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Microorganisms, Volume 10, Issue 10 (October 2022) – 216 articles

Cover Story (view full-size image): Biofilm formation by Salmonella typhimurium and Escherichia coli is a common ancient multicellular behavior relevant in cell–cell and inter-organism interactions equally, as in interaction with biotic and abiotic surfaces. Two characteristic extracellular matrix components amyloid curli fimbriae and the exopolysaccharide cellulose promote biofilm formation. The expression of these biofilm-promoting factors is regulated by the orphan transcriptional regulator CsgD. We found that GreA/GreB, proteins that interact with RNA polymerase to selectively overcome transcriptional pausing, are required for the expression of the csgD operon and consequently for biofilm formation. In the model proposed, the Gre factors suppress transcriptional pausing at the 5′-UTR of the csgD gene. View this paper
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13 pages, 2464 KB  
Article
Vaginal Lactobacillus Impair Candida Dimorphic Switching and Biofilm Formation
by Carola Parolin, Vanessa Croatti, Barbara Giordani and Beatrice Vitali
Microorganisms 2022, 10(10), 2091; https://doi.org/10.3390/microorganisms10102091 - 21 Oct 2022
Cited by 10 | Viewed by 3655
Abstract
Lactobacillus spp. generally dominate the vaginal microbiota and prevent pathogen adhesion and overgrowth, including Candida spp., by various mechanisms. Although Candida spp. can be commensal, in certain conditions they can become pathogenic, causing vulvovaginal candidiasis. The insurgence of candidiasis is related to the [...] Read more.
Lactobacillus spp. generally dominate the vaginal microbiota and prevent pathogen adhesion and overgrowth, including Candida spp., by various mechanisms. Although Candida spp. can be commensal, in certain conditions they can become pathogenic, causing vulvovaginal candidiasis. The insurgence of candidiasis is related to the expression of Candida virulence factors, including morphologic switching and biofilm formation. Germ tubes, pseudohyphae, and hyphae promote Candida tissue invasion, biofilms increase persistence and are often resistant to antifungals and host immune response. Here, we explored the inhibitory activity of vaginal Lactobacillus strains belonging to Lactobacillus crispatus, Lactobacillus gasseri, Limosilactobacillus vaginalis, and Lactiplantibacillus plantarum species towards Candida virulence factors. With the aim to investigate the interrelation between mode of growth and functionality, supernatants were collected from lactobacilli planktonic cultures and, for the first time, from adherent ones, and were evaluated towards Candida dimorphic switching and biofilm. Candida biofilms were analyzed by multiple methodologies, i.e., crystal violet staining, MTT assay, and confocal microscopy. Lactobacillus supernatants reduce Candida switching and biofilm formation. Importantly, L. crispatus supernatants showed the best profile of virulence suppression, especially when grown in adherence. These results highlight the role of such species as a hallmark of vaginal eubiosis and prompt its employment in new probiotics for women’s health. Full article
(This article belongs to the Special Issue The Role of Lactobacillus in Human Health)
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4 pages, 187 KB  
Brief Report
SARS-CoV-2 Omicron BA.2.75 Variant May Be Much More Infective than Preexisting Variants Based on In Silico Model
by Aki Sugano, Yutaka Takaoka, Haruyuki Kataguchi, Mika Ohta, Shigemi Kimura, Masatake Araki, Yoshitomo Morinaga and Yoshihiro Yamamoto
Microorganisms 2022, 10(10), 2090; https://doi.org/10.3390/microorganisms10102090 - 21 Oct 2022
Cited by 4 | Viewed by 2255
Abstract
Previously, we developed a mathematical model via molecular simulation analysis to predict the infectivity of six SARS-CoV-2 variants. In this report, we aimed to predict the relative risk of the recent new variants of SARS-CoV-2 based on our previous research. We subjected Omicron [...] Read more.
Previously, we developed a mathematical model via molecular simulation analysis to predict the infectivity of six SARS-CoV-2 variants. In this report, we aimed to predict the relative risk of the recent new variants of SARS-CoV-2 based on our previous research. We subjected Omicron BA.4/5 and BA.2.75 variants of SARS-CoV-2 to the analysis to determine the evolutionary distance of the spike protein gene (S gene) of the variants from the Wuhan variant so as to appreciate the changes in the spike protein. We performed molecular docking simulation analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) to understand the docking affinities of these variants. We then compared the evolutionary distances and the docking affinities of these variants with those of the variants that we had analyzed in our previous research. As a result, BA.2.75 has both the highest docking affinity (ratio per Wuhan variant) and the longest evolutionary distance of the S gene from the Wuhan variant. These results suggest that BA.2.75 infection can spread farther than can infections of preexisting variants. Full article
(This article belongs to the Special Issue Advances in SARS-CoV-2 Infection and Variants)
20 pages, 5228 KB  
Article
Screening of Endophytic Bacteria of Leucojum aestivum ‘Gravety Giant’ as a Potential Source of Alkaloids and as Antagonist to Some Plant Fungal Pathogens
by Yuka Munakata, Rosella Spina, Sophie Slezack-Deschaumes, Julie Genestier, Alain Hehn and Dominique Laurain-Mattar
Microorganisms 2022, 10(10), 2089; https://doi.org/10.3390/microorganisms10102089 - 21 Oct 2022
Cited by 10 | Viewed by 3711
Abstract
Leucojum aestivum is a medicinal plant belonging to the Amaryllidaceae family well known as a producer of alkaloids such as galanthamine and lycorine. However, the endophytic microbes that colonize different plant tissues without causing any damage have not been reported in this plant. [...] Read more.
Leucojum aestivum is a medicinal plant belonging to the Amaryllidaceae family well known as a producer of alkaloids such as galanthamine and lycorine. However, the endophytic microbes that colonize different plant tissues without causing any damage have not been reported in this plant. Here, we explored the different endophytic bacterial communities isolated from different surface disinfected tissues of L. aestivum ‘Gravety giant’ and screened bacterial isolates producing alkaloids and their potential use as biocontrol agent against wheat pathogens. For that purpose, endophytic bacteria were isolated from bulbs, roots and shoots of L. aestivum. After taxonomical characterization, these microorganisms were screened for their ability to produce alkaloids using high-performance thin-layer chromatography (HPTLC) and untargeted liquid chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS) strategies. We isolated 138 bacteria belonging to four phyla and 42 genera, mainly from roots and shoots. The most abundant genera were Rahnella in shoot, Patulibacter in bulb and Bacillus in roots. Among the different bacterial isolates, the methanolic extracts of Luteibacter rhizovicinus (LaBFB3301) and Commamonas denitrificans (LaBFS2103) slightly delayed the growth of F. graminearum colonies in in vitro dual tests against F. graminearum and M. nivale strains with 15.5% and 19.9% inhibition rates, respectively. These isolates are able to produce an indolic alkaloid tryptophol (C10H11NO, [M + H]+ 162.0913). These endophytic bacteria might be investigated to characterize the plant protection effect and the plant growth promotion effect. Full article
(This article belongs to the Special Issue Interaction of Plants and Endophytic Microorganisms: Community, Functions and Applications)
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14 pages, 2709 KB  
Article
StcU-2 Gene Mutation via CRISPR/Cas9 Leads to Misregulation of Spore-Cyst Formation in Ascosphaera apis
by Tessema Aynalem, Lifeng Meng, Awraris Getachew, Jiangli Wu, Huimin Yu, Jing Tan, Nannan Li and Shufa Xu
Microorganisms 2022, 10(10), 2088; https://doi.org/10.3390/microorganisms10102088 - 21 Oct 2022
Cited by 2 | Viewed by 2623
Abstract
Ascosphaera apis is the causative agent of honey bee chalkbrood disease, and spores are the only known source of infections. Interference with sporulation is therefore a promising way to manage A. apis. The versicolorin reductase gene (StcU-2) is a ketoreductase protein [...] Read more.
