@article {pmid34606847,
year = {2022},
author = {Lima, SF and Gogokhia, L and Viladomiu, M and Chou, L and Putzel, G and Jin, WB and Pires, S and Guo, CJ and Gerardin, Y and Crawford, CV and Jacob, V and Scherl, E and Brown, SE and Hambor, J and Longman, RS},
title = {Transferable Immunoglobulin A-Coated Odoribacter splanchnicus in Responders to Fecal Microbiota Transplantation for Ulcerative Colitis Limits Colonic Inflammation.},
journal = {Gastroenterology},
volume = {162},
number = {1},
pages = {166-178},
pmid = {34606847},
issn = {1528-0012},
support = {R01 DK114252/DK/NIDDK NIH HHS/United States ; R01 DK120985/DK/NIDDK NIH HHS/United States ; R01 DK128257/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteroidetes/genetics/*immunology/metabolism ; Clinical Trials as Topic ; Colitis/immunology/metabolism/microbiology/*therapy ; Colitis, Ulcerative/diagnosis/immunology/metabolism/microbiology ; Colon/immunology/metabolism/*microbiology ; Disease Models, Animal ; *Fecal Microbiota Transplantation ; Forkhead Transcription Factors/metabolism ; *Gastrointestinal Microbiome/genetics/immunology ; Germ-Free Life ; Humans ; Immunity, Mucosal ; Immunoglobulin A/genetics/*immunology/metabolism ; Intestinal Mucosa/immunology/metabolism/*microbiology ; Intraepithelial Lymphocytes/immunology/metabolism/microbiology ; Metagenome ; Metagenomics ; Mice, Inbred C57BL ; Mice, Knockout ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; T-Lymphocytes, Regulatory/immunology/metabolism/microbiology ; Treatment Outcome ; },
abstract = {BACKGROUND &amp; AIMS: Fecal microbiota transplantation (FMT) is an emerging treatment modality for ulcerative colitis (UC). Several randomized controlled trials have shown efficacy for FMT in the treatment of UC, but a better understanding of the transferable microbiota and their immune impact is needed to develop more efficient microbiome-based therapies for UC.<br><br>METHODS: Metagenomic analysis and strain tracking was performed on 60 donor and recipient samples receiving FMT for active UC. Sorting and sequencing of immunoglobulin (Ig) A-coated microbiota (called IgA-seq) was used to define immune-reactive microbiota. Colonization of germ-free or genetically engineered mice with patient-derived strains was performed to determine the mechanism of microbial impact on intestinal immunity.<br><br>RESULTS: Metagenomic analysis defined a core set of donor-derived transferable bacterial strains in UC subjects achieving clinical response, which predicted response in an independent trial of FMT for UC. IgA-seq of FMT recipient samples and gnotobiotic mice colonized with donor microbiota identified Odoribacter splanchnicus as a transferable strain shaping mucosal immunity, which correlated with clinical response and the induction of mucosal regulatory T cells. Colonization of mice with O splanchnicus led to an increase in Foxp3+/RORγt+ regulatory T cells, induction of interleukin (IL) 10, and production of short chain fatty acids, all of which were required for O splanchnicus to limit colitis in mouse models.<br><br>CONCLUSIONS: This work provides the first evidence of transferable, donor-derived strains that correlate with clinical response to FMT in UC and reveals O splanchnicus as a key component promoting both metabolic and immune cell protection from colitis. These mechanistic features will help enable strategies to enhance the efficacy of microbial therapy for UC. Clinicaltrials.gov ID NCT02516384.},
}
@article {pmid34245762,
year = {2021},
author = {Mihindukulasuriya, KA and Mars, RAT and Johnson, AJ and Ward, T and Priya, S and Lekatz, HR and Kalari, KR and Droit, L and Zheng, T and Blekhman, R and D'Amato, M and Farrugia, G and Knights, D and Handley, SA and Kashyap, PC},
title = {Multi-Omics Analyses Show Disease, Diet, and Transcriptome Interactions With the Virome.},
journal = {Gastroenterology},
volume = {161},
number = {4},
pages = {1194-1207.e8},
pmid = {34245762},
issn = {1528-0012},
support = {R01 DK114007/DK/NIDDK NIH HHS/United States ; RC2 DK116713/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Bacteriophages/genetics/growth &amp; development ; Case-Control Studies ; *Diet/adverse effects ; Female ; Gastrointestinal Microbiome ; Gene Expression Profiling ; Gene Expression Regulation ; Host-Pathogen Interactions ; Humans ; Intestines/microbiology/*virology ; Irritable Bowel Syndrome/diagnosis/genetics/microbiology/*virology ; Longitudinal Studies ; Male ; Metagenome ; Metagenomics ; Middle Aged ; *Transcriptome ; Virology ; *Virome ; Viruses/genetics/*growth &amp; development ; },
abstract = {BACKGROUND &amp; AIMS: The gut virome includes eukaryotic viruses and bacteriophages that can shape the gut bacterial community and elicit host responses. The virome can be implicated in diseases, such as irritable bowel syndrome (IBS), where gut bacteria play an important role in pathogenesis. We provide a comprehensive and longitudinal characterization of the virome, including DNA and RNA viruses and paired multi-omics data in a cohort of healthy subjects and patients with IBS.<br><br>METHODS: We selected 2 consecutive stool samples per subject from a longitudinal study cohort and performed metagenomic sequencing on DNA and RNA viruses after enriching for viral-like particles. Viral sequence abundance was evaluated over time, as well as in the context of diet, bacterial composition and function, metabolite levels, colonic gene expression, host genetics, and IBS subsets.<br><br>RESULTS: We found that the gut virome was temporally stable and correlated with the colonic transcriptome. We identified IBS-subset-specific changes in phage populations; Microviridae, Myoviridae, and Podoviridae species were elevated in diarrhea-predominant IBS, and other Microviridae and Myoviridae species were elevated in constipation-predominant IBS compared to healthy controls. We identified correlations between subsets of the virome and bacterial composition (unclassifiable "dark matter" and phages) and diet (eukaryotic viruses).<br><br>CONCLUSIONS: We found that the gut virome is stable over time but varies among subsets of patients with IBS. It can be affected by diet and potentially influences host function via interactions with gut bacteria and/or altering host gene expression.},
}
@article {pmid34207047,
year = {2021},
author = {Saad, N and Olmstead, JW and Varsani, A and Polston, JE and Jones, JB and Folimonova, SY and Harmon, PF},
title = {Discovery of Known and Novel Viruses in Wild and Cultivated Blueberry in Florida through Viral Metagenomic Approaches.},
journal = {Viruses},
volume = {13},
number = {6},
pages = {},
pmid = {34207047},
issn = {1999-4915},
mesh = {Blueberry Plants/*virology ; Florida ; Fruit/virology ; *Metagenome ; Metagenomics/*methods ; Plant Viruses/classification/*genetics/*isolation &amp; purification ; *Virome ; },
abstract = {Southern highbush blueberry (interspecific hybrids of Vaccinium corymbosum L.) is cultivated near wild V. corymbosum as well as closely related species in Florida, USA. The expansion of blueberry cultivation into new areas in Florida and deployment of new cultivars containing viruses can potentially increase the diversity of viruses in wild and cultivated V. corymbosum. In this study, viral diversity in wild and cultivated blueberries (V. corymbosum) is described using a metagenomic approach. RNA viromes from V. corymbosum plants collected from six locations (two cultivated and four wild) in North Central Florida were generated by high throughput sequencing (HTS) and analyzed using a bioinformatic analysis pipeline. De novo assembled contigs obtained from viromes of both commercial and wild sites produced sequences with similarities to plant virus species from a diverse range of families (Amalgaviridae, Caulimoviridae, Endornaviridae, Ophioviridae, Phenuiviridae, and Virgaviridae). In addition, this study has enabled the identification of blueberry latent virus (BlLV) and blueberry mosaic associated ophiovirus (BlMaV) for the first time in Florida, as well as a tentative novel tepovirus (blueberry virus T) (BlVT) in blueberry. To the best of our knowledge, this is the first study that compares viral diversity in wild and cultivated blueberry using a metagenomic approach.},
}
@article {pmid34175280,
year = {2021},
author = {Yang, K and Niu, J and Zuo, T and Sun, Y and Xu, Z and Tang, W and Liu, Q and Zhang, J and Ng, EKW and Wong, SKH and Yeoh, YK and Chan, PKS and Chan, FKL and Miao, Y and Ng, SC},
title = {Alterations in the Gut Virome in Obesity and Type 2 Diabetes Mellitus.},
journal = {Gastroenterology},
volume = {161},
number = {4},
pages = {1257-1269.e13},
doi = {10.1053/j.gastro.2021.06.056},
pmid = {34175280},
issn = {1528-0012},
mesh = {Adolescent ; Adult ; Aged ; Case-Control Studies ; Diabetes Mellitus, Type 2/diagnosis/microbiology/*virology ; Dysbiosis ; Feces/microbiology/virology ; Female ; Gastrointestinal Microbiome ; Hong Kong ; Host-Pathogen Interactions ; Humans ; Intestines/microbiology/*virology ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Obesity/diagnosis/microbiology/*virology ; *Virome/genetics ; Young Adult ; },
abstract = {BACKGROUND &amp; AIMS: Obesity and type 2 diabetes mellitus (T2DM) are associated with changes in the gut bacterial composition, but little is known about the role of the viral community (virome) in disease development. This study aims to characterize the gut virome alterations in obese subjects with or without T2DM.<br><br>METHODS: There were 128 obese subjects (body mass index ≥28 kg/m2) and 101 lean controls (body mass index ≥18.5 and <23 kg/m2) recruited from 2 regions in China (Hong Kong and Kunming). Fecal virome and bacteriome were profiled by shotgun metagenomic sequencing. Gut virome, bacteriome, and viral-bacterial correlations were compared between obese subjects and lean controls.<br><br>RESULTS: Obese subjects, especially those with T2DM (ObT2), had a decreased gut viral richness and diversity compared with lean controls in the Hong Kong cohort (P < .05), while no significant differences were observed in the Kunming cohort. Eleven viruses, including Escherichia phage, Geobacillus phage, and Lactobacillus phage were enriched in obese subjects (q < .1). Besides, 17 differentially abundant viruses were identified between ObT2 and lean controls (q < .1). Further ecologic analysis revealed that intensive transkingdom correlations between viruses and bacteria observed in lean controls were significantly decreased in ObT2 subjects (P < .001).<br><br>CONCLUSIONS: Obesity is characterized by altered viral taxonomic composition and weakened viral-bacterial correlations compared with lean controls. Obesity accompanied with T2DM may aggravate the obesity-associated virus signatures, signifying that the gut virome may play an important role in the development of obesity and T2DM. Geographic factors also contributed to the variations of gut virome in obesity and T2DM.},
}
@article {pmid34126062,
year = {2021},
author = {Nooij, S and Ducarmon, QR and Laros, JFJ and Zwittink, RD and Norman, JM and Smits, WK and Verspaget, HW and Keller, JJ and Terveer, EM and Kuijper, EJ and , },
title = {Fecal Microbiota Transplantation Influences Procarcinogenic Escherichia coli in Recipient Recurrent Clostridioides difficile Patients.},
journal = {Gastroenterology},
volume = {161},
number = {4},
pages = {1218-1228.e5},
doi = {10.1053/j.gastro.2021.06.009},
pmid = {34126062},
issn = {1528-0012},
mesh = {Adult ; Aged ; Aged, 80 and over ; Clostridioides difficile/*pathogenicity ; Clostridium Infections/diagnosis/microbiology/*therapy ; Dysbiosis ; Escherichia coli/enzymology/genetics/*growth &amp; development ; Escherichia coli Proteins/genetics/metabolism ; *Fecal Microbiota Transplantation/adverse effects ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Polyketide Synthases/genetics/metabolism ; Reinfection ; Retrospective Studies ; Time Factors ; Treatment Outcome ; },
abstract = {BACKGROUND &amp; AIMS: Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota transplantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarcinogenic polyketide synthase-positive (pks+) Escherichia coli. Here, we aim to determine whether the pks abundance and persistence of pks+E coli is influenced by pks status of the donor feces.<br><br>METHODS: In a cohort of 49 patients with rCDI treated with FMT and matching donor samples-the largest cohort of its kind, to our knowledge-we retrospectively screened fecal metagenomes for pks+E coli and compared the presence of pks in patients before and after treatment and to their respective donors.<br><br>RESULTS: The pks island was more prevalent (P = .026) and abundant (P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated (P = .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks+E coli in pks+ patients was correlated to pks in the donor (P = .004).<br><br>CONCLUSIONS: We conclude that FMT contributes to pks+E coli persistence or eradication in patients with rCDI but that donor-to-patient transmission of pks+E coli is unlikely.},
}
@article {pmid33958598,
year = {2021},
author = {Heinken, A and Hertel, J and Thiele, I},
title = {Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis.},
journal = {NPJ systems biology and applications},
volume = {7},
number = {1},
pages = {19},
pmid = {33958598},
issn = {2056-7189},
support = {RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; },
mesh = {Child ; *Crohn Disease ; Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; Metagenomics ; },
abstract = {Inflammatory bowel diseases, such as Crohn's Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal metabolites. We retrieve strain-level relative abundances from metagenomics data from a cohort of paediatric Crohn's Disease patients with and without dysbiosis and healthy control children and construct and interrogate a personalised microbiome model for each sample. Predicted faecal secretion profiles and strain-level contributions to each metabolite vary broadly between healthy, dysbiotic, and non-dysbiotic microbiomes. The reduced microbial diversity in IBD results in reduced numbers of secreted metabolites, especially in sulfur metabolism. We demonstrate that increased potential to synthesise amino acids is linked to Proteobacteria contributions, in agreement with experimental observations. The established modelling framework yields testable hypotheses that may result in novel therapeutic and dietary interventions targeting the host-gut microbiome-diet axis.},
}
@article {pmid33857456,
year = {2021},
author = {Shamsaddini, A and Gillevet, PM and Acharya, C and Fagan, A and Gavis, E and Sikaroodi, M and McGeorge, S and Khoruts, A and Albhaisi, S and Fuchs, M and Sterling, RK and Bajaj, JS},
title = {Impact of Antibiotic Resistance Genes in Gut Microbiome of Patients With Cirrhosis.},
journal = {Gastroenterology},
volume = {161},
number = {2},
pages = {508-521.e7},
doi = {10.1053/j.gastro.2021.04.013},
pmid = {33857456},
issn = {1528-0012},
support = {R21 TR003095/TR/NCATS NIH HHS/United States ; I01 CX001761/CX/CSRD VA/United States ; R21 TR002024/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Aged ; Anti-Bacterial Agents/adverse effects/*therapeutic use ; Bacteria/*drug effects/genetics ; Case-Control Studies ; Cross-Sectional Studies ; Disease Progression ; Drug Resistance, Bacterial/*genetics ; Dysbiosis ; Female ; Gastrointestinal Microbiome/*drug effects/genetics ; Hospitalization ; Humans ; Intestines/*microbiology ; Liver Cirrhosis/diagnosis/*drug therapy/microbiology/mortality ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Rifaximin/adverse effects/*therapeutic use ; Risk Assessment ; Risk Factors ; Time Factors ; Treatment Outcome ; Young Adult ; },
abstract = {BACKGROUND AND AIMS: Cirrhosis is associated with changes in intestinal microbiota that can lead to hepatic encephalopathy (HE) and infections, especially with antibiotic-resistant organisms. However, the impact of gut microbial antibiotic resistance gene (ARG) burden on clinical outcomes is unclear. The aims of the study were to determine the impact of ARGs in cirrhosis-related gut metagenome on outcomes and disease progression, study the effect of rifaximin on ARG burden, and compare ARGs in cirrhosis with chronic kidney disease (CKD) and diabetes.<br><br>METHODS: In outpatients with cirrhosis who underwent metagenomics, we evaluated change in ARG abundances with progression and their multivariable impact on 90-day hospitalizations and deaths over 1 year. We also studied ARGs pre- and 8 weeks post-rifaximin in patients with compensated cirrhosis in an open-label trial. Finally, ARGs from CKD and diabetes studies were compared with cirrhosis on machine learning.<br><br>RESULTS: A total of 163 patients with cirrhosis (43 compensated, 20 ascites-only, 30 HE-only, 70 both) and 40 controls were included. ARG abundances were higher in cirrhosis versus controls and worsened with advancing cirrhosis severity; 44 patients were hospitalized and 14 died. ARG abundances were associated with hospitalizations and mortality while controlling for cirrhosis complications, medications, and demographics. Rifaximin trial: ARG abundance patterns were minimally affected in 19 patients post-rifaximin. CKD/diabetes comparison: ARG abundance patterns in cirrhosis are distinguishable on machine learning and include more gram-positive ARGs.<br><br>CONCLUSIONS: Cirrhosis is associated with high gut microbial ARG gene burden compared with controls, which worsens with disease progression and may be different from CKD and diabetes. ARGs are not affected by rifaximin and are associated with hospitalizations and death.},
}
@article {pmid33827686,
year = {2021},
author = {Ducarmon, QR and Terveer, EM and Nooij, S and Bloem, MN and Vendrik, KEW and Caljouw, MAA and Sanders, IMJG and van Dorp, SM and Wong, MC and Zwittink, RD and Kuijper, EJ},
title = {Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home.},
journal = {Genome medicine},
volume = {13},
number = {1},
pages = {54},
pmid = {33827686},
issn = {1756-994X},
mesh = {Bacteria/genetics/isolation &amp; purification ; *Drug Resistance, Multiple, Bacterial/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Genome, Bacterial ; Humans ; Metagenome ; Microbial Sensitivity Tests ; Netherlands ; *Nursing Homes ; Principal Component Analysis ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; Time Factors ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs.<br><br>METHODS: We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016-April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study.<br><br>RESULTS: Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents.<br><br>CONCLUSIONS: Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation.},
}
@article {pmid34772759,
year = {2021},
author = {Kardos, M and Armstrong, EE and Fitzpatrick, SW and Hauser, S and Hedrick, PW and Miller, JM and Tallmon, DA and Funk, WC},
title = {The crucial role of genome-wide genetic variation in conservation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {48},
pages = {},
pmid = {34772759},
issn = {1091-6490},
support = {RL5 GM118990/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Biodiversity ; Conservation of Natural Resources ; Ecosystem ; Genetic Fitness/genetics ; Genetic Variation/*genetics ; Genetics ; Genetics, Population/methods ; Genome/*genetics ; Genomics ; Inbreeding ; Metagenomics/methods ; Population Dynamics/*trends ; },
abstract = {The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.},
}
@article {pmid34607029,
year = {2022},
author = {Sun, Y and Duan, C and Cao, N and Ding, C and Huang, Y and Wang, J},
title = {Biodegradable and conventional microplastics exhibit distinct microbiome, functionality, and metabolome changes in soil.},
journal = {Journal of hazardous materials},
volume = {424},
number = {Pt A},
pages = {127282},
doi = {10.1016/j.jhazmat.2021.127282},
pmid = {34607029},
issn = {1873-3336},
mesh = {Metabolome ; *Microbiota ; *Microplastics ; Plastics ; RNA, Ribosomal, 16S/genetics ; Soil ; },
abstract = {Environmental concerns with liberal petroleum-based plastic use have led to demand for sustainable biodegradable alternatives. However, the inadequate end-of-life treatment of plastics may emit microplastics, either conventional or biodegradable, to the terrestrial environment. It is essential to evaluate the possible effects of conventional and biodegradable microplastics on the composition and function of soil microbial communities. Therefore, we conducted a soil microcosm experiment with polyethylene (PE), polystyrene (PS), polylactide (PLA), or polybutylene succinate (PBS) microplastics. The soil microbiome and metabolome were evaluated via 16S rRNA gene sequencing, metagenomics, and untargeted metabolomics. We reported that the presence of conventional or biodegradable microplastics can significantly alter soil microbial community composition. Compared to the control soils, the microbiome in PBS and PLA amended soils exhibited higher potential for uptake of exogenous carbohydrates and amino acids, but a reduced capacity for related metabolic function, potentially due to catabolite repression. No differences in soil metabolome can be observed between conventional microplastic treatments and the control. The potential reason may be that the functional diversity was unaffected by PE and PS microplastics, while the biodegradable particles promoted the soil microbial multifunctionality. Our findings systematically shed light on the influence of conventional and biodegradable microplastics on soil microorganisms, facilitating microplastic regulation.},
}
@article {pmid33382948,
year = {2021},
author = {Liu, W and Sun, Z and Ma, C and Zhang, J and Ma, C and Zhao, Y and Wei, H and Huang, S and Zhang, H},
title = {Exposure to soil environments during earlier life stages is distinguishable in the gut microbiome of adult mice.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-13},
pmid = {33382948},
issn = {1949-0984},
mesh = {Animals ; *Environmental Exposure ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Housing, Animal ; Life Cycle Stages/*physiology ; Metagenomics ; Mice ; Soil ; *Soil Microbiology ; },
abstract = {Environmental exposure during earlier life stages can govern the assembly and development of gut microbiota, yet it is insufficiently understood. In this study, ex-germ-free mice were cohoused with distinct soil-microbiota (from desert, steppe, and forest) beddings within 60 days after birth and subsequently transferred to new soil beddings from 60 to 90th day. Using metagenomic shotgun sequencing, firstly, we found soil microbes from natural environments (birthplace) greatly influenced the gut community assembly in the housing experiment. About 27% microbial species and 12% functional components that associated with birthplaces at Day 60 were still discriminatory of birthplaces after transferring mice to new environments. Moreover, prior soil-exposure types are associated with the magnitude of temporal microbiome change due to environmental shifts. The appropriate soil-exposure (e.g., steppe) might help mice gut microbiome adapt to changing environments or host development. Our study demonstrated the continuous soil-exposure history earlier is associated with the gut microbiome individuality and development later.},
}
@article {pmid34763361,
year = {2021},
author = {Deka, N and Hassan, S and Seghal Kiran, G and Selvin, J},
title = {Insights into the role of vaginal microbiome in women's health.},
journal = {Journal of basic microbiology},
volume = {61},
number = {12},
pages = {1071-1084},
doi = {10.1002/jobm.202100421},
pmid = {34763361},
issn = {1521-4028},
mesh = {Dysbiosis ; Female ; Humans ; *Microbiota ; Vagina ; *Vaginosis, Bacterial ; Women's Health ; },
abstract = {The vaginal microbiome is a complex and dynamic microecosystem that fluctuates continually throughout a woman's life. Lactobacillus, a bacterium that possesses antibacterial properties dominates a healthy vaginal microbiome. Bacterial vaginosis is the most common vaginal disorder that has been linked with the dysbiosis of normal vaginal microbiota. Despite the importance of vaginal microbiome, little is known about functions it performs especially, how it helps in protecting the female reproductive tract. This knowledge gap is a significant impediment to the development of effective and feasible clinical treatments that might be required to improve women's health. Thus, a deeper understanding of the functional aspects and not just the composition of vaginal microbiome may aid in improving the diagnostics and treatment strategies. Recent advancement in molecular methods and computational biology have allowed researchers to acquire more knowledge about the vaginal microbiome. The use of metagenomics (culture-independent high-throughput technology) and bioinformatics tools have improved our understanding of the vaginal microbiome. In this review, we have attempted to explore the factors that may alter normal vaginal microbiota homeostasis such as age, sexual behavior, ethnicity, and hygiene, and so forth. We also discuss the role of probiotics in restoring healthy vaginal microbiome.},
}
@article {pmid34686940,
year = {2021},
author = {Sabater, C and Cobo-Díaz, JF and Álvarez-Ordóñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A},
title = {Novel methods of microbiome analysis in the food industry.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {24},
number = {4},
pages = {593-605},
pmid = {34686940},
issn = {1618-1905},
support = {818368//h2020 food/ ; RTI2018-095021-J-I00//agencia estatal de investigación/ ; AGL2016-78085-P//agencia estatal de investigación/ ; AGL2016-78311-R//agencia estatal de investigación/ ; FJC2019-042125-I//agencia estatal de investigación/ ; },
mesh = {Drug Resistance, Microbial ; Food Industry ; Metagenome ; *Metagenomics ; *Microbiota ; },
abstract = {The study of the food microbiome has gained considerable interest in recent years, mainly due to the wide range of applications that can be derived from the analysis of metagenomes. Among these applications, it is worth mentioning the possibility of using metagenomic analyses to determine food authenticity, to assess the microbiological safety of foods thanks to the detection and tracking of pathogens, antibiotic resistance genes and other undesirable traits, as well to identify the microorganisms responsible for food processing defects. Metataxonomics and metagenomics are currently the gold standard methodologies to explore the full potential of metagenomes in the food industry. However, there are still a number of challenges that must be solved in order to implement these methods routinely in food chain monitoring, and for the regulatory agencies to take them into account in their opinions. These challenges include the difficulties of analysing foods and food-related environments with a low microbial load, the lack of validated bioinformatics pipelines adapted to food microbiomes and the difficulty of assessing the viability of the detected microorganisms. This review summarizes the methods of microbiome analysis that have been used, so far, in foods and food-related environments, with a specific focus on those involving Next-Generation Sequencing technologies.},
}
@article {pmid34556654,
year = {2021},
author = {Belstrøm, D and Constancias, F and Drautz-Moses, DI and Schuster, SC and Veleba, M and Mahé, F and Givskov, M},
title = {Periodontitis associates with species-specific gene expression of the oral microbiota.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {76},
pmid = {34556654},
issn = {2055-5008},
mesh = {*Diabetes Mellitus, Type 2 ; Gene Expression ; Humans ; *Microbiota/genetics ; *Periodontitis ; RNA, Ribosomal, 16S ; },
abstract = {The purpose of the present investigation was to characterize species-specific bacterial activity of the oral microbiota in periodontitis. We tested the hypotheses that chronic inflammation, i.e., periodontitis, associates with bacterial gene expression of the oral microbiota. Oral microbial samples were collected from three oral sites-subgingival plaque, tongue, and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterization of taxonomic composition and to determine species-specific bacterial activity as expressed by the ratio of specific messenger RNA reads to their corresponding genomic DNA reads. Here, we show the association of periodontitis with bacterial gene expression of the oral microbiota. While oral site was the main determinant of taxonomic composition as well as bacterial gene expression, periodontitis was significantly associated with a reduction of carbohydrate metabolism of the oral microbiota at three oral sites (subgingival plaque, tongue, and saliva). Data from the present study revealed the association of periodontitis with bacterial gene expression of the oral microbiota. Conditions of periodontitis was associated with bacterial activity of local subgingival plaque, but also on tongue and the salivary microbiota. Collectively, data suggest that periodontitis associates with impaired carbohydrate metabolism of the oral microbiota. Future longitudinal and interventional studies are warranted to evaluate the potential pathogenic role of impaired bacterial carbohydrate metabolism not only in periodontitis but also in other diseases with low-grade inflammation, such as type 2 diabetes mellitus.},
