Microorganisms

22 pages, 5306 KiB

Open AccessArticle

Cupriavidus metallidurans CH34 Possesses Aromatic Catabolic Versatility and Degrades Benzene in the Presence of Mercury and Cadmium

by Pablo Alviz-Gazitua, Roberto E. Durán, Felipe A. Millacura, Franco Cárdenas, Luis A. Rojas and Michael Seeger

Microorganisms 2022, 10(2), 484; https://doi.org/10.3390/microorganisms10020484 - 21 Feb 2022

Cited by 6 | Viewed by 2760

Abstract

Heavy metal co-contamination in crude oil-polluted environments may inhibit microbial bioremediation of hydrocarbons. The model heavy metal-resistant bacterium Cupriavidus metallidurans CH34 possesses cadmium and mercury resistance, as well as genes related to the catabolism of hazardous BTEX aromatic hydrocarbons. The aims of this [...] Read more.

Heavy metal co-contamination in crude oil-polluted environments may inhibit microbial bioremediation of hydrocarbons. The model heavy metal-resistant bacterium Cupriavidus metallidurans CH34 possesses cadmium and mercury resistance, as well as genes related to the catabolism of hazardous BTEX aromatic hydrocarbons. The aims of this study were to analyze the aromatic catabolic potential of C. metallidurans CH34 and to determine the functionality of the predicted benzene catabolic pathway and the influence of cadmium and mercury on benzene degradation. Three chromosome-encoded bacterial multicomponent monooxygenases (BMMs) are involved in benzene catabolic pathways. Growth assessment, intermediates identification, and gene expression analysis indicate the functionality of the benzene catabolic pathway. Strain CH34 degraded benzene via phenol and 2-hydroxymuconic semialdehyde. Transcriptional analyses revealed a transition from the expression of catechol 2,3-dioxygenase (tomB) in the early exponential phase to catechol 1,2-dioxygenase (catA1 and catA2) in the late exponential phase. The minimum inhibitory concentration to Hg (II) and Cd (II) was significantly lower in the presence of benzene, demonstrating the effect of co-contamination on bacterial growth. Notably, this study showed that C. metallidurans CH34 degraded benzene in the presence of Hg (II) or Cd (II). Full article

(This article belongs to the Special Issue Microbial Bioremediation)

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Graphical abstract

13 pages, 357 KiB

Open AccessReview

Nonhemolytic Listeria monocytogenes—Prevalence Rate, Reasons Underlying Atypical Phenotype, and Methods for Accurate Hemolysis Assessment

by Iwona Kawacka, Agnieszka Olejnik-Schmidt and Marcin Schmidt

Microorganisms 2022, 10(2), 483; https://doi.org/10.3390/microorganisms10020483 - 21 Feb 2022

Cited by 2 | Viewed by 2080

Abstract

Listeria monocytogenes is a foodborne pathogen that typically presents β-hemolytic activity. However, there are literature reports indicating that L. monocytogenes strains are sometimes nonhemolytic or their zones of hemolysis are perceivable only after removal of the colonies from the agar plate. Nonhemolytic L. [...] Read more.

Listeria monocytogenes is a foodborne pathogen that typically presents β-hemolytic activity. However, there are literature reports indicating that L. monocytogenes strains are sometimes nonhemolytic or their zones of hemolysis are perceivable only after removal of the colonies from the agar plate. Nonhemolytic L. monocytogenes are most commonly encountered in food products, but some have also been detected in clinical samples. Usually, atypical bacteria of this species belong to serotype 1/2a. Mutations of the prfA gene sequence are the most common reason for changed phenotype, and mutations of the hly gene are the second most common cause. There are also reports that the methodology used for detecting hemolysis may influence the results. Sheep or horse blood, although most commonly used in modern studies, may not allow for the production of clear hemolytic zones on blood agar, whereas other types of blood (guinea pig, rabbit, piglet, and human) are more suitable according to some studies. Furthermore, the standard blood agar plate technique is less sensitive than its modifications such as bilayer or top-layer (overlay) techniques. The microplate technique (employing erythrocyte suspensions) is probably the most informative when assessing listerial hemolysis and is the least susceptible to subjective interpretation. Full article

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

13 pages, 2809 KiB

Open AccessArticle

Organic and Inorganic Amendments Shape Bacterial Indicator Communities That Can, In Turn, Promote Rice Yield

by Chongwen Qiu, Yuanyuan Bao, Evangelos Petropoulos, Yiming Wang, Zhenfang Zhong, Yaozhi Jiang, Xuhong Ye, Xiangui Lin and Youzhi Feng

Microorganisms 2022, 10(2), 482; https://doi.org/10.3390/microorganisms10020482 - 21 Feb 2022

Cited by 7 | Viewed by 2111

Abstract

The dynamic patterns of the belowground microbial communities and their corresponding metabolic functions, when exposed to various environmental disturbances, are important for the understanding and development of sustainable agricultural systems. In this study, a two-year field experiment with soils subjected to: chemical fertilization [...] Read more.

The dynamic patterns of the belowground microbial communities and their corresponding metabolic functions, when exposed to various environmental disturbances, are important for the understanding and development of sustainable agricultural systems. In this study, a two-year field experiment with soils subjected to: chemical fertilization (F), mushroom residues (MR), combined application of chemical fertilizers and mushroom residues (MRF), and no-fertilization (CK) was conducted to evaluate the effect of fertilization on the soil bacterial taxonomic and functional compositions as well as on the rice yield. The highest rice yield was obtained under MRF. Soil microbial properties (microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), urease, invertase, acid phosphatase, and soil dehydrogenase activities) reflected the rice yield better than soil chemical characteristics (soil organic matter (SOM), total N (TN), total K (TK), available P (AP), available K (AK), and pH). Although the dominant bacterial phyla were not significantly different among fertilizations, 10 bacterial indicator taxa that mainly belonged to Actinobacteria (Nocardioides, Marmoricola, Tetrasphaera, and unclassified Intrasporangiaceae) with functions of xenobiotic biodegradation and metabolism and amino acid and nucleotide metabolism were found to strongly respond to MRF. Random Forest (RF) modeling further revealed that these 10 bacterial indicator taxa act as drivers for soil dehydrogenase, acid phosphatase, pH, TK, and C/N cycling, which directly and/or indirectly determine the rice yield. Our study demonstrated the explicit links between bacterial indicator communities, community function, soil nutrient cycling, and crop yield under organic and inorganic amendments, and highlighted the advantages of the combined chemical and organic fertilization in agroecosystems. Full article

(This article belongs to the Special Issue Advances in Soil Microbiome)

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15 pages, 5586 KiB

Open AccessArticle

Community Assembly and Co-Occurrence Patterns of Microeukaryotes in Thermokarst Lakes of the Yellow River Source Area

by Ze Ren, Kang Ma, Xuan Jia, Qing Wang, Cheng Zhang and Xia Li

Microorganisms 2022, 10(2), 481; https://doi.org/10.3390/microorganisms10020481 - 21 Feb 2022

Cited by 7 | Viewed by 2190

Abstract

Thermokarst lakes are important aquatic ecosystems in cold regions, experiencing several changes due to global warming. However, the fundamental assembly mechanisms of microeukaryotic communities in thermokarst lakes are unknown. In this study, we examined the assembly processes and co-occurrence networks of microeukaryotic communities [...] Read more.

