Microorganisms

16 pages, 6676 KiB

Open AccessArticle

Multiplexed High-Throughput Serological Assay for Human Enteroviruses

by Niila V. V. Saarinen, Jussi Lehtonen, Riitta Veijola, Johanna Lempainen, Mikael Knip, Heikki Hyöty, Olli H. Laitinen and Vesa P. Hytönen

Microorganisms 2020, 8(6), 963; https://doi.org/10.3390/microorganisms8060963 - 26 Jun 2020

Cited by 5 | Viewed by 3789 | Correction

Abstract

Immunological assays detecting antibodies against enteroviruses typically use a single enterovirus serotype as antigen. This limits the ability of such assays to detect antibodies against different enterovirus types and to detect possible type-specific variation in antibody responses. We set out to develop a [...] Read more.

Immunological assays detecting antibodies against enteroviruses typically use a single enterovirus serotype as antigen. This limits the ability of such assays to detect antibodies against different enterovirus types and to detect possible type-specific variation in antibody responses. We set out to develop a multiplexed assay for simultaneous detection of antibodies against multiple enterovirus and rhinovirus types encompassing all human infecting species. Seven recombinant VP1 proteins from enteroviruses EV-A to EV-D and rhinoviruses RV-A to RV-C species were produced. Using Meso Scale Diagnostics U-PLEX platform we were able to study antibody reactions against these proteins as well as non-structural enterovirus proteins in a single well with 140 human serum samples. Adults had on average 33-fold stronger antibody responses to these antigens (p < 10⁻¹¹) compared to children, but children had less cross-reactivity between different enterovirus types. The results suggest that this new high-throughput assay offers clear benefits in the evaluation of humoral enterovirus immunity in children, giving more exact information than assays that are based on a single enterovirus type as antigen. Full article

(This article belongs to the Special Issue Enterovirus and Type 1 Diabetes)

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12 pages, 1257 KiB

Open AccessArticle

Antibacterial Activity of Four Plant Extracts Extracted from Traditional Chinese Medicinal Plants against Listeria monocytogenes, Escherichia coli, and Salmonella enterica subsp. enterica serovar Enteritidis

by R.L. McMurray, M.E.E. Ball, M.M. Tunney, N. Corcionivoschi and C. Situ

Microorganisms 2020, 8(6), 962; https://doi.org/10.3390/microorganisms8060962 - 26 Jun 2020

Cited by 13 | Viewed by 5043

Abstract

The worldwide ethnobotanical use of four investigated plants indicates antibacterial properties. The aim of this study was to screen and determine significant antibacterial activity of four plant extracts in vitro and in a poultry digest model. Using broth microdilution, the concentrations at which [...] Read more.

The worldwide ethnobotanical use of four investigated plants indicates antibacterial properties. The aim of this study was to screen and determine significant antibacterial activity of four plant extracts in vitro and in a poultry digest model. Using broth microdilution, the concentrations at which four plant extracts inhibited Listeria monocytogenes, Salmonella enteritidis, and Escherichia coli over 24 h was determined. Agrimonia pilosa Ledeb, Iris domestica (L.) Goldblatt and Mabb, Anemone chinensis Bunge, and Smilax glabra Roxb all exhibited a minimum inhibitory concentration (MIC) of 62.5 mg/L and a minimum bactericidal concentration (MBC) of 500 mg/L against one pathogen. A. pilosa Ledeb was the most effective against L. monocytogenes and E. coli with the exception of S. enteritidis, for which A. chinensis Bunge was the most effective. Time–kills of A. pilosa Ledeb and A. chinensis Bunge against L. monocytogenes, E. coli and S. enteritidis incubated in poultry cecum were used to determine bactericidal activity of these plant extracts. A. chinensis Bunge, significantly reduced S. enteritidis by ≥ 99.99% within 6 h. A. pilosa Ledeb exhibited effective significant bactericidal activity within 4 h against L. monocytogenes and E. coli. This paper highlights the potential of these plant extracts to control pathogens commonly found in the poultry gastrointestinal tract. Full article

(This article belongs to the Special Issue Control and Intervention Strategies to Reduce Foodborne Pathogens in Animal Agriculture)

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12 pages, 2289 KiB

Open AccessArticle

The Bacterial Gut Microbiota of Schoolchildren from High and Low Socioeconomic Status: A Study in an Urban Area of Makassar, Indonesia

by Aldian I. Amaruddin, Firdaus Hamid, Jan Pieter R. Koopman, Munawir Muhammad, Eric A.T. Brienen, Lisette van Lieshout, Anoecim R. Geelen, Sitti Wahyuni, Ed J. Kuijper, Erliyani Sartono, Maria Yazdanbakhsh and Romy D. Zwittink

Microorganisms 2020, 8(6), 961; https://doi.org/10.3390/microorganisms8060961 - 26 Jun 2020

Cited by 13 | Viewed by 5210

Abstract

To understand the relationship between the gut microbiota and the health profile of Indonesians, it is important to elucidate the characteristics of the bacterial communities that prevail in this population. To this end, we profiled the faecal bacterial community of 140 Indonesian schoolchildren [...] Read more.

To understand the relationship between the gut microbiota and the health profile of Indonesians, it is important to elucidate the characteristics of the bacterial communities that prevail in this population. To this end, we profiled the faecal bacterial community of 140 Indonesian schoolchildren in urban Makassar. The core microbiota of Indonesian schoolchildren consisted of Bifidobacterium, Collinsella, and multiple members of the Lachnospiraceae and Ruminicoccaceae families, but the relative abundance of these taxa varied greatly among children. Socioeconomic status (SES) was the main driver for differences in microbiota composition. Multiple bacterial genera were differentially abundant between high and low SES children, including Bifidobacterium, Lactobacillus, Prevotella, and Escherichia-Shigella. In addition, the microbiota of high SES children was less diverse and strongly associated with body mass index (BMI). In low SES children, helminth infection was prevalent and positively associated with Olsenella, Enterohabdus, Lactobacillus, and Mogibacterium abundance, while negatively associated with relative abundance of Prevotella. Protozoa infection was also prevalent, and positively associated with Rikenellaceae, while it was negatively associated with the relative abundance of Romboutsia and Prevotella. In conclusion, Indonesian schoolchildren living in urban Makassar share a core microbiota, but their microbiota varies in diversity and relative abundance of specific bacterial taxa depending on socioeconomic status, nutritional status, and intestinal parasites infection. Full article

(This article belongs to the Special Issue Gut Microbiota Dysbiosis)

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13 pages, 2626 KiB

Open AccessArticle

Antimicrobial and Antibiofilm Activities of Probiotic Lactobacilli on Antibiotic-Resistant Proteus mirabilis

by Mona Shaaban, Ola A. Abd El-Rahman, Bashair Al-Qaidi and Hossam M. Ashour

Microorganisms 2020, 8(6), 960; https://doi.org/10.3390/microorganisms8060960 - 26 Jun 2020

Cited by 22 | Viewed by 4338

Abstract

The emergence of biofilm-forming, multi-drug-resistant (MDR) Proteus mirabilis infections is a serious threat that necessitates non-antibiotic therapies. Antibiotic susceptibility and biofilm-forming activity of P. mirabilis isolates from urine samples were assessed by disc diffusion and crystal violet assays, respectively. Antimicrobial activities of probiotic [...] Read more.