}
@article {pmid34473943,
year = {2021},
author = {Vasquez, KS and Willis, L and Cira, NJ and Ng, KM and Pedro, MF and Aranda-Díaz, A and Rajendram, M and Yu, FB and Higginbottom, SK and Neff, N and Sherlock, G and Xavier, KB and Quake, SR and Sonnenburg, JL and Good, BH and Huang, KC},
title = {Quantifying rapid bacterial evolution and transmission within the mouse intestine.},
journal = {Cell host &amp; microbe},
volume = {29},
number = {9},
pages = {1454-1468.e4},
pmid = {34473943},
issn = {1934-6069},
support = {R35 GM131824/GM/NIGMS NIH HHS/United States ; RM1 GM135102/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Ciprofloxacin/*pharmacology ; DNA Barcoding, Taxonomic/*methods ; Escherichia coli/drug effects/*growth &amp; development/immunology ; Evolution, Molecular ; Gastrointestinal Microbiome/*genetics ; Genetics, Population/methods ; Germ-Free Life ; Intestines/*microbiology ; Mice ; Selection, Genetic/genetics ; Whole Genome Sequencing ; },
abstract = {Due to limitations on high-resolution strain tracking, selection dynamics during gut microbiota colonization and transmission between hosts remain mostly mysterious. Here, we introduced hundreds of barcoded Escherichia coli strains into germ-free mice and quantified strain-level dynamics and metagenomic changes. Mutations in genes involved in motility and metabolite utilization are reproducibly selected within days. Even with rapid selection, coprophagy enforced similar barcode distributions across co-housed mice. Whole-genome sequencing of hundreds of isolates revealed linked alleles that demonstrate between-host transmission. A population-genetics model predicts substantial fitness advantages for certain mutants and that migration accounted for ∼10% of the resident microbiota each day. Treatment with ciprofloxacin suggests interplay between selection and transmission. While initial colonization was mostly uniform, in two mice a bottleneck reduced diversity and selected for ciprofloxacin resistance in the absence of drug. These findings highlight the interplay between environmental transmission and rapid, deterministic selection during evolution of the intestinal microbiota.},
}
@article {pmid34410642,
year = {2021},
author = {Moore, NE and Weyrich, LS},
title = {A Standardized Approach for Shotgun Metagenomic Analysis of Ancient Dental Calculus.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2327},
number = {},
pages = {93-118},
pmid = {34410642},
issn = {1940-6029},
mesh = {DNA, Ancient ; *Dental Calculus ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {Ancient dental calculus provides a challenging, yet unparalleled, opportunity to reconstruct ancient oral microbial communities and trace the origins of modern microbiota-associated diseases. Metagenomic analysis of ancient dental calculus using high-throughput DNA sequencing has proven itself as an effective method to accurately reconstruct microorganisms that once lived in the mouths of ancient humans. Here, we provide the strategy, methodologies, and approaches used to establish an ancient dental calculus project, from project conception, community engagement, sampling, extracting DNA, and preparing shotgun metagenomic DNA libraries for sequencing on an Illumina platform. We also discuss techniques to minimize background or contaminant DNA by monitoring and reducing contamination in calculus data sets, utilizing appropriate protective gear, and employing the use of sample decontamination strategies. In this methodology chapter, we hope to promote transparency in the ancient dental calculus research field and encourage collaboration across the ancient DNA research community.},
}
@article {pmid34410641,
year = {2021},
author = {Marotz, C and Zuniga, C and Zaramela, L and Knight, R and Zengler, K},
title = {Host DNA Depletion in Saliva Samples for Improved Shotgun Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2327},
number = {},
pages = {87-92},
pmid = {34410641},
issn = {1940-6029},
mesh = {DNA/genetics ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Saliva ; Sequence Analysis, DNA ; },
abstract = {Host DNA makes up the majority of DNA in a saliva sample. Therefore, shotgun metagenomics can be an inefficient way to evaluate the microbial populations of saliva since often <10% of the sequencing reads are microbial. In this chapter, we describe a method to deplete human DNA from fresh or frozen saliva samples, allowing for more efficient shotgun metagenomic sequencing of the salivary microbial community.},
}
@article {pmid34410638,
year = {2021},
author = {Tansirichaiya, S and Reynolds, LJ and Roberts, AP},
title = {Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2327},
number = {},
pages = {31-50},
pmid = {34410638},
issn = {1940-6029},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; Drug Resistance, Bacterial/drug effects/genetics ; Humans ; Metagenome ; *Metagenomics ; *Microbiota ; },
abstract = {A large proportion of bacteria, from a multitude of environments, are not yet able to be grown in the laboratory, and therefore microbiological and molecular biological investigations of these bacteria are challenging. A way to circumvent this challenge is to analyze the metagenome, the entire collection of DNA molecules that can be isolated from a particular environment or sample. This collection of DNA molecules can be sequenced and assembled to determine what is present and infer functional potential, or used as a PCR template to detect known target DNA and potentially unknown regions of DNA nearby those targets; however assigning functions to new or conserved hypothetical, functionally cryptic, genes is difficult. Functional metagenomics allows researchers to determine which genes are responsible for selectable phenotypes, such as resistance to antimicrobials and metabolic capabilities, without the prerequisite needs to grow the bacteria containing those genes or to already know which genes are of interest. It is estimated that a third of the resident species of the human oral cavity is not yet cultivable and, together with the ease of sample acquisition, makes this metagenome particularly suited to functional metagenomic studies. Here we describe the methodology related to the collection of saliva samples, extraction of metagenomic DNA, construction of metagenomic libraries, as well as the description of functional assays that have previously led to the identification of new genes conferring antimicrobial resistance.},
}
@article {pmid34346706,
year = {2021},
author = {Ma, L and Keng, J and Cheng, M and Pan, H and Feng, B and Hu, Y and Feng, T and Yang, F},
title = {Gut Microbiome and Serum Metabolome Alterations Associated with Isolated Dystonia.},
journal = {mSphere},
volume = {6},
number = {4},
pages = {e0028321},
pmid = {34346706},
issn = {2379-5042},
mesh = {Adult ; Bacteria/classification/*genetics/*metabolism ; Biosynthetic Pathways/genetics ; Dysbiosis/microbiology ; Dystonia/*blood/*etiology/microbiology/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Male ; Mass Spectrometry ; *Metabolome ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Dystonia is a complex neurological movement disorder characterized by involuntary muscle contractions. Increasing studies implicate the microbiome as a possible key susceptibility factor for neurological disorders, but the relationship between the gut microbiota and dystonia remains poorly explored. Here, the gut microbiota of 57 patients with isolated dystonia and 27 age- and environment-matched healthy controls was analyzed by 16S rRNA gene amplicon sequencing. Further, integrative analysis of the gut microbiome and serum metabolome measured by high-performance liquid chromatography-mass spectrometry was performed. No difference in α-diversity was found, while β-diversity was significantly different, with a more heterogeneous community structure among dystonia patients than among controls. The most significant changes in dystonia highlighted an increase in Clostridiales, including Blautia obeum, Dorea longicatena, and Eubacterium hallii, and a reduction in Bacteroides vulgatus and Bacteroides plebeius. The functional analysis revealed that genes related to tryptophan and purine biosynthesis were more abundant in gut microbiota from patients with dystonia, while genes linked to citrate cycle, vitamin B6, and glycan metabolism were less abundant. The evaluation of serum metabolites revealed altered levels of l-glutamic acid, taurine, and d-tyrosine, suggesting changes in neurotransmitter metabolism. The most modified metabolites strongly inversely correlated with the abundance of members belonging to the Clostridiales, revealing the effect of the gut microbiota on neurometabolic activity. This study is the first to reveal gut microbial dysbiosis in patients with isolated dystonia and identified potential links between gut microbiota and serum neurotransmitters, providing new insight into the pathogenesis of isolated dystonia. IMPORTANCE Dystonia is the third most common movement disorder after essential tremor and Parkinson's disease. However, the cause for the majority of cases is not known. This is the first study so far that reveals significant alterations of gut microbiome and correlates the alteration of serum metabolites with gut dysbiosis in patients with isolated dystonia. We demonstrated a general overrepresentation of Clostridiales and underrepresentation of Bacteroidetes in patients with dystonia in comparison with healthy controls. The functional analysis found that genes related to the biosynthesis of tryptophan, which is the precursor of the neurotransmitter serotonin, were more active in isolated dystonia patients. Altered levels of several serum metabolites were found to be associated with microbial changes, such as d-tyrosine, taurine, and glutamate, indicating differences in neurotransmitter metabolism in isolated dystonia. Integrative analysis suggests that neurotransmitter system dysfunction may be a possible pathway by which the gut microbiome participates in the development of dystonia. The gut microbiome changes provide new insight into the pathogenesis of dystonia, suggesting new potential therapeutic directions.},
}
@article {pmid34346704,
year = {2021},
author = {Huang, X and Welsh, RM and Deming, C and Proctor, DM and Thomas, PJ and , and Gussin, GM and Huang, SS and Kong, HH and Bentz, ML and Vallabhaneni, S and Chiller, T and Jackson, BR and Forsberg, K and Conlan, S and Litvintseva, AP and Segre, JA},
title = {Skin Metagenomic Sequence Analysis of Early Candida auris Outbreaks in U.S. Nursing Homes.},
journal = {mSphere},
volume = {6},
number = {4},
pages = {e0028721},
pmid = {34346704},
issn = {2379-5042},
mesh = {Candida auris/*genetics ; Candidiasis/*epidemiology/microbiology ; Disease Outbreaks ; Humans ; Metagenome ; Metagenomics/*methods ; Mycobiome/genetics ; Nursing Homes/*statistics &amp; numerical data ; Risk Factors ; Skin/*microbiology ; United States/epidemiology ; },
abstract = {Candida auris is a human fungal pathogen classified as an urgent threat to the delivery of health care due to its extensive antimicrobial resistance and the high mortality rates associated with invasive infections. Global outbreaks have occurred in health care facilities, particularly, long-term care hospitals and nursing homes. Skin is the primary site of colonization for C. auris. To accelerate research studies, we developed microbiome sequencing protocols, including amplicon and metagenomic sequencing, directly from patient samples at health care facilities with ongoing C. auris outbreaks. We characterized the skin mycobiome with a database optimized to classify Candida species and C. auris to the clade level. While Malassezia species were the predominant skin-associated fungi, nursing home residents also harbored Candida species, including C. albicans, and C. parapsilosis. Amplicon sequencing was concordant with culturing studies to identify C. auris-colonized patients and provided further resolution that distinct clades of C. auris are colonizing facilities in New York and Illinois. Shotgun metagenomic sequencing from a clinical sample with a high fungal bioburden generated a skin-associated profile of the C. auris genome. Future larger scale clinical studies are warranted to more systematically investigate the effects of commensal microbes and patient risk factors on the colonization and transmission of C. auris. IMPORTANCE Candida auris is a human pathogen of high concern due to its extensive antifungal drug resistance and high mortality rates associated with invasive infections. Candida auris skin colonization and persistence on environmental surfaces make this pathogen difficult to control once it enters a health care facility. Residents in long-term care hospitals and nursing homes are especially vulnerable. In this study, we developed microbiome sequencing protocols directly from surveillance samples, including amplicon and metagenomic sequencing, demonstrating concordance between sequencing results and culturing.},
}
@article {pmid34287005,
year = {2021},
author = {Kang, Y and Sun, B and Chen, Y and Lou, Y and Zheng, M and Li, Z},
title = {Dental Plaque Microbial Resistomes of Periodontal Health and Disease and Their Changes after Scaling and Root Planing Therapy.},
journal = {mSphere},
volume = {6},
number = {4},
pages = {e0016221},
pmid = {34287005},
issn = {2379-5042},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/classification/*genetics ; Databases, Nucleic Acid ; Dental Plaque/*microbiology ; *Dental Scaling ; Drug Resistance, Microbial/*genetics ; Genes, Bacterial ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/drug effects/*genetics ; Periodontal Diseases/*microbiology/*therapy ; *Root Planing ; },
abstract = {The human oral microbial community has been considered a reservoir of antibiotic resistance. Currently, the effects of periodontitis and the scaling and root planing (SRP) treatment on the performance of antibiotic-resistant genes (ARGs) and metal-resistant genes (MRGs) in the dental plaque microbiota are not well characterized. To explore this issue, we selected 48 healthy-state (HS), 40 periodontitis-state (PS; before treatment), and 24 resolved-state (RS; after SRP treatment) metagenomic data of dental plaque samples from the Sequence Read Archive (SRA) database. NetShift analysis identified Fretibacterium fastidiosum, Tannerella forsythia, and Campylobacter rectus as key drivers during dental plaque microbiota alteration in the progression of periodontitis. Periodontitis and SRP treatment resulted in an increase in the number of ARGs and MRGs in dental plaque and significantly altered the composition of ARG and MRG profiles. Bacitracin, beta-lactam, macrolide-lincosamide-streptogramin (MLS), tetracycline, and multidrug resistance genes were the main classes of ARGs with high relative abundance, whereas multimetal, iron, chromium, and copper resistance genes were the primary types of MRGs in dental plaque microbiota. The cooccurrence of ARGs, MRGs, and mobile genetic elements (MGEs) indicated that a coselection phenomenon exists in the resistomes of dental plaque microbiota. Overall, our data provide new insights into the standing of the distribution of ARGs and MRGs in oral microbiota of periodontitis patients, and it was possible to contribute to the understanding of the complicated correlations among microorganisms, resistomes, and MGEs. IMPORTANCE The emergence and development of resistance to antibiotics in periodontal pathogens have affected the success rate of treatment for periodontitis. The development of new antibacterial strategies is urgently needed to help control and treat periodontal disease, and dental plaque microbiome studies offer a promising new angle of attack. In this study, we investigated the dental plaque microbiota and resistomes in periodontal health and disease states and their changes after SRP therapy. This is the first analysis of the profile of the microbial community and antibiotic and metal resistance genes in dental plaque by the metagenomic approach, to the best of our knowledge. Monitoring the profile of these resistomes has huge potential to provide reference levels for proper antibiotics use and the development of new antimicrobial strategies in periodontitis therapy and thereby improve actual efficacy of the treatment regimens.},
}
@article {pmid34884735,
year = {2021},
author = {Hernandez-Baixauli, J and Puigbò, P and Abasolo, N and Palacios-Jordan, H and Foguet-Romero, E and Suñol, D and Galofré, M and Caimari, A and Baselga-Escudero, L and Bas, JMD and Mulero, M},
title = {Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach.},
journal = {International journal of molecular sciences},
volume = {22},
number = {23},
pages = {},
pmid = {34884735},
issn = {1422-0067},
mesh = {Animals ; Biomarkers/blood/urine ; Male ; *Metabolome ; *Microbiota ; Rats, Wistar ; Stress, Psychological/*metabolism/microbiology ; },
abstract = {Stress disorders have dramatically increased in recent decades becoming the most prevalent psychiatric disorder in the United States and Europe. However, the diagnosis of stress disorders is currently based on symptom checklist and psychological questionnaires, thus making the identification of candidate biomarkers necessary to gain better insights into this pathology and its related metabolic alterations. Regarding the identification of potential biomarkers, omic profiling and metabolic footprint arise as promising approaches to recognize early biochemical changes in such disease and provide opportunities for the development of integrative candidate biomarkers. Here, we studied plasma and urine metabolites together with metagenomics in a 3 days Chronic Unpredictable Mild Stress (3d CUMS) animal approach that aims to focus on the early stress period of a well-established depression model. The multi-omics integration showed a profile composed by a signature of eight plasma metabolites, six urine metabolites and five microbes. Specifically, threonic acid, malic acid, alpha-ketoglutarate, succinic acid and cholesterol were proposed as key metabolites that could serve as key potential biomarkers in plasma metabolome of early stages of stress. Such findings targeted the threonic acid metabolism and the tricarboxylic acid (TCA) cycle as important pathways in early stress. Additionally, an increase in opportunistic microbes as virus of the Herpesvirales was observed in the microbiota as an effect of the primary stress stages. Our results provide an experimental biochemical characterization of the early stage of CUMS accompanied by a subsequent omic profiling and a metabolic footprinting that provide potential candidate biomarkers.},
}
@article {pmid34838108,
year = {2021},
author = {Lin, D and Zheng, X and Sanogo, B and Ding, T and Sun, X and Wu, Z},
title = {Bacterial composition of midgut and entire body of laboratory colonies of Aedes aegypti and Aedes albopictus from Southern China.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {586},
pmid = {34838108},
issn = {1756-3305},
support = {2020YFC1200100//the National Key R&amp;D Program of China/ ; 2016YFC1200500//the National Key R&amp;D Program of China/ ; 2019A1515012068//Natural Science Foundation of Guangdong Province/ ; 2020A1515010896//Natural Science Foundation of Guangdong Province/ ; 2021A1515010976//Natural Science Foundation of Guangdong Province/ ; 82072308//the National Natural Science Foundation of China/ ; 82002168//the National Natural Science Foundation of China/ ; 20201192//the 6th Nuclear Energy R&amp;D Project/ ; B12003//The 111 Project/ ; },
mesh = {Aedes/*microbiology ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Laboratories ; Metagenomics ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are invasive mosquito species and significantly impact human health in southern China. Microbiota are confirmed to affect the development and immunity of mosquitoes. However, scientists have focused more on midgut microbiota of female mosquitoes and bacterial differences between female and male Aedes mosquitoes. The relationship between the midgut and entire body microbiota of Aedes is unclear. In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.<br><br>METHODS: In this study, we collected mosquito samples reared under the same laboratory conditions and compared the microbial composition of midgut and entire bodies of Aedes aegypti and Aedes albopictus using 16S rRNA gene sequencing.<br><br>RESULTS: A total of 341 OTUs were identified, showing that Proteobacteria was the dominant phylum and Methylobacterium the dominant genus in both Aedes aegypti and Aedes albopictus. The bacterial diversity and community structures of the entire bodies were similar between males and females in both Aedes aegypti and Aedes albopictus. Conversely, the bacterial compositions of male and female Aedes aegypti and Aedes albopictus were significantly different. NMDS analysis, UPGMA analysis, diversity indices and OTU distribution demonstrated that compositions and structures in midgut microbiota were similar but significantly different in the entire bodies of Aedes aegypti and Aedes albopictus. Functional prediction analysis showed that metabolism and environmental information processing were the dominant KEGG pathways at level 1. Our study showed that there were significantly different level 2 and 3 KEGG pathways in the midgut microbiota (16 level 2 and 24 level 3) and the entire bodies (33 level 2 and 248 level 3) between female Aedes albopictus and Aedes Aegypti.<br><br>CONCLUSIONS: Our findings that Aedes aegypti and Aedes albopictus reared in the same laboratory harbor a similar gut bacterial microbiome but different entire body microbiota imply that the gut microbiota of adult mosquitoes is environmentally determined regardless of the host genotype, but the entire body microbiota is more genetically determined. Our findings improved the understanding of the microbiota in the entire and partial tissues of Aedes mosquitoes.},
}
@article {pmid34406852,
year = {2021},
author = {Cifuentes-Anticevic, J and Alcamán-Arias, ME and Alarcón-Schumacher, T and Tamayo-Leiva, J and Pedrós-Alió, C and Farías, L and Díez, B},
title = {Proteorhodopsin Phototrophy in Antarctic Coastal Waters.},
journal = {mSphere},
volume = {6},
number = {4},
pages = {e0052521},
pmid = {34406852},
issn = {2379-5042},
mesh = {Alphaproteobacteria/chemistry/classification/genetics ; Antarctic Regions ; Ecosystem ; Flavobacteriaceae/chemistry/classification/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; *Phototrophic Processes ; Phylogeny ; Rhodopsin/metabolism ; Rhodopsins, Microbial/analysis/*genetics ; Seawater/*microbiology ; },
abstract = {Microbial proton-pumping rhodopsins are considered the simplest strategy among phototrophs to conserve energy from light. Proteorhodopsins are the most studied rhodopsins thus far because of their ubiquitous presence in the ocean, except in Antarctica, where they remain understudied. We analyzed proteorhodopsin abundance and transcriptional activity in the Western Antarctic coastal seawaters. Combining quantitative PCR (qPCR) and metagenomics, the relative abundance of proteorhodopsin-bearing bacteria accounted on average for 17, 3.5, and 29.7% of the bacterial community in Chile Bay (South Shetland Islands) during 2014, 2016, and 2017 summer-autumn, respectively. The abundance of proteorhodopsin-bearing bacteria changed in relation to environmental conditions such as chlorophyll a and temperature. Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were the main bacteria that transcribed the proteorhodopsin gene during day and night. Although green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones, the latter were transcribed more intensely, resulting in >50% of the proteorhodopsin transcripts during the day and night. Flavobacteriia were the most abundant proteorhodopsin-bearing bacteria in the metagenomes; however, Alphaproteobacteria and Gammaproteobacteria were more represented in the metatranscriptomes, with qPCR quantification suggesting the dominance of the active SAR11 clade. Our results show that proteorhodopsin-bearing bacteria are prevalent in Antarctic coastal waters in late austral summer and early autumn, and their ecological relevance needs to be elucidated to better understand how sunlight energy is used in this marine ecosystem. IMPORTANCE Proteorhodopsin-bearing microorganisms in the Southern Ocean have been overlooked since their discovery in 2000. The present study identify taxonomy and quantify the relative abundance of proteorhodopsin-bearing bacteria and proteorhodopsin gene transcription in the West Antarctic Peninsula's coastal waters. This information is crucial to understand better how sunlight enters this marine environment through alternative ways unrelated to chlorophyll-based strategies. The relative abundance of proteorhodopsin-bearing bacteria seems to be related to environmental parameters (e.g., chlorophyll a, temperature) that change yearly at the coastal water of the West Antarctic Peninsula during the austral late summers and early autumns. Proteorhodopsin-bearing bacteria from Antarctic coastal waters are potentially able to exploit both the green and blue spectrum of sunlight and are a prevalent group during the summer in this polar environment.},
}
@article {pmid34180607,
year = {2021},
author = {Bruggeling, CE and Garza, DR and Achouiti, S and Mes, W and Dutilh, BE and Boleij, A},
title = {Optimized bacterial DNA isolation method for microbiome analysis of human tissues.},
journal = {MicrobiologyOpen},
volume = {10},
number = {3},
pages = {e1191},
pmid = {34180607},
issn = {2045-8827},
mesh = {Bacteria/classification/*genetics/*isolation &amp; purification ; Biopsy ; Colon/microbiology/pathology ; DNA, Bacterial/genetics/*isolation &amp; purification ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Recent advances in microbiome sequencing have rendered new insights into the role of the microbiome in human health with potential clinical implications. Unfortunately, the presence of host DNA in tissue isolates has hampered the analysis of host-associated bacteria. Here, we present a DNA isolation protocol for tissue, optimized on biopsies from resected human colons (~2-5 mm in size), which includes reduction of human DNA without distortion of relative bacterial abundance at the phylum level. We evaluated which concentrations of Triton and saponin lyse human cells and leave bacterial cells intact, in combination with DNAse treatment to deplete released human DNA. Saponin at a concentration of 0.0125% in PBS lysed host cells, resulting in a 4.5-fold enrichment of bacterial DNA while preserving the relative abundance of Firmicutes, Bacteroidetes, γ-Proteobacteria, and Actinobacteria assessed by qPCR. Our optimized protocol was validated in the setting of two large clinical studies on 521 in vivo acquired colon biopsies of 226 patients using shotgun metagenomics. The resulting bacterial profiles exhibited alpha and beta diversities that are similar to the diversities found by 16S rRNA amplicon sequencing. A direct comparison between shotgun metagenomics and 16S rRNA amplicon sequencing of 15 forceps tissue biopsies showed similar bacterial profiles and a similar Shannon diversity index between the sequencing methods. Hereby, we present the first protocol for enriching bacterial DNA from tissue biopsies that allows efficient isolation of all bacteria. Our protocol facilitates analysis of a wide spectrum of bacteria of clinical tissue samples improving their applicability for microbiome research.},
}
@article {pmid34030623,
year = {2021},
author = {Méndez-Salazar, EO and Vázquez-Mellado, J and Casimiro-Soriguer, CS and Dopazo, J and Çubuk, C and Zamudio-Cuevas, Y and Francisco-Balderas, A and Martínez-Flores, K and Fernández-Torres, J and Lozada-Pérez, C and Pineda, C and Sánchez-González, A and Silveira, LH and Burguete-García, AI and Orbe-Orihuela, C and Lagunas-Martínez, A and Vazquez-Gomez, A and López-Reyes, A and Palacios-González, B and Martínez-Nava, GA},
title = {Taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.},
journal = {Molecular medicine (Cambridge, Mass.)},
volume = {27},
number = {1},
pages = {50},
pmid = {34030623},
issn = {1528-3658},
mesh = {Biodiversity ; Computational Biology/methods ; *Dysbiosis ; *Gastrointestinal Microbiome ; Gout/etiology/*metabolism/pathology ; Humans ; *Metagenome ; *Metagenomics/methods ; Protein Interaction Mapping ; Protein Interaction Maps ; Uric Acid/*metabolism ; },