Ascosphaera apis is the causative agent of honey bee chalkbrood disease, and spores are the only known source of infections. Interference with sporulation is therefore a promising way to manage A. apis. The versicolorin reductase gene (StcU-2) is a ketoreductase protein related to sporulation and melanin biosynthesis. To study the StcU-2 gene in ascospore production of A. apis, CRISPR/Cas9 was used, and eight hygromycin B antibiotic-resistant transformants incorporating enhanced green fluorescent protein (EGFP) were made and analyzed. PCR amplification, gel electrophoresis, and sequence analysis were used for target gene editing analysis and verification. The CRISPR/Cas9 editing successfully knocked out the StcU-2 gene in A. apis. StcU-2 mutants had shown albino and non-functional spore-cyst development and lost effective sporulation. In conclusion, editing of StcU-2 gene has shown direct relation with sporulation and melanin biosynthesis of A. apis; this effective sporulation reduction would reduce the spread and pathogenicity of A. apis to managed honey bee. To the best of our knowledge, this is the first time CRISPR/Cas9-mediated gene editing has been efficiently performed in A. apis, a fungal honey bee brood pathogen, which offers a comprehensive set of procedural references that contributes to A. apis gene function studies and consequent control of chalkbrood disease. Full article
(This article belongs to the Special Issue Pathogen Infection in Wildlife)
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21 pages, 1667 KB  
Article
Lacticaseibacillus casei Strain Shirota Modulates Macrophage-Intestinal Epithelial Cell Co-Culture Barrier Integrity, Bacterial Sensing and Inflammatory Cytokines
by Andrew Foey, Neama Habil, Alex Strachan and Jane Beal
Microorganisms 2022, 10(10), 2087; https://doi.org/10.3390/microorganisms10102087 - 21 Oct 2022
Cited by 13 | Viewed by 4597
Abstract
Probiotic bacteria modulate macrophage immune inflammatory responses, with functional cytokine responses determined by macrophage subset polarisation, stimulation and probiotic strain. Mucosal macrophages exhibit subset functional heterogeneity but are organised in a 3-dimensional tissue, over-laid by barrier epithelial cells. This study aimed to investigate [...] Read more.
Probiotic bacteria modulate macrophage immune inflammatory responses, with functional cytokine responses determined by macrophage subset polarisation, stimulation and probiotic strain. Mucosal macrophages exhibit subset functional heterogeneity but are organised in a 3-dimensional tissue, over-laid by barrier epithelial cells. This study aimed to investigate the effects of the probiotic Lacticaseibacillus casei strain Shirota (LcS) on macrophage-epithelial cell cytokine responses, pattern recognition receptor (PRR) expression and LPS responses and the impacts on barrier integrity. THP-1-derived M1 and M2 subset macrophages were co-cultured in a transwell system with differentiated Caco-2 epithelial cells in the presence or absence of enteropathogenic LPS. Both Caco-2 cells in monoculture and macrophage co-culture were assayed for cytokines, PRR expression and barrier integrity (TEER and ZO-1) by RT-PCR, ELISA, IHC and electrical resistance. Caco-2 monocultures expressed distinct cytokine profiles (IL-6, IL-8, TNFα, endogenous IL-10), PRRs and barrier integrity, determined by inflammatory context (TNFα or IL-1β). In co-culture, LcS rescued ZO-1 and TEER in M2/Caco-2, but not M1/Caco-2. LcS suppressed TLR2, TLR4, MD2 expression in both co-cultures and differentially regulated NOD2, TLR9, Tollip and cytokine secretion. In conclusion, LcS selectively modulates epithelial barrier integrity, pathogen sensing and inflammatory cytokine profile; determined by macrophage subset and activation status. Full article
(This article belongs to the Topic Application of Probiotics and Their Potential Health Benefits)
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23 pages, 5010 KB  
Article
Endophytic Bacteria Associated with Origanum heracleoticum L. (Lamiaceae) Seeds
by Giulia Semenzato, Teresa Faddetta, Sara Falsini, Sara Del Duca, Antonia Esposito, Anna Padula, Claudia Greco, Nadia Mucci, Marco Zaccaroni, Anna Maria Puglia, Alessio Papini and Renato Fani
Microorganisms 2022, 10(10), 2086; https://doi.org/10.3390/microorganisms10102086 - 21 Oct 2022
Cited by 9 | Viewed by 2951
Abstract
Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic [...] Read more.
Seed-associated microbiota are believed to play a crucial role in seed germination, seedling establishment, and plant growth and fitness stimulation, due to the vertical transmission of a core microbiota from seeds to the next generations. It might be hypothesized that medicinal and aromatic plants could use the seeds as vectors to vertically transfer beneficial endophytes, providing plants with metabolic pathways that could influence phytochemicals production. Here, we investigated the localization, the structure and the composition of the bacterial endophytic population that resides in Origanum heracleoticum L. seeds. Endocellular bacteria, surrounded by a wall, were localized close to the aleurone layer when using light and transmission electron microscopy. From surface-sterilized seeds, cultivable endophytes were isolated and characterized through RAPD analysis and 16S RNA gene sequencing, which revealed the existence of a high degree of biodiversity at the strain level and the predominance of the genus Pseudomonas. Most of the isolates grew in the presence of six selected antibiotics and were able to inhibit the growth of clinical and environmental strains that belong to the Burkholderia cepacia complex. The endophytes production of antimicrobial compounds could suggest their involvement in plant secondary metabolites production and might pave the way to endophytes exploitation in the pharmaceutical field. Full article
(This article belongs to the Special Issue Endophytes: Improving Plants Performance)
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12 pages, 3120 KB  
Article
Antifungal Activities of Bacillus mojavensis BQ-33 towards the Kiwifruit Black Spot Disease Caused by the Fungal Pathogen Didymella glomerata
by Bingce Wang, Xia Lei, Jia Chen, Wenzhi Li, Youhua Long and Weizhen Wang
Microorganisms 2022, 10(10), 2085; https://doi.org/10.3390/microorganisms10102085 - 21 Oct 2022
Cited by 10 | Viewed by 2906
Abstract
‘Hongyang’ kiwifruit (Actinidia chinensis, cultivar ‘Hongyang’) black spot disease is caused by the fungal pathogen Didymella glomerata, and is a serious disease, causing considerable losses to the kiwifruit industry during growth of the fruit. Hence, we aimed to identify a [...] Read more.
‘Hongyang’ kiwifruit (Actinidia chinensis, cultivar ‘Hongyang’) black spot disease is caused by the fungal pathogen Didymella glomerata, and is a serious disease, causing considerable losses to the kiwifruit industry during growth of the fruit. Hence, we aimed to identify a potential biocontrol agent against D. glomerata. In this study, bacterial isolates from the rhizosphere soil of kiwifruit were tested for their potential antifungal activity against selected fungal pathogens. Based on a phylogenetic tree constructed using sequences of 16S rDNA and the gyrA gene, BQ-33 with the best antifungal activity was identified as Bacillus mojavensis. We evaluated the antagonistic activity and inhibitory mechanism of BQ-33 against D. glomerata. Confrontation experiments showed that both BQ-33 suspension and the sterile supernatant (SS) produced by BQ-33 possessed excellent broad-spectrum antifungal activity. Furthermore, the SS damaged the cell membrane and cell wall of the mycelia, resulting in the leakage of a large quantity of small ions (Na+, K+), soluble proteins and nucleic acids. Chitinase and β-1,3-glucanase activities in SS increased in correlation with incubation time and remained at a high level for several days. An in vivo control efficacy assay indicated that 400 mL L−1 of SS completely inhibited kiwifruit black spot disease caused by D. glomerata. Therefore, BQ-33 is a potential biocontrol agent against kiwifruit black spot and plant diseases caused by other fungal pathogens. To our knowledge, this is the first report of the use of a rhizosphere microorganism as a biocontrol agent against kiwifruit black spot disease caused by D. glomerata. Full article
(This article belongs to the Section Plant Microbe Interactions)
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15 pages, 6549 KB  
Article
Gene Regulatory Network of the Noncoding RNA Qrr5 Involved in the Cytotoxicity of Vibrio parahaemolyticus during Infection
by Fei Zha, Rui Pang, Shixuan Huang, Jumei Zhang, Juan Wang, Moutong Chen, Liang Xue, Qinghua Ye, Shi Wu, Meiyan Yang, Qihui Gu, Yu Ding, Hao Zhang and Qingping Wu
Microorganisms 2022, 10(10), 2084; https://doi.org/10.3390/microorganisms10102084 - 21 Oct 2022
Cited by 5 | Viewed by 2522
Abstract
Small non-coding RNAs (sRNAs) in bacteria are important regulatory molecules for controlling virulence. In Vibrio spp., Qrr sRNAs are critical for quorum-sensing pathways and regulating the release of some virulence factors. However, the detailed role of Qrr sRNAs in the virulence of Vibrio [...] Read more.