The emergence of biofilm-forming, multi-drug-resistant (MDR) Proteus mirabilis infections is a serious threat that necessitates non-antibiotic therapies. Antibiotic susceptibility and biofilm-forming activity of P. mirabilis isolates from urine samples were assessed by disc diffusion and crystal violet assays, respectively. Antimicrobial activities of probiotic Lactobacilli were evaluated by agar diffusion. Antibiofilm and anti-adherence activities were evaluated by crystal violet assays. While most P. mirabilis isolates were antibiotic-resistant to varying degrees, isolate P14 was MDR (resistant to ceftazidime, cefotaxime, amoxicillin-clavulanic acid, imipenem, ciprofloxacin, and amikacin) and formed strong biofilms. Cultures and cell-free supernatants of Lactobacillus casei and Lactobacillus reuteri exhibited antimicrobial and antibiofilm activities. The 1/16 concentration of untreated supernatants of L. casei and L. reuteri significantly reduced mature biofilm formation and adherence of P14 by 60% and 72%, respectively (for L. casei), and by 73% each (for L. reuteri). The 1/8 concentration of pH-adjusted supernatants of L. casei and L. reuteri significantly reduced mature biofilm formation and adherence of P14 by 39% and 75%, respectively (for L. casei), and by 73% each (for L. reuteri). Scanning electron microscopy (SEM) confirmed eradication of P14’s biofilm by L. casei. L. casei and L. reuteri could be utilized to combat Proteus-associated urinary tract infections. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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17 pages, 4416 KiB

Open AccessArticle

Clinical Detection of Chronic Rhinosinusitis through Next-Generation Sequencing of the Oral Microbiota

by Ben-Chih Yuan, Yao-Tsung Yeh, Ching-Chiang Lin, Cheng-Hsieh Huang, Hsueh-Chiao Liu and Chih-Po Chiang

Microorganisms 2020, 8(6), 959; https://doi.org/10.3390/microorganisms8060959 - 26 Jun 2020

Cited by 11 | Viewed by 2729

Abstract

Chronic rhinosinusitis (CRS) is the chronic inflammation of the sinus cavities of the upper respiratory tract, which can be caused by a disrupted microbiome. However, the role of the oral microbiome in CRS is not well understood. Polymicrobial and anaerobic infections of CRS [...] Read more.

Chronic rhinosinusitis (CRS) is the chronic inflammation of the sinus cavities of the upper respiratory tract, which can be caused by a disrupted microbiome. However, the role of the oral microbiome in CRS is not well understood. Polymicrobial and anaerobic infections of CRS frequently increased the difficulty of cultured and antibiotic therapy. This study aimed to elucidate the patterns and clinical feasibility of the oral microbiome in CRS diagnosis. Matched saliva and nasal swabs were collected from 18 CRS patients and 37 saliva specimens from normal volunteers were collected for 16S rRNA sequencing. The α-diversity of the saliva displayed no significant difference between control and CRS patients, whereas the β-diversity was significantly different (p = 0.004). Taxonomic indices demonstrated that Veillonella dispar, Rothia mucilaginosa, and Porphyromonas endodontalis were enriched, while Campylobacter and Cardiobacterium were reduced in the saliva of CRS patients. These microbial markers could significantly distinguish CRS patients from control (AUC = 0.939). It is noted that the 16S rRNA results of the nasal swab were consistent with the nasopharynx aerobic culture, and additionally detected multiple pathogens in CRS patients. In summary, these results indicated these oral microbiomes may provide a novel signal for CRS detection and that NGS may be an alternative approach for CRS diagnosis. Full article

(This article belongs to the Section Medical Microbiology)

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11 pages, 18406 KiB

Open AccessBrief Report

Variable Expression of Notch1 and Pax5 in Classical Hodgkin Lymphoma and Infection with Epstein–Barr in Pediatric Patients

by Icela Palma-Lara, Ana Elena Sánchez-Aldana, Elva Jiménez-Hernández, Octavio Martínez-Villegas, Juan Carlos Núñez-Enríquez, Juan Manuel Mejía-Aranguré, Sara A. Ochoa, Juan Xicohtencatl-Cortes, Ariadnna Cruz-Córdova, Sergio Zavala-Vega, Mariana García-Jiménez, Alejandra Contreras-Ramos, José Refugio Torres-Nava, Guillermo Mora-Ramiro and José Arellano-Galindo

Microorganisms 2020, 8(6), 958; https://doi.org/10.3390/microorganisms8060958 - 26 Jun 2020

Cited by 2 | Viewed by 2968

Abstract

NOTCH1 and PAX5 participate in the proliferation and differentiation of B and T lymphocytes. Their expression can be modified by activation of NOTCH1, induced by the Epstein–Barr (EBV) viral proteins identified as LMP1 and LMP2. To identify whether PAX5, NOTCH1, and EBV latency [...] Read more.

NOTCH1 and PAX5 participate in the proliferation and differentiation of B and T lymphocytes. Their expression can be modified by activation of NOTCH1, induced by the Epstein–Barr (EBV) viral proteins identified as LMP1 and LMP2. To identify whether PAX5, NOTCH1, and EBV latency genes participate in the oncogenic process of pediatric patients with classical Hodgkin lymphoma (cHL), the present study aimed to identify the variable expression of NOTCH1 among disease subtypes and to assess its effect on PAX5 expression. A total of 41 paraffin-embedded tissues from Mexican pediatric patients with cHL were analyzed. The expression of CD30, CD20, NOTCH1, PAX5, and LMP1 was evaluated by immunohistochemistry and immunofluorescence. EBV detection was performed by in situ hybridization. Out of all cases, 78% (32/41) of the cHL cases were EBV positive. NOTCH1 expression was detected in 78.1% (25/32) of EBV-positive cases, nodular sclerosis being the most frequent subtype (11/25, 44%). In cases where the expression of both genes was identified, double immunofluorescence assays were conducted, finding no colocalization. We found that Reed–Sternberg cells had aberrant expression compared to their cells of origin (B lymphocytes) due to the molecular mechanisms involved in the loss of expression of PAX5 and that the identification of NOTCH1 could be considered as a candidate diagnostic/prognostic marker and a therapeutic target in pediatric cHL. Full article

(This article belongs to the Special Issue Epstein–Barr Virus Infection and Associated Diseases)

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17 pages, 672 KiB

Open AccessArticle

Antimicrobial Susceptibility Pattern of Helicobacter heilmannii and Helicobacter ailurogastricus Isolates

by Rita Matos, Chloë De Witte, Annemieke Smet, Helena Berlamont, Sofie De Bruyckere, Irina Amorim, Fátima Gärtner and Freddy Haesebrouck

Microorganisms 2020, 8(6), 957; https://doi.org/10.3390/microorganisms8060957 - 25 Jun 2020

Cited by 14 | Viewed by 2913

Abstract

A combined agar and broth dilution method followed by qPCR was used to determine the antimicrobial susceptibility of feline H. heilmannii and H. ailurogastricus isolates. All H. ailurogastricus isolates showed a monomodal distribution of MICs for all the antimicrobial agents tested. For H. [...] Read more.

A combined agar and broth dilution method followed by qPCR was used to determine the antimicrobial susceptibility of feline H. heilmannii and H. ailurogastricus isolates. All H. ailurogastricus isolates showed a monomodal distribution of MICs for all the antimicrobial agents tested. For H. heilmannii, a bimodal distribution was observed for azithromycin, enrofloxacin, spectinomycin, and lincomycin. Single nucleotide polymorphisms (SNPs) were found in 50S ribosomal proteins L2 and L3 of the H. heilmannii isolate not belonging to the WT population for azithromycin, and in 30S ribosomal proteins S1, S7, and S12 of the isolate not belonging to the WT population for spectinomycin. The antimicrobial resistance mechanism to enrofloxacin and lincomycin remains unknown (2 and 1 H. heilmannii isolate(s), resp.). Furthermore, H. heilmannii isolates showed higher MICs for neomycin compared to H. ailurogastricus isolates which may be related to the presence of SNPs in several 30S and 50S ribosomal protein encoding genes and ribosomal RNA methyltransferase genes. This study shows that acquired resistance to azithromycin, spectinomycin, enrofloxacin, and lincomycin occasionally occurs in feline H. heilmannii isolates. As pets may constitute a source of infection for humans, this should be kept in mind when dealing with a human patient infected with H. heilmannii. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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18 pages, 3166 KiB

Open AccessArticle

Fungal Diversity Analysis of Grape Musts from Central Valley-Chile and Characterization of Potential New Starter Cultures

by Dinka Mandakovic, Rodrigo Pulgar, Jonathan Maldonado, Wladimir Mardones, Mauricio González, Francisco A. Cubillos and Verónica Cambiazo

Microorganisms 2020, 8(6), 956; https://doi.org/10.3390/microorganisms8060956 - 24 Jun 2020

Cited by 7 | Viewed by 3313

Abstract

Autochthonous microorganisms are an important source of the distinctive metabolites that influence the chemical profile of wine. However, little is known about the diversity of fungal communities associated with grape musts, even though they are the source of local yeast strains with potential [...] Read more.