abstract = {OBJECTIVE: To evaluate the taxonomic composition of the gut microbiome in gout patients with and without tophi formation, and predict bacterial functions that might have an impact on urate metabolism.<br><br>METHODS: Hypervariable V3-V4 regions of the bacterial 16S rRNA gene from fecal samples of gout patients with and without tophi (n = 33 and n = 25, respectively) were sequenced and compared to fecal samples from 53 healthy controls. We explored predictive functional profiles using bioinformatics in order to identify differences in taxonomy and metabolic pathways.<br><br>RESULTS: We identified a microbiome characterized by the lowest richness and a higher abundance of Phascolarctobacterium, Bacteroides, Akkermansia, and Ruminococcus_gnavus_group genera in patients with gout without tophi when compared to controls. The Proteobacteria phylum and the Escherichia-Shigella genus were more abundant in patients with tophaceous gout than in controls. Fold change analysis detected nine genera enriched in healthy controls compared to gout groups (Bifidobacterium, Butyricicoccus, Oscillobacter, Ruminococcaceae_UCG_010, Lachnospiraceae_ND2007_group, Haemophilus, Ruminococcus_1, Clostridium_sensu_stricto_1, and Ruminococcaceae_UGC_013). We found that the core microbiota of both gout groups shared Bacteroides caccae, Bacteroides stercoris ATCC 43183, and Bacteroides coprocola DSM 17136. These bacteria might perform functions linked to one-carbon metabolism, nucleotide binding, amino acid biosynthesis, and purine biosynthesis. Finally, we observed differences in key bacterial enzymes involved in urate synthesis, degradation, and elimination.<br><br>CONCLUSION: Our findings revealed that taxonomic variations in the gut microbiome of gout patients with and without tophi might have a functional impact on urate metabolism.},
}
@article {pmid33975870,
year = {2021},
author = {Brial, F and Chilloux, J and Nielsen, T and Vieira-Silva, S and Falony, G and Andrikopoulos, P and Olanipekun, M and Hoyles, L and Djouadi, F and Neves, AL and Rodriguez-Martinez, A and Mouawad, GI and Pons, N and Forslund, S and Le-Chatelier, E and Le Lay, A and Nicholson, J and Hansen, T and Hyötyläinen, T and Clément, K and Oresic, M and Bork, P and Ehrlich, SD and Raes, J and Pedersen, OB and Gauguier, D and Dumas, ME},
title = {Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health.},
journal = {Gut},
volume = {70},
number = {11},
pages = {2105-2114},
pmid = {33975870},
issn = {1468-3288},
support = {MR/L01632X/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Biodiversity ; Biomarkers/*metabolism ; Denmark ; Female ; *Gastrointestinal Microbiome ; Hippurates/*metabolism ; Humans ; Magnetic Resonance Spectroscopy ; Male ; Metabolome ; Metagenomics ; Mice ; Middle Aged ; Phenotype ; },
abstract = {OBJECTIVE: Gut microbial products are involved in regulation of host metabolism. In human and experimental studies, we explored the potential role of hippurate, a hepatic phase 2 conjugation product of microbial benzoate, as a marker and mediator of metabolic health.<br><br>DESIGN: In 271 middle-aged non-diabetic Danish individuals, who were stratified on habitual dietary intake, we applied 1H-nuclear magnetic resonance (NMR) spectroscopy of urine samples and shotgun-sequencing-based metagenomics of the gut microbiome to explore links between the urine level of hippurate, measures of the gut microbiome, dietary fat and markers of metabolic health. In mechanistic experiments with chronic subcutaneous infusion of hippurate to high-fat-diet-fed obese mice, we tested for causality between hippurate and metabolic phenotypes.<br><br>RESULTS: In the human study, we showed that urine hippurate positively associates with microbial gene richness and functional modules for microbial benzoate biosynthetic pathways, one of which is less prevalent in the Bacteroides 2 enterotype compared with Ruminococcaceae or Prevotella enterotypes. Through dietary stratification, we identify a subset of study participants consuming a diet rich in saturated fat in which urine hippurate concentration, independently of gene richness, accounts for links with metabolic health. In the high-fat-fed mice experiments, we demonstrate causality through chronic infusion of hippurate (20 nmol/day) resulting in improved glucose tolerance and enhanced insulin secretion.<br><br>CONCLUSION: Our human and experimental studies show that a high urine hippurate concentration is a general marker of metabolic health, and in the context of obesity induced by high-fat diets, hippurate contributes to metabolic improvements, highlighting its potential as a mediator of metabolic health.},
}
@article {pmid33848685,
year = {2021},
author = {Canova, R and Budaszewski, RF and Weber, MN and da Silva, MS and Puhl, DE and Battisti, LO and Soares, JF and Wagner, PG and Varela, APM and Mayer, FQ and Canal, CW},
title = {Spleen and lung virome analysis of South American fur seals (Arctocephalus australis) collected on the southern Brazilian coast.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {92},
number = {},
pages = {104862},
doi = {10.1016/j.meegid.2021.104862},
pmid = {33848685},
issn = {1567-7257},
mesh = {Anelloviridae/genetics ; Animals ; Brazil ; Circovirus/genetics ; Fur Seals/*virology ; Lung/*virology ; Metagenomics/methods ; Phylogeny ; Spleen/*virology ; Virome/*genetics ; },
abstract = {South American fur seals (Arctocephalus australis) are believed to reach the coast of Rio Grande do Sul (RS) through sea currents. They live in colonies and are frequently found resting on the beach. However, it is also common to find dead pinnipeds on beaches, sharing the environment with humans, domestic animals and other wild species on the coast and facilitating the transmission of pathogens. In the present study, a metagenomic approach was applied to evaluate the viral diversity in organs of fur seals found deceased along the coast of the state of RS, southern Brazil. The lungs and spleens of 29 animals were collected, macerated individually, pooled separately (one pool for lungs and another for spleens) and sequenced using the Illumina MiSeq platform. Sequences more closely related to members of the Anelloviridae and Circoviridae families were detected. Nine putative new species of anellovirus and one putative new genus, named Nitorquevirus, were described. Additionally, the circovirus sequences found in the lungs of A. australis have a common ancestor with PCV3, a proposed swine pathogen. Our study expanded the knowledge about viral communities in pinnipeds and could be useful for monitoring new viruses and potential viral sharing among wildlife, domestic animals, and humans.},
}
@article {pmid33328245,
year = {2021},
author = {Masi, AC and Embleton, ND and Lamb, CA and Young, G and Granger, CL and Najera, J and Smith, DP and Hoffman, KL and Petrosino, JF and Bode, L and Berrington, JE and Stewart, CJ},
title = {Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis.},
journal = {Gut},
volume = {70},
number = {12},
pages = {2273-2282},
doi = {10.1136/gutjnl-2020-322771},
pmid = {33328245},
issn = {1468-3288},
mesh = {Case-Control Studies ; Enterocolitis, Necrotizing/*microbiology/*prevention &amp; control ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Premature ; Male ; Milk, Human/*chemistry ; Oligosaccharides/*metabolism ; },
abstract = {OBJECTIVE: Necrotising enterocolitis (NEC) is a devastating intestinal disease primarily affecting preterm infants. The underlying mechanisms are poorly understood: mother's own breast milk (MOM) is protective, possibly relating to human milk oligosaccharide (HMO) and infant gut microbiome interplay. We investigated the interaction between HMO profiles and infant gut microbiome development and its association with NEC.<br><br>DESIGN: We performed HMO profiling of MOM in a large cohort of infants with NEC (n=33) with matched controls (n=37). In a subset of 48 infants (14 with NEC), we also performed longitudinal metagenomic sequencing of infant stool (n=644).<br><br>RESULTS: Concentration of a single HMO, disialyllacto-N-tetraose (DSLNT), was significantly lower in MOM received by infants with NEC compared with controls. A MOM threshold level of 241 nmol/mL had a sensitivity and specificity of 0.9 for NEC. Metagenomic sequencing before NEC onset showed significantly lower relative abundance of Bifidobacterium longum and higher relative abundance of Enterobacter cloacae in infants with NEC. Longitudinal development of the microbiome was also impacted by low MOM DSLNT associated with reduced transition into preterm gut community types dominated by Bifidobacterium spp and typically observed in older infants. Random forest analysis combining HMO and metagenome data before disease accurately classified 87.5% of infants as healthy or having NEC.<br><br>CONCLUSION: These results demonstrate the importance of HMOs and gut microbiome in preterm infant health and disease. The findings offer potential targets for biomarker development, disease risk stratification and novel avenues for supplements that may prevent life-threatening disease.},
}
@article {pmid34491886,
year = {2021},
author = {Hullar, MAJ and Jenkins, IC and Randolph, TW and Curtis, KR and Monroe, KR and Ernst, T and Shepherd, JA and Stram, DO and Cheng, I and Kristal, BS and Wilkens, LR and Franke, A and Le Marchand, L and Lim, U and Lampe, JW},
title = {Associations of the gut microbiome with hepatic adiposity in the Multiethnic Cohort Adiposity Phenotype Study.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1965463},
pmid = {34491886},
issn = {1949-0984},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; P30 CA071789/CA/NCI NIH HHS/United States ; U01 CA164973/CA/NCI NIH HHS/United States ; P01 CA168530/CA/NCI NIH HHS/United States ; UL1 TR000130/TR/NCATS NIH HHS/United States ; },
mesh = {Adiposity/*physiology ; Aged ; Bacteria/*classification/isolation &amp; purification ; Cross-Sectional Studies ; Endotoxins/metabolism ; Gastrointestinal Microbiome/*physiology ; Humans ; Inflammation/pathology ; Liver/pathology ; Male ; Middle Aged ; Non-alcoholic Fatty Liver Disease/*epidemiology/*ethnology ; Obesity/pathology ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; },
abstract = {Nonalcoholic fatty liver disease (NAFLD) is a risk factor for liver cancer and prevalence varies by ethnicity. Along with genetic and lifestyle factors, the gut microbiome (GM) may contribute to NAFLD and its progression to advanced liver disease. Our cross-sectional analysis assessed the association of the GM with hepatic adiposity among African American, Japanese American, White, Latino, and Native Hawaiian participants in the Multiethnic Cohort. We used MRI to measure liver fat and determine nonalcoholic fatty liver disease (NAFLD) status (n = 511 cases) in 1,544 participants, aged 60-77 years, with 12-53% overall adiposity (BMI of 17.8-46.2 kg/m2). The GM was measured by 16S rRNA gene sequencing and, on a subset, by metagenomic sequencing. Alpha diversity was lower overall with NAFLD and in certain ethnicities (African Americans, Whites, and Latinos). In models regressing genus on NAFLD status, 62 of 149 genera (40%) exhibited a significant interaction between NAFLD and ethnicity stratified analysis found 69 genera significantly associated with NAFLD in at least one ethnic group. No single genus was significantly associated with NAFLD across all ethnicities. In contrast, the same bacterial metabolic pathways were over-represented in participants with NAFLD regardless of ethnicity. Imputed secondary bile acid and carbohydrate pathways were associated with NAFLD, the latter of which was corroborated by metagenomics, although different genera in different ethnicities were associated with these pathways. Overall, we found that NAFLD was associated with altered bacterial composition and metabolism, and that bacterial endotoxin, assessed by plasma lipopolysaccharide binding protein (LBP), may mediate liver fat-associated systemic inflammation in a manner that seems to vary by ethnicity.},
}
@article {pmid34415535,
year = {2022},
author = {Marbouty, M and Koszul, R},
title = {Metagenomes Binning Using Proximity-Ligation Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2301},
number = {},
pages = {163-181},
pmid = {34415535},
issn = {1940-6029},
mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {Microbial communities are key components of all ecosystems, but characterization of their complete genomic structure remains challenging. Typical analysis tends to elude the complexity of the mixes in terms of species, strains, as well as extrachromosomal DNA molecules. Recently, approaches have been developed that bins DNA contigs into individual genomes and episomes according to their 3D contact frequencies. Those contacts are quantified by chromosome conformation capture experiments (3C, Hi-C), also known as proximity-ligation approaches, applied to metagenomics samples. Here, we present a simple computational pipeline that allows to recover high-quality Metagenomics Assemble Genomes (MAGs) starting from metagenomic 3C or Hi-C datasets and a metagenome assembly.},
}
@article {pmid34301806,
year = {2021},
author = {Xie, Y and Song, L and Yang, J and Tao, T and Yu, J and Shi, J and Jin, X},
title = {Small intestinal flora graft alters fecal flora, stool, cytokines and mood status in healthy mice.},
journal = {Life science alliance},
volume = {4},
number = {9},
pages = {},
pmid = {34301806},
issn = {2575-1077},
mesh = {*Affect ; Animals ; *Behavior, Animal ; Biomarkers ; Body Weight ; Cytokines/blood/*metabolism ; Drinking ; Eating ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Male ; Metagenome ; Metagenomics ; Mice ; },
abstract = {Fecal microbiota transplantation is widely used. Large intestinal microbiota (LIM) is more similar to fecal microbiota than small intestinal microbiota (SIM). The SIM communities are very different from those of LIM. Therefore, SIM transplantation (SIMT) and LIM transplantation (LIMT) might exert different influences. Here, healthy adult male C57Bl/6 mice received intragastric SIMT, LIMT, or sterile PBS administration. Microbiota graft samples were collected from small/large intestine of healthy mice of the same age, sex, and strain background. Compared with PBS treatment, SIMT increased pellet number, stool wet weight, and stool water percentage; induced a fecal microbiota profile shift toward the microbial composition of the SIM graft; induced a systemic anti-inflammatory cytokines profile; and ameliorated depressive-like behaviors in recipients. LIMT, however, induced merely a slight alteration in fecal microbial composition and no significant influence on the other aspects. In sum, SIMT, rather than LIMT, affected defecation features, fecal microbial composition, cytokines profile, and depressive-like behaviors in healthy mice. This study reveals the different effects of SIMT and LIMT, providing an interesting clue for further researches involving gut microbial composition change.},
}
@article {pmid33845884,
year = {2021},
author = {Garg, S},
title = {Computational methods for chromosome-scale haplotype reconstruction.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {101},
pmid = {33845884},
issn = {1474-760X},
mesh = {*Chromosomes ; Computational Biology/*methods ; Diploidy ; Genomics/*methods ; *Haplotypes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; Polyploidy ; Sequence Analysis, DNA/methods ; },
abstract = {High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.},
}
@article {pmid33845850,
year = {2021},
author = {Fremin, BJ and Bhatt, AS},
title = {Comparative genomics identifies thousands of candidate structured RNAs in human microbiomes.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {100},
pmid = {33845850},
issn = {1474-760X},
support = {AI148623-01//National Institute of Allergy and Infectious Diseases (US)/ ; 1S10OD02014101/CA/NCI NIH HHS/United States ; P50AG047366/NH/NIH HHS/United States ; },
mesh = {Computational Biology/methods ; Gastrointestinal Microbiome ; *Genomics/methods ; Humans ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Nucleic Acid Conformation ; RNA ; Workflow ; },
abstract = {BACKGROUND: Structured RNAs play varied bioregulatory roles within microbes. To date, hundreds of candidate structured RNAs have been predicted using informatic approaches that search for motif structures in genomic sequence data. The human microbiome contains thousands of species and strains of microbes. Yet, much of the metagenomic data from the human microbiome remains unmined for structured RNA motifs primarily due to computational limitations.<br><br>RESULTS: We sought to apply a large-scale, comparative genomics approach to these organisms to identify candidate structured RNAs. With a carefully constructed, though computationally intensive automated analysis, we identify 3161 conserved candidate structured RNAs in intergenic regions, as well as 2022 additional candidate structured RNAs that may overlap coding regions. We validate the RNA expression of 177 of these candidate structures by analyzing small fragment RNA-seq data from four human fecal samples.<br><br>CONCLUSIONS: This approach identifies a wide variety of candidate structured RNAs, including tmRNAs, antitoxins, and likely ribosome protein leaders, from a wide variety of taxa. Overall, our pipeline enables conservative predictions of thousands of novel candidate structured RNAs from human microbiomes.},
}
@article {pmid33785070,
year = {2021},
author = {Wirbel, J and Zych, K and Essex, M and Karcher, N and Kartal, E and Salazar, G and Bork, P and Sunagawa, S and Zeller, G},
title = {Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {93},
pmid = {33785070},
issn = {1474-760X},
mesh = {Computational Biology/*methods ; Confounding Factors, Epidemiologic ; Crohn Disease/etiology ; Databases, Genetic ; Gastrointestinal Microbiome ; Humans ; *Machine Learning ; Meta-Analysis as Topic ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; Models, Statistical ; ROC Curve ; *Software ; Workflow ; },
abstract = {The human microbiome is increasingly mined for diagnostic and therapeutic biomarkers using machine learning (ML). However, metagenomics-specific software is scarce, and overoptimistic evaluation and limited cross-study generalization are prevailing issues. To address these, we developed SIAMCAT, a versatile R toolbox for ML-based comparative metagenomics. We demonstrate its capabilities in a meta-analysis of fecal metagenomic studies (10,803 samples). When naively transferred across studies, ML models lost accuracy and disease specificity, which could however be resolved by a novel training set augmentation strategy. This reveals some biomarkers to be disease-specific, with others shared across multiple conditions. SIAMCAT is freely available from siamcat.embl.de .},
}
@article {pmid33691770,
year = {2021},
author = {Zimmermann, J and Kaleta, C and Waschina, S},
title = {gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {81},
pmid = {33691770},
issn = {1474-760X},
mesh = {Bacteria/enzymology/*genetics/*metabolism ; Computational Biology/*methods ; Databases, Factual ; *Energy Metabolism ; Fermentation ; Gastrointestinal Microbiome ; Genome, Bacterial ; Genomics/methods ; Humans ; *Metabolic Networks and Pathways ; Metagenome ; Metagenomics/methods ; *Software ; Soil Microbiology ; },
abstract = {Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq (https://github.com/jotech/gapseq), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.},
}
@article {pmid33662387,
year = {2021},
author = {Moll, JM and Myers, PN and Zhang, C and Eriksen, C and Wolf, J and Appelberg, KS and Lindberg, G and Bahl, MI and Zhao, H and Pan-Hammarström, Q and Cai, K and Jia, H and Borte, S and Nielsen, HB and Kristiansen, K and Brix, S and Hammarström, L},
title = {Gut Microbiota Perturbation in IgA Deficiency Is Influenced by IgA-Autoantibody Status.},
journal = {Gastroenterology},
volume = {160},
number = {7},
pages = {2423-2434.e5},
doi = {10.1053/j.gastro.2021.02.053},
pmid = {33662387},
issn = {1528-0012},
mesh = {Adult ; Aged ; Autoantibodies/*metabolism ; Case-Control Studies ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*immunology ; Humans ; IgA Deficiency/*immunology/*microbiology ; Immunoglobulin A/*metabolism ; Male ; Middle Aged ; },
abstract = {BACKGROUND &amp; AIMS: IgA exerts its primary function at mucosal surfaces, where it binds microbial antigens to regulate bacterial growth and epithelial attachment. One third of individuals with IgA deficiency (IgAD) suffers from recurrent mucosal infections, possibly related to an altered microbiota. We aimed to delineate the impact of IgAD and the IgA-autoantibody status on the composition and functional capacity of the gut microbiota.<br><br>METHODS: We performed a paired, lifestyle-balanced analysis of the effect of IgA on the gut microbiota composition and functionality based on fecal samples from individuals with IgAD and IgA-sufficient household members (n = 100), involving quantitative shotgun metagenomics, species-centric functional annotation of gut bacteria, and strain-level analyses. We supplemented the data set with 32 individuals with IgAD and examined the influence of IgA-autoantibody status on the composition and functionality of the gut microbiota.<br><br>RESULTS: The gut microbiota of individuals with IgAD exhibited decreased richness and diversity and was enriched for bacterial species encoding pathogen-related functions including multidrug and antimicrobial peptide resistance, virulence factors, and type III and VI secretion systems. These functional changes were largely attributed to Escherichia coli but were independent of E coli strain variations and most prominent in individuals with IgAD with IgA-specific autoreactive antibodies.<br><br>CONCLUSIONS: The microbiota of individuals with IgAD is enriched for species holding increased proinflammatory potential, thereby potentially decreasing the resistance to gut barrier-perturbing events. This phenotype is especially pronounced in individuals with IgAD with IgA-specific autoreactive antibodies, thus warranting a screening for IgA-specific autoreactive antibodies in IgAD to identify patients with IgAD with increased risk for gastrointestinal implications.},
}
@article {pmid32998876,
year = {2021},
author = {Bajaj, JS and Sikaroodi, M and Shamsaddini, A and Henseler, Z and Santiago-Rodriguez, T and Acharya, C and Fagan, A and Hylemon, PB and Fuchs, M and Gavis, E and Ward, T and Knights, D and Gillevet, PM},
title = {Interaction of bacterial metagenome and virome in patients with cirrhosis and hepatic encephalopathy.},
journal = {Gut},
volume = {70},
number = {6},
pages = {1162-1173},
doi = {10.1136/gutjnl-2020-322470},
pmid = {32998876},
issn = {1468-3288},
support = {R21 TR003095/TR/NCATS NIH HHS/United States ; R21 TR002024/TR/NCATS NIH HHS/United States ; R01 HS025412/HS/AHRQ HHS/United States ; },
mesh = {Aged ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Cross-Sectional Studies ; Disease Progression ; End Stage Liver Disease/etiology/*microbiology ; Faecalibacterium/genetics/virology ; Feces/microbiology ; Female ; Firmicutes/genetics/*virology ; Gastrointestinal Agents/therapeutic use ; Hepatic Encephalopathy/*microbiology ; Hospitalization ; Humans ; Lactococcus/genetics/virology ; Lactulose/therapeutic use ; Liver Cirrhosis/complications/drug therapy/*microbiology ; Male ; Metagenome/drug effects ; Metagenomics ; Microbial Interactions ; Microviridae/genetics ; Middle Aged ; Myoviridae/genetics ; Patient Acuity ; Rifaximin/pharmacology/*therapeutic use ; Streptococcus/genetics/virology ; Virome/drug effects ; },
abstract = {OBJECTIVE: Altered bacterial composition is associated with disease progression in cirrhosis but the role of virome, especially phages, is unclear.<br><br>DESIGN: Cross-sectional and pre/post rifaximin cohorts were enrolled. Cross-sectional: controls and cirrhotic outpatients (compensated, on lactulose (Cirr-L), on rifaximin (Cirr-LR)) were included and followed for 90-day hospitalisations. Pre/post: compensated cirrhotics underwent stool collection pre/post 8 weeks of rifaximin. Stool metagenomics for bacteria and phages and their correlation networks were analysed in controls versus cirrhosis, within cirrhotics, hospitalised/not and pre/post rifaximin.<br><br>RESULTS: Cross-sectional: 40 controls and 163 cirrhotics (63 compensated, 43 Cirr-L, 57 Cirr-LR) were enrolled. Cirr-L/LR groups were similar on model for end-stage liver disease (MELD) score but Cirr-L developed greater hospitalisations versus Cirr-LR (56% vs 30%, p=0.008). Bacterial alpha/beta diversity worsened from controls through Cirr-LR. While phage alpha diversity was similar, beta diversity was different between groups. Autochthonous bacteria linked negatively, pathobionts linked positively with MELD but only modest phage-MELD correlations were seen. Phage-bacterial correlation network complexity was highest in controls, lowest in Cirr-L and increased in Cirr-LR. Microviridae and Faecalibacterium phages were linked with autochthonous bacteria in Cirr-LR, but not Cirr-L hospitalised patients had greater pathobionts, lower commensal bacteria and phages focused on Streptococcus, Lactococcus and Myoviridae. Pre/post: No changes in alpha/beta diversity of phages or bacteria were seen postrifaximin. Phage-bacterial linkages centred around urease-producing Streptococcus species collapsed postrifaximin.<br><br>CONCLUSION: Unlike bacteria, faecal phages are sparsely linked with cirrhosis characteristics and 90-day outcomes. Phage and bacterial linkages centred on urease-producing, ammonia-generating Streptococcus species were affected by disease progression and rifaximin therapy and were altered in patients who experienced 90-day hospitalisations.},
}
@article {pmid35007432,
year = {2021},
author = {Ibrahim, A and Maatouk, M and Rajaonison, A and Zgheib, R and Haddad, G and Bou Khalil, J and Raoult, D and Bittar, F},
title = {Adapted Protocol for Saccharibacteria Cocultivation: Two New Members Join the Club of Candidate Phyla Radiation.},
journal = {Microbiology spectrum},
volume = {9},
number = {3},
pages = {e0106921},
doi = {10.1128/spectrum.01069-21},
pmid = {35007432},
issn = {2165-0497},
support = {10-IAHU-03//Agence Nationale de la Recherche (ANR)/ ; },
abstract = {The growing application of metagenomics to different ecological and microbiome niches in recent years has enhanced our knowledge of global microbial biodiversity. Among these abundant and widespread microbes, the candidate phyla radiation (CPR) group has been recognized as representing a large proportion of the microbial kingdom (>26%). CPR are characterized by their obligate symbiotic or exoparasitic activity with other microbial hosts, mainly bacteria. Currently, isolating CPR is still considered challenging for microbiologists. The idea of this study was to develop an adapted protocol for the coculture of CPR with a suitable bacterial host. Based on various sputum samples, we tried to enrich CPR (Saccharibacteria members) and to cocultivate them with pure hosts (Schaalia odontolytica). This protocol was monitored by TaqMan real-time quantitative PCR (qPCR) using a system specific for Saccharibacteria designed in this study, as well as by electron microscopy and sequencing. We succeeded in coculturing and sequencing the complete genomes of two new Saccharibacteria species, "Candidatus Minimicrobia naudis" and "Candidatus Minimicrobia vallesae." In addition, we noticed a decrease in the CT values of Saccharibacteria and a significant multiplication through their physical association with Schaalia odontolytica strains in the enriched medium that we developed. This work may help bridge gaps in the genomic database by providing new CPR members, and in the future, their currently unknown characteristics may be revealed. IMPORTANCE In this study, the first TaqMan real-time quantitative PCR (qPCR) system, targeting Saccharibacteria phylum, has been developed. This technique can specifically quantify Saccharibacteria members in any sample of interest in order to investigate their prevalence. In addition, another easy, specific, and sensitive protocol has been developed to maintain the viability of Saccharibacteria cells in an enriched medium with their bacterial host. The use of this protocol facilitates subsequent studies of the phenotypic characteristics of CPR and their physical interactions with bacterial species, as well as the sequencing of new genomes to improve the current database.},
}
@article {pmid34864063,
year = {2022},
author = {Pradhan, S and Ray, P and Aich, P},
title = {Microbiota transplantation from younger to older mice could restore lost immunity to effectively clear salmonella infection in Th2-biased BALB/c mice.},
journal = {Life sciences},
volume = {288},
number = {},
pages = {120201},
doi = {10.1016/j.lfs.2021.120201},
pmid = {34864063},
issn = {1879-0631},
mesh = {Animals ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*growth &amp; development ; Cecum/*transplantation ; Fecal Microbiota Transplantation/*methods ; Gastrointestinal Microbiome ; Homeostasis ; Immunity, Innate ; Male ; Metabolome ; Metagenomics ; Mice ; Mice, Inbred BALB C ; Salmonella/drug effects/genetics/*immunology/metabolism ; Salmonella Infections/immunology/metabolism/microbiology/*therapy ; Th2 Cells/*immunology ; },
