested at maturity then grain yield and yield components were measured. Compared to the non-inoculated control, virus infection severely reduced grain yield by up to 84% (1358 kg/ha) in wheat and 64% (1456 kg/ha) in barley. The yield component most affected by virus infection was grain number, which accounted for a large proportion of the yield loss. There were no significant differences between early (seedling stage) and later (early-tillering stage) infection for any of the parameters measured (plant height, biomass, yield, grain number, 1000-grain weight or grain size) for either wheat or barley. Additionally, this study provides an estimated yield loss value, or impact factor, of 0.91% (72 kg/ha) for each one percent increase in natural BYDV-PAV background infection. Yield losses varied considerably between experiments, demonstrating the important role of cultivar and environmental factors in BYDV epidemiology and highlighting the importance of conducting these experiments under varying conditions for specific cultivar–vector–virus combinations. Full article

(This article belongs to the Special Issue Plant Viruses: From Ecology to Control)

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18 pages, 5124 KiB

Open AccessArticle

Exogenous Probiotics Improve Fermentation Quality, Microflora Phenotypes, and Trophic Modes of Fermented Vegetable Waste for Animal Feed

by Guilin Du, Jiping Shi, Jingxian Zhang, Zhiguo Ma, Xiangcen Liu, Chenyang Yuan, Baoguo Zhang, Zhanying Zhang and Mark D. Harrison

Microorganisms 2021, 9(3), 644; https://doi.org/10.3390/microorganisms9030644 - 19 Mar 2021

Cited by 10 | Viewed by 2837

Abstract

The fermentation of leaf vegetable waste to produce animal feed reduces the environmental impact of vegetable production and transforms leaf vegetable waste into a commodity. We investigated the effect of exogenous probiotics and lignocellulose enzymes on the quality and microbial community of fermented [...] Read more.

The fermentation of leaf vegetable waste to produce animal feed reduces the environmental impact of vegetable production and transforms leaf vegetable waste into a commodity. We investigated the effect of exogenous probiotics and lignocellulose enzymes on the quality and microbial community of fermented feed (FF) produced from cabbage waste. The addition of exogenous probiotics resulted in increased crude protein (CP) content (p < 0.05), better odor (moderate organic acid and ethanol, with low ammonia-N, p < 0.05), and a lower relative abundance (RA) of pathogens (below 0.4%, p < 0.05) in FF, compared to without. With the addition of exogenous probiotics, only Pediococcus and Saccharomyces were enriched and symbiotic in FF; these were the keystone taxa to reduce the abundance of aerobic, form-biofilms, and pathogenic microorganisms, resulting in an efficient anaerobic fermentation system characterized by facultative anaerobic and Gram-positive bacterial communities, and undefined saprotroph fungal communities. Thus, inoculation of vegetable waste fermentation with exogenous probiotics is a promising strategy to enhance the biotransformation of vegetable waste into animal feed. Full article

(This article belongs to the Special Issue Yeasts and Lactic Acid Bacteria for Food Innovation and Byproduct Valorization)

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23 pages, 5605 KiB

Open AccessArticle

Relative Contribution of Each Component of the French Ante-Mortem Surveillance System for Bovine Tuberculosis in Its Overall Sensitivity

by Valentine Guétin-Poirier, Julie Rivière and Barbara Dufour

Microorganisms 2021, 9(3), 643; https://doi.org/10.3390/microorganisms9030643 - 19 Mar 2021

Viewed by 1804

Abstract

The aim of this study was to assess the contribution to the sensitivity of the French ante-mortem surveillance system for bovine tuberculosis in cattle of each of the system’s components (periodic screening, epidemiological investigations, and screening exchanged animals), on a local scale defined [...] Read more.

The aim of this study was to assess the contribution to the sensitivity of the French ante-mortem surveillance system for bovine tuberculosis in cattle of each of the system’s components (periodic screening, epidemiological investigations, and screening exchanged animals), on a local scale defined by administrative areas. These components were individually assessed in previous studies by scenario tree modeling. We used scenario tree modeling at the herd level and combined the results to evaluate the overall sensitivity of the ante-mortem surveillance system. The probability to detect at least one infected herd was consistent with the location of the outbreaks detected in 2016. In areas with a high apparent incidence, the probability of an infected herd to be detected was satisfactory (for an infected herd there was a 100% probability to be detected over a two-year period). Periodic screening was the most important component for the overall sensitivity in infected areas. In other areas, where periodic screening had stopped, tracing-on epidemiological investigation was the most sensitive component of the system. Screening exchanged animals had a negligible part in the overall sensitivity of the surveillance system. Full article

(This article belongs to the Special Issue Animal Tuberculosis Due to Mycobacterium tuberculosis complex Members)

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13 pages, 3181 KiB

Open AccessArticle

High Efficacy of Saliva in Detecting SARS-CoV-2 by RT-PCR in Adults and Children

by Michael Huber, Peter Werner Schreiber, Thomas Scheier, Annette Audigé, Roberto Buonomano, Alain Rudiger, Dominique L. Braun, Gerhard Eich, Dagmar I. Keller, Barbara Hasse, Jürg Böni, Christoph Berger, Huldrych F. Günthard, Amapola Manrique and Alexandra Trkola

Microorganisms 2021, 9(3), 642; https://doi.org/10.3390/microorganisms9030642 - 19 Mar 2021

Cited by 34 | Viewed by 4707

Abstract

Rising demands for repetitive SARS-CoV-2 screens and mass testing necessitate additional test strategies. Saliva may serve as an alternative to nasopharyngeal swab (NPS) as its collection is simple, non-invasive and amenable for mass- and home testing, but its rigorous validation, particularly in children, [...] Read more.