Autochthonous microorganisms are an important source of the distinctive metabolites that influence the chemical profile of wine. However, little is known about the diversity of fungal communities associated with grape musts, even though they are the source of local yeast strains with potential capacities to become starters during fermentation. By using internal transcribed spacer (ITS) amplicon sequencing, we identified the taxonomic structure of the yeast community in unfermented and fermented musts of a typical Vitis vinifera L. var. Sauvignon blanc from the Central Valley of Chile throughout two consecutive seasons of production. Unsurprisingly, Saccharomyces represented the most abundant fungal genus in unfermented and fermented musts, mainly due to the contribution of S. uvarum (42.7%) and S. cerevisiae (80%). Unfermented musts were highly variable between seasons and showed higher values of fungal diversity than fermented musts. Since microbial physiological characterization is primarily achieved in culture, we isolated nine species belonging to six genera of fungi from the unfermented must samples. All isolates were characterized for their potential capacities to be used as new starters in wine. Remarkably, only Metschnikowia pulcherrima could co-exist with a commercial Saccharomyces cerevisiae strain under fermentative conditions, representing a feasible candidate strain for wine production. Full article

(This article belongs to the Special Issue Wine Yeast 1.0)

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17 pages, 3226 KiB

Open AccessArticle

Novel Antifungal Activity of Lolium-Associated Epichloë Endophytes

by Krishni Fernando, Priyanka Reddy, Inoka K. Hettiarachchige, German C. Spangenberg, Simone J. Rochfort and Kathryn M. Guthridge

Microorganisms 2020, 8(6), 955; https://doi.org/10.3390/microorganisms8060955 - 24 Jun 2020

Cited by 12 | Viewed by 3405

Abstract

Asexual Epichloë spp. fungal endophytes have been extensively studied for their functional secondary metabolite production. Historically, research mostly focused on understanding toxicity of endophyte-derived compounds on grazing livestock. However, endophyte-derived compounds also provide protection against invertebrate pests, disease, and other environmental stresses, which [...] Read more.

Asexual Epichloë spp. fungal endophytes have been extensively studied for their functional secondary metabolite production. Historically, research mostly focused on understanding toxicity of endophyte-derived compounds on grazing livestock. However, endophyte-derived compounds also provide protection against invertebrate pests, disease, and other environmental stresses, which is important for ensuring yield and persistence of pastures. A preliminary screen of 30 strains using an in vitro dual culture bioassay identified 18 endophyte strains with antifungal activity. The novel strains NEA12, NEA21, and NEA23 were selected for further investigation as they are also known to produce alkaloids associated with protection against insect pests. Antifungal activity of selected endophyte strains was confirmed against three grass pathogens, Ceratobasidium sp., Dreschlera sp., and Fusarium sp., using independent isolates in an in vitro bioassay. NEA21 and NEA23 showed potent activity against Ceratobasidium sp. and NEA12 showed moderate inhibition against all three pathogens. Crude extracts from liquid cultures of NEA12 and NEA23 also inhibited growth of the phytopathogens Ceratobasidium sp. and Fusarium sp. and provided evidence that the compounds of interest are stable, constitutively expressed, and secreted. Comparative analysis of the in vitro and in planta metabolome of NEA12 and NEA23 using LCMS profile data revealed individual metabolites unique to each strain that are present in vitro and in planta. These compounds are the best candidates for the differential bioactivity observed for each strain. Novel endophyte strains show promise for endophyte-mediated control of phytopathogens impacting Lolium spp. pasture production and animal welfare. Full article

(This article belongs to the Special Issue Fungal Endophytes and Their Interactions with Plants)

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19 pages, 7805 KiB

Open AccessArticle

Combinatorial Effects of Soluble, Insoluble, and Organic Extracts from Jerusalem Artichokes on Gut Microbiota in Mice

by Hiroyuki Sasaki, Yijin Lyu, Yuki Nakayama, Fumiaki Nakamura, Aya Watanabe, Hiroki Miyakawa, Yoichi Nakao and Shigenobu Shibata

Microorganisms 2020, 8(6), 954; https://doi.org/10.3390/microorganisms8060954 - 24 Jun 2020

Cited by 8 | Viewed by 3111

Abstract

Jerusalem artichokes contain high amounts of inulin, which is a prebiotic that supports digestive health, as well as a variety of insoluble fibers and caffeoylquinic acid. The individual impact of these components on gut microbiota is well known; however, the combinatorial effects are [...] Read more.

Jerusalem artichokes contain high amounts of inulin, which is a prebiotic that supports digestive health, as well as a variety of insoluble fibers and caffeoylquinic acid. The individual impact of these components on gut microbiota is well known; however, the combinatorial effects are less clear. In this investigation, we fractionated Jerusalem artichokes into three parts (water-soluble extract, insoluble extract, and organic extract) and powdered them. Mice were fed a high-fat diet that included one or more of these extracts for 10 days, and then their cecal pH, cecal short-chain fatty acids (SCFAs), and fecal microbiota were evaluated. The combination of the water-soluble and organic extract decreased cecal pH and increased the concentration of SCFAs and led to dynamic changes in the composition of the gut microbiota. These results demonstrate that both the water-soluble and organic extracts in Jerusalem artichokes are bioactive substances that are capable of changing SCFA production and the composition of gut microbiota. Powdered Jerusalem artichokes, rather than inulin supplements, may be superior for promoting a healthy gut. Full article

(This article belongs to the Section Gut Microbiota)

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16 pages, 2815 KiB

Open AccessArticle

Effects of Crude β-Glucosidases from Issatchenkia terricola, Pichia kudriavzevii, Metschnikowia pulcherrima on the Flavor Complexity and Characteristics of Wines

by Wenxia Zhang, Xuanhan Zhuo, Lanlan Hu and Xiuyan Zhang

Microorganisms 2020, 8(6), 953; https://doi.org/10.3390/microorganisms8060953 - 24 Jun 2020

Cited by 28 | Viewed by 2540

Abstract

To investigate the effects of crude β-glucosidases from Issatchenkia terricola SLY-4 (SLY-4E), Pichia kudriavzevii F2-24 (F2-24E), and Metschnikowia pulcherrima HX-13 (HX-13E) on flavor complexity and characteristics of wines, grape juice was fermented by Saccharomyces cerevisiae with the addition of SLY-4E, F2-24E and [...] Read more.

To investigate the effects of crude β-glucosidases from Issatchenkia terricola SLY-4 (SLY-4E), Pichia kudriavzevii F2-24 (F2-24E), and Metschnikowia pulcherrima HX-13 (HX-13E) on flavor complexity and characteristics of wines, grape juice was fermented by Saccharomyces cerevisiae with the addition of SLY-4E, F2-24E and HX-13E, respectively. The growth and sugar consumption kinetics of S. cerevisiae, the physicochemical characteristics, the volatile compounds, and the sensory dimensions of wines were analyzed. Results showed that adding SLY-4E, F2-24E, and HX-13E into must had no negative effect on the fermentation and physicochemical characteristics of wines, but increased the content of terpenes, esters, and fatty acids, while decreased the C₆ compound content. Each wine had its typical volatile compound profiles. Adding SLY-4E or F2-24E into must could significantly improve the flavor complexity and characteristics of wines. These results would provide not only an approach to improve flavor complexity and characteristics of wines, but also references for application of β-glucosidases from other sources. Full article

(This article belongs to the Special Issue Wine Yeast 1.0)

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23 pages, 1422 KiB

Open AccessReview

Lactic Acid Bacteria as Antibacterial Agents to Extend the Shelf Life of Fresh and Minimally Processed Fruits and Vegetables: Quality and Safety Aspects

by Sofia Agriopoulou, Eygenia Stamatelopoulou, Monika Sachadyn-Król and Theodoros Varzakas

Microorganisms 2020, 8(6), 952; https://doi.org/10.3390/microorganisms8060952 - 24 Jun 2020

Cited by 106 | Viewed by 15991

Abstract

Eating fresh fruits and vegetables is, undoubtedly, a healthy habit that should be adopted by everyone (particularly due to the nutrients and functional properties of fruits and vegetables). However, at the same time, due to their production in the external environment, there is [...] Read more.