abstract = {AIMS: The composition, overtly abundance, and diversity of gut microbiota, play a significant role in maintaining physiological homeostasis with age. Reports revealed that the gut microbial profile might be correlated with immunity and metabolism. It is, therefore, tantamount to know if an older individual can achieve the immunity and metabolic profile of a younger individual by receiving the gut microbiome of a younger individual. In the current report, we have studied the effects of cecal microbiota transplantation (CMT) from younger to older mice.<br><br>MATERIALS AND METHODS: In this study, older BALB/c mice (23 weeks) received CMT from younger BALB/c mice (3 weeks).<br><br>KEY FINDINGS: CMT recipient mice showed altered expressions of immune and tight junction protein genes in the colon of mice, while the non-CMT recipient mice did not. Older mice were treated with AVNM to make them compatible with CMT. Further data from metabolite studies revealed that AVNM treatment mainly affected the aromatic amino acid biosynthesis pathway while CMT mostly affected the metabolism of different carbohydrates. We repeated the analysis in C57BL/6 mice without any significant effects of CMT.<br><br>SIGNIFICANCE: Results revealed that mice who received CMT showed more efficient restoration of gut microbiota than non-CMT recipient mice. CMT caused the alleviation of Salmonella infection and efficient recovery of the cecal index in the mice following antibiotics treatment.},
}
@article {pmid34563039,
year = {2021},
author = {Hakim, JA and Green, GBH and Watts, SA and Crowley, MR and Morrow, CD and Bej, AK},
title = {Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics.},
journal = {Current issues in molecular biology},
volume = {43},
number = {2},
pages = {978-995},
doi = {10.3390/cimb43020070},
pmid = {34563039},
issn = {1467-3045},
support = {P30AR050948//Comprehensive Cancer Center, University of Alabama at Birmingham/ ; P30DK0t56336efef/GF/NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/*genetics/metabolism ; *Computational Biology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Lytechinus/*microbiology ; *Metagenomics ; Sequence Analysis, DNA ; Strongylocentrotus purpuratus/*microbiology ; },
abstract = {This paper describes the microbial community composition and genes for key metabolic genes, particularly the nitrogen fixation of the mucous-enveloped gut digesta of green (Lytechinus variegatus) and purple (Strongylocentrotus purpuratus) sea urchins by using the shotgun metagenomics approach. Both green and purple urchins showed high relative abundances of Gammaproteobacteria at 30% and 60%, respectively. However, Alphaproteobacteria in the green urchins had higher relative abundances (20%) than the purple urchins (2%). At the genus level, Vibrio was dominant in both green (~9%) and purple (~10%) urchins, whereas Psychromonas was prevalent only in purple urchins (~24%). An enrichment of Roseobacter and Ruegeria was found in the green urchins, whereas purple urchins revealed a higher abundance of Shewanella, Photobacterium, and Bacteroides (q-value < 0.01). Analysis of key metabolic genes at the KEGG-Level-2 categories revealed genes for amino acids (~20%), nucleotides (~5%), cofactors and vitamins (~6%), energy (~5%), carbohydrates (~13%) metabolisms, and an abundance of genes for assimilatory nitrogen reduction pathway in both urchins. Overall, the results from this study revealed the differences in the microbial community and genes designated for the metabolic processes in the nutrient-rich sea urchin gut digesta, suggesting their likely importance to the host and their environment.},
}
@article {pmid34554392,
year = {2022},
author = {Sumbula, V and Kurian, PS and Girija, D and Cherian, KA},
title = {Impact of foliar application of fungicides on tomato leaf fungal community structure revealed by metagenomic analysis.},
journal = {Folia microbiologica},
volume = {67},
number = {1},
pages = {103-108},
pmid = {34554392},
issn = {1874-9356},
mesh = {*Fungicides, Industrial/pharmacology ; *Lycopersicon esculentum ; Metagenomics ; *Mycobiome ; Plant Leaves ; },
abstract = {Fungicides are commonly used to manage plant pathogens. However, little is known about their effects on the non-target fungal communities that inhabit inside and outside the plant. These fungicides may have adverse effects on beneficial microbial communities with possible consequences for plant health and productivity. Hence, a metagenomic approach, based on the ITS2 region of fungal rDNA, was used to study the impact of foliar application of two fungicides (propineb and iprodione + carbendazim) on non-target tomato leaf fungal communities, in the context of early blight disease management. Metagenomic analysis revealed that the richness and diversity of tomato leaf fungal populations were adversely affected by the chemical treatments tested. Among the two fungicides, propineb (contact fungicide) imparted less non-targeted microorganisms than iprodione + carbendazim (systemic fungicide). In addition, all samples showed association of pathogenic genera Cladosporium, Corynespora, Pseudocercospora along with early blight pathogen Alternaria on tomato leaves that otherwise were undetected. Metagenomic studies also revealed a new mode of action for fungicides and bioagents besides their direct effect that is shifting the microbial community structure so that it provides greater resistance against the pathogen.},
}
@article {pmid34341764,
year = {2021},
author = {Wen, M and Liu, T and Zhao, M and Dang, X and Feng, S and Ding, X and Xu, Z and Huang, X and Lin, Q and Xiang, W and Li, X and He, X and He, Q},
title = {Correlation Analysis between Gut Microbiota and Metabolites in Children with Systemic Lupus Erythematosus.},
journal = {Journal of immunology research},
volume = {2021},
number = {},
pages = {5579608},
pmid = {34341764},
issn = {2314-7156},
mesh = {Age Factors ; Biomarkers ; Case-Control Studies ; Child ; *Disease Susceptibility ; Dysbiosis ; Feces/microbiology ; Female ; Gas Chromatography-Mass Spectrometry/methods ; *Gastrointestinal Microbiome ; Humans ; Immunosuppressive Agents/therapeutic use ; Lupus Erythematosus, Systemic/drug therapy/*etiology/*metabolism/pathology ; Male ; *Metabolome ; Metabolomics/methods ; Metagenomics/methods ; },
abstract = {Systemic lupus erythematosus (SLE) is an autoimmune-mediated diffuse connective tissue disease characterized by immune inflammation with an unclear aetiology and pathogenesis. This work profiled the intestinal flora and faecal metabolome of patients with SLE using 16S RNA sequencing and gas chromatography-mass spectrometry (GC-MS). We identified unchanged alpha diversity and partially altered beta diversity of the intestinal flora. Another important finding was the increase in Proteobacteria and Enterobacteriales and the decrease in Ruminococcaceae among SLE patients. For metabolites, amino acids and short-chain fatty acids were enriched when long-chain fatty acids were downregulated in SLE faecal samples. KEGG analysis showed the significance of the protein digestion and absorption pathway, and association analysis revealed the key role of 3-phenylpropanoic acid and Sphingomonas. Sphingomonas were reported to be less abundant in healthy periodontal sites of SLE patients than in those of HCs, indicating transmission of oral species to the gut. This study contributes to the understanding of the pathogenesis of SLE disease from the perspective of intestinal microorganisms, explains the pathogenesis of SLE, and serves as a basis for exploring potential treatments for the disease.},
}
@article {pmid33811041,
year = {2021},
author = {Bolte, LA and Vich Vila, A and Imhann, F and Collij, V and Gacesa, R and Peters, V and Wijmenga, C and Kurilshikov, A and Campmans-Kuijpers, MJE and Fu, J and Dijkstra, G and Zhernakova, A and Weersma, RK},
title = {Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome.},
journal = {Gut},
volume = {70},
number = {7},
pages = {1287-1298},
pmid = {33811041},
issn = {1468-3288},
mesh = {Adult ; Bacteria/isolation &amp; purification ; *Beverages ; Colitis, Ulcerative/*microbiology ; Crohn Disease/*microbiology ; *Diet ; Feces/microbiology ; *Food ; *Gastrointestinal Microbiome ; Humans ; Inflammation/microbiology/physiopathology ; Irritable Bowel Syndrome/*microbiology ; Metagenomics ; Middle Aged ; Surveys and Questionnaires ; Time Factors ; },
abstract = {OBJECTIVE: The microbiome directly affects the balance of pro-inflammatory and anti-inflammatory responses in the gut. As microbes thrive on dietary substrates, the question arises whether we can nourish an anti-inflammatory gut ecosystem. We aim to unravel interactions between diet, gut microbiota and their functional ability to induce intestinal inflammation.<br><br>DESIGN: We investigated the relation between 173 dietary factors and the microbiome of 1425 individuals spanning four cohorts: Crohn's disease, ulcerative colitis, irritable bowel syndrome and the general population. Shotgun metagenomic sequencing was performed to profile gut microbial composition and function. Dietary intake was assessed through food frequency questionnaires. We performed unsupervised clustering to identify dietary patterns and microbial clusters. Associations between diet and microbial features were explored per cohort, followed by a meta-analysis and heterogeneity estimation.<br><br>RESULTS: We identified 38 associations between dietary patterns and microbial clusters. Moreover, 61 individual foods and nutrients were associated with 61 species and 249 metabolic pathways in the meta-analysis across healthy individuals and patients with IBS, Crohn's disease and UC (false discovery rate<0.05). Processed foods and animal-derived foods were consistently associated with higher abundances of Firmicutes, Ruminococcus species of the Blautia genus and endotoxin synthesis pathways. The opposite was found for plant foods and fish, which were positively associated with short-chain fatty acid-producing commensals and pathways of nutrient metabolism.<br><br>CONCLUSION: We identified dietary patterns that consistently correlate with groups of bacteria with shared functional roles in both, health and disease. Moreover, specific foods and nutrients were associated with species known to infer mucosal protection and anti-inflammatory effects. We propose microbial mechanisms through which the diet affects inflammatory responses in the gut as a rationale for future intervention studies.},
}
@article {pmid33794735,
year = {2021},
author = {Copeland, JK and Chao, G and Vanderhout, S and Acton, E and Wang, PW and Benchimol, EI and El Sohami, A and Croitoru, K and Gommerman, JL and Guttman, DS and , },
title = {The Impact of Migration on the Gut Metagenome of South Asian Canadians.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-29},
pmid = {33794735},
issn = {1949-0984},
support = {//CIHR/Canada ; },
mesh = {Adolescent ; Adult ; Asians ; Bacteria/classification/genetics ; Biodiversity ; Canada ; Cohort Studies ; DNA, Bacterial ; Diet ; Emigrants and Immigrants ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Immune System Diseases/*microbiology ; Inflammation/*microbiology ; Male ; *Metagenome ; Metagenomics/methods ; Prevotella/classification/genetics ; Sequence Analysis, DNA ; Young Adult ; },
abstract = {South Asian (SA) Canadian immigrants have a higher risk of developing certain immune-mediated inflammatory diseases compared to non-migrant SAs. We sought to investigate the effect of migration on the gut metagenome and to identify microbiological associations between migration and conditions that may influence the development of immune-mediated inflammatory diseases. Metagenomic analysis of 58 first-generation (GEN1) SA immigrants and 38 unrelated Canadian born children-of-immigrants (GEN2) determined that the time lived in Canada was associated with continued changes in gut microbial communities. Migration of GEN1 to Canada early in life results in a gut community with similarities to GEN2 SA Canadians and non-SA North Americans. Conversely, GEN1 immigrants who arrived recently to Canada exhibited pronounced differences from GEN2, while displaying microbial similarities to a non-migrating SA cohort. Multivariate analysis identified that community composition was primarily influenced by high abundance taxa. Prevotella copri dominated in GEN1 and non-migrant SAs. Clostridia and functionally related Bacteroidia spp. replaced P. copri dominance over generations in Canada. Mutually exclusive Dialister species occurred at differing relative abundances over time and generations in Canada. This shift in species composition is accompanied by a change in genes associated with carbohydrate utilization and short-chain fatty acid production. Total energy derived from carbohydrates compared to protein consumption was significantly higher for GEN1 recent immigrants, which may influence the functional requirements of the gut community. This study demonstrates the associations between migration and the gut microbiome, which may be further associated with the altered risk of immune-mediated inflammatory diseases observed for SA Canadians.},
}
@article {pmid33794724,
year = {2021},
author = {Manrique, P and Zhu, Y and van der Oost, J and Herrema, H and Nieuwdorp, M and de Vos, WM and Young, M},
title = {Gut bacteriophage dynamics during fecal microbial transplantation in subjects with metabolic syndrome.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-15},
pmid = {33794724},
issn = {1949-0984},
support = {R01 GM117361/GM/NIGMS NIH HHS/United States ; },
mesh = {Adult ; Aged ; Bacteria/*virology ; *Bacteriophages ; Biodiversity ; Fecal Microbiota Transplantation/*methods ; Feces/virology ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metabolic Syndrome/*microbiology/*therapy ; Middle Aged ; Pilot Projects ; Young Adult ; },
abstract = {Metabolic Syndrome (MetS) is a growing public health concern worldwide. Individuals with MetS have an increased risk for cardiovascular (CV) disease and type 2 diabetes (T2D). These diseases - in part preventable with the treatment of MetS - increase the chances of premature death and pose a great economic burden to health systems. A healthy gut microbiota is associated with a reduction in MetS, T2D, and CV disease. Treatment of MetS with fecal microbiota transplantation (FMT) can be effective, however, its success rate is intermediate and difficult to predict. Because bacteriophages significantly affect the microbiota membership and function, the aim of this pilot study was to explore the dynamics of the gut bacteriophage community after FMT in MetS subjects. We performed a longitudinal study of stool bacteriophages from healthy donors and MetS subjects before and after FMT treatment. Subjects were assigned to either a control group (self-stool transplant, n = 3) or a treatment group (healthy-donor-stool transplant; n-recipients = 6, n-donors = 5). Stool samples were collected over an 18-week period and bacteriophage-like particles were purified and sequenced. We found that FMT from healthy donors significantly alters the gut bacteriophage community. Subjects with better clinical outcome clustered closer to the heathy donor group, suggesting that throughout the treatment, their bacteriophage community was more similar to healthy donors. Finally, we identified bacteriophage groups that could explain these differences and we examined their prevalence in individuals from a larger cohort of MetS FMT trial.Trial information- http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=2705; NTR 2705.},
}
@article {pmid33722860,
year = {2021},
author = {Asnicar, F and Leeming, ER and Dimidi, E and Mazidi, M and Franks, PW and Al Khatib, H and Valdes, AM and Davies, R and Bakker, E and Francis, L and Chan, A and Gibson, R and Hadjigeorgiou, G and Wolf, J and Spector, TD and Segata, N and Berry, SE},
title = {Blue poo: impact of gut transit time on the gut microbiome using a novel marker.},
journal = {Gut},
volume = {70},
number = {9},
pages = {1665-1674},
pmid = {33722860},
issn = {1468-3288},
support = {/WT_/Wellcome Trust/United Kingdom ; R01 CA230551/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Akkermansia ; Bacteroides ; Bacteroidetes ; Biomarkers ; Coloring Agents ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; *Gastrointestinal Transit/genetics/physiology ; Humans ; Male ; Metagenomics ; Middle Aged ; },
abstract = {BACKGROUND AND AIMS: Gut transit time is a key modulator of host-microbiome interactions, yet this is often overlooked, partly because reliable methods are typically expensive or burdensome. The aim of this single-arm, single-blinded intervention study is to assess (1) the relationship between gut transit time and the human gut microbiome, and (2) the utility of the 'blue dye' method as an inexpensive and scalable technique to measure transit time.<br><br>METHODS: We assessed interactions between the taxonomic and functional potential profiles of the gut microbiome (profiled via shotgun metagenomic sequencing), gut transit time (measured via the blue dye method), cardiometabolic health and diet in 863 healthy individuals from the PREDICT 1 study.<br><br>RESULTS: We found that gut microbiome taxonomic composition can accurately discriminate between gut transit time classes (0.82 area under the receiver operating characteristic curve) and longer gut transit time is linked with specific microbial species such as Akkermansia muciniphila, Bacteroides spp and Alistipes spp (false discovery rate-adjusted p values <0.01). The blue dye measure of gut transit time had the strongest association with the gut microbiome over typical transit time proxies such as stool consistency and frequency.<br><br>CONCLUSIONS: Gut transit time, measured via the blue dye method, is a more informative marker of gut microbiome function than traditional measures of stool consistency and frequency. The blue dye method can be applied in large-scale epidemiological studies to advance diet-microbiome-health research. Clinical trial registry website https://clinicaltrials.gov/ct2/show/NCT03479866 and trial number NCT03479866.},
}
@article {pmid34960001,
year = {2021},
author = {Kaashyap, M and Cohen, M and Mantri, N},
title = {Microbial Diversity and Characteristics of Kombucha as Revealed by Metagenomic and Physicochemical Analysis.},
journal = {Nutrients},
volume = {13},
number = {12},
pages = {},
pmid = {34960001},
issn = {2072-6643},
mesh = {Acetobacter/isolation &amp; purification ; Bacteria/classification ; Chemical Phenomena ; Fermentation ; Humans ; Kombucha Tea/*analysis/*microbiology ; Metagenomics/*methods ; *Microbiota ; Phenols/analysis ; Probiotics/analysis ; Proteins/analysis ; RNA, Ribosomal, 16S/genetics ; Tea/chemistry ; Yeasts/classification ; },
abstract = {Kombucha is a fermented tea made from a Symbiotic Culture of Bacteria and Yeast (SCOBY) with a long history of use as a health tonic. It is likely that most health benefits come from the tea and fermentation metabolites from specific microbial communities. Despite its growing importance as a functional health drink, the microbial ecosystem present in kombucha has not been fully documented. To characterize the microbial composition and biochemical properties of 'The Good Brew' original base kombucha, we used metagenomics amplicon (16S rRNA and ITS) sequencing to identify the microbial communities at the taxonomic level. We identified 34 genera with 200 microbial species yet described in kombucha. The dominance of organic acid producing microorganisms Acetobacter, Komagataeibacter and Starmerella are healthy for the human gut and their glucose metabolising activities have a putative role in preventing conditions such as diabetes and obesity. Kombucha contains high protein (3.31 µg/mL), high phenolic content (290.4 mg/100 mL) and low sugars (glucose: 1.87 g/L; sucrose 1.11 g/L; fructose: 0.05 g/L) as compared to green tea. The broad microbial diversity with proven health benefits for the human gut suggests kombucha is a powerful probiotic. These findings are important to improve the commercial value of kombucha and uncover the immense prospects for health benefits.},
}
@article {pmid34767757,
year = {2021},
author = {Yap, CX and Henders, AK and Alvares, GA and Wood, DLA and Krause, L and Tyson, GW and Restuadi, R and Wallace, L and McLaren, T and Hansell, NK and Cleary, D and Grove, R and Hafekost, C and Harun, A and Holdsworth, H and Jellett, R and Khan, F and Lawson, LP and Leslie, J and Frenk, ML and Masi, A and Mathew, NE and Muniandy, M and Nothard, M and Miller, JL and Nunn, L and Holtmann, G and Strike, LT and de Zubicaray, GI and Thompson, PM and McMahon, KL and Wright, MJ and Visscher, PM and Dawson, PA and Dissanayake, C and Eapen, V and Heussler, HS and McRae, AF and Whitehouse, AJO and Wray, NR and Gratten, J},
title = {Autism-related dietary preferences mediate autism-gut microbiome associations.},
journal = {Cell},
volume = {184},
number = {24},
pages = {5916-5931.e17},
doi = {10.1016/j.cell.2021.10.015},
pmid = {34767757},
issn = {1097-4172},
mesh = {Adolescent ; Age Factors ; Autistic Disorder/diagnosis/*microbiology ; Behavior ; Child ; Child, Preschool ; Feces/microbiology ; *Feeding Behavior ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Phenotype ; Phylogeny ; Species Specificity ; },
abstract = {There is increasing interest in the potential contribution of the gut microbiome to autism spectrum disorder (ASD). However, previous studies have been underpowered and have not been designed to address potential confounding factors in a comprehensive way. We performed a large autism stool metagenomics study (n = 247) based on participants from the Australian Autism Biobank and the Queensland Twin Adolescent Brain project. We found negligible direct associations between ASD diagnosis and the gut microbiome. Instead, our data support a model whereby ASD-related restricted interests are associated with less-diverse diet, and in turn reduced microbial taxonomic diversity and looser stool consistency. In contrast to ASD diagnosis, our dataset was well powered to detect microbiome associations with traits such as age, dietary intake, and stool consistency. Overall, microbiome differences in ASD may reflect dietary preferences that relate to diagnostic features, and we caution against claims that the microbiome has a driving role in ASD.},
}
@article {pmid34677676,
year = {2022},
author = {Biassoni, R and Di Marco, E and Squillario, M and Ugolotti, E and Mosconi, M and Faticato, MG and Mattioli, G and Avanzini, S and Pini Prato, A},
title = {Pathways and microbiome modifications related to surgery and enterocolitis in Hirschsprung disease.},
journal = {Pediatric surgery international},
volume = {38},
number = {1},
pages = {83-98},
pmid = {34677676},
issn = {1437-9813},
support = {GR-2011-02347381//ministero della salute/ ; },
mesh = {*Enteric Nervous System ; *Enterocolitis ; Feces ; *Hirschsprung Disease/surgery ; Humans ; *Microbiota ; },
abstract = {BACKGROUND: Hirschsprung disease (HSCR) is a congenital anomaly of the enteric nervous system. Abnormal microbiome composition was reported in HSCR patients. In this study, we addressed and analyzed microbiome modifications with relation tosurgery and HSCR associated enterocolitis (HAEC).<br><br>METHODS: The faecal microbiome of 31 HSCR patients (overall 64 samples) was analyzed. HAEC was diagnosed and classified according to a combination of Pastor's and Elhalabi's criteria. Stool samples were analyzed by 16S sequencing (7 out of 9 polymorphic regions). Compositional and relative abundance profiles, as well as the functional potentials of the microbial community, were analyzed with the marker gene sequencing profiles using PICRUSt.<br><br>RESULTS: The relative abundance of Bacteroidetes showed a severe decrease with slow recovery after surgery. Conversely, Proteobacteria transiently increased their abundance. Noteworthy, a strong linkage has been found between Proteobacteria descendants and HAEC occurrences. The inferred functional analysis indicated that virulence factors and fimbriae or pili might be associated with HAEC.<br><br>CONCLUSIONS: Our study, addressing microbiome dynamics, demonstrated relevant changes after surgical manipulation. Alpha-diversity analyses indicated that surgery deeply affects microbiome composition. Proteobacteria and Enterobacteriaceae seem to play a pivotal role in HAEC occurrences. Several virulence factors, such as fimbriae or pili, might explain the HAEC-predisposing potential of selected microbiomes. These results suggest some innovative therapeutic approaches that deserve to be tested in appropriate clinical trials.},
}
@article {pmid34159880,
year = {2021},
author = {Fouladi, F and Carroll, IM and Sharpton, TJ and Bulik-Sullivan, E and Heinberg, L and Steffen, KJ and Fodor, AA},
title = {A microbial signature following bariatric surgery is robustly consistent across multiple cohorts.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1930872},
pmid = {34159880},
issn = {1949-0984},
support = {R01 DK112585/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Bariatric Surgery ; Cohort Studies ; DNA, Bacterial/genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenomics ; Middle Aged ; Obesity, Morbid/*microbiology/*surgery ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Bariatric surgery induces significant shifts in the gut microbiota which could potentially contribute to weight loss and metabolic benefits. The aim of this study was to characterize a microbial signature following Roux-en-Y Gastric bypass (RYGB) surgery using novel and existing gut microbiota sequence data. We generated 16S rRNA gene and metagenomic sequences from fecal samples from patients undergoing RYGB surgery (n = 61 for 16S rRNA gene and n = 135 for metagenomics) at pre-surgical baseline and one, six, and twelve-month post-surgery. We compared these data with three smaller publicly available 16S rRNA gene and one metagenomic datasets from patients who also underwent RYGB surgery. Linear mixed models and machine learning approaches were used to examine the presence of a common microbial signature across studies. Comparison of our new sequences with previous longitudinal studies revealed strikingly similar profiles in both fecal microbiota composition (r = 0.41 ± 0.10; p < .05) and metabolic pathways (r = 0.70 ± 0.05; p < .001) early after surgery across multiple datasets. Notably, Veillonella, Streptococcus, Gemella, Fusobacterium, Escherichia/Shigella, and Akkermansia increased after surgery, while Blautia decreased. Machine learning approaches revealed that the replicable gut microbiota signature associated with RYGB surgery could be used to discriminate pre- and post-surgical samples. Opportunistic pathogen abundance also increased post-surgery in a consistent manner across cohorts. Our study reveals a robust microbial signature involving many commensal and pathogenic taxa and metabolic pathways early after RYGB surgery across different studies and sites. Characterization of the effects of this robust microbial signature on outcomes of bariatric surgery could provide insights into the development of microbiome-based interventions for predicting or improving outcomes following surgery.},
}
@article {pmid33960282,
year = {2021},
author = {Wang, S and Zeng, S and Egan, M and Cherry, P and Strain, C and Morais, E and Boyaval, P and Ryan, CA and M Dempsey, E and Ross, RP and Stanton, C},
title = {Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-24},
pmid = {33960282},
issn = {1949-0984},
mesh = {Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Infant ; Male ; Metagenome ; Metagenomics ; Mothers ; Phylogeny ; },
abstract = {Emerging evidence indicates maternal microbiota as one major reservoir for pioneering microbes in infants. However, the global distinct and identical features of mother-infant gut microbiota at various taxonomic resolutions and metabolic functions across cohorts and potential of infant microbial prediction based on their paired mother's gut microbiota remain unclear. Here, we analyzed 376 mother-infant dyads (468 mother and 1024 infant samples) of eight studies from six countries and observed higher diversity at species and strain levels in maternal gut microbiota but not their metabolic functions. A number of 290 species were shared in at least one mother-infant dyad, with 26 species (five at strain level) observed across cohorts. The profile of mother-infant shared species and strains was further influenced by delivery mode and feeding regimen. The mother-sourced species in infants exhibited similar strain heterogeneity but more metabolic functions compared to other-sourced species, suggesting the comparable stability and fitness of shared and non-shared species and the potential role of shared species in the early gut microbial community, respectively. Predictive models showed moderate performance accuracy for shared species and strains occurrences in infants. These generalized mother-infant shared species and strains may be considered as the primary targets for future work toward infant microbiome development and probiotics exploration.},