Rising demands for repetitive SARS-CoV-2 screens and mass testing necessitate additional test strategies. Saliva may serve as an alternative to nasopharyngeal swab (NPS) as its collection is simple, non-invasive and amenable for mass- and home testing, but its rigorous validation, particularly in children, is missing. We conducted a large-scale head-to-head comparison of SARS-CoV-2 detection by RT-PCR in saliva and NPS of 1270 adults and children reporting to outpatient test centers and an emergency unit. In total, 273 individuals were tested positive for SARS-CoV-2 in either NPS or saliva. SARS-CoV-2 RT-PCR results in the two specimens showed a high agreement (overall percent agreement = 97.8%). Despite lower viral loads in the saliva of both adults and children, detection of SARS-CoV-2 in saliva fared well compared to NPS (positive percent agreement = 92.5%). Importantly, in children, SARS-CoV-2 infections were more often detected in saliva than NPS (positive predictive value = 84.8%), underlining that NPS sampling in children can be challenging. The comprehensive parallel analysis reported here establishes saliva as a generally reliable specimen for the detection of SARS-CoV-2, with particular advantages for testing children, that is readily applicable to increase and facilitate repetitive and mass testing in adults and children. Full article

(This article belongs to the Section Medical Microbiology)

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16 pages, 1369 KiB

Open AccessArticle

A Mouse Model Suggests That Heart Failure and Its Common Comorbidity Sleep Fragmentation Have No Synergistic Impacts on the Gut Microbiome

by Olfat Khannous-Lleiffe, Jesse R. Willis, Ester Saus, Ignacio Cabrera-Aguilera, Isaac Almendros, Ramon Farré, David Gozal, Nuria Farré and Toni Gabaldón

Microorganisms 2021, 9(3), 641; https://doi.org/10.3390/microorganisms9030641 - 19 Mar 2021

Cited by 4 | Viewed by 3484

Abstract

Heart failure (HF) is a common condition associated with a high rate of hospitalizations and adverse outcomes. HF is characterized by impairments of either the cardiac ventricular filling, ejection of blood capacity or both. Sleep fragmentation (SF) involves a series of short sleep [...] Read more.

Heart failure (HF) is a common condition associated with a high rate of hospitalizations and adverse outcomes. HF is characterized by impairments of either the cardiac ventricular filling, ejection of blood capacity or both. Sleep fragmentation (SF) involves a series of short sleep interruptions that lead to fatigue and contribute to cognitive impairments and dementia. Both conditions are known to be associated with increased inflammation and dysbiosis of the gut microbiota. In the present study, mice were distributed into four groups, and subjected for four weeks to either HF, SF, both HF and SF, or left unperturbed as controls. We used 16S metabarcoding to assess fecal microbiome composition before and after the experiments. Evidence for distinct alterations in several bacterial groups and an overall decrease in alpha diversity emerged in HF and SF treatment groups. Combined HF and SF conditions, however, showed no synergism, and observed changes were not always additive, suggesting preliminarily that some of the individual effects of either HF or SF cancel each other out when applied concomitantly. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Animal/Human Health and Disease)

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20 pages, 5340 KiB

Open AccessArticle

Isolation and Characterization of Potential Starter Cultures from the Nigerian Fermented Milk Product nono

by Olakunle Fagbemigun, Gyu-Sung Cho, Niels Rösch, Erik Brinks, Katrin Schrader, Wilhelm Bockelmann, Folarin A. Oguntoyinbo and Charles M. A. P. Franz

Microorganisms 2021, 9(3), 640; https://doi.org/10.3390/microorganisms9030640 - 19 Mar 2021

Cited by 11 | Viewed by 3393

Abstract

Nono, an important traditional fermented dairy food produced from cow’s milk in Nigeria, was studied for microbial diversity and for starter culture development for industrial production. On the basis of a polyphasic approach, including phenotypic and genotypic methods such as 16S rRNA [...] Read more.

Nono, an important traditional fermented dairy food produced from cow’s milk in Nigeria, was studied for microbial diversity and for starter culture development for industrial production. On the basis of a polyphasic approach, including phenotypic and genotypic methods such as 16S rRNA gene sequencing, repetitive element PCR (rep-PCR) fingerprinting metagenomics, and whole genome sequencing, we identified Lactobacillus (Lb.) helveticus, Limosilactobacillus (L.) fermentum, Lb. delbrueckii, and Streptococcus (S.) thermophilus as predominant bacterial species involved with milk fermentation during traditional nono production in Nigeria, while the predominant yeast species in nono was identified as Saccharomyces cerevisiae. Using metagenomics, Shigella and potential pathogens such as enterobacteria were detected at low levels of abundance. Strains of the predominant lactic acid bacteria (LAB) were selected for starter cultures combination on the basis of their capacities for rapid growth in milk and reduction of pH below 4.5 and their gelling characteristic, which was demonstrated noticeably only by the S. thermophilus strains. Whole genome sequence analysis of selected bacterial strains showed the largest assembled genome size to be 2,169,635 bp in Lb. helveticus 314, while the smallest genome size was 1,785,639 bp in Lb. delbrueckii 328M. Genes encoding bacteriocins were not detected in all the strains, but all the LAB possessed genes potentially involved in diacetyl production and citrate metabolism. These bacteria isolated from nono can thus be used to improve the microbial safety quality of nono in Nigeria, in addition to improving technological parameters such as gelling viscosity, palatability, and product consistency. Full article

(This article belongs to the Special Issue Beneficial and Detrimental Microorganisms Occurring in Fermented Foods)

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Microorganisms, Volume 9, Issue 3 (March 2021) – 205 articles

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