Eating fresh fruits and vegetables is, undoubtedly, a healthy habit that should be adopted by everyone (particularly due to the nutrients and functional properties of fruits and vegetables). However, at the same time, due to their production in the external environment, there is an increased risk of their being infected with various pathogenic microorganisms, some of which cause serious foodborne illnesses. In order to preserve and distribute safe, raw, and minimally processed fruits and vegetables, many strategies have been proposed, including bioprotection. The use of lactic acid bacteria in raw and minimally processed fruits and vegetables helps to better maintain their quality by extending their shelf life, causing a significant reduction and inhibition of the action of important foodborne pathogens. The antibacterial effect of lactic acid bacteria is attributed to its ability to produce antimicrobial compounds, including bacteriocins, with strong competitive action against many microorganisms. The use of bacteriocins, both separately and in combination with edible coatings, is considered a very promising approach for microbiological quality, and safety for postharvest storage of raw and minimally processed fruits and vegetables. Therefore, the purpose of the review is to discuss the biopreservation of fresh fruits and vegetables through the use of lactic acid bacteria as a green and safe technique. Full article

(This article belongs to the Special Issue Lactic Acid Bacteria, Biopreservation Agents for Fruit and Vegetables)

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14 pages, 2760 KiB

Open AccessArticle

Functional Associations and Resilience in Microbial Communities

by Maria-Luisa Avila-Jimenez, Gavin Burns, Zhili He, Jizhong Zhou, Andrew Hodson, Jose-Luis Avila-Jimenez and David Pearce

Microorganisms 2020, 8(6), 951; https://doi.org/10.3390/microorganisms8060951 - 24 Jun 2020

Cited by 10 | Viewed by 3646

Abstract

Microbial communities have inherently high levels of metabolic flexibility and functional redundancy, yet the structure of microbial communities can change rapidly with environmental perturbation. To understand whether such changes observed at the taxonomic level translate into differences at the functional level, we analyzed [...] Read more.

Microbial communities have inherently high levels of metabolic flexibility and functional redundancy, yet the structure of microbial communities can change rapidly with environmental perturbation. To understand whether such changes observed at the taxonomic level translate into differences at the functional level, we analyzed the structure of taxonomic and functional gene distribution across Arctic and Antarctic locations. Taxonomic diversity (in terms of alpha diversity and species richness) differed significantly with location. However, we found that functional genes distributed evenly across bacterial networks and that this functional distribution was also even across different geographic locations. For example, on average 15% of the functional genes were related to carbon cycling across all bacterial networks, slightly over 21% of the genes were stress-related and only 0.5% of the genes were linked to carbon degradation functions. In such a distribution, each bacterial network includes all of the functional groups distributed following the same proportions. However, the total number of functional genes that is included in each bacterial network differs, with some clusters including many more genes than others. We found that the proportion of times a specific gene must occur to be linked to a specific cluster is 8%, meaning the relationship between the total number of genes in the cluster and the number of genes per function follows a linear pattern: smaller clusters require a gene to appear less frequently to get fixed within the cluster, while larger clusters require higher gene frequencies. We suggest that this mechanism of functional association between equally rare or equally abundant genes could have implications for ecological resilience, as non-dominant genes also associate in fully functioning ecological networks, potentially suggesting that there are always pre-existing functional networks available to exploit new ecological niches (where they can become dominant) as they emerge; for example, in the case of rapid or sudden environmental change. Furthermore, this pattern did not correlate with taxonomic distribution, suggesting that bacteria associate based on functionality and this is independent of its taxonomic position. Our analyses based on ecological networks also showed no clear evidence of recent environmental impact on polar marine microbial communities at the functional level, unless all communities analyzed have changed exactly in the same direction and intensity, which is unlikely given we are comparing areas changing at different rates. Full article

(This article belongs to the Special Issue Extremophiles 2.0)

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24 pages, 930 KiB

Open AccessReview

Experimental Strategies to Explore Drug Action and Resistance in Kinetoplastid Parasites

by Magali Van den Kerkhof, Yann G.-J. Sterckx, Philippe Leprohon, Louis Maes and Guy Caljon

Microorganisms 2020, 8(6), 950; https://doi.org/10.3390/microorganisms8060950 - 24 Jun 2020

Cited by 11 | Viewed by 3789

Abstract

Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of [...] Read more.

Kinetoplastids are the causative agents of leishmaniasis, human African trypanosomiasis, and American trypanosomiasis. They are responsible for high mortality and morbidity in (sub)tropical regions. Adequate treatment options are limited and have several drawbacks, such as toxicity, need for parenteral administration, and occurrence of treatment failure and drug resistance. Therefore, there is an urgency for the development of new drugs. Phenotypic screening already allowed the identification of promising new chemical entities with anti-kinetoplastid activity potential, but knowledge on their mode-of-action (MoA) is lacking due to the generally applied whole-cell based approach. However, identification of the drug target is essential to steer further drug discovery and development. Multiple complementary techniques have indeed been used for MoA elucidation. In this review, the different ‘omics’ approaches employed to define the MoA or mode-of-resistance of current reference drugs and some new anti-kinetoplastid compounds are discussed. Full article

(This article belongs to the Special Issue Treatment of Leishmaniasis)

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12 pages, 1057 KiB

Open AccessArticle

Identification and Pathogenic Potential of Bacillus cereus Strains Isolated from a Dairy Processing Plant Producing PDO Taleggio Cheese

by Erica Tirloni, Simone Stella, Cristian Bernardi, Diletta Mazzantini, Francesco Celandroni and Emilia Ghelardi

Microorganisms 2020, 8(6), 949; https://doi.org/10.3390/microorganisms8060949 - 24 Jun 2020

Cited by 19 | Viewed by 3120

Abstract

Low levels of contamination by Bacillus cereus at the cheese farm is essential for reducing any opportunity for growth prior consumption. In this study, B. cereus distribution in a plant producing Protected Designation of Origin Taleggio cheese was investigated and the virulence potential [...] Read more.