}
@article {pmid33757378,
year = {2021},
author = {Bellali, S and Lagier, JC and Million, M and Anani, H and Haddad, G and Francis, R and Kuete Yimagou, E and Khelaifia, S and Levasseur, A and Raoult, D and Bou Khalil, J},
title = {Running after ghosts: are dead bacteria the dark matter of the human gut microbiota?.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-12},
pmid = {33757378},
issn = {1949-0984},
mesh = {Bacteria/classification/growth &amp; development ; *Bacterial Physiological Phenomena ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenome ; Metagenomics ; *Microbial Viability ; Phylogeny ; },
abstract = {The human gut microbiota has been explored by a wide range of culture-dependent and culture-independent methods, revealing that many microbes remain uncharacterized and uncultured. In this work, we aimed to confirm the hypothesis that some of the species present in the human gut microbiota remain uncultured not because of culture limitations, but because all members of such species are dead before reaching the end of the gastro-intestinal tract.We evaluate this phenomenon by studying the microbial viability and culturability of the human gut microbiota from the fresh fecal materials of eight healthy adults. For the first time, we applied fluorescence-activated cell sorting (FACS) combined with 16S metagenomics analysis and microbial culturomics.We identified a total of 1,020 bacterial OTUs and 495 bacterial isolates through metagenomics and culturomics, respectively. Among the FACS metagenomics results, only 735 bacterial OTUs were alive, comprising on average 42% of known species and 87% of relative abundance per individual. The remaining uncultured bacteria were rare, dead, or injured.Our strategy allowed us to shed light on the dark matter of the human gut microbiota and revealed that both metagenomics and culturomics approaches are needed for greater insight into the diversity and richness of bacteria in the human gut microbiota. Further work on culture is needed to enhance the repertoire of cultured gut bacteria by targeting low abundance bacteria and optimizing anaerobic sample conditioning and processing to preserve the viability of bacteria.},
}
@article {pmid33651661,
year = {2021},
author = {Ruuskanen, MO and Åberg, F and Männistö, V and Havulinna, AS and Méric, G and Liu, Y and Loomba, R and Vázquez-Baeza, Y and Tripathi, A and Valsta, LM and Inouye, M and Jousilahti, P and Salomaa, V and Jain, M and Knight, R and Lahti, L and Niiranen, TJ},
title = {Links between gut microbiome composition and fatty liver disease in a large population sample.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-22},
pmid = {33651661},
issn = {1949-0984},
support = {R01 ES027595/ES/NIEHS NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 DK124318/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; R01 DK121378/DK/NIDDK NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Age Factors ; Bacteria/*classification/genetics/*growth &amp; development/metabolism ; Clostridium/classification/genetics/growth &amp; development/metabolism ; Cohort Studies ; Ethanol/metabolism ; Fatty Liver/*microbiology ; Female ; Fermentation ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Humans ; Male ; Metagenome ; Middle Aged ; Phylogeny ; Sex Factors ; },
abstract = {Fatty liver disease is the most common liver disease in the world. Its connection with the gut microbiome has been known for at least 80 y, but this association remains mostly unstudied in the general population because of underdiagnosis and small sample sizes. To address this knowledge gap, we studied the link between the Fatty Liver Index (FLI), a well-established proxy for fatty liver disease, and gut microbiome composition in a representative, ethnically homogeneous population sample of 6,269 Finnish participants. We based our models on biometric covariates and gut microbiome compositions from shallow metagenome sequencing. Our classification models could discriminate between individuals with a high FLI (≥60, indicates likely liver steatosis) and low FLI (<60) in internal cross-region validation, consisting of 30% of the data not used in model training, with an average AUC of 0.75 and AUPRC of 0.56 (baseline at 0.30). In addition to age and sex, our models included differences in 11 microbial groups from class Clostridia, mostly belonging to orders Lachnospirales and Oscillospirales. Our models were also predictive of the high FLI group in a different Finnish cohort, consisting of 258 participants, with an average AUC of 0.77 and AUPRC of 0.51 (baseline at 0.21). Pathway analysis of representative genomes of the positively FLI-associated taxa in (NCBI) Clostridium subclusters IV and XIVa indicated the presence of, e.g., ethanol fermentation pathways. These results support several findings from smaller case-control studies, such as the role of endogenous ethanol producers in the development of the fatty liver.},
}
@article {pmid33310751,
year = {2021},
author = {He, X and Gao, J and Peng, L and Hu, T and Wan, Y and Zhou, M and Zhen, P and Cao, H},
title = {Bacterial O-GlcNAcase genes abundance decreases in ulcerative colitis patients and its administration ameliorates colitis in mice.},
journal = {Gut},
volume = {70},
number = {10},
pages = {1872-1883},
pmid = {33310751},
issn = {1468-3288},
mesh = {Animals ; Bacteroidetes/enzymology ; Colitis, Ulcerative/*enzymology/*genetics ; Firmicutes/enzymology ; Gastrointestinal Microbiome ; Humans ; Metagenomics ; Mice ; N-Acetylglucosaminyltransferases/*genetics/pharmacology ; },
abstract = {OBJECTIVE: O-linked N-acetylglucosaminylation (O-GlcNAcylation), controlled by O-GlcNAcase (OGA) and O-GlcNAc transferase (OGT), is an important post-translational modification of eukaryotic proteins and plays an essential role in regulating gut inflammation. Gut microbiota encode various enzymes involved in O-GlcNAcylation. However, the characteristics, abundance and function of these enzymes are unknown.<br><br>DESIGN: We first investigated the structure and taxonomic distribution of bacterial OGAs and OGTs. Then, we performed metagenomic analysis to explore the OGA genes abundance in health samples and different diseases. Finally, we employed in vitro and in vivo experiments to determine the effects and mechanisms of bacterial OGAs to hydrolyse O-GlcNAcylated proteins in host cells and suppress inflammatory response in the gut.<br><br>RESULTS: We found OGAs, instead of OGTs, are enriched in Bacteroidetes and Firmicutes, the major bacterial divisions in the human gut. Most bacterial OGAs are secreted enzymes with the same conserved catalytic domain as human OGAs. A pooled analysis on 1999 metagenomic samples encompassed six diseases revealed that bacterial OGA genes were conserved in healthy human gut with high abundance, and reduced exclusively in ulcerative colitis. In vitro studies showed that bacterial OGAs could hydrolyse O-GlcNAcylated proteins in host cells, including O-GlcNAcylated NF-κB-p65 subunit, which is important for activating NF-κB signalling. In vivo studies demonstrated that gut bacteria-derived OGAs could protect mice from chemically induced colonic inflammation through hydrolysing O-GlcNAcylated proteins.<br><br>CONCLUSION: Our results reveal a previously unrecognised enzymatic activity by which gut microbiota influence intestinal physiology and highlight bacterial OGAs as a promising therapeutic strategy in colonic inflammation.},
}
@article {pmid34551705,
year = {2021},
author = {Bjerre, RD and Holm, JB and Palleja, A and Sølberg, J and Skov, L and Johansen, JD},
title = {Skin dysbiosis in the microbiome in atopic dermatitis is site-specific and involves bacteria, fungus and virus.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {256},
pmid = {34551705},
issn = {1471-2180},
mesh = {Adult ; Bacteria/classification/*genetics/isolation &amp; purification/pathogenicity ; Case-Control Studies ; Dermatitis, Atopic/*microbiology/pathology ; Dysbiosis/*microbiology ; Female ; Fungi/classification/*genetics/isolation &amp; purification/pathogenicity ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Skin/*microbiology ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/pathogenicity ; Viruses/classification/*genetics/isolation &amp; purification/pathogenicity ; },
abstract = {BACKGROUND: Microbial dysbiosis with increased Staphylococcus aureus (S. aureus) colonization on the skin is a hallmark of atopic dermatitis (AD), however most microbiome studies focus on bacteria in the flexures and the microbial composition at other body sites have not been studied systematically.<br><br>OBJECTIVES: The aim of the study is to characterize the skin microbiome, including bacteria, fungi and virus, at different body sites in relation to AD, lesional state, and S. aureus colonization, and to test whether the nares could be a reservoir for S. aureus strain colonization.<br><br>METHODS: Using shotgun metagenomics we characterized microbial compositions from 14 well defined skin sites from 10 patients with AD and 5 healthy controls.<br><br>RESULTS: We found clear differences in microbial composition between AD and controls at multiple skin sites, most pronounced on the flexures and neck. The flexures exhibited lower alpha-diversity and were colonized by S. aureus, accompanied by S. epidermidis in lesions. Malassezia species were absent on the neck in AD. Virus mostly constituted Propionibacterium and Staphylococcus phages, with increased abundance of Propionibacterium phages PHL041 and PHL092 and Staphylococcus epidermidis phages CNPH82 and PH15 in AD. In lesional samples, both the genus Staphylococcus and Staphylococcus phages were more abundant. S. aureus abundance was higher across all skin sites except from the feet. In samples where S. aureus was highly abundant, lower abundances of S. hominis and Cutibacterium acnes were observed. M. osloensis and M. luteus were more abundant in AD. By single nucleotide variant analysis of S. aureus we found strains to be subject specific. On skin sites some S. aureus strains were similar and some dissimilar to the ones in the nares.<br><br>CONCLUSIONS: Our data indicate a global and site-specific dysbiosis in AD, involving both bacteria, fungus and virus. When defining targeted treatment clinicians should both consider the individual and skin site and future research into potential crosstalk between microbiota in AD yields high potential.},
}
@article {pmid34544375,
year = {2021},
author = {Koo, H and Morrow, CD},
title = {Incongruence between dominant commensal donor microbes in recipient feces post fecal transplant and response to anti-PD-1 immunotherapy.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {251},
pmid = {34544375},
issn = {1471-2180},
mesh = {Clostridium Infections/*prevention &amp; control ; Fecal Microbiota Transplantation/*methods/standards ; Feces/*microbiology ; Gastrointestinal Microbiome/*genetics/*physiology ; Humans ; Immunotherapy/*adverse effects ; Longitudinal Studies ; Melanoma/immunology/therapy ; *Symbiosis ; },
abstract = {BACKGROUND: To understand inter-individual variability of fecal microbe transplantation (FMT) to enhance anti-PD-1 immunotherapy (IT) for melanoma, we analyzed the data sets from two recent publications with a microbial strain-tracking tool to determine if donor strains were dominant in the recipient feces following FMT.<br><br>RESULTS: Analysis of the Baruch et al. data set found that the presence of commensal donor microbes in recipient feces post-FMT did not correlate with the patient response to IT. From the Davar et al., data set, we found 4 patients that responded to IT had donor's related strain post-FMT, while 2 patients that did not respond to the IT also had donor's strain post-FMT. Importantly, we identified no donor microbes in the feces in one recipient post-FMT that responded to IT. Furthermore, in depth analysis from two patients who responded to IT revealed both donor and recipient strains at different times post-FMT. Colonization of the gastrointestinal tract niches is important for the interaction with the host immune system. Using a separate data set, we show that mucosa from the cecum, transverse colon, and sigmoid colon share strains, providing a large reservoir of niches containing recipient microbes.<br><br>CONCLUSIONS: We demonstrated using strain-tracking analysis individual variation with the respect to the presence of fecal dominant donor microbes in the recipient following FMT that did not correlate with the response to anti-PD-1 immunotherapy. The inter-individual differences of FMT to enhance IT might be explained by the variability of the donor microbes to occupy and outcompete recipient microbes for the gastrointestinal niches. The result from our study supports the use of new approaches to clear the niches in the gastrointestinal tract to promote donor colonization to reduce inter-individual variability of IT for melanoma and potentially other cancers.},
}
@article {pmid34475403,
year = {2021},
author = {Yan, Y and Ren, S and Duan, Y and Lu, C and Niu, Y and Wang, Z and Inglis, B and Ji, W and Zheng, Y and Si, W},
title = {Gut microbiota and metabolites of α-synuclein transgenic monkey models with early stage of Parkinson's disease.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {69},
pmid = {34475403},
issn = {2055-5008},
mesh = {Animals ; Animals, Genetically Modified ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*physiology ; Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism ; Humans ; Macaca mulatta ; Male ; Metagenomics ; Mice ; Neurodegenerative Diseases ; Parkinson Disease/*metabolism ; alpha-Synuclein/genetics/*metabolism ; },
abstract = {Parkinson's disease (PD) is the second most prevalent neurodegenerative disease. However, it is unclear whether microbiota and metabolites have demonstrated changes at early PD due to the difficulties in diagnosis and identification of early PD in clinical practice. In a previous study, we generated A53T transgenic monkeys with early Parkinson's symptoms, including anxiety and cognitive impairment. Here we analyzed the gut microbiota by metagenomic sequencing and metabolites by targeted gas chromatography. The gut microbiota analysis showed that the A53T monkeys have higher degree of diversity in gut microbiota with significantly elevated Sybergistetes, Akkermansia, and Eggerthella lenta compared with control monkeys. Prevotella significantly decreased in A53T transgenic monkeys. Glyceric acid, L-Aspartic acid, and p-Hydroxyphenylacetic acid were significantly elevated, whereas Myristic acid and 3-Methylindole were significantly decreased in A53T monkeys. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (KO0131) and the oxidative phosphorylation reaction (KO2147) were significantly increased in metabolic pathways of A53T monkeys. Our study suggested that the transgenic A53T and α-syn aggregation may affect the intestine microbiota and metabolites of rhesus monkeys, and the identified five compositional different metabolites that are mainly associated with mitochondrial dysfunction may be related to the pathogenesis of PD.},
}
@article {pmid34407769,
year = {2021},
author = {Goolam Mahomed, T and Peters, R and Pretorius, G and Goolam Mahomed, A and Ueckermann, V and Kock, MM and Ehlers, MM},
title = {Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {228},
pmid = {34407769},
issn = {1471-2180},
mesh = {Aged ; Aged, 80 and over ; DNA, Bacterial/genetics ; Female ; Humans ; Lung/*microbiology ; Male ; Metagenomics/*methods/*standards ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Software/*standards ; Sputum/microbiology ; },
abstract = {BACKGROUND: Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients.<br><br>METHODS: Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method.<br><br>RESULTS: Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods' data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly.<br><br>CONCLUSIONS: It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.},
}
@article {pmid34373464,
year = {2021},
author = {Chu, Y and Sun, S and Huang, Y and Gao, Q and Xie, X and Wang, P and Li, J and Liang, L and He, X and Jiang, Y and Wang, M and Yang, J and Chen, X and Zhou, C and Zhao, Y and Ding, F and Zhang, Y and Wu, X and Bai, X and Wu, J and Wei, X and Chen, X and Yue, Z and Fang, X and Huang, Q and Wang, Z and Huang, R},
title = {Metagenomic analysis revealed the potential role of gut microbiome in gout.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {66},
pmid = {34373464},
issn = {2055-5008},
mesh = {Adolescent ; Adult ; Aged ; Arthritis ; Bacteria/classification ; Butyrates/analysis ; Diabetes Mellitus, Type 2/genetics ; Dysbiosis/microbiology ; Fatty Acids, Volatile ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Gout/*microbiology ; Humans ; Inflammation ; Male ; Metabolic Diseases ; *Metagenome ; Metagenomics/methods ; Middle Aged ; Spondylitis, Ankylosing ; Uric Acid/blood ; Young Adult ; },
abstract = {Emerging evidence indicates an association between gut microbiome and arthritis diseases including gout. However, how and which gut bacteria affect host urate degradation and inflammation in gout remains unclear. Here we performed a metagenome analysis on 307 fecal samples from 102 gout patients and 86 healthy controls. Gout metagenomes significantly differed from those of healthy controls. The relative abundances of Prevotella, Fusobacterium, and Bacteroides were increased in gout, whereas those of Enterobacteriaceae and butyrate-producing species were decreased. Functionally, gout patients had greater abundances for genes in fructose, mannose metabolism and lipid A biosynthesis, and lower for genes in urate degradation and short chain fatty acid production. A three-pronged association between metagenomic species, functions and clinical parameters revealed that decreased abundances of species in Enterobacteriaceae were associated with reduced amino acid metabolism and environmental sensing, which together contribute to increased serum uric acid and C-reactive protein levels in gout. A random forest classifier based on three gut microbial genes showed high predictivity for gout in both discovery and validation cohorts (0.91 and 0.80 accuracy), with high specificity in the context of other chronic disorders. Longitudinal analysis showed that uric-acid-lowering and anti-inflammatory drugs partially restored gut microbiota after 24-week treatment. Comparative analysis with obesity, type 2 diabetes, ankylosing spondylitis and rheumatoid arthritis indicated that gout metagenomes were more similar to those of autoimmune than metabolic diseases. Our results suggest that gut dysbiosis was associated with dysregulated host urate degradation and systemic inflammation and may be used as non-invasive diagnostic markers for gout.},
}
@article {pmid34362295,
year = {2021},
author = {Shaw, AG and Sim, K and Rose, G and Wooldridge, DJ and Li, MS and Misra, RV and Gharbia, S and Kroll, JS},
title = {Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {225},
pmid = {34362295},
issn = {1471-2180},
mesh = {Bayes Theorem ; DNA, Bacterial/genetics ; Enterocolitis, Necrotizing/immunology/*microbiology ; Epithelial Cells/*immunology/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/immunology/*microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Toll-Like Receptor 4/genetics/*immunology ; },
abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Bayesian regression was used to segregate cases from control samples using both microbial and clinical data.<br><br>RESULTS: We found that the infants suffering from NEC fell into two groups based on their microbiota; one with low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We propose that these two patterns represent the stimulation of a common pathway at extremes; the LPS-enriched microbiome suggesting overstimulation of TLR4, whilst a microbial community with low levels of CpG DNA suggests reduction of the counterbalance to TLR4 overstimulation.<br><br>CONCLUSIONS: The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.},
}
@article {pmid34354062,
year = {2021},
author = {Schaan, AP and Sarquis, D and Cavalcante, GC and Magalhães, L and Sacuena, ERP and Costa, J and Fonseca, D and Mello, VJ and Guerreiro, JF and Ribeiro-Dos-Santos, Â},
title = {The structure of Brazilian Amazonian gut microbiomes in the process of urbanisation.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {65},
pmid = {34354062},
issn = {2055-5008},
mesh = {Bacteria/*classification/genetics ; Biodiversity ; Brazil ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Life Style ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Rural Population ; Urban Population ; *Urbanization ; },
abstract = {Shifts in subsistence strategy among Native American people of the Amazon may be the cause of typically western diseases previously linked to modifications of gut microbial communities. Here, we used 16S ribosomal RNA sequencing to characterise the gut microbiome of 114 rural individuals, namely Xikrin, Suruí and Tupaiú, and urban individuals from Belém city, in the Brazilian Amazon. Our findings show the degree of potential urbanisation occurring in the gut microbiome of rural Amazonian communities characterised by the gradual loss and substitution of taxa associated with rural lifestyles, such as Treponema. Comparisons to worldwide populations indicated that Native American groups are similar to South American agricultural societies and urban groups are comparable to African urban and semi-urban populations. The transitioning profile observed among traditional populations is concerning in light of increasingly urban lifestyles. Lastly, we propose the term "tropical urban" to classify the microbiome of urban populations living in tropical zones.},
}
@article {pmid34259891,
year = {2021},
author = {Yen, S and Johnson, JS},
title = {Metagenomics: a path to understanding the gut microbiome.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {32},
number = {4},
pages = {282-296},
pmid = {34259891},
issn = {1432-1777},
support = {/DH_/Department of Health/United Kingdom ; },
mesh = {Computational Biology/*standards ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/*standards ; Humans ; Metagenome/genetics ; *Metagenomics ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.},
}
@article {pmid34058706,
year = {2021},
author = {Hayer, J and Wille, M and Font, A and González-Aravena, M and Norder, H and Malmberg, M},
title = {Four novel picornaviruses detected in Magellanic Penguins (Spheniscus magellanicus) in Chile.},
journal = {Virology},
volume = {560},
number = {},
pages = {116-123},
doi = {10.1016/j.virol.2021.05.010},
pmid = {34058706},
issn = {1096-0341},
mesh = {Animals ; Chile/epidemiology ; Endangered Species ; Phylogeny ; Picornaviridae/*classification/genetics/*isolation &amp; purification ; Picornaviridae Infections/*epidemiology/*veterinary ; Spheniscidae/*virology ; },
abstract = {Members of the Picornaviridae family comprise a significant burden on the poultry industry, causing diseases such as gastroenteritis and hepatitis. However, with the advent of metagenomics, a number of picornaviruses have now been revealed in apparently healthy wild birds. In this study, we identified four novel viruses belonging to the family Picornaviridae in healthy Magellanic penguins, a near threatened species. All samples were subsequently screened by RT-PCR for these new viruses, and approximately 20% of the penguins were infected with at least one of these viruses. The viruses were distantly related to members of the genera Hepatovirus, Tremovirus, Gruhelivirus and Crahelvirus. Further, they had more than 60% amino acid divergence from other picornaviruses, and therefore likely constitute novel genera. Our results demonstrate the vast undersampling of wild birds for viruses, and we expect the discovery of numerous avian viruses that are related to hepatoviruses and tremoviruses in the future.},
}
@article {pmid33689000,
year = {2021},
author = {Ericsson, AC and Franklin, CL},
title = {The gut microbiome of laboratory mice: considerations and best practices for translational research.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {32},
number = {4},
pages = {239-250},
pmid = {33689000},
issn = {1432-1777},
support = {U42 OD010918/OD/NIH HHS/United States ; },
mesh = {Animals ; Disease Models, Animal ; Gastrointestinal Microbiome/*genetics ; Humans ; Mice ; *Translational Research, Biomedical ; },
abstract = {Just as the gut microbiota (GM) is now recognized as an integral mediator of environmental influences on human physiology, susceptibility to disease, and response to pharmacological intervention, so too does the GM of laboratory mice affect the phenotype of research using mouse models. Multiple experimental factors have been shown to affect the composition of the GM in research mice, as well as the model phenotype, suggesting that the GM represents a major component in experimental reproducibility. Moreover, several recent studies suggest that manipulation of the GM of laboratory mice can substantially improve the predictive power or translatability of data generated in mouse models to the human conditions under investigation. This review provides readers with information related to these various factors and practices, and recommendations regarding methods by which issues with poor reproducibility or translatability can be transformed into discoveries.},
}
@article {pmid33651197,
year = {2021},
author = {Brubaker, L and Putonti, C and Dong, Q and Wolfe, AJ},
title = {The human urobiome.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {32},
number = {4},
pages = {232-238},
pmid = {33651197},
issn = {1432-1777},
support = {R01 DK104718/DK/NIDDK NIH HHS/United States ; R01 AI116706/AI/NIAID NIH HHS/United States ; },
mesh = {Female ; Humans ; Male ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Urinary Bladder/*microbiology ; },
abstract = {Traditionally, the healthy urinary bladder has been considered to be sterile. Several teams have used metagenomic (DNA-dependent) and metaculturomic (culture-dependent) methods to debunk this longstanding dogma. In fact, resident microbial communities (urobiome) have been detected in both adult females and males. Although the field is young, several observations have been made. For example, the urobiome differs between men and women, likely due to anatomical and hormonal differences. Importantly, the urobiome has been associated with a variety of lower urinary tract disorders, including overactive bladder and post-operative urinary tract infection, raising the possibility that clinicians might one day treat symptoms by modifying the urobiome instead of killing the suspected uropathogen. Little is known concerning the relationship between the urobiome and host genetics; so far, only a single paper has reported such a study. However, major efforts have gone into understanding the genomics of the urobiome itself, a process facilitated by the fact that many urobiome studies have used metaculturomic methods to detect and identify microbes. In this narrative review, we will introduce the urobiome with separate sections on the female and male urobiomes, discuss challenges specific to the urobiome, describe newly discovered associations between the urobiome and lower urinary tract symptoms, and highlight the one study that has attempted to relate host genetics and the urobiome. We will finish with a section on how metagenomic surveys and whole genome sequencing of bacterial isolates are improving our understanding of the urobiome and its relationship to lower urinary tract health and disorders.},
}
@article {pmid33596669,
year = {2021},
author = {Shi, H and Zhang, B and Abo-Hamzy, T and Nelson, JW and Ambati, CSR and Petrosino, JF and Bryan, RM and Durgan, DJ},
title = {Restructuring the Gut Microbiota by Intermittent Fasting Lowers Blood Pressure.},
journal = {Circulation research},
volume = {128},
number = {9},
pages = {1240-1254},
pmid = {33596669},
issn = {1524-4571},
support = {R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS102594/NS/NINDS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Bile Acids and Salts/metabolism ; Cecum/microbiology ; Cholic Acid/administration &amp; dosage ; Dysbiosis/blood/complications/metabolism/*prevention &amp; control ; Fasting/*physiology ; Gastrointestinal Microbiome/genetics/*physiology ; Germ-Free Life ; Hypotension/etiology/*prevention &amp; control ; Metabolome/*physiology ; Oleanolic Acid/pharmacology ; Random Allocation ; Rats ; Rats, Inbred SHR ; Rats, Inbred WKY ; Receptors, G-Protein-Coupled/agonists/blood/metabolism ; Specific Pathogen-Free Organisms ; Time Factors ; Whole Genome Sequencing ; },
abstract = {[Figure: see text].},
}
@article {pmid34143954,
year = {2021},
author = {Henrick, BM and Rodriguez, L and Lakshmikanth, T and Pou, C and Henckel, E and Arzoomand, A and Olin, A and Wang, J and Mikes, J and Tan, Z and Chen, Y and Ehrlich, AM and Bernhardsson, AK and Mugabo, CH and Ambrosiani, Y and Gustafsson, A and Chew, S and Brown, HK and Prambs, J and Bohlin, K and Mitchell, RD and Underwood, MA and Smilowitz, JT and German, JB and Frese, SA and Brodin, P},