Small non-coding RNAs (sRNAs) in bacteria are important regulatory molecules for controlling virulence. In Vibrio spp., Qrr sRNAs are critical for quorum-sensing pathways and regulating the release of some virulence factors. However, the detailed role of Qrr sRNAs in the virulence of Vibrio parahaemolyticus remains poorly understood. In this study, we identified a Vibrio sRNA Qrr5 that positively regulates cytotoxicity and adherence in Caco-2 cells by primarily regulating the T3SS1 gene cluster. A number of 185, 586, 355, and 74 differentially expressed genes (DEGs) detected at 0, 2, 4, and 6 h post-infection, respectively, were mainly associated with ABC transporters and two-component system pathways. The DEGs exhibited a dynamic change in expression at various time points post-infection owing to the deletion of Qrr5. Accordingly, 17 related genes were identified in the co-expression network, and their interaction with Qrr5 was determined based on weighted co-expression network analysis during infection. Taken together, our results provide a comprehensive transcriptome profile of V. parahaemolyticus during infection in Caco-2 cells. Full article
(This article belongs to the Special Issue Foodborne Pathogens: Infections and Pathogenesis)
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13 pages, 2041 KB  
Article
Microbiome of Citrullus colocynthis (L.) Schrad. Reveals a Potential Association with Non-Photosynthetic Cyanobacteria
by Miranda Procter, Biduth Kundu, Naganeeswaran Sudalaimuthuasari, Raja S. AlMaskari, Esam E. Saeed, Khaled M. Hazzouri and Khaled M. A. Amiri
Microorganisms 2022, 10(10), 2083; https://doi.org/10.3390/microorganisms10102083 - 21 Oct 2022
Cited by 5 | Viewed by 3018
Abstract
Citrullus colocynthis grows in the sandy desert soil of the Arabian Peninsula with limited access to water, aside from occasional precipitation or dew. Understanding its ability to produce water-filled fruit and nutrient-rich seeds despite the harsh environment, can be useful for agricultural applications. [...] Read more.
Citrullus colocynthis grows in the sandy desert soil of the Arabian Peninsula with limited access to water, aside from occasional precipitation or dew. Understanding its ability to produce water-filled fruit and nutrient-rich seeds despite the harsh environment, can be useful for agricultural applications. However, information regarding the microbiome of C. colocynthis is lacking. We hypothesized that C. colocynthis associates with bacteria that aid its survival, like what has been observed in other desert plants. Here, we used 16S rRNA gene data to gain insight into the microbiome of C. colocynthis to identify its associated bacteria. In total, 9818 and 6983 OTUs were generated from root, soil, and leaf samples combined. Overall, bulk soils had the highest alpha diversity, followed by rhizosphere and root zone soils. Furthermore, C. colocynthis is associated with known plant-growth-promoting bacteria (including Acidobacteria, Bacterioidetes, and Actinobacteria), and interestingly a class of non-photosynthetic Cyanobacteria (Melainabacteria) that is more abundant on the inside and outside of the root surface than control samples, suggesting its involvement in the rhizophagy process. This study will provide a foundation for functional studies to further understand how C. colocynthis-microbes interactions help them grow in the desert, paving the path for possible agricultural applications. Full article
(This article belongs to the Section Plant Microbe Interactions)
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16 pages, 2992 KB  
Article
Translocation and Dissemination of Gut Bacteria after Severe Traumatic Brain Injury
by Weijian Yang, Qiang Yuan, Zhiqi Li, Zhuoying Du, Gang Wu, Jian Yu and Jin Hu
Microorganisms 2022, 10(10), 2082; https://doi.org/10.3390/microorganisms10102082 - 21 Oct 2022
Cited by 19 | Viewed by 2922
Abstract
Enterobacteriaceae are often found in the lungs of patients with severe Traumatic Brain Injury (sTBI). However, it is unknown whether these bacteria come from the gut microbiota. To investigate this hypothesis, the mice model of sTBI was used in this study. After sTBI, [...] Read more.
Enterobacteriaceae are often found in the lungs of patients with severe Traumatic Brain Injury (sTBI). However, it is unknown whether these bacteria come from the gut microbiota. To investigate this hypothesis, the mice model of sTBI was used in this study. After sTBI, Chao1 and Simpson index peaking at 7 d in the lungs (p < 0.05). The relative abundance of Acinetobacter in the lungs increased to 16.26% at 7 d after sTBI. The chao1 index of gut microbiota increased after sTBI and peaked at 7 d (p < 0.05). Three hours after sTBI, the conditional pathogens such as Lachnoclostridium, Acinetobacter, Bacteroides and Streptococcus grew significantly. At 7 d and 14 d, the histology scores in the sTBI group were significantly higher than the control group (p < 0.05). The myeloperoxidase (MPO) activity increased at all-time points after sTBI and peaked at 7 d (p < 0.05). The LBP and sCD14 peaking 7 d after sTBI (p < 0.05). The Zonulin increased significantly at 3 d after sTBI and maintained the high level (p < 0.05). SourceTracker identified that the lung tissue microbiota reflects 49.69% gut source at 7 d after sTBI. In the small intestine, sTBI induced gastrointestinal dysfunction with increased apoptosis and decreasing antimicrobial peptides. There was a negative correlation between gut conditional pathogens and the expression level of antimicrobial peptides in Paneth cells. Our data indicate that gut bacteria translocated to the lungs after sTBI, and Paneth cells may regulate gut microbiota stability and translocation. Full article
(This article belongs to the Special Issue Microbiota-Gut-Brain Axis in Health and Disease, and Future Therapies)
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22 pages, 4273 KB  
Article
Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments
by Asha Z. Goodman, Bhavya Papudeshi, Michael P. Doane, Maria Mora, Emma Kerr, Melissa Torres, Jennifer Nero Moffatt, Lais Lima, Andrew P. Nosal and Elizabeth Dinsdale
Microorganisms 2022, 10(10), 2081; https://doi.org/10.3390/microorganisms10102081 - 21 Oct 2022
Cited by 4 | Viewed by 2878
Abstract
Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in [...] Read more.
Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for <1 year in duration and scheduled for release; Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients. Full article
(This article belongs to the Special Issue Genome Analysis of Microbial Communities in Environments)
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16 pages, 693 KB  
Review
The Widespread Use of Nanomaterials: The Effects on the Function and Diversity of Environmental Microbial Communities
by Chunshui Sun, Ke Hu, Dashuai Mu, Zhijun Wang and Xiuxia Yu
Microorganisms 2022, 10(10), 2080; https://doi.org/10.3390/microorganisms10102080 - 21 Oct 2022
Cited by 29 | Viewed by 3738
Abstract
In recent years, as an emerging material, nanomaterials have rapidly expanded from laboratories to large-scale industrial productions. Along with people’s productive activities, these nanomaterials can enter the natural environment of soil, water and atmosphere through various ways. At present, a large number of [...] Read more.