Thermokarst lakes are important aquatic ecosystems in cold regions, experiencing several changes due to global warming. However, the fundamental assembly mechanisms of microeukaryotic communities in thermokarst lakes are unknown. In this study, we examined the assembly processes and co-occurrence networks of microeukaryotic communities in sediment and water of thermokarst lakes in the Yellow River Source Area. Sediment microeukaryotic communities had a significantly lower α-diversity but higher β-diversity than water microeukaryotic communities. pH, sediment organic carbon, and total phosphorus significantly affected taxonomic and phylogenetic diversity of sediment communities, while conductivity was a significant driver for water communities. Both sediment and water microeukaryotic communities were strongly governed by dispersal limitation. However, deterministic processes, especially homogenous selection, were more relevant in structuring microeukaryotic communities in water than those in sediment. Changes in total nitrogen and phosphorus in sediment could contribute to shift its microeukaryotic communities from homogeneous selection to stochastic processes. Co-occurrence networks showed that water microeukaryotic communities are more complex and interconnected but have lower modularity than sediment microeukaryotic communities. The water microeukaryotic network had more modules than the sediment microeukaryotic network. These modules were dominated by different taxonomic groups and associated to different environmental variables. Full article

(This article belongs to the Section Environmental Microbiology)

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23 pages, 2434 KiB

Open AccessArticle

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

by Tatyana V. Butina, Ivan S. Petrushin, Igor V. Khanaev and Yurij S. Bukin

Microorganisms 2022, 10(2), 480; https://doi.org/10.3390/microorganisms10020480 - 21 Feb 2022

Cited by 6 | Viewed by 2117

Abstract

Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge [...] Read more.

Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges. Full article

(This article belongs to the Special Issue Ecology, Physiology and Phylogeny of Microbes in Lakes and Their Catchments)

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14 pages, 909 KiB

Open AccessArticle

Shallow-Water Hydrothermal Vents as Natural Accelerators of Bacterial Antibiotic Resistance in Marine Coastal Areas

by Erika Arcadi, Eugenio Rastelli, Michael Tangherlini, Carmen Rizzo, Monique Mancuso, Marilena Sanfilippo, Valentina Esposito, Franco Andaloro and Teresa Romeo

Microorganisms 2022, 10(2), 479; https://doi.org/10.3390/microorganisms10020479 - 21 Feb 2022

Cited by 5 | Viewed by 2123

Abstract

Environmental contamination by heavy metals (HMs) poses several indirect risks to human health, including the co-spreading of genetic traits conferring resistance to both HMs and antibiotics among micro-organisms. Microbial antibiotic resistance (AR) acquisition is enhanced at sites anthropogenically polluted by HMs, as well [...] Read more.

Environmental contamination by heavy metals (HMs) poses several indirect risks to human health, including the co-spreading of genetic traits conferring resistance to both HMs and antibiotics among micro-organisms. Microbial antibiotic resistance (AR) acquisition is enhanced at sites anthropogenically polluted by HMs, as well as in remote systems naturally enriched in HMs, such as hydrothermal vents in the deep sea. However, to date, the possible role of hydrothermal vents at shallower water depths as hot spots of microbial AR gain and spreading has not been tested, despite the higher potential risks associated with the closer vicinity of such ecosystems to coasts and human activities. In this work, we collected waters and sediments at the Panarea shallow-water hydrothermal vents, testing the presence of culturable marine bacteria and their sensitivity to antibiotics and HMs. All of the bacterial isolates showed resistance to at least one antibiotic and one HM and, most notably, 80% of them displayed multi-AR on average to 12 (min 8, max 15) different antibiotics, as well as multi-HM tolerance. We show that our isolates displayed high similarity (≥99%) to common marine bacteria, affiliating with Actinobacteria, Gammaproteobacteria, Alphaproteobacteria and Firmicutes, and all displayed wide growth ranges for temperature and salinity during in vitro physiological tests. Notably, the analysis of the genomes available in public databases for their closest relatives highlighted the lack of genes for AR, posing new questions on the origin of multi-AR acquisition in this peculiar HM-rich environment. Overall, our results point out that shallow-water hydrothermal vents may contribute to enhance AR acquisition and spreading among common marine bacteria in coastal areas, highlighting this as a focus for future research. Full article

(This article belongs to the Section Environmental Microbiology)

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8 pages, 7006 KiB

Open AccessCommunication

Emergence of Novel Chlamydia trachomatis Sequence Types among Chlamydia Patients in the Republic of Belarus

by Valentina A. Feodorova, Yury V. Saltykov, Anna A. Kolosova, Liudmila V. Rubanik, Nikolay N. Poleshchuk and Vladimir L. Motin

Microorganisms 2022, 10(2), 478; https://doi.org/10.3390/microorganisms10020478 - 21 Feb 2022

Cited by 4 | Viewed by 1858

Abstract

Chlamydia trachomatis (CT) is a major cause of sexually transmitted diseases worldwide. The multilocus sequence typing (MLST) of clinical samples from random heterosexual chlamydia patients who were either asymptomatic or reported clinical manifestations of genital chlamydiosis (n = 63) in each of [...] Read more.

Chlamydia trachomatis (CT) is a major cause of sexually transmitted diseases worldwide. The multilocus sequence typing (MLST) of clinical samples from random heterosexual chlamydia patients who were either asymptomatic or reported clinical manifestations of genital chlamydiosis (n = 63) in each of the seven major regions of the Republic of Belarus in 2017–2018 revealed 12 different CT sequence types (STs). We found seven known STs, ST4, ST6, ST9, ST13, ST38, ST95 and ST110, and five novel variants, namely ST271–ST275, which have not been detected elsewhere thus far. The ST4 variant was predominant (27/63, 42.9%) and detected in six out of seven regions. The two most common STs, ST9 and ST13, were regularly seen in four out of seven regions. In contrast, the remaining STs, ST6, ST38, ST95, ST110, and novel STs271-275, surfaced randomly in different parts of the country. The emergence of novel STs was registered in two regions, namely Minsk (ST271 and ST275) and Brest (ST271, ST272, ST273, and ST274). All the STs of detected CT strains were clustered into two Groups, I and III, which are characteristic of CT urogenital strains. No STs typical for Group II, specific to the LGV strains, were revealed. Our study contributes to better understanding the genetic diversity and molecular evolution of CT, one of the most important pathogens in public health worldwide. Full article

(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens)

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3 pages, 184 KiB

Open AccessEditorial

Special Issue: Microbial Impact on Cholesterol and Bile Acid Metabolism

by Jason M. Ridlon

Microorganisms 2022, 10(2), 477; https://doi.org/10.3390/microorganisms10020477 - 21 Feb 2022

Cited by 2 | Viewed by 1579

Abstract

An important current focus in microbiome science is the biotransformation and degradation of cholesterol, steroids, and bile acids [...] Full article

(This article belongs to the Special Issue Microbial Impact on Cholesterol and Bile Acid Metabolism)

8 pages, 3090 KiB

Open AccessTechnical Note

Easy Removal of Epiphytic Bacteria on Ulva (Ulvophyceae, Chlorophyta) by Vortex with Silica Sands

by Xiaojie Liu, Jin Zhao and Peng Jiang

Microorganisms 2022, 10(2), 476; https://doi.org/10.3390/microorganisms10020476 - 21 Feb 2022

Cited by 5 | Viewed by 2018

Abstract

Macroalgae-associated bacteria play an important role in their algal hosts’ biological processes. They are localized on surfaces of the host thalli, as well as between and even within algal cells. To examine the differences in community structures and functions between epi- and endo- [...] Read more.