title = {Bifidobacteria-mediated immune system imprinting early in life.},
journal = {Cell},
volume = {184},
number = {15},
pages = {3884-3898.e11},
doi = {10.1016/j.cell.2021.05.030},
pmid = {34143954},
issn = {1097-4172},
support = {S10 OD018174/OD/NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology ; Bifidobacterium/*physiology ; Biomarkers/metabolism ; Breast Feeding ; CD4-Positive T-Lymphocytes/immunology ; Cell Polarity ; Cell Proliferation ; Cytokines/metabolism ; Feces/chemistry/microbiology ; Galectin 1/metabolism ; Gastrointestinal Microbiome ; Humans ; Immune System/*growth &amp; development/*microbiology ; Indoles/metabolism ; Infant, Newborn ; Inflammation/blood/genetics ; Intestinal Mucosa/immunology ; Metabolome ; Milk, Human/chemistry ; Oligosaccharides/metabolism ; Th17 Cells/immunology ; Th2 Cells/immunology ; Water ; },
abstract = {Immune-microbe interactions early in life influence the risk of allergies, asthma, and other inflammatory diseases. Breastfeeding guides healthier immune-microbe relationships by providing nutrients to specialized microbes that in turn benefit the host's immune system. Such bacteria have co-evolved with humans but are now increasingly rare in modern societies. Here we show that a lack of bifidobacteria, and in particular depletion of genes required for human milk oligosaccharide (HMO) utilization from the metagenome, is associated with systemic inflammation and immune dysregulation early in life. In breastfed infants given Bifidobacterium infantis EVC001, which expresses all HMO-utilization genes, intestinal T helper 2 (Th2) and Th17 cytokines were silenced and interferon β (IFNβ) was induced. Fecal water from EVC001-supplemented infants contains abundant indolelactate and B. infantis-derived indole-3-lactic acid (ILA) upregulated immunoregulatory galectin-1 in Th2 and Th17 cells during polarization, providing a functional link between beneficial microbes and immunoregulation during the first months of life.},
}
@article {pmid34043940,
year = {2021},
author = {Danko, D and Bezdan, D and Afshin, EE and Ahsanuddin, S and Bhattacharya, C and Butler, DJ and Chng, KR and Donnellan, D and Hecht, J and Jackson, K and Kuchin, K and Karasikov, M and Lyons, A and Mak, L and Meleshko, D and Mustafa, H and Mutai, B and Neches, RY and Ng, A and Nikolayeva, O and Nikolayeva, T and Png, E and Ryon, KA and Sanchez, JL and Shaaban, H and Sierra, MA and Thomas, D and Young, B and Abudayyeh, OO and Alicea, J and Bhattacharyya, M and Blekhman, R and Castro-Nallar, E and Cañas, AM and Chatziefthimiou, AD and Crawford, RW and De Filippis, F and Deng, Y and Desnues, C and Dias-Neto, E and Dybwad, M and Elhaik, E and Ercolini, D and Frolova, A and Gankin, D and Gootenberg, JS and Graf, AB and Green, DC and Hajirasouliha, I and Hastings, JJA and Hernandez, M and Iraola, G and Jang, S and Kahles, A and Kelly, FJ and Knights, K and Kyrpides, NC and Łabaj, PP and Lee, PKH and Leung, MHY and Ljungdahl, PO and Mason-Buck, G and McGrath, K and Meydan, C and Mongodin, EF and Moraes, MO and Nagarajan, N and Nieto-Caballero, M and Noushmehr, H and Oliveira, M and Ossowski, S and Osuolale, OO and Özcan, O and Paez-Espino, D and Rascovan, N and Richard, H and Rätsch, G and Schriml, LM and Semmler, T and Sezerman, OU and Shi, L and Shi, T and Siam, R and Song, LH and Suzuki, H and Court, DS and Tighe, SW and Tong, X and Udekwu, KI and Ugalde, JA and Valentine, B and Vassilev, DI and Vayndorf, EM and Velavan, TP and Wu, J and Zambrano, MM and Zhu, J and Zhu, S and Mason, CE and , },
title = {A global metagenomic map of urban microbiomes and antimicrobial resistance.},
journal = {Cell},
volume = {184},
number = {13},
pages = {3376-3393.e17},
pmid = {34043940},
issn = {1097-4172},
support = {R01 AI151059/AI/NIAID NIH HHS/United States ; R25 EB020393/EB/NIBIB NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; U01 DA053941/DA/NIDA NIH HHS/United States ; UL1 TR000457/TR/NCATS NIH HHS/United States ; },
mesh = {Biodiversity ; Databases, Genetic ; Drug Resistance, Bacterial/*genetics ; Humans ; *Metagenomics ; Microbiota/*genetics ; *Urban Population ; },
abstract = {We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.},
}
@article {pmid34742104,
year = {2022},
author = {Yan, Y and Li, H and Fayyaz, A and Gai, Y},
title = {Metagenomic and network analysis revealed wide distribution of antibiotic resistance genes in monkey gut microbiota.},
journal = {Microbiological research},
volume = {254},
number = {},
pages = {126895},
doi = {10.1016/j.micres.2021.126895},
pmid = {34742104},
issn = {1618-0623},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Gastrointestinal Microbiome/drug effects/genetics ; *Haplorhini/microbiology ; Metagenomics ; },
abstract = {The emergence and spread of drug-resistant microorganisms that have acquired new resistance mechanisms, leading to antibiotic resistance, continue to threaten the health of humans and animals worldwide. Non-human primates (NHPs), as close living relatives of human beings in the world, have a high degree of genetic and physiological similarity to humans. However, despite its importance, we lack a comprehensive characterization or understanding of the similarities and differences of the antibiotic resistance genes of the gut microbiome carried by non-human primates and humans. In the present study, the diversity and abundance of antibiotic resistance genes carried by the gut microbiota of cynomolgus monkeys (Macaca fascicularis) were investigated by metagenomic analysis. In total, 60 resistance types conferring resistance to 11 categories of antibiotics were identified in the gut microbiome of cynomolgus monkeys. Interestingly, the composition and abundance of ARGs carried by the gut microbiota of cynomolgus monkeys can be significantly affected by dietary changes. Moreover, we found that all ARG types carried by humans are also present in cynomolgus monkeys. The tetracycline resistance gene tet(37) is evolutionarily conserved and highly homologous. Taken together, our study provides a comprehensive overview of the diversity and richness of ARGs in the gut microbiota of cynomolgus monkeys and underlines the potentially crucial role of diet in the gut health of monkeys and humans.},
}
@article {pmid34970896,
year = {2021},
author = {Peng, X and Zhao, Y and Lin, T and Shu, X and Hou, L and Gao, L and Wang, H and Ge, N and Yue, J},
title = {[Research of relationship between frailty and gut microbiota on middle-aged and the aged patients with diabetes].},
journal = {Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi},
volume = {38},
number = {6},
pages = {1126-1133},
doi = {10.7507/1001-5515.202101083},
pmid = {34970896},
issn = {1001-5515},
mesh = {Aged ; *Diabetes Mellitus ; *Epstein-Barr Virus Infections ; *Frailty ; *Gastrointestinal Microbiome ; Herpesvirus 4, Human ; Humans ; Middle Aged ; },
abstract = {Gut microbiota plays an important role in development of diabetes with frailty. Therefore, it is of great significance to study the structural and functional characteristics of gut microbiota in Chinese with frailty. Totally 30 middle-aged and the aged participants in communities with diabetes were enrolled in this study, and their feces were collected. At the same time, we developed a metagenome analysis to explore the different of the structural and functional characteristics between diabetes with frailty and diabetes without frailty. The results showed the alpha diversity of intestinal microbiota in diabetes with frailty was lower. Collinsella and Butyricimonas were more abundant in diabetes with frailty. The functional characteristics showed that histidine metabolism, Epstein-Barr virus infection, sulfur metabolism, and biosynthesis of type Ⅱ polyketide products were upregulated in diabetes with frailty. Otherwise, butanoate metabolism and phenylalanine metabolism were down-regulated in diabetes with frailty. This research provides theoretical basic for exploring the mechanism of the gut microbiota on the occurrence and development of diabetes with frailty, and provides a basic for prevention and intervention of it.},
}
@article {pmid34824209,
year = {2021},
author = {Kandathil, AJ and Cox, AL and Page, K and Mohr, D and Razaghi, R and Ghanem, KG and Tuddenham, SA and Hsieh, YH and Evans, JL and Coller, KE and Timp, W and Celentano, DD and Ray, SC and Thomas, DL},
title = {Plasma virome and the risk of blood-borne infection in persons with substance use disorder.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {6909},
pmid = {34824209},
issn = {2041-1723},
support = {U19 AI159822/AI/NIAID NIH HHS/United States ; R01 DA016017/DA/NIDA NIH HHS/United States ; R21 DA053145/DA/NIDA NIH HHS/United States ; },
mesh = {Adult ; Amino Acid Sequence ; Anelloviridae ; *Blood-Borne Infections ; Blood-Borne Pathogens ; Female ; Hepatitis C/epidemiology ; Humans ; Knowledge ; Male ; Metagenomics ; Phylogeny ; *Plasma ; Public Health ; *Substance-Related Disorders ; *Virome ; Young Adult ; },
abstract = {There is an urgent need for innovative methods to reduce transmission of bloodborne pathogens like HIV and HCV among people who inject drugs (PWID). We investigate if PWID who acquire non-pathogenic bloodborne viruses like anelloviruses and pegiviruses might be at greater risk of acquiring a bloodborne pathogen. PWID who later acquire HCV accumulate more non-pathogenic viruses in plasma than matched controls who do not acquire HCV infection. Additionally, phylogenetic analysis of those non-pathogenic virus sequences reveals drug use networks. Here we find first in Baltimore and confirm in San Francisco that the accumulation of non-pathogenic viruses in PWID is a harbinger for subsequent acquisition of pathogenic viruses, knowledge that may guide the prioritization of the public health resources to combat HIV and HCV.},
}
@article {pmid34708327,
year = {2021},
author = {de Medeiros Azevedo, T and Aburjaile, FF and Ferreira-Neto, JRC and Pandolfi, V and Benko-Iseppon, AM},
title = {The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {37},
number = {12},
pages = {206},
pmid = {34708327},
issn = {1573-0972},
mesh = {Agricultural Inoculants ; Agriculture ; Biotechnology/*methods ; Computational Biology ; *Endophytes ; Humans ; Metagenomics/methods ; *Microbiota ; Plant Roots/microbiology ; Plants/*microbiology ; Soil ; Soil Microbiology ; },
abstract = {Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.},
}
@article {pmid34580777,
year = {2021},
author = {Kunda, P and Mukherjee, A and Dhal, PK},
title = {Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {37},
number = {11},
pages = {184},
pmid = {34580777},
issn = {1573-0972},
mesh = {Bacteria/*classification/genetics/*isolation &amp; purification ; Biodiversity ; Endophytes/*classification/genetics/*isolation &amp; purification ; India ; Metagenomics ; Microbiota ; Oryza/*microbiology ; *Phylogeny ; Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil ; },
abstract = {Endophytes have recently garnered importance worldwide and multiple studies are being conducted to understand their important role and mechanism of interaction inside plants. But before we indulge in their functions it is necessary to dig into the microbiome. This will help to get a complete picture of the microbes intrinsic to their host and understand changes in community composition with respect to their habitats. To fulfil this requirement in our study we have attempted to dissect the endophytic diversity in roots of rice plant grown across the various agro-ecological zones of West Bengal by undergoing amplicon analysis of their 16S rRNA gene. Based on the measured environmental parameters agro-ecological zones can be divided into two groups: nutrient dense groups, representing zones like Gangetic, Northern hill and Terai-Teesta zone characterised by soil with higher levels of nitrogen (N) and total organic carbon and nutrient low groups representing Coastal saline, Red-laterite and Vindhyan zone mainly characterised by high electroconductivity and pH. Gammaproteobacteria, Alphaproteobacteria, Bacilli and Bacteroidetes were mostly abundant in nutrient dense sites whereas Clostridia and Planctomycetes were concentrated in nutrient low sites. Few genera (Aeromonas, Sulfurospirillum, Uliginosibacterium and Acidaminococcus) are present in samples cultivated in all the zones representing the core microbiome of rice in West Bengal, while some other genera like Lactococcus, Dickeya, Azonexus and Pectobacterium are unique to specific zone. Hence it can be concluded that this study has provided some insight in to the endophytic status of rice grown across the state of West Bengal.},
}
@article {pmid34490704,
year = {2021},
author = {Li, L and Zhang, Y and Speakman, JR and Hu, S and Song, Y and Qin, S},
title = {The gut microbiota and its products: Establishing causal relationships with obesity related outcomes.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {22},
number = {12},
pages = {e13341},
doi = {10.1111/obr.13341},
pmid = {34490704},
issn = {1467-789X},
mesh = {Causality ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Obesity ; },
abstract = {Gut microorganisms not only participate in the metabolism of carbohydrate, lipids, protein, and polypeptides in the intestine but also directly affect the metabolic phenotypes of the host. Although many studies have described the apparent effects of gut microbiota on human health, the development of metagenomics and culturomics in the past decade has generated a large amount of evidence suggesting a causal relationship between gut microbiota and obesity. The interaction between the gut microbiota and host is realized by microbial metabolites with multiple biological functions. We concentrated here on several representative beneficial species connected with obesity as well as the mechanisms, with particular emphasis on microbiota-dependent metabolites. Finally, we consider the potential clinical significance of these relationships to fuel the conception and realization of novel therapeutic and preventive strategies.},
}
@article {pmid34380135,
year = {2021},
author = {Corralo, DJ and Ev, LD and Damé-Teixeira, N and Maltz, M and Arthur, RA and Do, T and Fatturi Parolo, CC},
title = {Functionally Active Microbiome in Supragingival Biofilms in Health and Caries.},
journal = {Caries research},
volume = {55},
number = {6},
pages = {603-616},
doi = {10.1159/000518963},
pmid = {34380135},
issn = {1421-976X},
mesh = {Adolescent ; Adult ; Aged ; Biofilms ; *Dental Caries ; Dental Caries Susceptibility ; Humans ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S ; Young Adult ; },
abstract = {The oral microbiome is unique at inter and intra-individual levels at various sites due to physical and biological factors. This study aimed to compare the bacterial composition of supragingival biofilms collected from enamel sites with different caries activity, from active and inactive-caries subjects, and from caries-free (CF) subjects. Twenty-two individuals (aged between 13 and 76 years old; med = 23.5 years old) were allocated into 3 groups: caries-active (CA) (n = 10), caries-inactive (CI) (n = 6), and CF (n = 6). From the CA group, 3 sites were sampled: CA (active non-cavitated lesion), CI (inactive non-cavitated lesion), and sound enamel surface (S). From the subjects of the CI group, biofilm from a CI lesion was collected (INCL), while for the CF subjects, a pool of biofilm from sound enamel surfaces was sampled. The total RNA was extracted, and cDNA libraries were prepared and paired-end sequenced (Illumina HiSeq 3,000). Final dental biofilm samples analysed from CA was 16 (ANCL-CA = 6, INCL-CA = 4, S-CA = 6); from CI, 3 (INCL-CI = 3); and from CF, 6 (S-CF = 6) (some samples were lost by insufficient genetic material). Read sequences were processed and analysed using the Metagenomics RAST server. High-quality sequences (3,542,190) were clustered into operational taxonomic units (97% identity; SILVA SSU), representing 915 genera belonging to 29 phyla (higher abundant: Actinobacteria, Firmicutes, Bacteroidetes, and Fusobacteria). The presence of a core microbiome was observed (123 shared genera). The alpha diversity analysis showed less bacterial diversity in disease (S-CA) compared to health (S-CF). The dominant genera included Actinomyces, Corynebacterium, Capnocytophaga, Leptotrichia, Veillonella, Prevotella, Streptococcus, Eubacterium, and Neisseria. Veillonella and Leptotrichia were related with disease and Prevotella with health. Corynebacterium, Capnocytophaga, and Actinomyces clustered together presenting high abundance in health and disease. The Metric Multidimensional Scaling Ordination analysis shows that sites from active subjects (ANCL-CA, INCL-CA, and S-CA) are closer to each other than either INCL-CI subjects or S-CF subjects. In conclusion, supragingival bacterial communities presented intra-individual similarities, but inter-individual diversity and difference in bacterial composition reveal that the subject's caries activity status matters more than sites.},
}
@article {pmid34190603,
year = {2021},
author = {Castro-Severyn, J and Pardo-Esté, C and Mendez, KN and Fortt, J and Marquez, S and Molina, F and Castro-Nallar, E and Remonsellez, F and Saavedra, CP},
title = {Living to the High Extreme: Unraveling the Composition, Structure, and Functional Insights of Bacterial Communities Thriving in the Arsenic-Rich Salar de Huasco Altiplanic Ecosystem.},
journal = {Microbiology spectrum},
volume = {9},
number = {1},
pages = {e0044421},
pmid = {34190603},
issn = {2165-0497},
mesh = {Arsenic/*metabolism ; Bacteria/classification/genetics/*metabolism ; Biodiversity ; Chile ; DNA, Bacterial ; *Ecosystem ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Salinity ; },
abstract = {Microbial communities inhabiting extreme environments such as Salar de Huasco (SH) in northern Chile are adapted to thrive while exposed to several abiotic pressures and the presence of toxic elements such as arsenic (As). Hence, we aimed to uncover the role of As in shaping bacterial composition, structure, and functional potential in five different sites in this altiplanic wetland using a shotgun metagenomic approach. The sites exhibit wide gradients of As (9 to 321 mg/kg), and our results showed highly diverse communities and a clear dominance exerted by the Proteobacteria and Bacteroidetes phyla. Functional potential analyses show broadly convergent patterns, contrasting with their great taxonomic variability. As-related metabolism, as well as other functional categories such as those related to the CH4 and S cycles, differs among the five communities. Particularly, we found that the distribution and abundance of As-related genes increase as the As concentration rises. Approximately 75% of the detected genes for As metabolism belong to expulsion mechanisms; arsJ and arsP pumps are related to sites with higher As concentrations and are present almost exclusively in Proteobacteria. Furthermore, taxonomic diversity and functional potential are reflected in the 12 reconstructed high-quality metagenome assembled genomes (MAGs) belonging to the Bacteroidetes (5), Proteobacteria (5), Cyanobacteria (1), and Gemmatimonadetes (1) phyla. We conclude that SH microbial communities are diverse and possess a broad genetic repertoire to thrive under extreme conditions, including increasing concentrations of highly toxic As. Finally, this environment represents a reservoir of unknown and undescribed microorganisms, with great metabolic versatility, which needs further study. IMPORTANCE As microbial communities inhabiting extreme environments are fundamental for maintaining ecosystems, many studies concerning composition, functionality, and interactions have been carried out. However, much is still unknown. Here, we sampled microbial communities in the Salar de Huasco, an extreme environment subjected to several abiotic stresses (high UV radiation, salinity and arsenic; low pressure and temperatures). We found that although microbes are taxonomically diverse, functional potential seems to have an important degree of convergence, suggesting high levels of adaptation. Particularly, arsenic metabolism showed differences associated with increasing concentrations of the metalloid throughout the area, and it effectively exerts a significant pressure over these organisms. Thus, the significance of this research is that we describe highly specialized communities thriving in little-explored environments subjected to several pressures, considered analogous of early Earth and other planets, that have the potential for unraveling technologies to face the repercussions of climate change in many areas of interest.},
}
@article {pmid33563544,
year = {2021},
author = {Liwinski, T and Leshem, A and Elinav, E},
title = {Breakthroughs and Bottlenecks in Microbiome Research.},
journal = {Trends in molecular medicine},
volume = {27},
number = {4},
pages = {298-301},
doi = {10.1016/j.molmed.2021.01.003},
pmid = {33563544},
issn = {1471-499X},
mesh = {Diet ; Fecal Microbiota Transplantation ; Host Microbial Interactions ; Humans ; Metagenomics/methods ; *Microbiota/drug effects/genetics/immunology ; Phage Therapy ; Precision Medicine/trends ; Probiotics ; },
abstract = {Over the past 15 years, the research community has witnessed unprecedented progress in microbiome research. We review this increasing knowledge and first attempts of its clinical application, and also limitations and challenges faced by the research community, in mechanistically understanding host-microbiome interactions and integrating these insights into clinical practice.},
}
@article {pmid34758050,
year = {2021},
author = {Alkema, W and Boekhorst, J and Eijlander, RT and Schnittger, S and De Gruyter, F and Lukovac, S and Schilling, K and Kortman, GAM},
title = {Charting host-microbe co-metabolism in skin aging and application to metagenomics data.},
journal = {PloS one},
volume = {16},
number = {11},
pages = {e0258960},
pmid = {34758050},
issn = {1932-6203},
mesh = {Adult ; Aged ; Bacteria/genetics/metabolism ; Ceramides/metabolism ; Fatty Acids/metabolism ; Female ; Genes, Bacterial ; Healthy Volunteers ; Host Microbial Interactions/genetics ; Humans ; Markov Chains ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Signal Transduction/genetics ; Skin/metabolism/*microbiology ; Skin Aging/*genetics ; Skin Pigmentation/genetics ; },
abstract = {During aging of human skin, a number of intrinsic and extrinsic factors cause the alteration of the skin's structure, function and cutaneous physiology. Many studies have investigated the influence of the skin microbiome on these alterations, but the molecular mechanisms that dictate the interplay between these factors and the skin microbiome are still not fully understood. To obtain more insight into the connection between the skin microbiome and the human physiological processes involved in skin aging, we performed a systematic study on interconnected pathways of human and bacterial metabolic processes that are known to play a role in skin aging. The bacterial genes in these pathways were subsequently used to create Hidden Markov Models (HMMs), which were applied to screen for presence of defined functionalities in both genomic and metagenomic datasets of skin-associated bacteria. These models were further applied on 16S rRNA gene sequencing data from skin microbiota samples derived from female volunteers of two different age groups (25-28 years ('young') and 59-68 years ('old')). The results show that the main bacterial pathways associated with aging skin are those involved in the production of pigmentation intermediates, fatty acids and ceramides. This study furthermore provides evidence for a relation between skin aging and bacterial enzymes involved in protein glycation. Taken together, the results and insights described in this paper provide new leads for intervening with bacterial processes that are associated with aging of human skin.},
}
@article {pmid34611216,
year = {2021},
author = {Goolam Mahomed, T and Peters, RPH and Allam, M and Ismail, A and Mtshali, S and Goolam Mahomed, A and Ueckermann, V and Kock, MM and Ehlers, MM},
title = {Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {19758},
pmid = {34611216},
issn = {2045-2322},
mesh = {Aged ; Biodiversity ; Disease Progression ; Female ; Humans ; Lung/*microbiology ; Male ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Pulmonary Disease, Chronic Obstructive/*diagnosis/*etiology ; Risk Factors ; South Africa/epidemiology ; Sputum/microbiology ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations triggered by infections. The aim of this study was to determine the composition of the lung microbiome and lung virome in patients with COPD in an African setting and to compare their composition between the stable and exacerbated states. Twenty-four adult COPD patients were recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There were no considerable differences for alpha and beta diversity measures between the disease states. However, a difference in the abundances between disease states was observed for: (i) Serratia (3% lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5% higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058 virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the first to report lung microbiome composition in COPD patients from Africa. In this small sample set, no differences in alpha or beta diversity between stable and exacerbated disease state was observed, but an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the need for further research of the lung microbiome of COPD patients in African settings.},
}
@article {pmid34961896,
year = {2021},
author = {Johny, TK and Puthusseri, RM and Bhat, SG},
title = {Metagenomic landscape of taxonomy, metabolic potential and resistome of Sardinella longiceps gut microbiome.},
journal = {Archives of microbiology},
volume = {204},
number = {1},
pages = {87},
pmid = {34961896},
issn = {1432-072X},
support = {MOES/10-MLR/2/2007//centre for marine living resources &amp; ecology- ministry of earth sciences, government of india/ ; MOES/10-MLRTD/03/2013//centre for marine living resources &amp; ecology- ministry of earth sciences, government of india/ ; },
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Fishes ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {Fish gut microbiota, encompassing a colossal reserve of microbes represents a dynamic ecosystem, influenced by a myriad of environmental and host factors. The current study presents a comprehensive insight into Sardinella longiceps gut microbiome using whole metagenome shotgun sequencing. Taxonomic profiling identified the predominance of phylum Proteobacteria, comprising of Photobacterium, Vibrio and Shewanella sp. Functional annotation revealed the dominance of Clustering based subsystems, Carbohydrate, and Amino acids and derivatives. Analysis of Virulence, disease and defense subsystem identified genes conferring resistance to antibiotics and toxic compounds, like multidrug resistance efflux pumps and resistance genes for fluoroquinolones and heavy metals like cobalt, zinc, cadmium and copper. The presence of overlapping genetic mechanisms of resistance to antibiotics and heavy metals, like the efflux pumps is a serious cause of concern as it is likely to aggravate co-selection pressure, leading to an increased dissemination of these resistance genes to fish and humans.},
}
@article {pmid33550118,
year = {2021},
author = {Paim, WP and Maggioli, MF and Weber, MN and Rezabek, G and Narayanan, S and Ramachandran, A and Canal, CW and Bauermann, FV},
title = {Virome characterization in serum of healthy show pigs raised in Oklahoma demonstrated great diversity of ssDNA viruses.},
journal = {Virology},
volume = {556},
number = {},
pages = {87-95},
doi = {10.1016/j.virol.2021.01.006},
pmid = {33550118},
issn = {1096-0341},
mesh = {Animals ; Animals, Domestic/*virology ; Oklahoma ; Swine/*virology ; *Virome ; },
abstract = {In the United States, show pigs are raised to compete in agricultural events. These animals are usually raised in small herds with extensive human, domestic, and wild animal contact. Therefore, pathogen monitoring in this animal category is critical for improved disease surveillance and preparedness. This study characterized the virome of healthy show pigs using high-throughput sequencing using pooled serum samples from 2018 or 2019 (200 samples each pool). Results demonstrated the presence of DNA viral families (Parvoviridae, Circoviridae, and Herpesviridae) and RNA families (Arteriviridae, Flaviviridae, and Retroviridae). Twenty-three viral species were identified, including the first detection of porcine bufavirus in the US. Moreover, important swine pathogens identified included porcine reproductive and respiratory syndrome virus, atypical porcine pestivirus, and porcine circovirus (PCV). Additionally, complete coding genomes of 17 viruses from the Parvoviridae, Anelloviridae, and Circoviridae families were retrieved and included the first near full-length genomes of US Ungulate bocaparvovirus 3 species.},