In recent years, as an emerging material, nanomaterials have rapidly expanded from laboratories to large-scale industrial productions. Along with people’s productive activities, these nanomaterials can enter the natural environment of soil, water and atmosphere through various ways. At present, a large number of reports have proved that nanomaterials have certain toxic effects on bacteria, algae, plants, invertebrates, mammalian cell lines and mammals in these environments, but people still know little about the ecotoxicology of nanomaterials. Most relevant studies focus on the responses of model strains to nanomaterials in pure culture conditions, but these results do not fully represent the response of microbial communities to nanomaterials in natural environments. Over the years, the effect of nanomaterials infiltrated into the natural environment on the microbial communities has become a popular topic in the field of nano-ecological environment research. It was found that under different environmental conditions, nanomaterials have various effects on the microbial communities. The medium; the coexisting pollutants in the environment and the structure, particle size and surface modification of nanomaterials may cause changes in the structure and function of microbial communities. This paper systematically summarizes the impacts of different nanomaterials on microbial communities in various environments, which can provide a reference for us to evaluate the impacts of nanomaterials released into the environment on the microecology and has certain guiding significance for strengthening the emission control of nanomaterials pollutants. Full article
(This article belongs to the Section Environmental Microbiology)
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16 pages, 1711 KB  
Article
Plant and Soil Core Mycobiomes in a Two-Year Sorghum–Legume Intercropping System of Underutilized Crops in South Africa
by Gilmore T. Pambuka, Tonjock Rosemary Kinge, Soumya Ghosh, Errol D. Cason, Martin M. Nyaga and Marieka Gryzenhout
Microorganisms 2022, 10(10), 2079; https://doi.org/10.3390/microorganisms10102079 - 20 Oct 2022
Cited by 9 | Viewed by 2968
Abstract
Fungal communities form close beneficial (mutualists) or detrimental (pathogens) associations with their plant hosts. Their diversity and abundance can be affected by agricultural practices which include cropping systems such as rotations and intercropping. Despite the importance of cropping systems in increasing productivity, knowledge [...] Read more.
Fungal communities form close beneficial (mutualists) or detrimental (pathogens) associations with their plant hosts. Their diversity and abundance can be affected by agricultural practices which include cropping systems such as rotations and intercropping. Despite the importance of cropping systems in increasing productivity, knowledge of the fungal mycobiome and the core inhabitants for under-utilised cereal and legume crops, particularly over a period, is still limited. The core mycobiomes in plant tissues and bulk soils of a cereal–legume intercrop were characterized over two years using high-throughput sequencing. The intercropping trial consisted of sorghum, Bambara groundnut, cowpea, dry bean, and soybean. A greater number of molecular operational taxonomic units (MOTUs) were found in plant tissues compared to those from the soils and between year one and year two. Principal coordinate analyses revealed that fungal communities for each year were relatively distinct, particularly for the soils. The core mycobiome was dominated by a Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Didymellaceae sp. 2 (Epicoccum), Fusarium sp. 2, Unidentified (Ascomycota), and Cryptococcus MOTUs that were present in all plant tissues and soils of year one and two. Other key MOTUs were only specific to a year, substrate, or crop. Although the mycobiome of sorghum were more distinct than the cores of the legumes, there were still MOTUs dominant across all of the crops. Characterization of this baseline core across two years provides insight into those fungi that are always present in these crops, and that could be utilized in improving crop performance and productivity. Full article
(This article belongs to the Special Issue Microbiomes and Mycobiomes in Crop Health and Disease)
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16 pages, 3061 KB  
Article
Influence of Biochar on Soil Nutrients and Associated Rhizobacterial Communities of Mountainous Apple Trees in Northern Loess Plateau China
by Rafiq Ahmad, Jianen Gao, Zhe Gao, Abdullah Khan, Izhar Ali and Shah Fahad
Microorganisms 2022, 10(10), 2078; https://doi.org/10.3390/microorganisms10102078 - 20 Oct 2022
Cited by 15 | Viewed by 2779
Abstract
Biochar application can enhance soil health and alter soil bacterial community structure. However, knowledge relating to biochar on soil nutrients of mountainous apple orchards and then assessing its effect on soil health, especially on soil microorganisms, is still scanty. Therefore, we evaluated the [...] Read more.
Biochar application can enhance soil health and alter soil bacterial community structure. However, knowledge relating to biochar on soil nutrients of mountainous apple orchards and then assessing its effect on soil health, especially on soil microorganisms, is still scanty. Therefore, we evaluated the responses of six biochar treatments [Ck (0), T1 (2), T2 (4), T3 (6), T4 (8), and T5 (10) Mg hm−2] with a basal dose of chemical fertilizer on the soil nutrients under potted apple trees across 3, 6, 9, and 12 months, and then investigated the responses of the rhizobacterial communities. Experimental findings demonstrated that: (i) Across the months, the biochar-applied treatment (T5) compared to the control significantly enhanced soil nutrients, including soil pH (2.12 to 2.29%), soil organic matter (35 to 40%), total nitrogen (59 to 65%), ammonium nitrogen (25 to 33%), nitrate nitrogen (163 to 169%), and the activities of urease (76 to 81%), alkaline phosphatase (30 to 33%), catalase (8.89 to 11.70%), and sucrase (23 to 29%). (ii) Compared to the control, the biochar-applied treatment (T5) had a more desirable relative abundance of the bacterial phylum Proteobacteria (35.47%), followed by Actinobacteria (8.59%), Firmicutes (5.74%), and Bacteroidota (2.77%). Similarly, the relative abundance of the bacterial genera in the T5 was Sphingomonas (8.23%) followed by RB41 (3.81%), Ellin6055 (3.42%), Lachnospiracea (1.61%), Bacillus (1.43%), Kineosporia (1.37%), Massilia (0.84%), and Odoribacter (0.34%) than the control. (iii) Among the alpha diversity, the biochar-applied treatment (T5) revealed the highest Chao1 (20%) and ACE (19.23%) indexes, while Shannon (1.63%) and Simpson (1.02%) had relatively lower indexes than the control. Furthermore, positive correlations were found between the soil nutrients and some of the abundant bacterial phyla. Overall, the findings of this research demonstrated that biochar application at 10 Mg hm−2 (T5) along with the required chemical fertilizer is beneficial to improve soil health and pave the way for sustainable production in apple orchards of the northern loess plateau. Full article
(This article belongs to the Section Environmental Microbiology)
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17 pages, 4124 KB  
Article
Functional Characterization of Saccharomyces cerevisiae P5C Reductase, the Enzyme at the Converging Point of Proline and Arginine Metabolism
by Giuseppe Forlani, Giuseppe Sabbioni and Milosz Ruszkowski
Microorganisms 2022, 10(10), 2077; https://doi.org/10.3390/microorganisms10102077 - 20 Oct 2022
Cited by 2 | Viewed by 2686
Abstract
The enzyme that, in Saccharomyces cerevisiae, catalyzes the last step in both proline synthesis and arginine catabolism, δ1-pyrroline-5-carboxylate (P5C) reductase, was purified to near homogeneity and characterized thoroughly. Retention patterns upon gel permeation chromatography were consistent with a homodecameric composition of [...] Read more.