Macroalgae-associated bacteria play an important role in their algal hosts’ biological processes. They are localized on surfaces of the host thalli, as well as between and even within algal cells. To examine the differences in community structures and functions between epi- and endo- bacteria, an effective approach for maximizing epiphyte removal from delicate seaweeds while retaining endophyte fidelity must be developed. In this study, a variety of surface sterilization methods for Ulva prolifera were compared, including mechanical, chemical, and enzymatical treatments. According to the results of scanning electron microscope (SEM) and denaturing gradient gel electrophoresis (DGGE) analysis, almost complete removal of epiphytic bacteria on Ulva was obtained simply by co-vortex of seaweeds with silica sands, causing minimal disturbance to endosymbionts when compared to previous published methods. In addition, the adaptability was also confirmed in additional U. prolifera strains and Ulva species with blade-like or narrow tubular thallus shapes. This easy mechanical method would enable the analysis of community composition and host specificity for Ulva-associated epi- and endo-bacteria separately. Full article

(This article belongs to the Special Issue Algal Host-Microbe Interactions)

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16 pages, 3267 KiB

Open AccessArticle

Identification of a Novel Biosurfactant with Antimicrobial Activity Produced by Rhodococcus opacus R7

by Jessica Zampolli, Alessandra De Giani, Alessandra Di Canito, Guido Sello and Patrizia Di Gennaro

Microorganisms 2022, 10(2), 475; https://doi.org/10.3390/microorganisms10020475 - 21 Feb 2022

Cited by 12 | Viewed by 2854

Abstract

Rhodococcus members excrete secondary metabolites, especially compounds which act as biosurfactants. In this work, we demonstrated the ability of Rhodococcus opacus R7 to produce a novel bioactive compound belonging to the class of biosurfactants with antimicrobial properties during the growth on naphthalene. Chemical [...] Read more.

Rhodococcus members excrete secondary metabolites, especially compounds which act as biosurfactants. In this work, we demonstrated the ability of Rhodococcus opacus R7 to produce a novel bioactive compound belonging to the class of biosurfactants with antimicrobial properties during the growth on naphthalene. Chemical and biochemical analyses of the isolated compound demonstrated that the biosurfactant could be classified as a hydrophobic peptide. The ESI-full mass spectrometry revealed that the isolated biosurfactant showed a molecular weight of 1292 Da and NMR spectra evidenced the composition of the following amino acid residues: Ala, Thr, Asp, Gly, Ser. Surfactant activity of the R. opacus R7 compound was quantified by the critical micelle dilution (CMD) method and the critical micelle concentration (CMC) was estimated around 20 mg L⁻¹ with a corresponding surface tension of 48 mN m⁻¹. Moreover, biological assays demonstrated that R. opacus R7 biosurfactant peptide exhibited antimicrobial activity against Escherichia coli ATCC 29522 and Staphylococcus aureus ATCC 6538 with the minimum inhibition growth concentration (MIC) values of 2.6 mg mL⁻¹ and 1.7 mg mL⁻¹, respectively. In this study for the first time, a hydrophobic peptide with both biosurfactant and antimicrobial activity was isolated from a bacterium belonging to Rhodococcus genus. Full article

(This article belongs to the Special Issue Antimicrobial Lipopeptide Biosurfactant)

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4 pages, 215 KiB

Open AccessEditorial

Gut Microbiota and Metabolism in Different Stages of Life and Health

by Shanthi G. Parkar and Pramod K. Gopal

Microorganisms 2022, 10(2), 474; https://doi.org/10.3390/microorganisms10020474 - 21 Feb 2022

Viewed by 1677

Abstract

In a very fascinating read, John Goodsir, a Scottish surgeon, describes how he isolated “vegetable organisms” from the “ejected fluid” from the stomach of his 19-year-old patient [...] Full article

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

15 pages, 1393 KiB

Open AccessArticle

Urinary Tract Infections and Associated Factors among Patients with Indwelling Urinary Catheters Attending Bugando Medical Centre a Tertiary Hospital in Northwestern Tanzania

by Asteria L. M. Ndomba, Rose M. Laisser, Vitus Silago, Benson R. Kidenya, Joseph Mwanga, Jeremiah Seni and Stephen E. Mshana

Microorganisms 2022, 10(2), 473; https://doi.org/10.3390/microorganisms10020473 - 21 Feb 2022

Cited by 9 | Viewed by 4066

Abstract

Complications of indwelling urinary catheterization (IUC) are associated with significant morbidity and mortality, thus affecting patient’s well-being. Understanding the magnitude and factors associated with complications is crucial in designing appropriate preventive strategies. A cross-sectional study was conducted at Bugando Medical Centre, involving patients [...] Read more.

Complications of indwelling urinary catheterization (IUC) are associated with significant morbidity and mortality, thus affecting patient’s well-being. Understanding the magnitude and factors associated with complications is crucial in designing appropriate preventive strategies. A cross-sectional study was conducted at Bugando Medical Centre, involving patients with long-term and short-term IUC from December 2016 to September 2017. The data were analyzed by STATA 13.0. Catheter-associated urinary tract infection (CA-UTI) was the leading (56.8%; 250/440) complication among patients with IUC. Gram-negative bacteria were predominantly isolated (98.1%, 252/257), whereas E. coli (30.7%, 79/257) and Klebsiella spp. (29.6%, 76/257) were the leading pathogens. CA-UTI was significantly higher among out-patients than in-patients (82.2% v 35.3%, p < 0.001). Older age (OR: 1.3, (95%CI: 1.1–1.5), p < 0.001), level of education (OR: 1.8, (95%CI: 1.1–3.1), p = 0.029) and catheter duration of ≥6 weeks (OR: 2.43, (95%CI: 1.1–5.5), p = 0.031) independently predicted CA-UTI among outpatients, while female gender (OR: 2.1, (95%CI: 1.2–3.7), p = 0.014), catheter bags not freely hanging (OR: 0.4, (95%CI: 0.2–0.7), p = 0.002) and residing outside Mwanza region (OR: 0.4, (95%CI: 0.2–0.6), p < 0.001) predicted CA-UTI among in-patients. CA-UTI is the common complication among patients with IUC, significantly higher in out-patients than in-patients. We recommend involving patients and carers in infection prevention and control measures in out-patients living with IUC. Full article

(This article belongs to the Section Medical Microbiology)

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8 pages, 1800 KiB

Open AccessArticle

Current Production Capability of Drug-Resistant Pathogen Enables Its Rapid Label-Free Detection Applicable to Wastewater-Based Epidemiology

by Waheed Miran, Xizi Long, Wenyuan Huang and Akihiro Okamoto

Microorganisms 2022, 10(2), 472; https://doi.org/10.3390/microorganisms10020472 - 20 Feb 2022

Cited by 3 | Viewed by 2232

Abstract

A rapid and label-free method for the detection of drug-resistant pathogens is in high demand for wastewater-based epidemiology. As recently shown, the extent of electrical current production (I_c) is a useful indicator of a pathogen’s metabolic activity. Therefore, if drug-resistant [...] Read more.