}
@article {pmid34613762,
year = {2021},
author = {Wagner, E and Fagerlund, A and Langsrud, S and Møretrø, T and Jensen, MR and Moen, B},
title = {Surveillance of Listeria monocytogenes: Early Detection, Population Dynamics, and Quasimetagenomic Sequencing during Selective Enrichment.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {24},
pages = {e0177421},
pmid = {34613762},
issn = {1098-5336},
support = {294910//Norges Forskningsråd (Forskningsrådet)/ ; 314743//Foundation for Research Levy on Agricultural Products (FFL)/ ; },
mesh = {*Food Microbiology ; Genes, Bacterial ; *Listeria monocytogenes/genetics/isolation &amp; purification ; Metagenomics ; *Microbiota ; Population Dynamics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In this study, we addressed different aspects regarding the implementation of quasimetagenomic sequencing as a hybrid surveillance method in combination with enrichment for early detection of Listeria monocytogenes in the food industry. Different experimental enrichment cultures were used, comprising seven L. monocytogenes strains of different sequence types (STs), with and without a background microbiota community. To assess whether the proportions of the different STs changed over time during enrichment, the growth and population dynamics were assessed using dapE colony sequencing and dapE and 16S rRNA amplicon sequencing. There was a tendency of some STs to have a higher relative abundance during the late stage of enrichment when L. monocytogenes was enriched without background microbiota. When coenriched with background microbiota, the population dynamics of the different STs was more consistent over time. To evaluate the earliest possible time point during enrichment that allows the detection of L. monocytogenes and at the same time the generation of genetic information that enables an estimation regarding the strain diversity in a sample, quasimetagenomic sequencing was performed early during enrichment in the presence of the background microbiota using Oxford Nanopore Technologies Flongle and Illumina MiSeq sequencing. The application of multiple displacement amplification (MDA) enabled detection of L. monocytogenes (and the background microbiota) after only 4 h of enrichment using both applied sequencing approaches. The MiSeq sequencing data additionally enabled the prediction of cooccurring L. monocytogenes strains in the samples. IMPORTANCE We showed that a combination of a short primary enrichment combined with MDA and Nanopore sequencing can accelerate the traditional process of cultivation and identification of L. monocytogenes. The use of Illumina MiSeq sequencing additionally allowed us to predict the presence of cooccurring L. monocytogenes strains. Our results suggest quasimetagenomic sequencing is a valuable and promising hybrid surveillance tool for the food industry that enables faster identification of L. monocytogenes during early enrichment. Routine application of this approach could lead to more efficient and proactive actions in the food industry that prevent contamination and subsequent product recalls and food destruction, economic and reputational losses, and human listeriosis cases.},
}
@article {pmid34613754,
year = {2021},
author = {Mickol, RL and Eddie, BJ and Malanoski, AP and Yates, MD and Tender, LM and Glaven, SM},
title = {Metagenomic and Metatranscriptomic Characterization of a Microbial Community That Catalyzes Both Energy-Generating and Energy-Storing Electrode Reactions.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {24},
pages = {e0167621},
pmid = {34613754},
issn = {1098-5336},
support = {//DOD | USN | U.S. Naval Research Laboratory (NRL)/ ; },
mesh = {*Deltaproteobacteria/genetics/metabolism ; *Electrodes ; *Metagenomics ; *Microbiota ; *Transcriptome ; },
abstract = {Electroactive bacteria are living catalysts, mediating energy-generating reactions at anodes or energy storage reactions at cathodes via extracellular electron transfer (EET). The Cathode-ANode (CANode) biofilm community was recently shown to facilitate both reactions; however, the identities of the primary constituents and underlying molecular mechanisms remain unknown. Here, we used metagenomics and metatranscriptomics to characterize the CANode biofilm. We show that a previously uncharacterized member of the family Desulfobulbaceae, Desulfobulbaceae-2, which had <1% relative abundance, had the highest relative gene expression and accounted for over 60% of all differentially expressed genes. At the anode potential, differential expression of genes for a conserved flavin oxidoreductase (Flx) and heterodisulfide reductase (Hdr) known to be involved in ethanol oxidation suggests a source of electrons for the energy-generating reaction. Genes for sulfate and carbon dioxide reduction pathways were expressed by Desulfobulbaceae-2 at both potentials and are the proposed energy storage reactions. Reduction reactions may be mediated by direct electron uptake from the electrode or from hydrogen generated at the cathode potential. The Desulfobulbaceae-2 genome is predicted to encode at least 85 multiheme (≥3 hemes) c-type cytochromes, some with as many as 26 heme-binding domains, that could facilitate reversible electron transfer with the electrode. Gene expression in other CANode biofilm species was also affected by the electrode potential, although to a lesser extent, and we cannot rule out their contribution to observed current. Results provide evidence of gene expression linked to energy storage and energy-generating reactions and will enable development of the CANode biofilm as a microbially driven rechargeable battery. IMPORTANCE Microbial electrochemical technologies (METs) rely on electroactive bacteria to catalyze energy-generating and energy storage reactions at electrodes. Known electroactive bacteria are not equally capable of both reactions, and METs are typically configured to be unidirectional. Here, we report on genomic and transcriptomic characterization of a recently described microbial electrode community called the Cathode-ANode (CANode). The CANode community is able to generate or store electrical current based on the electrode potential. During periods where energy is not needed, electrons generated from a renewable source, such as solar power, could be converted into energy storage compounds to later be reversibly oxidized by the same microbial catalyst. Thus, the CANode system can be thought of as a living "rechargeable battery." Results show that a single organism may be responsible for both reactions demonstrating a new paradigm for electroactive bacteria.},
}
@article {pmid34946200,
year = {2021},
author = {Bordugo, A and Salvetti, E and Rodella, G and Piazza, M and Dianin, A and Amoruso, A and Piacentini, G and Pane, M and Torriani, S and Vitulo, N and Felis, GE},
title = {Assessing Gut Microbiota in an Infant with Congenital Propionic Acidemia before and after Probiotic Supplementation.},
journal = {Microorganisms},
volume = {9},
number = {12},
pages = {},
doi = {10.3390/microorganisms9122599},
pmid = {34946200},
issn = {2076-2607},
abstract = {Propionic Acidemia (PA) is a rare inherited metabolic disorder caused by the enzymatic block of propionyl-CoA carboxylase with the consequent accumulation of propionic acid, which is toxic for the brain and cardiac cells. Since a considerable amount of propionate is produced by intestinal bacteria, interest arose in the attempt to reduce propionate-producing bacteria through a monthly antibiotic treatment of metronidazole. In the present study, we investigated the gut microbiota structure of an infant diagnosed at 4 days of life through Expanded Newborn Screening (NBS) and treated the child following international guidelines with a special low-protein diet, specific medications and strict biochemical monitoring. Microbiota composition was assessed during the first month of life, and the presence of Bacteroides fragilis, known to be associated with propionate production, was effectively decreased by metronidazole treatment. After five antibiotic therapy cycles, at 4 months of age, the infant was supplemented with a daily mixture of three bifidobacterial strains, known not to be propionate producers. The supplementation increased the population of bifidobacteria, with Bifidobacterium breve as the dominating species; Ruminococcus gnavus, an acetate and formate producer, was also identified. Metabarcoding analysis, compared with low coverage whole metagenome sequencing, proved to capture all the microbial biodiversity and could be the elected tool for fast and cost-effective monitoring protocols to be implemented in the follow up of rare metabolic disorders such as PA. Data obtained could be a possible starting point to set up tailored microbiota modification treatment studies in the attempt to improve the quality of life of people affected by propionic acidemia.},
}
@article {pmid34795375,
year = {2021},
author = {Van Goethem, MW and Osborn, AR and Bowen, BP and Andeer, PF and Swenson, TL and Clum, A and Riley, R and He, G and Koriabine, M and Sandor, L and Yan, M and Daum, CG and Yoshinaga, Y and Makhalanyane, TP and Garcia-Pichel, F and Visel, A and Pennacchio, LA and O'Malley, RC and Northen, TR},
title = {Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {1302},
pmid = {34795375},
issn = {2399-3642},
support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; },
mesh = {Bacteria/genetics/*metabolism ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Multigene Family ; *Secondary Metabolism ; *Soil Microbiology ; Utah ; },
abstract = {Microbial biosynthetic gene clusters (BGCs) encoding secondary metabolites are thought to impact a plethora of biologically mediated environmental processes, yet their discovery and functional characterization in natural microbiomes remains challenging. Here we describe deep long-read sequencing and assembly of metagenomes from biological soil crusts, a group of soil communities that are rich in BGCs. Taking advantage of the unusually long assemblies produced by this approach, we recovered nearly 3,000 BGCs for analysis, including 712 full-length BGCs. Functional exploration through metatranscriptome analysis of a 3-day wetting experiment uncovered phylum-specific BGC expression upon activation from dormancy, elucidating distinct roles and complex phylogenetic and temporal dynamics in wetting processes. For example, a pronounced increase in BGC transcription occurs at night primarily in cyanobacteria, implicating BGCs in nutrient scavenging roles and niche competition. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional dynamics of BGCs in environmental processes and suggests a central role of secondary metabolites in maintaining phylogenetically conserved niches within biocrusts.},
}
@article {pmid34795236,
year = {2021},
author = {Darnaud, M and De Vadder, F and Bogeat, P and Boucinha, L and Bulteau, AL and Bunescu, A and Couturier, C and Delgado, A and Dugua, H and Elie, C and Mathieu, A and Novotná, T and Ouattara, DA and Planel, S and Saliou, A and Šrůtková, D and Yansouni, J and Stecher, B and Schwarzer, M and Leulier, F and Tamellini, A},
title = {A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {6686},
pmid = {34795236},
issn = {2041-1723},
support = {U2C DK119886/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/genetics ; Body Weight/genetics/physiology ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; *Germ-Free Life ; Male ; Metagenomics/methods ; Mice, Inbred C57BL ; Phenotype ; Species Specificity ; *Specific Pathogen-Free Organisms ; Whole Genome Sequencing/*methods ; },
abstract = {Mus musculus is the classic mammalian model for biomedical research. Despite global efforts to standardize breeding and experimental procedures, the undefined composition and interindividual diversity of the microbiota of laboratory mice remains a limitation. In an attempt to standardize the gut microbiome in preclinical mouse studies, here we report the development of a simplified mouse microbiota composed of 15 strains from 7 of the 20 most prevalent bacterial families representative of the fecal microbiota of C57BL/6J Specific (and Opportunistic) Pathogen-Free (SPF/SOPF) animals and the derivation of a standardized gnotobiotic mouse model called GM15. GM15 recapitulates extensively the functionalities found in the C57BL/6J SOPF microbiota metagenome, and GM15 animals are phenotypically similar to SOPF or SPF animals in two different facilities. They are also less sensitive to the deleterious effects of post-weaning malnutrition. In this work, we show that the GM15 model provides increased reproducibility and robustness of preclinical studies by limiting the confounding effect of fluctuation in microbiota composition, and offers opportunities for research focused on how the microbiota shapes host physiology in health and disease.},
}
@article {pmid34737748,
year = {2021},
author = {Pallikkuth, S and Mendez, R and Russell, K and Sirupangi, T and Kvistad, D and Pahwa, R and Villinger, F and Banerjee, S and Pahwa, S},
title = {Age Associated Microbiome and Microbial Metabolites Modulation and Its Association With Systemic Inflammation in a Rhesus Macaque Model.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {748397},
pmid = {34737748},
issn = {1664-3224},
support = {R01 AI123048/AI/NIAID NIH HHS/United States ; R01 AG068110/AG/NIA NIH HHS/United States ; P30 AI073961/AI/NIAID NIH HHS/United States ; },
mesh = {Aging/*immunology ; Animals ; Bacteria/metabolism ; C-Reactive Protein/analysis ; Cytokines/blood ; Disease Models, Animal ; Dysbiosis/immunology/metabolism/*microbiology ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome/physiology ; Inflammation/immunology/metabolism/*microbiology ; Macaca mulatta ; Male ; Symbiosis ; Tandem Mass Spectrometry ; Tumor Necrosis Factor-alpha/blood ; },
abstract = {Aging is associated with declining immunity and inflammation as well as alterations in the gut microbiome with a decrease of beneficial microbes and increase in pathogenic ones. The aim of this study was to investigate the age associated gut microbiome in relation to immunologic and metabolic profile in a non-human primate (NHP) model. 12 geriatric (age 19-24 years) and 4 young adult (age 3-4 years) Rhesus macaques were included in this study. Immune cell subsets were characterized in peripheral blood mononuclear cells (PBMC) by flow cytometry and plasma cytokines levels were determined by bead based multiplex cytokine analysis. Stool samples were collected by ileal loop and investigated for microbiome analysis by shotgun metagenomics. Serum, gut microbial lysate, and microbe-free fecal extract were subjected to metabolomic analysis by mass-spectrometry. Our results showed that the gut microbiome in geriatric animals had higher abundance of Archaeal and Proteobacterial species and lower Firmicutes than the young adults. Highly abundant microbes in the geriatric animals showed a direct association with plasma biomarkers of inflammation and immune activation such as neopterin, CRP, TNF, IL-2, IL-6, IL-8 and IFN-γ. Significant enrichment of metabolites that contribute to inflammatory and cytotoxic pathways was observed in serum and feces of geriatric animals compared to the young adults. We conclude that aging NHP undergo immunosenescence and age associated alterations in the gut microbiome that has a distinct metabolic profile. Aging NHP can serve as a model for investigating the relationship of the gut microbiome to particular age-associated comorbidities and for strategies aimed at modulating the microbiome.},
}
@article {pmid34661515,
year = {2021},
author = {Barraza, A and Montes-Sánchez, JJ and Caamal-Chan, MG and Loera-Muro, A},
title = {Characterization of microbial communities from rumen and large intestine of lactating creole goats grazing in arid plant communities.},
journal = {Microbiology (Reading, England)},
volume = {167},
number = {10},
pages = {},
doi = {10.1099/mic.0.001092},
pmid = {34661515},
issn = {1465-2080},
mesh = {Animals ; Archaea/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Ribosomal/genetics ; Desert Climate ; Diet/veterinary ; Feces/chemistry/microbiology ; Female ; Fungi/classification/genetics/isolation &amp; purification ; Gastrointestinal Contents/chemistry ; *Gastrointestinal Microbiome ; Goats/*microbiology ; Intestine, Large/chemistry/*microbiology ; Lactation ; Rumen/chemistry/*microbiology ; Seasons ; },
abstract = {Arid plant communities provide variable diets that can affect digestive microbial communities of free-foraging ruminants. Thus, we used next-generation sequencing of 16S and 18S rDNA to characterize microbial communities in the rumen (regurgitated digesta) and large intestine (faeces) and diet composition of lactating creole goats from five flocks grazing in native plant communities in the Sonoran Desert in the rainy season. The bacterial communities in the rumen and large intestine of the five flocks had similar alpha diversity (Chao1, Shannon, and Simpson indices). However, bacterial community compositions were different: a bacterial community dominated by Proteobacteria in the rumen transitioned to a community dominated by Firmicutes in the large intestine. Bacterial communities of rumen were similar across flocks; similarly occurred with large-intestine communities. Archaea had a minimum presence in the goat digestive tract. We detected phylum Basidiomycota, Ascomycota, and Apicomplexa as the main fungi and protozoa. Analyses suggested different diet compositions; forbs and grasses composed the bulk of plants in the rumen and forbs and shrubs in faeces. Therefore, lactating goats consuming different diets in the Sonoran Desert in the rainy season share a similar core bacterial community in the rumen and another in the large intestine and present low archaeal communities.},
}
@article {pmid34630388,
year = {2021},
author = {Kong, L and Wang, Z and Xiao, C and Zhu, Q and Song, Z},
title = {Glycerol Monolaurate Ameliorated Intestinal Barrier and Immunity in Broilers by Regulating Intestinal Inflammation, Antioxidant Balance, and Intestinal Microbiota.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {713485},
pmid = {34630388},
issn = {1664-3224},
mesh = {Animals ; Antioxidants/*metabolism ; Chickens ; Cytokines/biosynthesis ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Regulation/drug effects ; Immunity, Mucosal/*drug effects ; Immunoglobulin G/blood/immunology ; Intestinal Mucosa/*immunology/*metabolism/pathology ; Laurates/*pharmacology ; Metagenome ; Metagenomics/methods ; Monoglycerides/*pharmacology ; Mucins/genetics/metabolism ; },
abstract = {This study was conducted to investigate the impact of glycerol monolaurate (GML) on performance, immunity, intestinal barrier, and cecal microbiota in broiler chicks. A total of 360 one-day-old broilers (Arbor Acres) with an average weight of 45.7 g were randomly allocated to five dietary groups as follows: basal diet and basal diets complemented with 300, 600, 900, or 1200 mg/kg GML. Samples were collected at 7 and 14 days of age. Results revealed that feed intake increased (P < 0.05) after 900 and 1200 mg/kg GML were administered during the entire 14-day experiment period. Dietary GML decreased (P < 0.05) crypt depth and increased the villus height-to-crypt depth ratio of the jejunum. In the serum and jejunum, supplementation with more than 600 mg/kg GML reduced (P < 0.05) interleukin-1β, tumor necrosis factor-α, and malondialdehyde levels and increased (P < 0.05) the levels of immunoglobulin G, jejunal mucin 2, total antioxidant capacity, and total superoxide dismutase. GML down-regulate (P < 0.05) jejunal interleukin-1β and interferon-γ expression and increased (P < 0.05) the mRNA level of zonula occludens 1 and occludin. A reduced (P < 0.05) expression of toll-like receptor 4 and nuclear factor kappa-B was shown in GML-treated groups. In addition, GML modulated the composition of the cecal microbiota of the broilers, improved (P < 0.05) microbial diversity, and increased (P < 0.05) the abundance of butyrate-producing bacteria. Spearman's correlation analysis revealed that the genera Barnesiella, Coprobacter, Lachnospiraceae, Faecalibacterium, Bacteroides, Odoriacter, and Parabacteroides were related to inflammation and intestinal integrity. In conclusion, GML ameliorated intestinal morphology and barrier function in broiler chicks probably by regulating intestinal immune and antioxidant balance, as well as intestinal microbiota.},
}
@article {pmid34611253,
year = {2021},
author = {Kačírová, J and Maďari, A and Mucha, R and Fecskeová, LK and Mujakic, I and Koblížek, M and Nemcová, R and Maďar, M},
title = {Study of microbiocenosis of canine dental biofilms.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {19776},
pmid = {34611253},
issn = {2045-2322},
mesh = {Animals ; Bacteria/classification/genetics ; *Biofilms ; Dogs ; Metagenome ; Metagenomics/methods ; *Microbiota ; Periodontium/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tooth/*microbiology ; },
abstract = {Dental biofilm is a complex microbial community influenced by many exogenous and endogenous factors. Despite long-term studies, its bacterial composition is still not clearly understood. While most of the research on dental biofilms was conducted in humans, much less information is available from companion animals. In this study, we analyzed the composition of canine dental biofilms using both standard cultivation on solid media and amplicon sequencing, and compared the two approaches. The 16S rRNA gene sequences were used to define the bacterial community of canine dental biofilm with both, culture-dependent and culture-independent methods. After DNA extraction from each sample, the V3-V4 region of the 16S rRNA gene was amplified and sequenced via Illumina MiSeq platform. Isolated bacteria were identified using universal primers and Sanger sequencing. Representatives of 18 bacterial genera belonging to 5 phyla were isolated from solid media. Amplicon sequencing largely expanded this information identifying in total 284 operational taxonomic units belonging to 10 bacterial phyla. Amplicon sequencing revealed much higher diversity of bacteria in the canine dental biofilms, when compared to standard cultivation approach. In contrast, cultured representatives of several bacterial families were not identified by amplicon sequencing.},
}
@article {pmid34611238,
year = {2021},
author = {Rahman, MS and Hoque, MN and Puspo, JA and Islam, MR and Das, N and Siddique, MA and Hossain, MA and Sultana, M},
title = {Microbiome signature and diversity regulates the level of energy production under anaerobic condition.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {19777},
pmid = {34611238},
issn = {2045-2322},
mesh = {*Anaerobiosis ; *Biodiversity ; Chemical Phenomena ; Computational Biology/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; *Renewable Energy ; },
abstract = {The microbiome of the anaerobic digester (AD) regulates the level of energy production. To assess the microbiome diversity and composition in different stages of anaerobic digestion, we collected 16 samples from the AD of cow dung (CD) origin. The samples were categorized into four groups (Group-I, Group-II, Group-III and Group-IV) based on the level of energy production (CH4%), and sequenced through whole metagenome sequencing (WMS). Group-I (n = 2) belonged to initial time of energy production whereas Group-II (n = 5), Group-III (n = 5), and Group-IV (n = 4) had 21-34%, 47-58% and 71-74% of CH4, respectively. The physicochemical analysis revealed that level of energy production (CH4%) had significant positive correlation with digester pH (r = 0.92, p < 0.001), O2 level (%) (r = 0.54, p < 0.05), and environmental temperature (°C) (r = 0.57, p < 0.05). The WMS data mapped to 2800 distinct bacterial, archaeal and viral genomes through PathoScope (PS) and MG-RAST (MR) analyses. We detected 768, 1421, 1819 and 1774 bacterial strains in Group-I, Group-II, Group-III and Group-IV, respectively through PS analysis which were represented by Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes and Fibrobacteres phyla (> 93.0% of the total abundances). Simultaneously, 343 archaeal strains were detected, of which 95.90% strains shared across four metagenomes. We identified 43 dominant species including 31 bacterial and 12 archaeal species in AD microbiomes, of which only archaea showed positive correlation with digester pH, CH4 concentration, pressure and temperature (Spearman correlation; r > 0.6, p < 0.01). The indicator species analysis showed that the species Methanosarcina vacuolate, Dehalococcoides mccartyi, Methanosarcina sp. Kolksee and Methanosarcina barkeri were highly specific for energy production. The correlation network analysis showed that different strains of Euryarcheota and Firmicutes phyla exhibited significant correlation (p = 0.021, Kruskal-Wallis test; with a cutoff of 1.0) with the highest level (74.1%) of energy production (Group-IV). In addition, top CH4 producing microbiomes showed increased genomic functional activities related to one carbon and biotin metabolism, oxidative stress, proteolytic pathways, membrane-type-1-matrix-metalloproteinase (MT1-MMP) pericellular network, acetyl-CoA production, motility and chemotaxis. Importantly, the physicochemical properties of the AD including pH, CH4 concentration (%), pressure, temperature and environmental temperature were found to be positively correlated with these genomic functional potentials and distribution of ARGs and metal resistance pathways (Spearman correlation; r > 0.5, p < 0.01). This study reveals distinct changes in composition and diversity of the AD microbiomes including different indicator species, and their genomic features that are highly specific for energy production.},
}
@article {pmid34608200,
year = {2021},
author = {Ito, T and Totoki, T and Takada, S and Otsuka, S and Maruyama, I},
title = {Potential roles of 1,5-anhydro-D-fructose in modulating gut microbiome in mice.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {19648},
pmid = {34608200},
issn = {2045-2322},
mesh = {Animals ; Diet ; Dietary Supplements ; Fructose/*analogs &amp; derivatives/metabolism/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metagenome ; Metagenomics/methods ; Mice ; NAD/biosynthesis ; Nutrients/biosynthesis ; Vitamins/biosynthesis ; },
abstract = {The gut microbiota has tremendous potential to affect the host's health, in part by synthesizing vitamins and generating nutrients from food that is otherwise indigestible by the host. 1,5-Anhydro-D-fructose (1,5-AF) is a monosaccharide with a wide range of bioactive potentials, including anti-oxidant, anti-inflammatory, and anti-microbial effects. Based on its potential benefits and minimal toxicity, it is anticipated that 1,5-AF will be used as a dietary supplement to support general health. However, the effects of 1,5-AF on the gut microbiota are yet to be clarified. Here, using an unbiased metagenomic approach, we profiled the bacterial taxa and functional genes in the caecal microbiota of mice fed a diet containing either 2% 1,5-AF or a reference sweetener. Supplementation with 1,5-AF altered the composition of the gut microbiota, enriching the proportion of Faecalibacterium prausnitzii. 1,5-AF also altered the metabolomic profile of the gut microbiota, enriching genes associated with nicotinamide adenine dinucleotide biosynthesis. These findings support the potential benefits of 1,5-AF, but further studies are required to clarify the impact of 1,5-AF on health and disease.},
}
@article {pmid34599245,
year = {2021},
author = {Ikegami, H and Noguchi, S and Fukuda, K and Akata, K and Yamasaki, K and Kawanami, T and Mukae, H and Yatera, K},
title = {Refinement of microbiota analysis of specimens from patients with respiratory infections using next-generation sequencing.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {19534},
pmid = {34599245},
issn = {2045-2322},
mesh = {Aged ; Aged, 80 and over ; Disease Susceptibility ; Female ; Gene Library ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Respiratory Mucosa/*microbiology ; Respiratory Tract Infections/diagnosis/*etiology ; Retrospective Studies ; },