The enzyme that, in Saccharomyces cerevisiae, catalyzes the last step in both proline synthesis and arginine catabolism, δ1-pyrroline-5-carboxylate (P5C) reductase, was purified to near homogeneity and characterized thoroughly. Retention patterns upon gel permeation chromatography were consistent with a homodecameric composition of the holomer. High lability of the purified preparations and stabilization by reducing compounds suggested susceptibility to reactive-oxygen-species-mediated damage. Both NADH and NADPH were used as the electron donor, the latter resulting in a 3-fold higher Vmax. However, a higher affinity toward NADH was evident, and the NADPH-dependent activity was inhibited by NAD+, proline, arginine, and a variety of anions. With proline and arginine, the inhibition was of the competitive type with respect to the specific substrate, and of the uncompetitive- or mixed-type with respect to NADPH, respectively. The results suggest that, contrary to the enzyme from higher plants, yeast P5C reductase may preferentially use NADH in vivo. An in silico analysis was also performed to investigate the structural basis of such enzyme features. Superposition of the protein model with the experimental structure of P5C reductase from Medicago truncatula allowed us to hypothesize on the possible allosteric sites for arginine and anion binding, and the cysteine pairs that may be involved in disulfide formation. Full article
(This article belongs to the Special Issue Yeasts Biochemistry and Biotechnology)
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11 pages, 875 KB  
Article
Direct MALDI-TOF MS and Antimicrobial Susceptibility Testing of Positive Blood Cultures Using the FASTTM System and FAST-PBC Prep Cartridges—Performance Evaluation in a Clinical Microbiology Laboratory Serving High-Risk Patients
by Khay Ugaban, Pil Pak and Rosemary C. She
Microorganisms 2022, 10(10), 2076; https://doi.org/10.3390/microorganisms10102076 - 20 Oct 2022
Cited by 7 | Viewed by 3608
Abstract
Bloodstream infections are a leading cause of morbidity and mortality. The rapid diagnostic testing of positive blood cultures (PBCs) shortens times to effective therapy and the de-escalation of broad-spectrum empiric therapy. This is the first study examining the Qvella FASTTM System for [...] Read more.
Bloodstream infections are a leading cause of morbidity and mortality. The rapid diagnostic testing of positive blood cultures (PBCs) shortens times to effective therapy and the de-escalation of broad-spectrum empiric therapy. This is the first study examining the Qvella FASTTM System for the rapid (~20 min) purification of microorganisms directly from PBCs using BacT/Alert® FA/FAN bottles in the bioMérieux Virtuo instrument. We compared the performance of the FASTTM System Liquid ColonyTM (LC), for immediate downstream ID and phenotypic AST, to standard workflow involving colonies obtained by overnight subculture. The LC yielded a concordant species ID by VITEK MS in 121/138 (87.7%) samples, identifying 32 different Gram-positive and Gram-negative species with 3/123 (2.6%) discordances. Compared to standard workflow, direct AST of the LC using VITEK® 2 yielded 98.4% categorical agreement and 98.0% essential agreement. Very major error, major error, and minor error rates were 1.0%, 0.0%, and 1.8%, respectively, for Gram-negative organisms; and 1.9%, 0.2%, and 1.2%, respectively, for Gram-positive organisms. The median times from positive blood culture flag to results by FASTTM System for ID and AST were 7.8 h and 15.7 h, respectively, versus 22.4 h and 36.6 h for standard workflow, respectively. In conclusion, the FASTTM System provides reliable results for direct ID and AST from PBCs with significantly decreased turnaround times. Full article
(This article belongs to the Special Issue Application of MALDI-TOF MS in Microbiology)
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14 pages, 1593 KB  
Article
Epidemiological and Cytokine Profile of Patients with Pulmonary and Extrapulmonary Tuberculosis in a Population of the Brazilian Amazon
by Maria Alice Freitas Queiroz, Sandra Souza Lima, Ednelza da Silva Graça Amoras, Francisca Dayse Martins de Sousa, Iury de Paula Souza, Juliana Abreu Lima Nunes, Igor Brasil-Costa, Izaura Maria Vieira Cayres-Vallinoto, Ricardo Ishak and Antonio Carlos Rosário Vallinoto
Microorganisms 2022, 10(10), 2075; https://doi.org/10.3390/microorganisms10102075 - 20 Oct 2022
Cited by 4 | Viewed by 2192
Abstract
Several factors are associated with the development of different clinical forms of tuberculosis (TB). The present study evaluated epidemiological variables and cytokine levels in samples from 89 patients with TB (75 with pulmonary TB and 14 with extrapulmonary TB) and 45 controls. Cytokines [...] Read more.
Several factors are associated with the development of different clinical forms of tuberculosis (TB). The present study evaluated epidemiological variables and cytokine levels in samples from 89 patients with TB (75 with pulmonary TB and 14 with extrapulmonary TB) and 45 controls. Cytokines were measured by flow cytometry (Human Th1/Th2/Th17 Cytometric Bead Array kit). The TB group had a higher frequency of individuals who were 39 years of age or older, married, with primary education or illiterate and had a lower family income (p < 0.05). All individuals with extrapulmonary TB reported that they were not working, and the main reasons were related to disease symptoms or treatment. The levels of IFN-γ (OR = 4.06) and IL-4 (OR = 2.62) were more likely to be elevated in the TB group (p = 0.05), and IFN-γ levels were lower in patients with extrapulmonary TB compared to those with pulmonary TB (OR = 0.11; p = 0.0050). The ROC curve was applied to investigate the diagnostic accuracy of IFN-γ levels between the different clinical forms of tuberculosis, resulting in high AUC (0.8661; p < 0.0001), sensitivity (93.85%) and specificity median (65.90%), suggesting that IFN-γ levels are useful to differentiate pulmonary TB from extrapulmonary TB. The dysregulation of pro- and anti-inflammatory cytokine levels represent a risk for the development of TB and contribute to the pathogenesis of the disease, especially variation in IFN-γ levels, which may determine protection or risk for extrapulmonary TB. Full article
(This article belongs to the Section Public Health Microbiology)
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9 pages, 260 KB  
Article
Trends in Asymptomatic Nasopharyngeal Streptococcus pneumoniae Carriage with qPCR and Culture Analysis
by Julie-Anne Lemay, Leah J. Ricketson and James D. Kellner
Microorganisms 2022, 10(10), 2074; https://doi.org/10.3390/microorganisms10102074 - 20 Oct 2022
Cited by 1 | Viewed by 2111
Abstract
We previously reported trends in pneumococcal nasopharyngeal carriage in the post-PCV13 era as detected by conventional culture methods. Our current aim is to assess if there are fundamental differences in the clinical and demographic features of children who have pneumococcal carriage detected by [...] Read more.
We previously reported trends in pneumococcal nasopharyngeal carriage in the post-PCV13 era as detected by conventional culture methods. Our current aim is to assess if there are fundamental differences in the clinical and demographic features of children who have pneumococcal carriage detected by qPCR compared with culture analysis. The CASPER team conducted point-prevalence surveys in 2016 in healthy children in Calgary to determine trends in overall and serotype-specific pneumococcal nasopharyngeal carriage. Being 18 months of age (p = 0.009), having at least one sibling under 2 years of age (p = 0.04), having only sibling(s) over 2 years of age (p = 0.001), and childcare attendance (p = 0.005) were associated with carriage by qPCR methods only. Having only sibling(s) older than 2 years of age was associated with carriage detected by both qPCR and culture methods (p = 0.001). No clinical factors were associated with carriage detected by both qPCR and culture compared to qPCR methods only. Both analyses are suitable methods to detect carriage; however, qPCR analysis is more sensitive and more cost-effective. As there are no fundamental differences in the children that have pneumococcal nasopharyngeal carriage detectable by qPCR methods compared to conventional culture methods, molecular analysis may be a preferable option for future carriage studies. Full article
(This article belongs to the Special Issue Recent Advances of Respiratory Infections)
17 pages, 2066 KB  
Article
Initial pH Conditions Shape the Microbial Community Structure of Sewage Sludge in Batch Fermentations for the Improvement of Volatile Fatty Acid Production
by Ylenia Di Leto, Fanny Claire Capri, Antonio Mineo, Alida Cosenza, Giuseppe Gallo, Rosa Alduina and Giorgio Mannina
Microorganisms 2022, 10(10), 2073; https://doi.org/10.3390/microorganisms10102073 - 20 Oct 2022
Cited by 15 | Viewed by 3168
Abstract
Conversion of wastewater treatment plants into biorefineries is a sustainable alternative for obtaining valuable compounds, thus reducing pollutants and costs and protecting the environment and human health. Under specific operating conditions, microbial fermentative products of sewage sludge are volatile fatty acids (VFA) that [...] Read more.