Low levels of contamination by Bacillus cereus at the cheese farm is essential for reducing any opportunity for growth prior consumption. In this study, B. cereus distribution in a plant producing Protected Designation of Origin Taleggio cheese was investigated and the virulence potential of the isolates was evaluated. Seventy-four samples were collected from Food and Non Food Contact Surfaces (FCS, NFCS), saline curd, and Taleggio. The eleven isolates were identified, typified, and clustered. Strains were tested for the production of hemolysins, hemolysin BL (HBL), phosphatidylcholine-specific phospholipase C (PC-PLC), proteases, and biofilm, and for the presence of chromosomal toxin-encoding genes (sph, plcA, cytK, entFM, bcet, entS, nheA, nheB, nheC). B. cereus was detected on NFCS, FCS, and curd, but not in Taleggio. The isolates were grouped into six clusters, and all produced PC-PLC, hemolysins, and proteases, and most of them HBL (66.7%). All the clusters harbored the nheA, sph, plcA, entFM, and cytK genes, and some also nheB (83.3%), nheC (66.7%), bcet (50.0%), and entS (66.7%). All strains showed biofilm-forming ability. Our data reveal possible contamination of production plants and cheese curd by potentially virulent B. cereus, but bacterial absence in Taleggio highlights the efficacy of a proper management of the production phases in assuring consumer’s protection. Full article

(This article belongs to the Special Issue Bacillus: Molecular Considerations)

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21 pages, 4442 KiB

Open AccessArticle

Plant Growth Enhancement using Rhizospheric Halotolerant Phosphate Solubilizing Bacterium Bacillus licheniformis QA1 and Enterobacter asburiae QF11 Isolated from Chenopodium quinoa Willd

by Ismail Mahdi, Nidal Fahsi, Mohamed Hafidi, Abdelmounaaim Allaoui and Latefa Biskri

Microorganisms 2020, 8(6), 948; https://doi.org/10.3390/microorganisms8060948 - 24 Jun 2020

Cited by 66 | Viewed by 5978

Abstract

Plant growth-promoting rhizobacteria represent a promising solution to enhancing agricultural productivity. Here, we screened phosphate solubilizing bacteria from the rhizospheric soil of Chenopodium quinoa Willd and assessed their plant-growth promoting rhizobacteria (PGPR) properties including production of indole-3-acetic acid (IAA), siderophores, hydrogen cyanide (HCN), [...] Read more.

Plant growth-promoting rhizobacteria represent a promising solution to enhancing agricultural productivity. Here, we screened phosphate solubilizing bacteria from the rhizospheric soil of Chenopodium quinoa Willd and assessed their plant-growth promoting rhizobacteria (PGPR) properties including production of indole-3-acetic acid (IAA), siderophores, hydrogen cyanide (HCN), ammonia and extracellular enzymes. We also investigated their tolerance to salt stress and their capacity to form biofilms. Two isolated strains, named QA1 and QF11, solubilized phosphate up to 346 mg/L, produced IAA up to 795.31 µg/mL, and tolerated up to 2 M NaCl in vitro. 16S rRNA and Cpn60 gene sequencing revealed that QA1 and QF11 belong to the genus Bacillus licheniformis and Enterobacter asburiae, respectively. In vivo, early plant growth potential showed that quinoa seeds inoculated either with QA1 or QF11 displayed higher germination rates and increased seedling growth. Under saline irrigation conditions, QA1 enhanced plant development/growth. Inoculation with QA1 increased leaf chlorophyll content index, enhanced P and K⁺ uptake and decreased plant Na⁺ uptake. Likewise, plants inoculated with QF11 strain accumulated more K⁺ and had reduced Na⁺ content. Collectively, our findings support the use of QA1 and QF11 as potential biofertilizers. Full article

(This article belongs to the Special Issue Plant Microbiome Augmentation and Stimulation: New Strategies to Grow Crops with Reduced Agrochemicals)

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9 pages, 1792 KiB

Open AccessCommunication

First Demonstration of Clinical Fusarium Strains Causing Cross-Kingdom Infections from Humans to Plants

by Thuluz Meza-Menchaca, Rupesh Kumar Singh, Jesús Quiroz-Chávez, Luz María García-Pérez, Norma Rodríguez-Mora, Manuel Soto-Luna, Guadalupe Gastélum-Contreras, Virginia Vanzzini-Zago, Lav Sharma and Francisco Roberto Quiroz-Figueroa

Microorganisms 2020, 8(6), 947; https://doi.org/10.3390/microorganisms8060947 - 23 Jun 2020

Cited by 8 | Viewed by 3329

Abstract

Mycotoxins from the Fusarium genus are widely known to cause economic losses in crops, as well as high mortalities rates among immunocompromised humans. However, to date, no correlation has been established for the ability of Fusarium to cause cross-kingdom infection between plants and [...] Read more.

Mycotoxins from the Fusarium genus are widely known to cause economic losses in crops, as well as high mortalities rates among immunocompromised humans. However, to date, no correlation has been established for the ability of Fusarium to cause cross-kingdom infection between plants and humans. The present investigation aims to fill this gap in the literature by examining cross-kingdom infection caused by Furasium strains isolated from non-immunocompromised or non-immunosuppressed humans, which were subsequently reinfected in plants and on human tissue. The findings document for the first time cross-kingdom infective events in Fusarium species, thus enhancing our existing knowledge of how mycopathogens continue to thrive in different hosts. Full article

(This article belongs to the Special Issue Fusarium: Mycotoxins, Taxonomy and Pathogenicity)

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19 pages, 3162 KiB

Open AccessArticle

Characterization of the Phenanthrene-Degrading Sphingobium yanoikuyae SJTF8 in Heavy Metal Co-Existing Liquid Medium and Analysis of Its Metabolic Pathway

by Chong Yin, Weiliang Xiong, Hua Qiu, Wanli Peng, Zixin Deng, Shuangjun Lin and Rubing Liang

Microorganisms 2020, 8(6), 946; https://doi.org/10.3390/microorganisms8060946 - 23 Jun 2020

Cited by 15 | Viewed by 3679

Abstract

Polycyclic aromatic hydrocarbons (PAHs) are common organic pollutants with great carcinogenic threaten, and metal/PAH-contaminated environments represent one of the most difficult remedial challenges. In this work, Sphingobium yanoikuyae SJTF8 was isolated and identified with great and stable PAH-degrading efficiency even under stress conditions. [...] Read more.

Polycyclic aromatic hydrocarbons (PAHs) are common organic pollutants with great carcinogenic threaten, and metal/PAH-contaminated environments represent one of the most difficult remedial challenges. In this work, Sphingobium yanoikuyae SJTF8 was isolated and identified with great and stable PAH-degrading efficiency even under stress conditions. It could utilize typical PAHs (naphthalene, phenanthrene, and anthracene) and heterocyclic and halogenated aromatic compounds (dibenzothiophene and 9-bromophenanthrene) as the sole carbon source. It could degrade over 98% of 500 mg/L phenanthrene in 4 days, and the cis-3,4-dihydrophenanthrene-3,4-diol was the first-step intermediate. Notably, strain SJTF8 showed great tolerance to heavy metals and acidic pH. Supplements of 0.30 mM of Cu²⁺, 1.15 mM of Zn²⁺, and 0.01 mM of Cd²⁺ had little effect on its cell growth and phenanthrene degradation; phenanthrene of 250 mg/L could still be degraded completely in 48 h. Further, the whole genome sequence of S. yanoikuyae SJTF8 was obtained, and three plasmids were found. The potential genes participating in stress-tolerance and PAH-degradation were annotated and were found mostly distributed in plasmids 1 and 2. Elimination of plasmid 2 resulted in the loss of the PAH-degradation ability. On the basis of genome mining results, the possible degrading pathway and the metabolites of S. yanoikuyae SJTF8 to phenanthrene were predicted. Full article

(This article belongs to the Section Environmental Microbiology)

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18 pages, 2426 KiB

Open AccessArticle

Biotransformation of Carboxylic Acids to Alcohols: Characterization of Thermoanaerobacter Strain AK152 and 1-Propanol Production via Propionate Reduction

by Sean Michael Scully and Johann Orlygsson

Microorganisms 2020, 8(6), 945; https://doi.org/10.3390/microorganisms8060945 - 23 Jun 2020

Cited by 5 | Viewed by 3042

Abstract

Thermoanaerobacter strains have recently gained interest because of their ability to convert short chain fatty acids to alcohols using actively growing cells. Thermoanaerobacter thermohydrosulfuricus strain AK152 was physiologically investigated for its ethanol and other alcohol formation. The temperature and pH optimum of the [...] Read more.