A rapid and label-free method for the detection of drug-resistant pathogens is in high demand for wastewater-based epidemiology. As recently shown, the extent of electrical current production (I_c) is a useful indicator of a pathogen’s metabolic activity. Therefore, if drug-resistant bacteria have extracellular electron transport (EET) capability, a simple electric sensor may be able to detect not only the growth as a conventional plating technique but also metabolic activity specific for drug-resistant bacteria in the presence of antibiotics. Here, one of the multidrug-resistant pathogens in wastewater, Klebsiella pneumoniae, was shown to generate I_c, and the extent of I_c was unaffected by the microbial growth inhibitor, kanamycin, while the current was markedly decreased in environmental EET bacteria Shewanella oneidensis. Kanamycin differentiated I_c in K. pneumonia and S. oneidensis within 3 h. Furthermore, the detection of K. pneumoniae was successful in the presence of S. oneidensis in the electrochemical cell. These results clarify the advantage of detecting drug-resistant bacteria using whole-cell electrochemistry as a simple and rapid method to detect on-site drug-resistant pathogens in wastewater, compared with conventional colony counting, which takes a few days. Full article

(This article belongs to the Special Issue New Electrogenic Microbes)

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14 pages, 2130 KiB

Open AccessArticle

Lactobacilli Strain Mixture Alleviates Bacterial Vaginosis through Antibacterial and Antagonistic Activity in Gardnerella vaginalis-Infected C57BL/6 Mice

by Soo-Im Choi, GaYeong Won, YongGyeong Kim, Chang-Ho Kang and Gun-Hee Kim

Microorganisms 2022, 10(2), 471; https://doi.org/10.3390/microorganisms10020471 - 20 Feb 2022

Cited by 10 | Viewed by 2843

Abstract

The present study investigated the anti-bacterial vaginitis (BV) effects of a mixture of five lactobacilli strains (LM5), containing equal amounts of Ligilactobacillus salivarius MG242, Limosilactobacillus fermentum MG901, Lactiplantibacillus plantarum MG989, Lacticaseibacillus paracasei MG4272, and Lacticaseibacillus rhamnosus MG4288), in HeLa cells and Gardnerella vaginalis [...] Read more.

The present study investigated the anti-bacterial vaginitis (BV) effects of a mixture of five lactobacilli strains (LM5), containing equal amounts of Ligilactobacillus salivarius MG242, Limosilactobacillus fermentum MG901, Lactiplantibacillus plantarum MG989, Lacticaseibacillus paracasei MG4272, and Lacticaseibacillus rhamnosus MG4288), in HeLa cells and Gardnerella vaginalis (GV)-infected BV mice. All strains produced lactic acid and hydrogen peroxide, and were resistant to nonoxynol-9. LM5 significantly inhibited GV growth by 80%, exhibited good adhesion to HeLa cells, and significantly inhibited GV adhesion to these cells. In GV-infected mice, LM5 administered orally at 5 × 10⁹ CFU/mouse significantly inhibited GV proliferation in the vaginal tract and significantly reduced myeloperoxidase activity, pro-inflammatory cytokine (TNF-α, IL-1β, and IL-6) levels, and nitric oxide levels in vaginal tissue lysates. Histopathological analysis of vaginal tissues revealed that LM5 markedly suppressed the exfoliation of vaginal epithelial cells. Overall, these results suggest that LM5 might alleviate BV by direct antibacterial and antagonistic activity in vaginal tissues of GV-infected mice. Full article

(This article belongs to the Section Medical Microbiology)

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16 pages, 307 KiB

Open AccessArticle

The Combination of In Vitro Assessment of Stress Tolerance Ability, Autoaggregation, and Vitamin B-Producing Ability for New Probiotic Strain Introduction

by Natalya Yu. Khromova, Julia M. Epishkina, Boris A. Karetkin, Natalia V. Khabibulina, Andrey V. Beloded, Irina V. Shakir and Victor I. Panfilov

Microorganisms 2022, 10(2), 470; https://doi.org/10.3390/microorganisms10020470 - 19 Feb 2022

Cited by 12 | Viewed by 2772

Abstract

The health benefits of probiotics are beyond doubt. The positive effects of lactobacilli and bifidobacteria on the function of many body systems have been repeatedly proven by various studies. To completely realize the potential of probiotic microorganisms, the strains should be tested by [...] Read more.

The health benefits of probiotics are beyond doubt. The positive effects of lactobacilli and bifidobacteria on the function of many body systems have been repeatedly proven by various studies. To completely realize the potential of probiotic microorganisms, the strains should be tested by the greatest combination of characteristics that contribute to the wellness of the host. In this work, for the first time, a combined assessment of the probiotic properties and vitamin B-producing potential of various species and strains of bifidobacteria and lactobacilli was carried out. The presence of an additional advantage, such as vitamin-producing ability, can prevent vitamin deficiency both at the level of the consumption of fermented foods, when the enrichment will occur naturally on the spot, and during colonization by these intestinal strains, when synthesis will occur in vivo. To select potential probiotics, the stress tolerance ability of 16 lactic acid bacteria and bifidobacteria strains to low pH values, bile, and proteolytic enzymes, as well as their ability to autoaggregate, were studied under conditions of modeling the gastrointestinal tract in vitro. The ability of the strains to extracellularly accumulate water-soluble B vitamins was evaluated by capillary electrophoresis. Among the tested strains of bifidobacteria, B. adolescentis VKPM AC-1662 is of interest; it was characterized by the greatest stress tolerance ability and the ability to autoaggregate, in addition to the extracellular synthesis of riboflavin and pyridoxine. Among lactic acid bacteria, L. sakei VKPM B-8936 demonstrated the greatest tolerance to low pH, L. plantarum VKPM B–11007 to duodenal conditions, L. acidophilus VKPM B-2213 to pepsin, and L. salivarius VKPM B–2214 to pancreatin. The highest percentage of autoaggregation was observed in L. salivarius VKPM B-2214, which also accumulated the largest amount of pantothenic acid, but it was sensitive to stress conditions. The obtained results could be used to create new products enriched with probiotics and B vitamins. Full article

(This article belongs to the Special Issue Studies on Lactic Acid Bacteria: Metabolism, Genomics and Applications)

13 pages, 1804 KiB

Open AccessArticle

Molecular Epidemiology of Multidrug-Resistant Pneumococci among Ghanaian Children under Five Years Post PCV13 Using MLST

by Richael O. Mills, Mohammed R. Abdullah, Samuel A. Akwetey, Dorcas C. Sappor, Gustavo Gámez and Sven Hammerschmidt

Microorganisms 2022, 10(2), 469; https://doi.org/10.3390/microorganisms10020469 - 19 Feb 2022

Cited by 3 | Viewed by 1857

Abstract

Antibiotic resistance in pneumococci contributes to the high pneumococcal deaths in children. We assessed the molecular characteristics of multidrug-resistant (MDR) pneumococci isolated from healthy vaccinated children under five years of age in Cape Coast, Ghana. A total of 43 MDR isolates were selected [...] Read more.

Antibiotic resistance in pneumococci contributes to the high pneumococcal deaths in children. We assessed the molecular characteristics of multidrug-resistant (MDR) pneumococci isolated from healthy vaccinated children under five years of age in Cape Coast, Ghana. A total of 43 MDR isolates were selected from 151 pneumococcal strains obtained from nasopharyngeal carriage. All isolates were previously serotyped by multiplex PCR and Quellung reaction. Susceptibility testing was performed using either the E-test or disk diffusion method. Virulence and antibiotic resistance genes were identified by PCR. Molecular epidemiology was analyzed using multilocus sequence typing (MLST). Vaccine-serotypes 23F and 19F were predominant. The lytA and pavB virulence genes were present in all isolates, whiles 14–86% of the isolates carried pilus-islets 1 and 2, pcpA, and psrP genes. Penicillin, tetracycline, and cotrimoxazole resistance were evident in >90% of the isolates. The ermB, mefA, and tetM genes were detected in (n = 7, 16.3%), (n = 4, 9.3%) and (n = 43, 100%) of the isolates, respectively. However, >60% showed alteration in the pbp2b gene. MLST revealed five novel and six known sequence types (STs). ST156 (Spain^9V-3) and ST802 were identified as international antibiotic-resistant clones. The emergence of international-MDR clones in Ghana requires continuous monitoring of the pneumococcus through a robust surveillance system. Full article

(This article belongs to the Special Issue Pneumococcal Pneumonia: Epidemiology, Pathophysiology, Treatment and Vaccines)

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19 pages, 4676 KiB

Open AccessArticle

A Parallel Tracking of Salivary and Gut Microbiota Profiles Can Reveal Maturation and Interplay of Early Life Microbial Communities in Healthy Infants

by Sofia Reddel, Giuseppe Rubens Pascucci, Silvia Foligno, Federica Del Chierico, Pamela Vernocchi, Alessandra Marzullo, Maria Grazia Pattumelli, Paolo Palma, Guglielmo Salvatori and Lorenza Putignani

Microorganisms 2022, 10(2), 468; https://doi.org/10.3390/microorganisms10020468 - 18 Feb 2022

Cited by 4 | Viewed by 2148

Abstract

In this study, the onset and shaping of the salivary and gut microbiota in healthy newborns during the first period of life has been followed, evaluating the impact of salivary microbiota on the development of early fecal microbial communities. The microbiota of 80 [...] Read more.