Conversion of wastewater treatment plants into biorefineries is a sustainable alternative for obtaining valuable compounds, thus reducing pollutants and costs and protecting the environment and human health. Under specific operating conditions, microbial fermentative products of sewage sludge are volatile fatty acids (VFA) that can be precursors of polyhydroxyalkanoate thermoplastic polyesters. The role of various operating parameters in VFA production has yet to be elucidated. This study aimed to correlate the levels of VFA yields with prokaryotic microbiota structures of sewage sludge in two sets of batch fermentations with an initial pH of 8 and 10. The sewage sludge used to inoculate the batch fermentations was collected from a Sicilian WWTP located in Marineo (Italy) as a case study. Gas chromatography analysis revealed that initial pH 10 stimulated chemical oxygen demands (sCOD) and VFA yields (2020 mg COD/L) in comparison with initial pH 8. Characterization of the sewage sludge prokaryotic community structures—analyzed by next-generation sequencing of 16S rRNA gene amplicons—demonstrated that the improved yield of VFA paralleled the increased abundance of fermenting bacteria belonging to Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes phyla and, conversely, the reduced abundance of VFA-degrading strains, such as archaeal methanogens. Full article
(This article belongs to the Special Issue Microbial Ecosystems in Water and Wastewater Treatment)
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17 pages, 841 KB  
Review
Opposite Sides of Pantoea agglomerans and Its Associated Commercial Outlook
by Adriana Sturion Lorenzi, Maria Letícia Bonatelli, Mathias Ahii Chia, Leonardo Peressim and Maria Carolina Quecine
Microorganisms 2022, 10(10), 2072; https://doi.org/10.3390/microorganisms10102072 - 20 Oct 2022
Cited by 37 | Viewed by 8176
Abstract
Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct [...] Read more.
Multifaceted microorganisms such as the bacterium Pantoea colonize a wide range of habitats and can exhibit both beneficial and harmful behaviors, which provide new insights into microbial ecology. In the agricultural context, several strains of Pantoea spp. can promote plant growth through direct or indirect mechanisms. Members of this genus contribute to plant growth mainly by increasing the supply of nitrogen, solubilizing ammonia and inorganic phosphate, and producing phytohormones (e.g., auxins). Several other studies have shown the potential of strains of Pantoea spp. to induce systemic resistance and protection against pests and pathogenic microorganisms in cultivated plants. Strains of the species Pantoea agglomerans deserve attention as a pest and phytopathogen control agent. Several of them also possess a biotechnological potential for therapeutic purposes (e.g., immunomodulators) and are implicated in human infections. Thus, the differentiation between the harmful and beneficial strains of P. agglomerans is mandatory to apply this bacterium safely as a biofertilizer or biocontroller. This review specifically evaluates the potential of the strain-associated features of P. agglomerans for bioprospecting and agricultural applications through its biological versatility as well as clarifying its potential animal and human health risks from a genomic point of view. Full article
(This article belongs to the Special Issue Microbial Biotechnology in Agriculture)
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16 pages, 984 KB  
Article
Long-Term Effects of Single-Dose Cephalosporin or Macrolide Use on the Prevalence of AmpC and Extended-Spectrum β-Lactamase Producing Escherichia coli in the Feces of Beef Cattle
by Gizem Levent, Ashlynn Schlochtermeier, Javier Vinasco, Jenny Jennings, John Richeson, Samuel E. Ives, Keri N. Norman, Sara D. Lawhon, Guy H. Loneragan and H. Morgan Scott
Microorganisms 2022, 10(10), 2071; https://doi.org/10.3390/microorganisms10102071 - 20 Oct 2022
Cited by 3 | Viewed by 3147
Abstract
Extended-spectrum-β-lactamase (ESBL) and AmpC-lactamase-producing Enterobacteriaceae are serious public health threats. Due to an increasing number of reports of ESBL and AmpC producing Escherichia coli in agricultural settings, it is critical to understand the relationship between the use of two of the highest priority [...] Read more.
Extended-spectrum-β-lactamase (ESBL) and AmpC-lactamase-producing Enterobacteriaceae are serious public health threats. Due to an increasing number of reports of ESBL and AmpC producing Escherichia coli in agricultural settings, it is critical to understand the relationship between the use of two of the highest priority critically important human antibiotics (e.g., third generation cephalosporins [3GC] and macrolides) in food animals and their potential contribution to the selection of ESBL/AmpC E. coli. The objective of our randomized controlled feedlot trial was to measure the effects of ceftiofur crystalline-free acid and tulathromycin on 3GC resistant fecal E. coli populations in cattle before and at various time points after treatment up to and including at slaughter. Multi-level mixed-effects linear regression showed no effect of ceftiofur and tulathromycin on 3GC E. coli CFU counts at slaughter (Day 99); however, a significant (p < 0.05) population shift was observed from susceptible to 3GC resistant E. coli immediately after ceftiofur administration (Day 7). Among 799 fecal samples screened using selective media, 17.7% were ESBL/AmpC E. coli positive, which were further tested for phenotypic antibiotic susceptibility. The majority of the isolates from these plates were multidrug-resistant (94.3%) and expressed either AmpC (78.1%) or ESBL (28.1%) phenotype. A subset of isolates was whole-genome sequenced (n = 20) and identified to harbor chromosomal and/or plasmidal bla genes such as CMY-2, CTX-M, and TEM. Our findings show a time-dependent selection of antibiotics on 3GC-resistant E. coli. High prevalence of multidrug-resistant ESBL/AmpC E. coli found in cattle feces highlights the importance of prudent use of antibiotics in livestock. Full article
(This article belongs to the Special Issue Pathogens and Antimicrobial Drug Resistance in the Food Chain)
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15 pages, 1732 KB  
Article
Evaluation of Safety and Probiotic Potential of Enterococcus faecalis MG5206 and Enterococcus faecium MG5232 Isolated from Kimchi, a Korean Fermented Cabbage
by YongGyeong Kim, Soo-Im Choi, Yulah Jeong and Chang-Ho Kang
Microorganisms 2022, 10(10), 2070; https://doi.org/10.3390/microorganisms10102070 - 20 Oct 2022
Cited by 24 | Viewed by 7095
Abstract
The purpose of this study was to evaluate the genotypic and phenotypic toxicity of Enterococcus faecalis MG5206 and Enterococcus faecium MG5232 isolated from kimchi (fermented vegetable cabbage). In this study, the genotypic toxicity of the strains MG5206 and MG5232 was identified through whole-genome [...] Read more.