Thermoanaerobacter strains have recently gained interest because of their ability to convert short chain fatty acids to alcohols using actively growing cells. Thermoanaerobacter thermohydrosulfuricus strain AK152 was physiologically investigated for its ethanol and other alcohol formation. The temperature and pH optimum of the strain was 70 °C and pH 7.0 and the strain degraded a variety of compounds present in lignocellulosic biomass like monosaccharides, disaccharides, and starch. The strain is highly ethanologenic, producing up to 86% of the theoretical ethanol yield form hexoses. Strain AK152 was inhibited by relatively low initial substrate (30 mM) concentration, leading to inefficient degradation of glucose and levelling up of all end-product formation. The present study shows that the strain produces alcohols from most of the tested carboxylic acids, with the highest yields for propionate conversion to propanol (40.7%) with kinetic studies demonstrating that the maximum conversion happens within the first 48 h of fermentation. Various physiological tests were performed to maximize the acid conversion to the alcohol which reveals that the optimum pH for propionate conversion is pH 6.7 which affords a 57.3% conversion. Kinetic studies reveal that propionate conversion is rapid, achieving a maximum conversion within the first 48 h of fermentation. Finally, by using ¹³C NMR, it was shown that the addition of propionate indeed converted to propanol. Full article

(This article belongs to the Special Issue Extremophiles and Extremozymes in Academia and Industries)

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21 pages, 7030 KiB

Open AccessArticle

Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple

by Ahmed Abdelfattah, Susan R. Whitehead, Dumitru Macarisin, Jia Liu, Erik Burchard, Shiri Freilich, Christopher Dardick, Samir Droby and Michael Wisniewski

Microorganisms 2020, 8(6), 944; https://doi.org/10.3390/microorganisms8060944 - 23 Jun 2020

Cited by 52 | Viewed by 5669

Abstract

There is growing recognition of the role that the microbiome plays in the health and physiology of many plant species. However, considerably less research has been conducted on the postharvest microbiome of produce and the impact that postharvest processing may have on its [...] Read more.

There is growing recognition of the role that the microbiome plays in the health and physiology of many plant species. However, considerably less research has been conducted on the postharvest microbiome of produce and the impact that postharvest processing may have on its composition. Here, amplicon sequencing was used to study the effect of washing, waxing, and low-temperature storage at 2 °C for six months on the bacterial and fungal communities of apple calyx-end, stem-end, and peel tissues. The results of the present work reveal that tissue-type is the main factor defining fungal and bacterial diversity and community composition on apple fruit. Both postharvest treatments and low temperature storage had a strong impact on the fungal and bacterial diversity and community composition of these tissue types. Distinct spatial and temporal changes in the composition and diversity of the microbiota were observed in response to various postharvest management practices. The greatest impact was attributed to sanitation practices with major differences among unwashed, washed and washed-waxed apples. The magnitude of the differences, however, was tissue-specific, with the greatest impact occurring on peel tissues. Temporally, the largest shift occurred during the first two months of low-temperature storage, although fungi were more affected by storage time than bacteria. In general, fungi and bacteria were impacted equally by sanitation practices, especially the epiphytic microflora of peel tissues. This research provides a foundation for understanding the impact of postharvest management practices on the microbiome of apple and its potential subsequent effects on postharvest disease management and food safety. Full article

(This article belongs to the Special Issue Applying Metaorganism Studies to the Fruit Microbiome: A New Frontier)

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21 pages, 4434 KiB

Open AccessArticle

Cryo-EM Structure and Molecular Dynamics Analysis of the Fluoroquinolone Resistant Mutant of the AcrB Transporter from Salmonella

by Rachel M. Johnson, Chiara Fais, Mayuriben Parmar, Harish Cheruvara, Robert L. Marshall, Sophie J. Hesketh, Matthew C. Feasey, Paolo Ruggerone, Attilio V. Vargiu, Vincent L. G. Postis, Stephen P. Muench and Vassiliy N. Bavro

Microorganisms 2020, 8(6), 943; https://doi.org/10.3390/microorganisms8060943 - 23 Jun 2020

Cited by 22 | Viewed by 5232

Abstract

Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of [...] Read more.

Salmonella is an important genus of Gram-negative pathogens, treatment of which has become problematic due to increases in antimicrobial resistance. This is partly attributable to the overexpression of tripartite efflux pumps, particularly the constitutively expressed AcrAB-TolC. Despite its clinical importance, the structure of the Salmonella AcrB transporter remained unknown to-date, with much of our structural understanding coming from the Escherichia coli orthologue. Here, by taking advantage of the styrene maleic acid (SMA) technology to isolate membrane proteins with closely associated lipids, we report the very first experimental structure of Salmonella AcrB transporter. Furthermore, this novel structure provides additional insight into mechanisms of drug efflux as it bears the mutation (G288D), originating from a clinical isolate of Salmonella Typhimurium presenting an increased resistance to fluoroquinolones. Experimental data are complemented by state-of-the-art molecular dynamics (MD) simulations on both the wild type and G288D variant of Salmonella AcrB. Together, these reveal several important differences with respect to the E. coli protein, providing insights into the role of the G288D mutation in increasing drug efflux and extending our understanding of the mechanisms underlying antibiotic resistance. Full article

(This article belongs to the Special Issue Multidrug Efflux Pumps)

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15 pages, 3094 KiB

Open AccessArticle

Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling Three Representative Locations of the Victoria Land

by Claudia Coleine, Nuttapon Pombubpa, Laura Zucconi, Silvano Onofri, Benedetta Turchetti, Pietro Buzzini, Jason E. Stajich and Laura Selbmann

Microorganisms 2020, 8(6), 942; https://doi.org/10.3390/microorganisms8060942 - 23 Jun 2020

Cited by 12 | Viewed by 3666

Abstract

The endolithic niche represents an ultimate refuge to microorganisms in the Mars-like environment of the Antarctic desert. In an era of rapid global change and desertification, the interest in these border ecosystems is increasing due to speculation on how they maintain balance and [...] Read more.

The endolithic niche represents an ultimate refuge to microorganisms in the Mars-like environment of the Antarctic desert. In an era of rapid global change and desertification, the interest in these border ecosystems is increasing due to speculation on how they maintain balance and functionality at the dry limits of life. To assure a reliable estimation of microbial diversity, proper sampling must be planned in order to avoid the necessity of re-sampling as reaching these remote locations is risky and requires tremendous logistical and economical efforts. In this study, we seek to determine the minimum number of samples for uncovering comprehensive bacterial and fungal diversity, comparing communities in strict vicinity to each other. We selected three different locations of the Victoria Land (Continental Antarctica) at different altitudes and showing sandstone outcrops of a diverse nature and origin—Battleship promontory (834 m above sea level (a.s.l.), Southern VL), Trio Nunatak (1,470 m a.s.l., Northern VL) and Mt New Zealand (3,100 m a.s.l., Northern VL). Overall, we found that a wider sampling would be required to capture the whole amplitude of microbial diversity, particularly in Northern VL. We concluded that the inhomogeneity of the rock matrix and the stronger environmental pressure at higher altitudes may force the communities to a higher local diversification. Full article

(This article belongs to the Special Issue Polar Microbial Ecology: The Role of Microbes in the Functioning of Extremely Cold Ecosystems)

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15 pages, 4022 KiB

Open AccessArticle

Metagenomic Characterization of Gut Microbiota of Carriers of Extended-Spectrum Beta-Lactamase or Carbapenemase-Producing Enterobacteriaceae Following Treatment with Oral Antibiotics and Fecal Microbiota Transplantation: Results from a Multicenter Randomized Trial

by Stefano Leo, Vladimir Lazarevic, Myriam Girard, Nadia Gaïa, Jacques Schrenzel, Victoire de Lastours, Bruno Fantin, Marc Bonten, Yehuda Carmeli, Emilie Rondinaud, Stephan Harbarth and Benedikt D. Huttner

Microorganisms 2020, 8(6), 941; https://doi.org/10.3390/microorganisms8060941 - 23 Jun 2020

Cited by 21 | Viewed by 3363

Abstract

Background: The R-GNOSIS (Resistance in Gram-Negative Organisms: Studying Intervention Strategies) WP3 study was the first multicenter randomized clinical trial systematically investigating fecal microbiota transplantation (FMT) for intestinal decolonization of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) or carbapenemase-producing Enterobacteriaceae (CPE). Here, we characterized the temporal dynamics [...] Read more.