In this study, the onset and shaping of the salivary and gut microbiota in healthy newborns during the first period of life has been followed, evaluating the impact of salivary microbiota on the development of early fecal microbial communities. The microbiota of 80 salivary and 82 fecal samples that were collected from healthy newborns in the first six months of life, was investigated by 16S rRNA amplicon profiling. The microbial relationship within and between the saliva and gut ecosystems was determined by correlation heatmaps and co-occurrence networks. Streptococcus and Staphylococcus appeared as early commensals in the salivary microbiota, dominating this ecosystem through the time, while Fusobacterium, Prevotella, Porphyromonas, Granulicatella, and Veillonella were late colonizers. Enterobacteriaceae, Staphylococcus and Streptococcus were gut pioneers, followed by the anaerobic Bifidobacterium, Veillonella, Eggerthella, and Bacteroides. Streptococcus, Staphylococcus, and Veillonella were shared by the gut and saliva ecosystems. The saliva and gut microbiota seem to evolve independently, driven by local adaptation strategies, except for the oral Streptococcus and Veillonella that are involved in gut microbiota development as seeding species. This study offers a piece of knowledge on how the oral microbiota may affect the gut microbiota in healthy newborns, shedding light onto new microbial targets for the development of therapies for early life intestinal dysbiosis. Full article

(This article belongs to the Special Issue Network Analysis of Microbiome and Metabolome in Health and Disease)

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19 pages, 9504 KiB

Open AccessArticle

Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect?

by Taha Menasria and Margarita Aguilera

Microorganisms 2022, 10(2), 467; https://doi.org/10.3390/microorganisms10020467 - 18 Feb 2022

Cited by 10 | Viewed by 3083

Abstract

Here, we report a first comprehensive genomic analysis of SARS-CoV-2 variants circulating in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with respect to genomic clades and mutational patterns. As of December 2021, a total of 1669 high-coverage whole-genome sequences [...] Read more.

Here, we report a first comprehensive genomic analysis of SARS-CoV-2 variants circulating in North African countries, including Algeria, Egypt, Libya, Morocco, Sudan and Tunisia, with respect to genomic clades and mutational patterns. As of December 2021, a total of 1669 high-coverage whole-genome sequences submitted to EpiCoV GISAID database were analyzed to infer clades and mutation annotation compared with the wild-type variant Wuhan-Hu-1. Phylogenetic analysis of SARS-CoV-2 genomes revealed the existence of eleven GISAID clades with GR (variant of the spike protein S-D614G and nucleocapsid protein N-G204R), GH (variant of the ORF3a coding protein ORF3a-Q57H) and GK (variant S-T478K) being the most common with 25.9%, 19.9%, and 19.6%, respectively, followed by their parent clade G (variant S-D614G) (10.3%). Lower prevalence was noted for GRY (variant S-N501Y) (5.1%), S (variant ORF8-L84S) (3.1%) and GV (variant of the ORF3a coding protein NS3-G251V) (2.0%). Interestingly, 1.5% of total genomes were assigned as GRA (Omicron), the newly emerged clade. Across the North African countries, 108 SARS-CoV-2 lineages using the Pangolin assignment were identified, whereby most genomes fell within six major lineages and variants of concern (VOC) including B.1, the Delta variants (AY.X, B.1.617.2), C.36, B.1.1.7 and B.1.1. The effect of mutations in SAR-CoV-2 genomes highlighted similar profiles with D614G spike (S) and ORF1b-P314L variants as the most changes found in 95.3% and 87.9% of total sequences, respectively. In addition, mutations affecting other viral proteins appeared frequently including; N:RG203KR, N:G212V, NSP3:T428I, ORF3a:Q57H, S:N501Y, M:I82T and E:V5F. These findings highlight the importance of genomic surveillance for understanding the SARS-CoV-2 genetic diversity and its spread patterns, leading to a better guiding of public health intervention measures. The know-how analysis of the present work could be implemented worldwide in order to overcome this health crisis through harmonized approaches. Full article

(This article belongs to the Section Virology)

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11 pages, 9094 KiB

Open AccessReview

Bacterial Biofilms Utilize an Underlying Extracellular DNA Matrix Structure That Can Be Targeted for Biofilm Resolution

by Steven D. Goodman and Lauren O. Bakaletz

Microorganisms 2022, 10(2), 466; https://doi.org/10.3390/microorganisms10020466 - 18 Feb 2022

Cited by 12 | Viewed by 2908

Abstract

Bacterial biofilms contribute significantly to the antibiotic resistance, pathogenesis, chronicity and recurrence of bacterial infections. Critical to the stability and survival of extant biofilms is the extracellular DNA (eDNA)-dependent matrix which shields the resident bacteria from hostile environments, allows a sessile metabolic state, [...] Read more.

Bacterial biofilms contribute significantly to the antibiotic resistance, pathogenesis, chronicity and recurrence of bacterial infections. Critical to the stability and survival of extant biofilms is the extracellular DNA (eDNA)-dependent matrix which shields the resident bacteria from hostile environments, allows a sessile metabolic state, but also encourages productive interactions with biofilm-inclusive bacteria. Given the importance of the eDNA, approaches to this area of research have been to target not just the eDNA, but also the additional constituent structural components which appear to be widespread. Chief among these is a ubiquitous two-member family of bacterial nucleoid associated proteins (the DNABII proteins) responsible for providing structural integrity to the eDNA and thereby the biofilm. Moreover, this resultant novel eDNA-rich secondary structure can also be targeted for disruption. Here, we provide an overview of both what is known about the eDNA-dependent matrix, as well as the resultant means that have resulted in biofilm resolution. Results obtained to date have been highly supportive of continued development of DNABII-targeted approaches, which is encouraging given the great global need for improved methods to medically manage, or ideally prevent biofilm-dependent infections, which remains a highly prevalent burden worldwide. Full article

(This article belongs to the Special Issue Biofilm Formation and Survival Strategies)

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20 pages, 12811 KiB

Open AccessArticle

From Rest to Growth: Life Collisions of Gordonia polyisoprenivorans 135

by Nataliya E. Suzina, Vladimir V. Sorokin, Valentina N. Polivtseva, Violetta V. Klyueva, Elena V. Emelyanova and Inna P. Solyanikova

Microorganisms 2022, 10(2), 465; https://doi.org/10.3390/microorganisms10020465 - 18 Feb 2022

Cited by 4 | Viewed by 2026

Abstract

In the process of evolution, living organisms develop mechanisms for population preservation to survive in unfavorable conditions. Spores and cysts are the most obvious examples of dormant forms in microorganisms. Non-spore-forming bacteria are also capable of surviving in unfavorable conditions, but the patterns [...] Read more.