The purpose of this study was to evaluate the genotypic and phenotypic toxicity of Enterococcus faecalis MG5206 and Enterococcus faecium MG5232 isolated from kimchi (fermented vegetable cabbage). In this study, the genotypic toxicity of the strains MG5206 and MG5232 was identified through whole-genome sequencing analysis, and phenotypic virulence, such as susceptibility to antibiotics, hemolytic activity, and gelatinase and hyaluronidase activities, was also evaluated. In addition, the in vivo toxicity of both strains was evaluated using an acute oral administration test in Sprague–Dawley rats. In all the tests, both the strains were determined to be safety by confirming that they did not show antibiotic resistance or virulence factors. In addition, these strains exhibited a low level of autoaggregation ability (37.2–66.3%) and hydrophobicity, as well as a high survival rate in gastrointestinal condition in vitro. Therefore, the safety and high gastrointestinal viability of E. faecalis MG5206 and E. faecium MG5232 suggests that both the strains could be utilized in food as potential probiotics in the future. Full article
(This article belongs to the Special Issue Emerging Issues and Approaches in Microbial Food Safety)
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20 pages, 1446 KB  
Review
Fermentation of Microalgal Biomass for Innovative Food Production
by Cristiana Garofalo, Alessandra Norici, Lorenzo Mollo, Andrea Osimani and Lucia Aquilanti
Microorganisms 2022, 10(10), 2069; https://doi.org/10.3390/microorganisms10102069 - 19 Oct 2022
Cited by 48 | Viewed by 7678
Abstract
Fermentation is an ancient method used worldwide to process and preserve food while enhancing its nutraceutical profile. Alga-based fermented products have recently been developed and tested due to growing interest in healthy sustainable diets, which demands the development of innovative practices in food [...] Read more.
Fermentation is an ancient method used worldwide to process and preserve food while enhancing its nutraceutical profile. Alga-based fermented products have recently been developed and tested due to growing interest in healthy sustainable diets, which demands the development of innovative practices in food production, operating for both human health and Earth sustainability. Algae, particularly microalgae such as Arthrospira platensis, Chlorella vulgaris, and Dunaliella salina, are already cultivated as sources of food due to their valuable compounds, including proteins, pigments, lipids, carotenoids, polyunsaturated fatty acids, steroids, and vitamins. Due to their nutritional composition, functional diversity, and flexible metabolism, microalgae represent good fermentation substrates for lactic acid bacteria (LAB) and yeasts. This review presents an overview of the scientific studies on microalga fermentation underlining microalgae’s properties and health benefits coupled with the advantages of LAB and yeast fermentation. The potential applications of and future perspectives on such functional foods are discussed. Full article
(This article belongs to the Special Issue Microorganisms Possibility for Future Bioproduction)
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19 pages, 8720 KB  
Article
Effect of Lactobacteria on Bioactive Peptides and Their Sequence Identification in Mature Cheese
by Marina Kurbanova, Roman Voroshilin, Oksana Kozlova and Victor Atuchin
Microorganisms 2022, 10(10), 2068; https://doi.org/10.3390/microorganisms10102068 - 19 Oct 2022
Cited by 17 | Viewed by 3364
Abstract
An in silico study that featured the effect of starter cultures on the bioactivity and other health benefits of peptides in semi-hard cheese is presented in this contribution. Model Caciotta-type cheese samples were obtained in laboratory conditions in two variations. Sample A included [...] Read more.
An in silico study that featured the effect of starter cultures on the bioactivity and other health benefits of peptides in semi-hard cheese is presented in this contribution. Model Caciotta-type cheese samples were obtained in laboratory conditions in two variations. Sample A included starter cultures of Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris. Sample B included starter cultures of Lactococcus lactis subsp. lactis, Lactococcus lactis subsp. cremoris, and a culture of lactobacilli Lacticaseibacillus casei. The in silico method showed that the peptides inhibited angiotensin-converting enzymes (ACE) and ipeptidyl peptidase IV (DPP-4), as well as possessed antioxidant properties. Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris had a greater effect on the formation of bioactive peptides. Full article
(This article belongs to the Special Issue Benefical Properties and Safety of Lactic Acid Bacteria)
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6 pages, 512 KB  
Brief Report
Outliers Matter—Correlation between S1 IgG SARS-CoV-2 Antibodies and Neutralizing SARS-CoV-2 Antibodies
by Berthold Hocher, Anne Schönbrunn, Xin Chen, Bernhard K. Krämer and Volker von Baehr
Microorganisms 2022, 10(10), 2067; https://doi.org/10.3390/microorganisms10102067 - 19 Oct 2022
Cited by 3 | Viewed by 2101
Abstract
Vaccination against the SARS-CoV-2 virus or infection with SARS-CoV-2 will lead to the development of IgG antibodies against the S1 protein of the SARS-CoV-2 virus. However, even despite having high levels of IgG antibodies against the S1 protein of the SARS-CoV-2 virus, (re-)infection [...] Read more.
Vaccination against the SARS-CoV-2 virus or infection with SARS-CoV-2 will lead to the development of IgG antibodies against the S1 protein of the SARS-CoV-2 virus. However, even despite having high levels of IgG antibodies against the S1 protein of the SARS-CoV-2 virus, (re-)infection may occur. We thus examined 2994 consecutive blood samples of outpatients from the Berlin-Brandenburg area in Germany in which IgG antibodies against the S1 protein of the SARS-CoV-2 virus as well as neutralizing SARS-CoV-2 virus antibodies were determined from the same sample. When analyzing the entire study population (2994 outpatients), we saw that S1 IgG antibodies (women: 223.98 ± 3.81; men: 207.80 ± 4.59; p = 0.014) and neutralizing antibodies (women: 66.65 ± 0.82; men: 62.88 ± 1.01; p = 0.021) are slightly higher in women than in men. Curve fitting revealed a good non-linear relationship between S1 IgG and neutralizing SARS-CoV-2 antibodies. However, 51 out of the 2994 blood samples from individual subjects were positive with regard to the neutralizing antibodies and at the same time negative for S1 IgG antibodies, and 112 out of the 2994 blood samples from individual subjects were negative with regard to the neutralizing antibodies and at the same time positive for S1 IgG antibodies. In conclusion, our study shows that there is a relevant number of patients who, despite developing significant titers of S1 antibodies, do not have relevant amounts of neutralizing antibody titers and are probably at high risk of (re-)infection. Full article
(This article belongs to the Special Issue SARS-CoV-2 Systemic Effects: New Clues)
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16 pages, 2280 KB  
Review
The Changes in Bacterial Microbiome Associated with Immune Disorder in Allergic Respiratory Disease
by Juanjuan Lyu, Fangfang Kou, Xiangyu Men, Yinhui Liu, Li Tang and Shu Wen
Microorganisms 2022, 10(10), 2066; https://doi.org/10.3390/microorganisms10102066 - 19 Oct 2022
Cited by 6 | Viewed by 2764
Abstract
Allergic respiratory disease is a worldwide and increasingly prevalent health problem. Many researchers have identified complex changes in the microbiota of the respiratory and intestinal tracts in patients with allergic respiratory diseases. These affect immune response and influence the progression of disease. However, [...] Read more.
Allergic respiratory disease is a worldwide and increasingly prevalent health problem. Many researchers have identified complex changes in the microbiota of the respiratory and intestinal tracts in patients with allergic respiratory diseases. These affect immune response and influence the progression of disease. However, the diversity of bacterial changes in such cases make it difficult to identify a specific microorganism to target for adjustment. Recent research evidence suggests that common bacterial variations present in allergic respiratory disease are associated with immune disorders. This finding could lead to the discovery of potential therapeutic targets in cases of allergic respiratory disease. In this review, we summarize current knowledge of bacteria changes in cases of allergic respiratory disease, to identify changes commonly associated with immune disorders, and thus provide a theoretical basis for targeting therapies of allergic respiratory disease through effective modulation of key bacteria. Full article
(This article belongs to the Special Issue Airborne Microbes and Their Potential Influence)
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13 pages, 636 KB  
Article
Plasma Gut Microbe-Derived Metabolites Associated with Peripheral Artery Disease and Major Adverse Cardiac Events
by Karen J. Ho, Joel L. Ramirez, Rohan Kulkarni, Katharine G. Harris, Irene Helenowski, Liqun Xiong, C. Keith Ozaki and S. Marlene Grenon
Microorganisms 2022, 10(10), 2065; https://doi.org/10.3390/microorganisms10102065 - 19 Oct 2022
Cited by 17 | Viewed by 3525
Abstract
Cardiovascular diseases are associated with gut dysbiosis, but the role of microbe-derived metabolites as biomarkers or modulators of cardiovascular disease are not well understood. This is a targeted metabolomics study to investigate the association of nine microbe-derived metabolites with lower extremity peripheral artery [...] Read more.