Background: The R-GNOSIS (Resistance in Gram-Negative Organisms: Studying Intervention Strategies) WP3 study was the first multicenter randomized clinical trial systematically investigating fecal microbiota transplantation (FMT) for intestinal decolonization of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) or carbapenemase-producing Enterobacteriaceae (CPE). Here, we characterized the temporal dynamics of fecal microbiota changes in a sub-cohort of the R-GNOSIS WP3 participants before and after antibiotics/FMT using whole metagenome shotgun sequencing. Methods: We sequenced fecal DNA obtained from 16 ESBL-E/CPE carriers having received oral colistin/neomycin followed by FMT and their corresponding seven donors. Ten treatment-naïve controls from the same trial were included. Fecal samples were collected at baseline (V0), after antibiotics but before FMT (V2) and three times after FMT (V3, V4 and V5). Results: Antibiotic treatment transiently decreased species richness and diversity and increased the abundance of antibiotic resistance determinants (ARDs). Bifidobacterium species, together with butyrate- and propionate-producing species from Lachnospiraceae and Ruminococcaceae families were significantly enriched in post-FMT microbiota of treated carriers. After FMT, the proportion of Enterobacteriaceae was lower compared to baseline but without statistical significance. Conclusions: Combined antibiotic and FMT treatment resulted in enrichment of species that are likely to limit the gut colonization by ESBL-E/CPE. Full article

(This article belongs to the Special Issue Therapeutic Potential of Fecal Microbiota Therapy (FMT))

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25 pages, 15432 KiB

Open AccessArticle

Asexual Evolution and Forest Conditions Drive Genetic Parallelism in Phytophthora ramorum

by Jennifer David Yuzon, Renaud Travadon, Mathu Malar C, Sucheta Tripathy, Nathan Rank, Heather K. Mehl, David M. Rizzo, Richard Cobb, Corinn Small, Tiffany Tang, Haley E. McCown, Matteo Garbelotto and Takao Kasuga

Microorganisms 2020, 8(6), 940; https://doi.org/10.3390/microorganisms8060940 - 22 Jun 2020

Cited by 4 | Viewed by 3097

Abstract

It is commonly assumed that asexual lineages are short-lived evolutionarily, yet many asexual organisms can generate genetic and phenotypic variation, providing an avenue for further evolution. Previous work on the asexual plant pathogen Phytophthora ramorum NA1 revealed considerable genetic variation in the form [...] Read more.

It is commonly assumed that asexual lineages are short-lived evolutionarily, yet many asexual organisms can generate genetic and phenotypic variation, providing an avenue for further evolution. Previous work on the asexual plant pathogen Phytophthora ramorum NA1 revealed considerable genetic variation in the form of Structural Variants (SVs). To better understand how SVs arise and their significance to the California NA1 population, we studied the evolutionary histories of SVs and the forest conditions associated with their emergence. Ancestral state reconstruction suggests that SVs arose by somatic mutations among multiple independent lineages, rather than by recombination. We asked if this unusual phenomenon of parallel evolution between isolated populations is transmitted to extant lineages and found that SVs persist longer in a population if their genetic background had a lower mutation load. Genetic parallelism was also found in geographically distant demes where forest conditions such as host density, solar radiation, and temperature, were similar. Parallel SVs overlap with genes involved in pathogenicity such as RXLRs and have the potential to change the course of an epidemic. By combining genomics and environmental data, we identified an unexpected pattern of repeated evolution in an asexual population and identified environmental factors potentially driving this phenomenon. Full article

(This article belongs to the Section Plant Microbe Interactions)

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16 pages, 1378 KiB

Open AccessArticle

Genome Analysis of Endobacterium cerealis, a Novel Genus and Species Isolated from Zea mays Roots in North Spain

by Esther Menéndez, Jose David Flores-Félix, Martha Helena Ramírez-Bahena, Jose M. Igual, Paula García-Fraile, Alvaro Peix and Encarna Velázquez

Microorganisms 2020, 8(6), 939; https://doi.org/10.3390/microorganisms8060939 - 22 Jun 2020

Cited by 9 | Viewed by 3659

Abstract

In the present work, we analyse the genomic and phenotypic characteristics of a strain named RZME27^T isolated from roots of a Zea mays plant grown in Spain. The phylogenetic analyses of 16S rRNA gene and whole genome sequences showed that the strain [...] Read more.

In the present work, we analyse the genomic and phenotypic characteristics of a strain named RZME27^T isolated from roots of a Zea mays plant grown in Spain. The phylogenetic analyses of 16S rRNA gene and whole genome sequences showed that the strain RZME27^T clustered with the type strains of Neorhizobium galegae and Pseudorhizobium pelagicum from the family Rhizobiaceae. This family encompasses several genera establishing symbiosis with legumes, but the genes involved in nodulation and nitrogen fixation are absent in its genome. Nevertheless, genes related to plant colonization, such as those involved in motility, chemotaxis, quorum sensing, exopolysaccharide biosynthesis and hydrolytic enzymes production were found. The comparative pangenomic analyses showed that 78 protein clusters present in the strain RZME27^T were not found in the type strains of its closest relatives N. galegae and P. pelagicum. The calculated average nucleotide identity (ANI) values between the strain RZME27^T and the type strains of N. galegae and P. pelagicum were 75.61% and 75.1%, respectively, similar or lower than those found for other genera from family Rhizobiaceae. Several phenotypic differences were also found, highlighting the absence of the fatty acid C_19:0 cyclo ω8c and propionate assimilation. These results support the definition of a novel genus and species named Endobacterium cerealis gen. nov. sp. nov. whose type strain is RZME27^T. Full article

(This article belongs to the Special Issue Plant Microbial Interactions)

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19 pages, 2416 KiB

Open AccessArticle

Sex-Specific Associations between Gut Prevotellaceae and Host Genetics on Adiposity

by Amanda Cuevas-Sierra, José Ignacio Riezu-Boj, Elizabeth Guruceaga, Fermín Ignacio Milagro and José Alfredo Martínez

Microorganisms 2020, 8(6), 938; https://doi.org/10.3390/microorganisms8060938 - 22 Jun 2020

Cited by 28 | Viewed by 4266

Abstract

The gut microbiome has been recognized as a tool for understanding adiposity accumulation and for providing personalized nutrition advice for the management of obesity and accompanying metabolic complications. The genetic background is also involved in human energy homeostasis. In order to increase the [...] Read more.

The gut microbiome has been recognized as a tool for understanding adiposity accumulation and for providing personalized nutrition advice for the management of obesity and accompanying metabolic complications. The genetic background is also involved in human energy homeostasis. In order to increase the value of nutrigenetic dietary advice, the interplay between genetics and microbiota must be investigated. The purpose of the present study was to evaluate interactive associations between gut microbiota composition and 95 obesity-related single nucleotide polymorphisms (SNPs) searched in the literature. Oral mucosa and fecal samples from 360 normal weight, overweight and obese subjects were collected. Next generation genotyping of these 95 SNPs and fecal 16S rRNA sequencing were performed. A genetic risk score (GRS) was constructed with 10 SNPs statistically or marginally associated with body mass index (BMI). Several microbiome statistical analyses at family taxonomic level were applied (LEfSe, Canonical Correspondence Analysis, MetagenomeSeq and Random Forest), and Prevotellaceae family was found in all of them as one of the most important bacterial families associated with BMI and GRS. Thus, in this family it was further analyzed the interactive association between BMI and GRS with linear regression models. Interestingly, women with higher abundance of Prevotellaceae and higher GRS were more obese, compared to women with higher GRS and lower abundance of Prevotellaceae. These findings suggest relevant interrelationships between Prevotellaceae and the genetic background that may determine interindividual BMI differences in women, which opens the way to new precision nutrition-based treatments for obesity. Full article

(This article belongs to the Special Issue Host-Gut Microbiota Interactions)

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22 pages, 2168 KiB

Open AccessArticle

Genetic Variants and Phenotypic Characteristics of Salmonella Typhimurium-Resistant Mutants after Exposure to Carvacrol

by Daniel Berdejo, Natalia Merino, Elisa Pagán, Diego García-Gonzalo and Rafael Pagán

Microorganisms 2020, 8(6), 937; https://doi.org/10.3390/microorganisms8060937 - 22 Jun 2020

Cited by 9 | Viewed by 2635

Abstract

The emergence of antimicrobial resistance has raised questions about the safety of essential oils and their individual constituents as food preservatives and as disinfection agents. Further research is required to understand how and under what conditions stable genotypic resistance might occur in food [...] Read more.