In the process of evolution, living organisms develop mechanisms for population preservation to survive in unfavorable conditions. Spores and cysts are the most obvious examples of dormant forms in microorganisms. Non-spore-forming bacteria are also capable of surviving in unfavorable conditions, but the patterns of their behavior and adaptive reactions have been studied in less detail compared to spore-forming organisms. The purpose of this work was to study the features of transition from dormancy to active vegetative growth in one of the non-spore-forming bacteria, Gordonia polisoprenivorans 135, which is known as a destructor of such aromatic compounds as benzoate, 3-chlorobenzoate, and phenol. It was shown that G. polyisoprenivorans 135 under unfavorable conditions forms cyst-like cells with increased thermal resistance. Storage for two years does not lead to complete cell death. When the cells were transferred to fresh nutrient medium, visible growth was observed after 3 h. Immobilized cells stored at 4 °C for at least 10 months regenerated their metabolic activity after only 30 min of aeration. A study of the ultrathin organization of resting cells by transmission electron microscopy combined with X-ray microanalysis revealed intracytoplasmic electron-dense spherical membrane ultrastructures with significant similarity to previously described acidocalcisomas. The ability of some resting G. polyisoprenivorans 135 cells in the population to secrete acidocalcisome-like ultrastructures into the extracellular space was also detected. These structures contain predominantly calcium (Ca) and, to a lesser extent, phosphorus (P), and are likely to serve as depots of vital macronutrients to maintain cell viability during resting and provide a quick transition to a metabolically active state under favorable conditions. The study revealed the features of transitions from active growth to dormant state and vice versa of non-spore-forming bacteria G. polyisoprenivorans 135 and the possibility to use them as the basis of biopreparations with a long shelf life. Full article

(This article belongs to the Special Issue Microbial Biocatalysis and Biodegradation)

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17 pages, 1664 KiB

Open AccessReview

Vaccination against Tick-Borne Encephalitis (TBE) in Italy: Still a Long Way to Go

by Donatella Panatto, Alexander Domnich, Daniela Amicizia, Paolo Reggio and Raffaella Iantomasi

Microorganisms 2022, 10(2), 464; https://doi.org/10.3390/microorganisms10020464 - 18 Feb 2022

Cited by 11 | Viewed by 4845

Abstract

Tick-borne encephalitis (TBE) is endemic in several European countries, and its incidence has recently increased. Various factors may explain this phenomenon: social factors (changes in human behavior, duration and type of leisure activities and increased tourism in European high-risk areas), ecological factors (e.g., [...] Read more.

Tick-borne encephalitis (TBE) is endemic in several European countries, and its incidence has recently increased. Various factors may explain this phenomenon: social factors (changes in human behavior, duration and type of leisure activities and increased tourism in European high-risk areas), ecological factors (e.g., effects of climate change on the tick population and reservoir animals), and technological factors (improved diagnostics, increased medical awareness). Furthermore, the real burden of TBE is not completely known, as the performance of surveillance systems is suboptimal and cases of disease are under-reported in several areas. Given the potentially severe clinical course of the disease, the absence of any antiviral therapy, and the impossibility of interrupting the transmission of the virus in nature, vaccination is the mainstay of prevention and control. TBE vaccines are effective (protective effect of approximately 95% after completion of the basic vaccination—three doses) and well tolerated. However, their uptake in endemic areas is suboptimal. In the main endemic countries where vaccination is included in the national/regional immunization program (with reimbursed vaccination programs), this decision was driven by a cost-effectiveness assessment (CEA), which is a helpful tool in the decision-making process. All CEA studies conducted have demonstrated the cost-effectiveness of TBE vaccination. Unfortunately, CEA is still lacking in many endemic countries, including Italy. In the future, it will be necessary to fill this gap in order to introduce an effective vaccination strategy in endemic areas. Finally, raising awareness of TBE, its consequences and the benefit of vaccination is critical in order to increase vaccination coverage and reduce the burden of the disease. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

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12 pages, 1290 KiB

Open AccessArticle

Probiotic Potentiality from Versatile Lactiplantibacillus plantarum Strains as Resource to Enhance Freshwater Fish Health

by Massimo Iorizzo, Gianluca Albanese, Francesco Letizia, Bruno Testa, Patrizio Tremonte, Franca Vergalito, Silvia Jane Lombardi, Mariantonietta Succi, Raffaele Coppola and Elena Sorrentino

Microorganisms 2022, 10(2), 463; https://doi.org/10.3390/microorganisms10020463 - 17 Feb 2022

Cited by 22 | Viewed by 2845

Abstract

Dietary probiotic supplementation has the potential to enhance the health of fish and their disease resistance. In this study, some properties of ten Lactiplantibacillus plantarum strains have been evaluated, for their potential use as probiotics in freshwater fish diet. In particular, antimicrobial activity, [...] Read more.

Dietary probiotic supplementation has the potential to enhance the health of fish and their disease resistance. In this study, some properties of ten Lactiplantibacillus plantarum strains have been evaluated, for their potential use as probiotics in freshwater fish diet. In particular, antimicrobial activity, antioxidant activity, the potentiality to survive the gastrointestinal transit and persist in the intestine, were evaluated in vitro. The experimental tests were carried out at 15 °C and 30 °C to determine the suitability of these lactic acid bacteria to be used as probiotics in the diet of fish grown at different temperatures. The results demonstrated that the evaluated Lp. plantarum strains, which often have significant differences among themselves, are characterized by important functional characteristics such as cell surface properties (auto-aggregation and hydrophobicity), ability to produce antioxidant substances, capacity to survive in the presence of 0.3% bile salts and acidic environment (2.5 pH), antagonistic activity against some fish opportunistic pathogens (A. salmonicida, Ps. aeruginosa, E. coli and C. freundii) and other unwanted bacteria present in fish products (S. aureus and L. innocua). The outcomes suggest that these Lp. plantarum strains may be candidates as probiotics in warm- and cold-water aquaculture. Full article

(This article belongs to the Special Issue Lactobacillus: Identification, Characterization and Application in Conventional and Functional Foods)

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19 pages, 5411 KiB

Open AccessArticle

Long-Term Application of Bio-Compost Increased Soil Microbial Community Diversity and Altered Its Composition and Network

by Xiayan Liu, Yu Shi, Lingyu Kong, Lihong Tong, Haoxuan Cao, Hu Zhou and Yizhong Lv

Microorganisms 2022, 10(2), 462; https://doi.org/10.3390/microorganisms10020462 - 17 Feb 2022

Cited by 24 | Viewed by 3190

Abstract

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of [...] Read more.

The influence of bio-compost on the diversity, composition and structure of soil microbial communities is less understood. Here, Illumina MiSeq sequencing and a network analysis were used to comprehensively characterize the effects of 25 years of bio-compost application on the microbial diversity of soil and community composition. High dosages of bio-compost significantly increased the bacterial and fungal richness. The compositions of bacterial and fungal communities were significantly altered by bio-compost addition. Bio-compost addition enriched the relative abundance of beneficial microorganisms (such as Sphingomonas, Acidibacter, Nocardioides, etc.) and reduced the relative abundance of harmful microorganisms (such as Stachybotrys and Aspergillus). Electrical conductivity, soil organic matter and total phosphorus were the key factors in shaping soil microbial community composition. The bacterial network was more complex than fungal network, and bacteria were more sensitive to changes in environmental factors than fungi. Positive interactions dominated both the bacterial and fungal networks, with stronger positive interactions found in the bacterial network. Functional prediction suggested that bio-composts altered the soil bacterial-community metabolic function with respect to carbon, nitrogen and phosphorus cycles and fungal community trophic modes. In conclusion, suitable bio-compost addition is beneficial to the improvement of soil health and crop quality and therefore the sustainability of agriculture. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 2286 KiB

Open AccessArticle

Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques

by Hanka Brangsch, Anatolii Golovko, Nataliia Pinchuk, Oleg Deriabin, Tetiana Kyselova, Jörg Linde, Falk Melzer and Mandy Carolina Elschner

Microorganisms 2022, 10(2), 461; https://doi.org/10.3390/microorganisms10020461 - 17 Feb 2022

Cited by 7 | Viewed by 3650

Abstract

Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining [...] Read more.

Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining long- and short-read next-generation sequencing techniques, highly accurate genomes were reconstructed, enabling detailed in silico genotyping. Thus, the strains could be assigned to the Tsiankovskii subgroup of the “TransEurAsia” clade, which is commonly found in this region. Their high genetic similarity suggests that the four strains are members of the endemic population whose progenitor was once introduced in the Ukraine and bordering regions. This study provides information on B. anthracis strains from a region where there is little knowledge of the local population, thereby adding to the picture of global B. anthracis genotype distribution. We also emphasize the importance of surveillance and prevention methods regarding anthrax outbreaks, as other studies predicted a higher number of cases in the future due to global warming. Full article

(This article belongs to the Section Medical Microbiology)

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14 pages, 1494 KiB

Open AccessArticle

Culture-Free Enumeration of Mycobacterium tuberculosis in Mouse Tissues Using the Molecular Bacterial Load Assay for Preclinical Drug Development

by Dimitrios Evangelopoulos, Carolyn M. Shoen, Isobella Honeyborne, Simon Clark, Ann Williams, Galina V. Mukamolova, Michael H. Cynamon and Timothy D. McHugh

Microorganisms 2022, 10(2), 460; https://doi.org/10.3390/microorganisms10020460 - 17 Feb 2022

Cited by 3 | Viewed by 2257

Abstract

Background: The turnaround times for phenotypic tests used to monitor the bacterial load of Mycobacterium tuberculosis, in both clinical and preclinical studies, are delayed by the organism’s slow growth in culture media. The existence of differentially culturable populations of M.tuberculosis may [...] Read more.

Background: The turnaround times for phenotypic tests used to monitor the bacterial load of Mycobacterium tuberculosis, in both clinical and preclinical studies, are delayed by the organism’s slow growth in culture media. The existence of differentially culturable populations of M.tuberculosis may result in an underestimate of the true number. Moreover, culture methods are susceptible to contamination resulting in loss of critical data points. Objectives: We report the adaptation of our robust, culture-free assay utilising 16S ribosomal RNA, developed for sputum, to enumerate the number of bacteria present in animal tissues as a tool to improve the read-outs in preclinical drug efficacy studies. Methods: Initial assay adaptation was performed using naïve mouse lungs spiked with known quantities of M. tuberculosis and an internal RNA control. Tissues were homogenised, total RNA extracted, and enumeration performed using RT-qPCR. We then evaluated the utility of the assay, in comparison to bacterial counts estimated using growth assays on solid and liquid media, to accurately inform bacterial load in tissues from M. tuberculosis-infected mice before and during treatment with a panel of drug combinations. Results: When tested on lung tissues derived from infected mice, the MBL assay produced comparable results to the bacterial counts in solid culture (colony forming units: CFU). Notably, under specific drug treatments, the MBL assay was able to detect a significantly higher number of M. tuberculosis compared to CFU, likely indicating the presence of bacteria that were unable to produce colonies in solid-based culture. Additionally, growth recovery in liquid media using the most probable number (MPN) assay was able to account for the discrepancy between the MBL assay and CFU number, suggesting that the MBL assay detects differentially culturable sub-populations of M. tuberculosis. Conclusions: The MBL assay can enumerate the bacterial load in animal tissues in real time without the need to wait for extended periods for cultures to grow. The readout correlates well with CFUs. Importantly, we have shown that the MBL is able to measure specific populations of bacteria not cultured on solid agar. The adaptation of this assay for preclinical studies has the potential to decrease the readout time of data acquisition from animal experiments and could represent a valuable tool for tuberculosis drug discovery and development. Full article

(This article belongs to the Special Issue Mycobacterial Infections: Diagnostics, Biomarkers and Treatment)

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20 pages, 2752 KiB

Open AccessArticle

Mycobiome-Host Coevolution? The Mycobiome of Ancestral Human Populations Seems to Be Different and Less Diverse Than Those of Extant Native and Urban-Industrialized Populations

by Jelissa Reynoso-García, Yvonne Narganes-Storde, Tasha M. Santiago-Rodriguez and Gary A. Toranzos

Microorganisms 2022, 10(2), 459; https://doi.org/10.3390/microorganisms10020459 - 16 Feb 2022

Cited by 3 | Viewed by 3075

Abstract

Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico [...] Read more.

Few data exist on the human gut mycobiome in relation to lifestyle, ethnicity, and dietary habits. To understand the effect of these factors on the structure of the human gut mycobiome, we analyzed sequences belonging to two extinct pre-Columbian cultures inhabiting Puerto Rico (the Huecoid and Saladoid) and compared them to coprolite samples found in Mexico and Ötzi, the Iceman’s large intestine. Stool mycobiome samples from extant populations in Peru and urban cultures from the United States were also included. The ancient Puerto Rican cultures exhibited a lower fungal diversity in comparison to the extant populations. Dissimilarity distances showed that the Huecoid gut mycobiome resembled that from ancient Mexico. Fungal genera including Aspergillus spp., Penicillium spp., Rasamsonia spp., Byssochlamys spp., Talaromyces spp., Blastomyces spp., Monascus spp., and Penicilliopsis spp. were differentially abundant in the ancient and extant populations. Despite cultural differences, certain fungal taxa were present in all samples. These results suggest that culture and diet may impact the gut mycobiome and emphasize that modern lifestyles could be associated with the alteration of gut mycobiome diversity. The present study presents data on ancient and extant human gut mycobiomes in terms of lifestyle, ethnicity, and diet in the Americas. Full article

(This article belongs to the Special Issue Understanding Ancient Microbiomes)

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13 pages, 1689 KiB

Open AccessArticle

Enhanced Production of (R)-3-Hydroxybutyrate Oligomers by Coexpression of Molecular Chaperones in Recombinant Escherichia coli Harboring a Polyhydroxyalkanoate Synthase Derived from Bacillus cereus YB-4

by Saki Goto, Yuki Miyahara, Seiichi Taguchi, Takeharu Tsuge and Ayaka Hiroe

Microorganisms 2022, 10(2), 458; https://doi.org/10.3390/microorganisms10020458 - 16 Feb 2022

Cited by 1 | Viewed by 2514

Abstract

The biodegradable polyester poly-(R)-3-hydroxybutyrate [P(3HB)] is synthesized by a polymerizing enzyme called polyhydroxyalkanoate (PHA) synthase and accumulates in a wide variety of bacterial cells. Recently, we demonstrated the secretory production of a (R)-3HB oligomer (3HBO), a low-molecular-weight P(3HB), by [...] Read more.