Cardiovascular diseases are associated with gut dysbiosis, but the role of microbe-derived metabolites as biomarkers or modulators of cardiovascular disease are not well understood. This is a targeted metabolomics study to investigate the association of nine microbe-derived metabolites with lower extremity peripheral artery disease (PAD), a form of atherosclerosis, and major adverse cardiac events (MACE). The study cohort consists of individuals with intermittent claudication and ankle-brachial index (ABI) < 0.9 (N = 119) and controls without clinically-apparent atherosclerosis (N = 37). The primary endpoint was MACE, a composite endpoint of myocardial infarction, coronary revascularization, stroke, transient ischemic attack, or cardiac-related death. Plasma metabolite concentrations differed significantly between the PAD and control groups. After adjustment for traditional atherosclerosis risk factors, kynurenine, hippuric acid, indole-3-propionic acid (IPA), and indole-3-aldehyde (I3A) concentrations were negatively associated with PAD, whereas indoxyl sulfate and 3-hydroxyanthranilic acid were positively associated. Hippuric acid, IPA, and I3A correlated with ABI, a surrogate for atherosclerotic disease burden. Those in the highest I3A concentration quartile had significantly improved freedom from MACE during follow-up compared to those in the lowest quartile. This study identifies specific indole- and phenyl-derived species impacted by gut microbial metabolic pathways that could represent novel microbiome-related biomarkers of PAD. Full article
(This article belongs to the Special Issue The Microbial Population of the Gastrointestinal Tract of Animals: Impacts on Host Physiology)
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12 pages, 1579 KB  
Article
Dynamics of Microbial Community during the Co-Composting of Swine and Poultry Manure with Spent Mushroom Substrates at an Industrial Scale
by Wan-Rou Lin, Han-Yun Li, Lei-Chen Lin and Sung-Yuan Hsieh
Microorganisms 2022, 10(10), 2064; https://doi.org/10.3390/microorganisms10102064 - 19 Oct 2022
Cited by 5 | Viewed by 2321
Abstract
Spent mushroom substrates (SMSs) can be developed as a biofertilizer through composting. Here, we investigated the dynamics of bacterial and fungal communities during commercial composting and the effect of swine and poultry manure on their communities through MiSeq pyrosequencing. Weissella paramesenteroides and Lactobacillus [...] Read more.
Spent mushroom substrates (SMSs) can be developed as a biofertilizer through composting. Here, we investigated the dynamics of bacterial and fungal communities during commercial composting and the effect of swine and poultry manure on their communities through MiSeq pyrosequencing. Weissella paramesenteroides and Lactobacillus helveticus were dominant bacterial species in the composts with soy waste (SMS-SW), whereas Thermotogaceae sp. and Ureibacillus sp. were dominant in the composts with swine and poultry manure (SMS-PM). For the fungal community, Flammulina velutipes was dominant in SMS-SW, whereas Trichosporon asahii, Candida catenulate, Aspergillus fumigatus, and Candida tropicalis were dominant in SMS-PM. The addition of manure affected the bacterial community significantly. Redundancy analysis indicated that bacterial communities were affected by temperature, potassium, and potassium oxide and fungal communities by temperature, Kjeldahl nitrogen, organic matter, and ammonium nitrogen. Our findings can guide future research on composting microbiology. Full article
(This article belongs to the Section Microbial Biotechnology)
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19 pages, 2723 KB  
Article
Geno- and Phenotypic Characteristics of a Klebsiella pneumoniae ST20 Isolate with Unusual Colony Morphology
by Katharina Sydow, Elias Eger, Michael Schwabe, Stefan E. Heiden, Jürgen A. Bohnert, Sören Franzenburg, Christoph Jurischka, Peter Schierack and Katharina Schaufler
Microorganisms 2022, 10(10), 2063; https://doi.org/10.3390/microorganisms10102063 - 19 Oct 2022
Cited by 8 | Viewed by 6361
Abstract
Klebsiella pneumoniae is a common member of the intestinal flora of vertebrates. In addition to opportunistic representatives, hypervirulent (hvKp) and antibiotic-resistant K. pneumoniae (ABR-Kp) occur. While ABR-Kp isolates often cause difficult-to-treat diseases due to limited therapeutic options, hvKp is a pathotype that can [...] Read more.
Klebsiella pneumoniae is a common member of the intestinal flora of vertebrates. In addition to opportunistic representatives, hypervirulent (hvKp) and antibiotic-resistant K. pneumoniae (ABR-Kp) occur. While ABR-Kp isolates often cause difficult-to-treat diseases due to limited therapeutic options, hvKp is a pathotype that can infect healthy individuals often leading to recurrent infection. Here, we investigated the clinical K. pneumoniae isolate PBIO3459 obtained from a blood sample, which showed an unusual colony morphology. By combining whole-genome and RNA sequencing with multiple in vitro and in vivo virulence-associated assays, we aimed to define the respective Klebsiella subtype and explore the unusual phenotypic appearance. We demonstrate that PBIO3459 belongs to sequence type (ST)20 and carries no acquired resistance genes, consistent with phenotypic susceptibility tests. In addition, the isolate showed low-level virulence, both at genetic and phenotypic levels. We thus suggest that PBIO3459 is an opportunistic (commensal) K. pneumoniae isolate. Genomic comparison of PBIO3459 with closely related ABR-Kp ST20 isolates revealed that they differed only in resistance genes. Finally, the unusual colony morphology was mainly associated with carbohydrate and amino acid transport and metabolism. In conclusion, our study reveals the characteristics of a Klebsiella sepsis isolate and suggests that opportunistic representatives likely acquire and accumulate antibiotic resistances that subsequently enable their emergence as ABR-Kp pathogens. Full article
(This article belongs to the Special Issue Virulence and Resistance of Klebsiella pneumoniae, 2nd Edition)
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Article
Performance of Urine Reagent Strips in Detecting the Presence and Estimating the Prevalence and Intensity of Schistosoma haematobium Infection
by Abraham Degarege, Abebe Animut, Yohannes Negash and Berhanu Erko
Microorganisms 2022, 10(10), 2062; https://doi.org/10.3390/microorganisms10102062 - 19 Oct 2022
Cited by 8 | Viewed by 2250
Abstract
The performance of the urine reagent strips (URS) in detecting the presence and estimating the intensity of Schistosoma haematobium infection was evaluated using urine filtration microscopy as a reference standard. Urine samples collected from 1288 school-age children living in five villages of the [...] Read more.
The performance of the urine reagent strips (URS) in detecting the presence and estimating the intensity of Schistosoma haematobium infection was evaluated using urine filtration microscopy as a reference standard. Urine samples collected from 1288 school-age children living in five villages of the Afar and one village in the Gambella Regional States of Ethiopia between October 2021 and April 2022 were examined using urine filtration and URS. The prevalence of S. haematobium infection was 31.6% based on urine filtration and 32.1% using URS. Using results of the urine filtration as a reference, the sensitivity, specificity, negative predictive values, and accuracy of the URS in detecting S. haematobium egg-positive urine specimens were 73.7%, 87.8%, 87.1%, and 82.8%, respectively. Sensitivity increased significantly with an increase in the urine egg count. Specificity was greater in low prevalence settings and among children aged 5–9 years. The level of hematuria detected was trace (19.1%), weak (30.2%), moderate (36.0%), or high (14.7%). The log odds of showing higher-level hematuria significantly increased as the number of egg counts in urine increased. In conclusion, URS remains good in rapidly screening individuals for S. haematobium infection, but the sensitivity of the test could be lower, particularly when the intensity of the infection is light. Full article
(This article belongs to the Special Issue Childhood Infections)
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