The emergence of antimicrobial resistance has raised questions about the safety of essential oils and their individual constituents as food preservatives and as disinfection agents. Further research is required to understand how and under what conditions stable genotypic resistance might occur in food pathogens. Evolution experiments on Salmonella Typhimurium cyclically exposed to sublethal and lethal doses of carvacrol permitted the isolation of SeSCar and SeLCar strains, respectively. Both evolved strains showed a significant increase in carvacrol resistance, assessed by minimum inhibitory and bactericidal concentrations, the study of growth kinetics in the presence of carvacrol, and the evaluation of survival under lethal conditions. Moreover, antibiotic susceptibility tests revealed a development of SeLCar resistance to a wide range of antibiotics. Whole genome sequencing allowed the identification of single nucleotide variations in transcriptional regulators of oxidative stress-response: yfhP in SeSCar and soxR in SeLCar, which could be responsible for the increased resistance by improving the response to carvacrol and preventing its accumulation inside the cell. This study demonstrates the emergence of S. Typhimurium-resistant mutants against carvacrol, which might pose a risk to food safety and should therefore be considered in the design of food preservation strategies, or of cleaning and disinfection treatments. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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20 pages, 4305 KiB

Open AccessArticle

A Differential Metabarcoding Approach to Describe Taxonomy Profiles of Bacteria and Archaea in the Saltern of Margherita di Savoia (Italy)

by Claudia Leoni, Mariateresa Volpicella, Bruno Fosso, Caterina Manzari, Elisabetta Piancone, Maria C.G. Dileo, Erika Arcadi, Michail Yakimov, Graziano Pesole and Luigi R. Ceci

Microorganisms 2020, 8(6), 936; https://doi.org/10.3390/microorganisms8060936 - 22 Jun 2020

Cited by 17 | Viewed by 3633

Abstract

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing [...] Read more.

Microorganisms inhabiting saline environments are an interesting ecological model for the study of the adaptation of organisms to extreme living conditions and constitute a precious resource of enzymes and bioproducts for biotechnological applications. We analyzed the microbial communities in nine ponds with increasing salt concentrations (salinity range 4.9–36.0%) of the Saltern of Margherita di Savoia (Italy), the largest thalassohaline saltern in Europe. A deep-metabarcoding NGS procedure addressing separately the V5-V6 and V3-V4 hypervariable regions of the 16S rRNA gene of Bacteria and Archaea, respectively, and a CARD-FISH (catalyzed reporter deposition fluorescence in situ hybridization) analysis allowed us to profile the dynamics of microbial populations at the different salt concentrations. Both the domains were detected throughout the saltern, even if the low relative abundance of Archaea in the three ponds with the lowest salinities prevented the construction of the relative amplicon libraries. The highest cell counts were recorded at 14.5% salinity for Bacteria and at 24.1% salinity for Archaea. While Bacteria showed the greatest number of genera in the first ponds (salinity range 4.9–14.5%), archaeal genera were more numerous in the last ponds of the saltern (salinity 24.1–36.0%). Among prokaryotes, Salinibacter was the genus with the maximum abundance (~49% at 34.6% salinity). Other genera detected at high abundance were the archaeal Haloquadratum (~43% at 36.0% salinity) and Natronomonas (~18% at 13.1% salinity) and the bacterial “Candidatus Aquiluna” (~19% at 14.5% salinity). Interestingly, “Candidatus Aquiluna” had not been identified before in thalassohaline waters. Full article

(This article belongs to the Special Issue Extremophiles 2.0)

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40 pages, 665 KiB

Open AccessReview

Antibiotic Resistance Profiles, Molecular Mechanisms and Innovative Treatment Strategies of Acinetobacter baumannii

by Corneliu Ovidiu Vrancianu, Irina Gheorghe, Ilda Barbu Czobor and Mariana Carmen Chifiriuc

Microorganisms 2020, 8(6), 935; https://doi.org/10.3390/microorganisms8060935 - 21 Jun 2020

Cited by 98 | Viewed by 11484

Abstract

Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its [...] Read more.

Antibiotic resistance is one of the biggest challenges for the clinical sector and industry, environment and societal development. One of the most important pathogens responsible for severe nosocomial infections is Acinetobacter baumannii, a Gram-negative bacterium from the Moraxellaceae family, due to its various resistance mechanisms, such as the β-lactamases production, efflux pumps, decreased membrane permeability and altered target site of the antibiotic. The enormous adaptive capacity of A. baumannii and the acquisition and transfer of antibiotic resistance determinants contribute to the ineffectiveness of most current therapeutic strategies, including last-line or combined antibiotic therapy. In this review, we will present an update of the antibiotic resistance profiles and underlying mechanisms in A. baumannii and the current progress in developing innovative strategies for combating multidrug-resistant A. baumannii (MDRAB) infections. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: From the Environment to Human Health)

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21 pages, 4008 KiB

Open AccessArticle

Rapid Microscopic Detection of Bacillus anthracis by Fluorescent Receptor Binding Proteins of Bacteriophages

by Peter Braun, Immanuel Wolfschläger, Leonie Reetz, Lilia Bachstein, Ana Clara Jacinto, Carolina Tocantins, Johannes Poppe and Gregor Grass

Microorganisms 2020, 8(6), 934; https://doi.org/10.3390/microorganisms8060934 - 21 Jun 2020

Cited by 12 | Viewed by 5747

Abstract

Bacillus anthracis, the etiological agent of anthrax disease, is typically diagnosed by immunological and molecular methods such as polymerase chain reaction (PCR). Alternatively, mass spectrometry techniques may aid in confirming the presence of the pathogen or its toxins. However, because of the [...] Read more.

Bacillus anthracis, the etiological agent of anthrax disease, is typically diagnosed by immunological and molecular methods such as polymerase chain reaction (PCR). Alternatively, mass spectrometry techniques may aid in confirming the presence of the pathogen or its toxins. However, because of the close genetic relationship between B. anthracis and other members of the Bacillus cereus sensu lato group (such as Bacillus cereus or Bacillus thuringiensis) mis- or questionable identification occurs frequently. Also, bacteriophages such as phage gamma (which is highly specific for B. anthracis) have been in use for anthrax diagnostics for many decades. Here we employed host cell-specific receptor binding proteins (RBP) of (pro)-phages, also known as tail or head fibers, to develop a microscopy-based approach for the facile, rapid and unambiguous detection of B. anthracis cells. For this, the genes of (putative) RBP from Bacillus phages gamma, Wip1, AP50c and from lambdoid prophage 03 located on the chromosome of B. anthracis were selected. Respective phage genes were heterologously expressed in Escherichia coli and purified as fusions with fluorescent proteins. B. anthracis cells incubated with either of the reporter fusion proteins were successfully surface-labeled. Binding specificity was confirmed as RBP fusion proteins did not bind to most isolates of a panel of other B. cereus s.l. species or to more distantly related bacteria. Remarkably, RBP fusions detected encapsulated B. anthracis cells, thus RBP were able to penetrate the poly-γ-d-glutamate capsule of B. anthracis. From these results we anticipate this RBP-reporter assay may be useful for rapid confirmative identification of B. anthracis. Full article

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

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