The biodegradable polyester poly-(R)-3-hydroxybutyrate [P(3HB)] is synthesized by a polymerizing enzyme called polyhydroxyalkanoate (PHA) synthase and accumulates in a wide variety of bacterial cells. Recently, we demonstrated the secretory production of a (R)-3HB oligomer (3HBO), a low-molecular-weight P(3HB), by using recombinant Escherichia coli expressing PHA synthases. The 3HBO has potential value as an antibacterial substance and as a building block for various polymers. In this study, to construct an efficient 3HBO production system, the coexpression of molecular chaperones and a PHA synthase derived from Bacillus cereus YB-4 (PhaRC_YB4) was examined. First, genes encoding enzymes related to 3HBO biosynthesis (phaRC_YB4, phaA and phaB derived from Ralstonia eutropha H16) and two types of molecular chaperones (groEL, groES, and tig) were introduced into the E. coli strains BW25113 and BW25113ΔadhE. As a result, coexpression of the chaperones promoted the enzyme activity of PHA synthase (approximately 2–3-fold) and 3HBO production (approximately 2-fold). The expression assay of each chaperone and PHA synthase subunit (PhaR_YB4 and PhaC_YB4) indicated that the combination of the two chaperone systems (GroEL-GroES and TF) supported the folding of PhaR_YB4 and PhaC_YB4. These results suggest that the utilization of chaperone proteins is a valuable approach to enhance the formation of active PHA synthase and the productivity of 3HBO. Full article

(This article belongs to the Special Issue Development of Eco-friendly Bioplastics Using Microbes)

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19 pages, 4028 KiB

Open AccessArticle

Bermudagrass Cultivars with Different Tolerance to Nematode Damage Are Characterized by Distinct Fungal but Similar Bacterial and Archaeal Microbiomes

by Chang Jae Choi, Jacqueline Valiente, Marco Schiavon, Braham Dhillon, William T. Crow and Ulrich Stingl

Microorganisms 2022, 10(2), 457; https://doi.org/10.3390/microorganisms10020457 - 16 Feb 2022

Cited by 2 | Viewed by 3028

Abstract

Turfgrass landscapes have expanded rapidly in recent decades and are a major vegetation type in urbanizing ecosystems. While turfgrass areas provide numerous ecosystem services in urban environments, ecological side effects from intensive management are raising concerns regarding their sustainability. One potentially promising approach [...] Read more.

Turfgrass landscapes have expanded rapidly in recent decades and are a major vegetation type in urbanizing ecosystems. While turfgrass areas provide numerous ecosystem services in urban environments, ecological side effects from intensive management are raising concerns regarding their sustainability. One potentially promising approach to ameliorate the ecological impact and decrease the use of agricultural chemicals is to take advantage of naturally evolved turfgrass-associated microbes by harnessing beneficial services provided by microbiomes. Unfortunately, especially compared to agricultural crops, the microbiomes of turfgrasses are not well understood. Here, we analyzed microbial communities inhabiting the leaf and root endospheres as well as soil in two bermudagrass cultivars, ‘Latitude 36’ and ‘TifTuf’, which exhibit distinct tolerance to nematode damage, with the goal of identifying potential differences in the microbiomes that might explain their distinct phenotype. We used 16S rRNA gene V4 and ITS2 amplicon sequencing to characterize the microbiomes in combination with microbial cultivation efforts to identify potentially beneficial endophytic fungi and bacteria. Our results show that Latitude 36 and TifTuf showed markedly different fungal microbiomes, each harboring unique taxa from Ascomycota and Glomeromycota, respectively. In contrast, less difference was observed from bacterial and archaeal microbiomes, which were dominated by Bacteroidetes and Thaumarchaeota, respectively. The TifTuf microbiomes exhibited lower microbial diversity compared to Latitude 36. Many sequences could not be classified to a higher taxonomic resolution, indicating a relatively high abundance of hitherto undescribed microorganisms. Our results provide new insights into the structure and composition of turfgrass microbiomes but also raise important questions regarding the functional attributes of key taxa. Full article

(This article belongs to the Special Issue Feature Collection in Environmental Microbiology Section 2021-2022)

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14 pages, 1622 KiB

Open AccessArticle

Combination of High-Pressure Treatment at 500 MPa and Biopreservation with a Lactococcus lactis Strain for Lowering the Bacterial Growth during Storage of Diced Cooked Ham with Reduced Nitrite Salt

by Stéphane Chaillou, Mihanta Ramaroson, Gwendoline Coeuret, Albert Rossero, Valérie Anthoine, Marie Champomier-Vergès, Nicolas Moriceau, Sandrine Rezé, Jean-Luc Martin, Sandrine Guillou and Monique Zagorec

Microorganisms 2022, 10(2), 456; https://doi.org/10.3390/microorganisms10020456 - 16 Feb 2022

Cited by 5 | Viewed by 2219

Abstract

We investigated the combined effects of biopreservation and high-pressure treatment on bacterial communities of diced cooked ham prepared with diminished nitrite salt. First, bacterial communities of four commercial brands of diced cooked ham from local supermarkets were characterized and stored frozen. Second, sterile [...] Read more.

We investigated the combined effects of biopreservation and high-pressure treatment on bacterial communities of diced cooked ham prepared with diminished nitrite salt. First, bacterial communities of four commercial brands of diced cooked ham from local supermarkets were characterized and stored frozen. Second, sterile diced cooked ham, prepared with reduced levels of nitrite, was inoculated with two different microbiota collected from the aforementioned commercial samples together with a nisin-producing Lactococcus lactis protective strain able to recover from a 500 MPa high-pressure treatment. Samples were then treated at 500 MPa for 5 min, and bacterial dynamics were monitored during storage at 8 °C. Depending on samples, the ham microbiota was dominated by different Proteobacteria (Pseudomonas, Serratia, Psychrobacter, or Vibrio) or by Firmicutes (Latilactobacillus and Leuconostoc). Applied alone, none of the treatments stabilized during the growth of the ham microbiota. Nevertheless, the combination of biopreservation and high-pressure treatment was efficient in reducing the growth of Proteobacteria spoilage species. However, this effect was dependent on the nature of the initial microbiota, showing that the use of biopreservation and high-pressure treatment, as an alternative to nitrite reduction for ensuring cooked ham microbial safety, merits attention but still requires improvement. Full article

(This article belongs to the Section Food Microbiology)

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20 pages, 1494 KiB

Open AccessArticle

New Alphaproteobacteria Thrive in the Depths of the Ocean with Oxygen Gradient

by Miguel Angel Cevallos and Mauro Degli Esposti

Microorganisms 2022, 10(2), 455; https://doi.org/10.3390/microorganisms10020455 - 16 Feb 2022

Cited by 7 | Viewed by 2884

Abstract

We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in [...] Read more.

We survey here the Alphaproteobacteria, a large class encompassing physiologically diverse bacteria which are divided in several orders established since 2007. Currently, there is considerable uncertainty regarding the classification of an increasing number of marine metagenome-assembled genomes (MAGs) that remain poorly defined in their taxonomic position within Alphaproteobacteria. The traditional classification of NCBI taxonomy is increasingly complemented by the Genome Taxonomy Database (GTDB), but the two taxonomies differ considerably in the classification of several Alphaproteobacteria, especially from ocean metagenomes. We analyzed the classification of Alphaproteobacteria lineages that are most common in marine environments, using integrated approaches of phylogenomics and functional profiling of metabolic features that define their aerobic metabolism. Using protein markers such as NuoL, the largest membrane subunit of complex I, we have identified new clades of Alphaproteobacteria that are specific to marine niches with steep oxygen gradients (oxycline). These bacteria have relatives among MAGs found in anoxic strata of Lake Tanganyika and together define a lineage that is distinct from either Rhodospirillales or Sneathiellales. We characterized in particular the new ‘oxycline’ clade. Our analysis of Alphaproteobacteria also reveals new clues regarding the ancestry of mitochondria, which likely evolved in oxycline marine environments. Full article

(This article belongs to the Special Issue Bacterial Evolution – Molecular Adaptation to Oxygen)

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