abstract = {Next-generation sequencing (NGS) technologies have been applied in bacterial flora analysis. However, there is no standardized protocol, and the optimal clustering threshold for estimating bacterial species in respiratory infection specimens is unknown. This study was conducted to investigate the optimal threshold for clustering 16S ribosomal RNA gene sequences into operational taxonomic units (OTUs) by comparing the results of NGS technology with those of the Sanger method, which has a higher accuracy of sequence per single read than NGS technology. This study included 45 patients with pneumonia with aspiration risks and 35 patients with lung abscess. Compared to Sanger method, the concordance rates of NGS technology (clustered at 100%, 99%, and 97% homology) with the predominant phylotype were 78.8%, 71.3%, and 65.0%, respectively. With respect to the specimens dominated by the Streptococcus mitis group, containing several important causative agents of pneumonia, Bray Curtis dissimilarity revealed that the OTUs obtained at 100% clustering threshold (versus those obtained at 99% and 97% thresholds; medians of 0.35, 0.69, and 0.71, respectively) were more similar to those obtained by the Sanger method, with statistical significance (p < 0.05). Clustering with 100% sequence identity is necessary when analyzing the microbiota of respiratory infections using NGS technology.},
}
@article {pmid34586901,
year = {2021},
author = {Fernandes-Martins, MC and Keller, LM and Munro-Ehrlich, M and Zimlich, KR and Mettler, MK and England, AM and Clare, R and Surya, K and Shock, EL and Colman, DR and Boyd, ES},
title = {Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {23},
pages = {e0159821},
pmid = {34586901},
issn = {1098-5336},
support = {CSP 504081//Department of Energy/ ; EAR-1820658//National Science Foundation (NSF)/ ; },
mesh = {*Atmosphere ; Carbon ; *Hot Springs/microbiology ; Metagenomics ; *Microbiota ; Oxygen ; Wyoming ; },
abstract = {Little is known of how the confluence of subsurface and surface processes influences the assembly and habitability of hydrothermal ecosystems. To address this knowledge gap, the geochemical and microbial composition of a high-temperature, circumneutral hot spring in Yellowstone National Park was examined to identify the sources of solutes and their effect on the ecology of microbial inhabitants. Metagenomic analysis showed that populations comprising planktonic and sediment communities are archaeal dominated, are dependent on chemical energy (chemosynthetic), share little overlap in their taxonomic composition, and are differentiated by their inferred use of/tolerance to oxygen and mode of carbon metabolism. The planktonic community is dominated by putative aerobic/aerotolerant autotrophs, while the taxonomic composition of the sediment community is more evenly distributed and comprised of anaerobic heterotrophs. These observations are interpreted to reflect sourcing of the spring by anoxic, organic carbon-limited subsurface hydrothermal fluids and ingassing of atmospheric oxygen that selects for aerobic/aerotolerant organisms that have autotrophic capabilities in the water column. Autotrophy and consumption of oxygen by the planktonic community may influence the assembly of the anaerobic and heterotrophic sediment community. Support for this inference comes from higher estimated rates of genome replication in planktonic populations than sediment populations, indicating faster growth in planktonic populations. Collectively, these observations provide new insight into how mixing of subsurface waters and atmospheric oxygen create dichotomy in the ecology of hot spring communities and suggest that planktonic and sediment communities may have been less differentiated taxonomically and functionally prior to the rise of oxygen at ∼2.4 billion years ago (Gya). IMPORTANCE Understanding the source and availability of energy capable of supporting life in hydrothermal environments is central to predicting the ecology of microbial life on early Earth when volcanic activity was more widespread. Little is known of the substrates supporting microbial life in circumneutral to alkaline springs, despite their relevance to early Earth habitats. Using metagenomic and informatics approaches, water column and sediment habitats in a representative circumneutral hot spring in Yellowstone were shown to be dichotomous, with the former largely hosting aerobic/aerotolerant autotrophs and the latter primarily hosting anaerobic heterotrophs. This dichotomy is attributed to influx of atmospheric oxygen into anoxic deep hydrothermal spring waters. These results indicate that the ecology of microorganisms in circumneutral alkaline springs sourced by deep hydrothermal fluids was different prior to the rise of atmospheric oxygen ∼2.4 Gya, with planktonic and sediment communities likely to be less differentiated than contemporary circumneutral hot springs.},
}
@article {pmid33542492,
year = {2021},
author = {Jones-Freeman, B and Chonwerawong, M and Marcelino, VR and Deshpande, AV and Forster, SC and Starkey, MR},
title = {The microbiome and host mucosal interactions in urinary tract diseases.},
journal = {Mucosal immunology},
volume = {14},
number = {4},
pages = {779-792},
pmid = {33542492},
issn = {1935-3456},
mesh = {Animals ; Disease Management ; Disease Susceptibility ; Feedback, Physiological ; Gastrointestinal Microbiome ; Homeostasis ; *Host Microbial Interactions ; *Host-Pathogen Interactions ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mucous Membrane/*microbiology ; Organ Specificity ; Urinary Tract Infections/diagnosis/*etiology/therapy ; },
abstract = {The urinary tract consists of the bladder, ureters, and kidneys, and is an essential organ system for filtration and excretion of waste products and maintaining systemic homeostasis. In this capacity, the urinary tract is impacted by its interactions with other mucosal sites, including the genitourinary and gastrointestinal systems. Each of these sites harbors diverse ecosystems of microbes termed the microbiota, that regulates complex interactions with the local and systemic immune system. It remains unclear whether changes in the microbiota and associated metabolites may be a consequence or a driver of urinary tract diseases. Here, we review the current literature, investigating the impact of the microbiota on the urinary tract in homeostasis and disease including urinary stones, acute kidney injury, chronic kidney disease, and urinary tract infection. We propose new avenues for exploration of the urinary microbiome using emerging technology and discuss the potential of microbiome-based medicine for urinary tract conditions.},
}
@article {pmid32857289,
year = {2021},
author = {Wang, Y and Liu, F and Zhang, G and Su, Y and Sun, X and Chen, Q and Wang, C and Fu, H and He, Y and Zhu, X and Liu, X and Lv, M and Zhao, X and Zhao, X and Li, Y and Wang, Q and Huang, X and Zhang, X},
title = {Gut microbiome alterations and its link to corticosteroid resistance in immune thrombocytopenia.},
journal = {Science China. Life sciences},
volume = {64},
number = {5},
pages = {766-783},
pmid = {32857289},
issn = {1869-1889},
mesh = {Adrenal Cortex Hormones/*administration &amp; dosage ; Drug Resistance/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenomics ; Protein Interaction Maps ; Purpura, Thrombocytopenic, Idiopathic/*drug therapy/*microbiology ; },
abstract = {Quantitative metagenomic studies have linked the gut microbiota to autoimmune disorders. Here, we performed deep shotgun metagenomic sequencing of fecal samples from 99 immune thrombocytopenia (ITP) patients and 52 healthy controls. Dysbiosis in the gut microbiome of ITP was detected phylogenetically and functionally, and classifier based on species markers distinguished individuals with ITP from healthy controls. In particular, the abundance of Ruminococcus gnavus, Bifidobacterium longum and Akkermansia muciniphila was markedly increased in treatment-naïve ITP patients, and the alterations of microbial species were correlated with clinical indices. Functionally, the secondary bile acid biosynthesis and flagellar assembly were depleted in the gut microbiota of ITP, which may contribute to the onset of ITP by affecting the immune system. Furthermore, we found that corticosteroid treatment affected the gut microbiome of ITP. Compared with corticosteroid-sensitive ITP patients, we identified that the corticosteroid-resistant ITP patients displayed a distinct gut microbiome, which was different from that of the treatment-naïve ITP patients. Together, we provided support for the critical role of gut microbiota in the development of ITP and established a foundation for further research characterizing gut microbiota in relation to corticosteroid resistance of ITP.},
}
@article {pmid32394199,
year = {2021},
author = {Liu, YX and Qin, Y and Chen, T and Lu, M and Qian, X and Guo, X and Bai, Y},
title = {A practical guide to amplicon and metagenomic analysis of microbiome data.},
journal = {Protein &amp; cell},
volume = {12},
number = {5},
pages = {315-330},
pmid = {32394199},
issn = {1674-8018},
mesh = {*Algorithms ; Computational Biology ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics ; Microbiota/*genetics ; *Software ; },
abstract = {Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and beta-diversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a step-by-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.},
}
@article {pmid34819495,
year = {2021},
author = {Hafner, L and Pichon, M and Burucoa, C and Nusser, SHA and Moura, A and Garcia-Garcera, M and Lecuit, M},
title = {Listeria monocytogenes faecal carriage is common and depends on the gut microbiota.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {6826},
pmid = {34819495},
issn = {2041-1723},
mesh = {Animals ; Carrier State/diagnosis/*epidemiology/microbiology ; DNA, Bacterial/isolation &amp; purification ; Datasets as Topic ; Disease Models, Animal ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Listeria monocytogenes/genetics/*isolation &amp; purification/pathogenicity ; Male ; Metagenomics/statistics &amp; numerical data ; Mice ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Virulence ; },
abstract = {Listeria genus comprises two pathogenic species, L. monocytogenes (Lm) and L. ivanovii, and non-pathogenic species. All can thrive as saprophytes, whereas only pathogenic species cause systemic infections. Identifying Listeria species' respective biotopes is critical to understand the ecological contribution of Listeria virulence. In order to investigate the prevalence and abundance of Listeria species in various sources, we retrieved and analyzed 16S rRNA datasets from MG-RAST metagenomic database. 26% of datasets contain Listeria sensu stricto sequences, and Lm is the most prevalent species, most abundant in soil and host-associated environments, including 5% of human stools. Lm is also detected in 10% of human stool samples from an independent cohort of 900 healthy asymptomatic donors. A specific microbiota signature is associated with Lm faecal carriage, both in humans and experimentally inoculated mice, in which it precedes Lm faecal carriage. These results indicate that Lm faecal carriage is common and depends on the gut microbiota, and suggest that Lm faecal carriage is a crucial yet overlooked consequence of its virulence.},
}
@article {pmid34619218,
year = {2022},
author = {Prado, T and Shubo, T and Freitas, L and Leomil, L and Maranhão, AG and Miagostovich, MP},
title = {Virome in roof-harvested rainwater of a densely urbanized low-income region.},
journal = {The Science of the total environment},
volume = {807},
number = {Pt 2},
pages = {150778},
doi = {10.1016/j.scitotenv.2021.150778},
pmid = {34619218},
issn = {1879-1026},
mesh = {Brazil ; Cities ; Metagenomics ; *Poverty ; Rain/*virology ; *Virome ; },
abstract = {Rainwater harvesting has been considered an affordable practice to supplement the conventional sources of water supply for potable and non-potable uses worldwide. This study characterizes the viral community found in roof-harvested rainwater (RHRW) samples obtained under different rain volumes in a densely urbanized low-income region in Rio de Janeiro, Brazil. Three pilot-scale standardized metal-sheet roofs (same catchment area, material age, and slope - 3%) were installed in the study area aiming at obtaining more reliable and representative samples. Fifty-four samples were collected from six rainfall events from January to April 2019 and concentrated by the skimmed-milk flocculation method. Pools of different rainfall volumes were submitted to high throughput sequencing using the shotgun metagenomic approach. Sequencing was performed on NextSeq platform. Genomic analysis of the virus community revealed that most are RNA non-human viruses, including two main families: Dicistroviridae and Iflaviridae, recognized for infecting arthropods. Bacteriophages were also relatively abundant, with a predominance of DNA phages belonging to Microviridae and Siphoviridae families, showing percentages from 5.3 and 3.7% of the total viral hits present in these samples, respectively. Viral genomic RNA viruses (77%) predominated over DNA viruses (23%). Concerning number of viral species identified, a higher percentage was observed for plant viruses (12 families, 58%). Hepatitis A virus and human klassevirus 1 were detected among the established human pathogens, suggesting the need for RHRW treatment before it is considered for human consumption. Australian bat lyssavirus was also detected, emphasizing the importance of environmental monitoring facing emerging viruses. The results corroborate the influence of the surrounding area on the rainwater quality.},
}
@article {pmid34469196,
year = {2021},
author = {Yap, M and Gleeson, D and O'Toole, PW and O'Sullivan, O and Cotter, PD},
title = {Seasonality and Geography Have a Greater Influence than the Use of Chlorine-Based Cleaning Agents on the Microbiota of Bulk Tank Raw Milk.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {22},
pages = {e0108121},
pmid = {34469196},
issn = {1098-5336},
mesh = {Animals ; *Chlorine/pharmacology ; Dairying ; Disinfectants/pharmacology ; Equipment Contamination/prevention &amp; control ; *Geography ; Ireland ; *Microbiota ; Milk/*microbiology ; *Seasons ; },
abstract = {Cleaning of the production environment is vital to ensure the safety and quality of dairy products. Although cleaning with chlorine-based agents is widely adopted, it has been associated with detrimental effects on milk quality and safety, which has garnered increasing interest in chlorine-free cleaning. However, the influence of these methods on the milk microbiota is not well documented. This study investigated the factors that influence the raw milk microbiota, with a focus on the differences when chlorine-based and chlorine-free cleaning of milking equipment are used. Bulk tank raw milk was sampled during three sampling months (April, August, and November), from farms across Ireland selected to capture the use of different cleaning methods, i.e., exclusively chlorine-based (n = 51) and chlorine-free cleaning (n = 92) and farms that used chlorine-free agents for the bulk tank and chlorine-based cleaning agents for the rest of the equipment (n = 28). Shotgun metagenomic analysis revealed the significant influence of seasonal and geographic factors on the bulk tank milk microbiota, indicated by differences in diversity, taxonomic composition, and functional characteristics. Taxonomic and functional profiles of samples collected in November clustered separately from those of samples collected in other months. In contrast, cleaning methods only accounted for 1% of the variation in the bulk tank milk bacterial community, and samples collected from farms using chlorine-based versus chlorine-free cleaning did not differ significantly, suggesting that the chlorine-free approaches used did not negatively impact microbiological quality. This study shows the value of shotgun metagenomics in advancing our knowledge of the raw milk microbiota. IMPORTANCE The microbiota of raw milk is affected by many factors that can control or promote the introduction of undesirable microorganisms. Chlorine-based cleaning agents have been commonly used due to their effectiveness in controlling undesirable microorganisms, but they have been associated with the formation of chlorine residues that are detrimental to product quality and may impact consumer health. Chlorine-free alternatives have been recommended in some countries, but the influence of cleaning agents on the milk microbiota is unknown. Here, we investigated the influence of cleaning methods and other factors on bulk tank raw milk. Results showed that season and location had a greater influence on the milk microbiota than the cleaning agents used. Indeed, the similar microbiota compositions of raw milk from farms that used chlorine-based and those that used chlorine-free cleaning methods supports the further use of chlorine-free cleaning agents in dairy production.},
}
@article {pmid34372696,
year = {2021},
author = {Kachroo, N and Lange, D and Penniston, KL and Stern, J and Tasian, G and Bajic, P and Wolfe, AJ and Suryavanshi, M and Ticinesi, A and Meschi, T and Monga, M and Miller, AW},
title = {Meta-analysis of Clinical Microbiome Studies in Urolithiasis Reveal Age, Stone Composition, and Study Location as the Predominant Factors in Urolithiasis-Associated Microbiome Composition.},
journal = {mBio},
volume = {12},
number = {4},
pages = {e0200721},
pmid = {34372696},
issn = {2150-7511},
mesh = {Humans ; Male ; *Metagenome ; Microbiota/*genetics/physiology ; Urinary Calculi/*chemistry ; Urinary Tract/microbiology/pathology ; Urolithiasis/*microbiology ; },
abstract = {To determine whether functionally relevant questions associated with the urinary or gut microbiome and urinary stone disease (USD) can be answered from metagenome-wide association studies (MWAS), we performed the most comprehensive meta-analysis of published clinical MWAS in USD to date, using publicly available data published prior to April 2021. Six relevant studies met inclusion criteria. For alpha-diversity, significant differences were noted between USD status, stone composition, sample type, study location, age, diet, and sex. For beta-diversity, significant differences were noted by USD status, stone composition, sample type, study location, antibiotic use (30 days and 12 months before sampling), sex, hypertension, water intake, body habitus, and age. Prevotella and Lactobacillus in the gut and urinary tract, respectively, were associated with healthy individuals, while Enterobacteriaceae was associated with USD in the urine and stones. Paradoxically, other Prevotella strains were also strongly associated with USD in the gut microbiome. When data were analyzed together, USD status, stone composition, age group, and study location were the predominant factors associated with microbiome composition. Meta-analysis showed significant microbiome differences based on USD status, stone composition, age group or study location. However, analyses were limited by a lack of public data from published studies, metadata collected, and differing study protocols. Results highlight the need for field-specific standardization of experimental protocols in terms of sample collection procedures and the anatomical niches to assess, as well as in defining clinically relevant metadata and subphenotypes such as stone composition. IMPORTANCE Studies focused on the microbiome broadly support the hypothesis that the microbiome influences the onset of chronic diseases such as urinary stone disease. However, it is unclear what environmental factors shape the microbiome in ways that increase the risk for chronic disease. In addition, it is unclear how differences in study methodology can impact the results of clinical metagenome-wide association studies. In the current meta-analysis, we show that age, stone composition, and study location are the predominant factors that associate with the microbiome and USD status. Furthermore, we reveal differences in results based on specific analytical protocols, which impacts the interpretation of any microbiome study.},
}
@article {pmid34281401,
year = {2021},
author = {Chu, ND and Crothers, JW and Nguyen, LTT and Kearney, SM and Smith, MB and Kassam, Z and Collins, C and Xavier, R and Moses, PL and Alm, EJ},
title = {Dynamic Colonization of Microbes and Their Functions after Fecal Microbiota Transplantation for Inflammatory Bowel Disease.},
journal = {mBio},
volume = {12},
number = {4},
pages = {e0097521},
pmid = {34281401},
issn = {2150-7511},
mesh = {Bacteria/classification/genetics/*metabolism ; Butyrates/analysis/metabolism ; Cohort Studies ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/microbiology/*therapy ; Longitudinal Studies ; Metagenomics/methods ; },
abstract = {For fecal microbiota transplantation (FMT) to be successful in immune diseases like inflammatory bowel disease, it is assumed that therapeutic microbes and their beneficial functions and immune interactions must colonize a recipient patient and persist in sufficient quantity and for a sufficient period of time to produce a clinical benefit. Few studies, however, have comprehensively profiled the colonization and persistence of transferred microbes along with the transfer of their microbial functions and interactions with the host immune system. Using 16S, metagenomic, and immunoglobulin A (IgA) sequencing, we analyzed hundreds of longitudinal microbiome samples from a randomized controlled trial of 12 patients with ulcerative colitis who received fecal transplant or placebo for 12 weeks. We uncovered diverse competitive dynamics among donor and patient strains, showing that persistence of transferred microbes is far from static. Indeed, one patient experienced a dramatic loss of donor bacteria 10 weeks into the trial, coinciding with a bloom of pathogenic bacteria and worsening symptoms. We evaluated the transfer of microbial functions, including desired ones, such as butyrate production, and unintended ones, such as antibiotic resistance. By profiling bacteria coated with IgA, we identified bacteria associated with inflammation and found that microbial interactions with the host immune system can be transferred across people, which could play a role in gut microbiome therapeutics for immune-related diseases. Our findings shed light on the colonization dynamics of gut microbes and their functions in the context of FMT to treat a complex disease-information that may provide a foundation for developing more-targeted therapeutics. IMPORTANCE Fecal microbiota transplantation (FMT)-transferring fecal microbes from a healthy donor to a sick patient-has shown promise for gut diseases such as inflammatory bowel disease. Unlike pharmaceuticals, however, fecal transplants are complex mixtures of living organisms, which must then interact with the microbes and immune system of the recipient. We sought to understand these interactions by tracking the microbes of 12 inflammatory bowel disease patients who received fecal transplants for 12 weeks. We uncovered a range of dynamics. For example, one patient experienced successful transfer of donor bacteria, only to lose them after 10 weeks. We similarly evaluated transfer of microbial functions, including how they interacted with the recipient's immune system. Our findings shed light on the colonization dynamics of gut microbes, as well as their functions in the context of FMT-information that may provide a critical foundation for the development of more-targeted therapeutics.},
}
@article {pmid34044101,
year = {2021},
author = {Gonzales-Luna, AJ and Spinler, JK and Oezguen, N and Khan, MAW and Danhof, HA and Endres, BT and Alam, MJ and Begum, K and Lancaster, C and Costa, GP and Savidge, TC and Hurdle, JG and Britton, R and Garey, KW},
title = {Systems biology evaluation of refractory Clostridioides difficile infection including multiple failures of fecal microbiota transplantation.},
journal = {Anaerobe},
volume = {70},
number = {},
pages = {102387},
pmid = {34044101},
issn = {1095-8274},
support = {F32 AI136404/AI/NIAID NIH HHS/United States ; R01 AI139261/AI/NIAID NIH HHS/United States ; U01 AI124290/AI/NIAID NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/administration &amp; dosage ; Bacteria/classification/genetics/isolation &amp; purification ; Clostridioides difficile/drug effects/genetics/isolation &amp; purification/*physiology ; Clostridium Infections/drug therapy/microbiology/*therapy ; *Fecal Microbiota Transplantation ; Feces ; Female ; Gastrointestinal Microbiome/drug effects ; Humans ; Microbial Sensitivity Tests ; Polymorphism, Single Nucleotide ; Treatment Failure ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) aims to cure Clostridioides difficile infection (CDI) through reestablishing a healthy microbiome and restoring colonization resistance. Although often effective after one infusion, patients with continued microbiome disruptions may require multiple FMTs. In this N-of-1 study, we use a systems biology approach to evaluate CDI in a patient receiving chronic suppressive antibiotics with four failed FMTs over two years.<br><br>METHODS: Seven stool samples were obtained between 2016-18 while the patient underwent five FMTs. Stool samples were cultured for C. difficile and underwent microbial characterization and functional gene analysis using shotgun metagenomics. C. difficile isolates were characterized through ribotyping, whole genome sequencing, metabolic pathway analysis, and minimum inhibitory concentration (MIC) determinations.<br><br>RESULTS: Growing ten strains from each sample, the index and first four recurrent cultures were single strain ribotype F078-126, the fifth was a mixed culture of ribotypes F002 and F054, and the final culture was ribotype F002. One single nucleotide polymorphism (SNP) variant was identified in the RNA polymerase (RNAP) β-subunit RpoB in the final isolated F078-126 strain when compared to previous F078-126 isolates. This SNV was associated with metabolic shifts but phenotypic differences in fidaxomicin MIC were not observed. Microbiome differences were observed over time during vancomycin therapy and after failed FMTs.<br><br>CONCLUSION: This study highlights the importance of antimicrobial stewardship in patients receiving FMT. Continued antibiotics play a destructive role on a transplanted microbiome and applies selection pressure for resistance to the few antibiotics available to treat CDI.},
}
@article {pmid34369304,
year = {2021},
author = {Singhal, R and Donde, H and Ghare, S and Stocke, K and Zhang, J and Vadhanam, M and Reddy, S and Gobejishvili, L and Chilton, P and Joshi-Barve, S and Feng, W and McClain, C and Hoffman, K and Petrosino, J and Vital, M and Barve, S},
title = {Decrease in acetyl-CoA pathway utilizing butyrate-producing bacteria is a key pathogenic feature of alcohol-induced functional gut microbial dysbiosis and development of liver disease in mice.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1946367},
pmid = {34369304},
issn = {1949-0984},
support = {P20 GM113226/GM/NIGMS NIH HHS/United States ; P50 AA024337/AA/NIAAA NIH HHS/United States ; U01 AA022618/AA/NIAAA NIH HHS/United States ; },
mesh = {Animals ; Butyrates/*metabolism ; Chemical and Drug Induced Liver Injury/*etiology/*physiopathology ; Coenzyme A-Transferases/*metabolism ; Disease Models, Animal ; Dysbiosis/*chemically induced/physiopathology ; Ethanol/*metabolism ; Gastrointestinal Microbiome/*drug effects ; Humans ; Metabolic Networks and Pathways ; Mice ; Ruminococcus/*metabolism ; },
abstract = {Emerging research evidence has established the critical role of the gut-liver axis in the development of alcohol-associated liver disease (ALD). The present study employed 16S rRNA gene and whole genome shotgun (WGS) metagenomic analysis in combination with a revised microbial dataset to comprehensively detail the butyrate-producing microbial communities and the associated butyrate metabolic pathways affected by chronic ethanol feeding. Specifically, the data demonstrated that a decrease in several butyrate-producing bacterial genera belonging to distinct families within the Firmicutes phyla was a significant component of ethanol-induced dysbiosis. WGS analysis of total bacterial genomes encompassing butyrate synthesizing pathways provided the functional characteristics of the microbiome associated with butyrate synthesis. The data revealed that in control mice microbiome, the acetyl-coenzyme A (CoA) butyrate synthesizing pathway was the most prevalent and was significantly and maximally decreased by chronic ethanol feeding. Further WGS analysis i) validated the ethanol-induced decrease in the acetyl-CoA pathway by identifying the decrease in two critical genes but - (butyryl-CoA: acetate CoA transferase) and buk - (butyrate kinase) that encode the terminal condensing enzymes required for converting butyryl-CoA to butyrate and ii) detection of specific taxa of butyrate-producing bacteria containing but and buk genes. Notably, the administration of tributyrin (Tb) - a butyrate prodrug - significantly prevented ethanol-induced decrease in butyrate-producing bacteria, hepatic steatosis, inflammation, and injury. Taken together, our findings strongly suggest that the loss of butyrate-producing bacteria using the acetyl-CoA pathway is a significant pathogenic feature of ethanol-induced microbial dysbiosis and ALD and can be targeted for therapy.},
}
@article {pmid34346283,
year = {2021},
author = {Bajaj, JS and Shamsaddini, A and Fagan, A and McGeorge, S and Gavis, E and Sikaroodi, M and Brenner, LA and Wade, JB and Gillevet, PM},
title = {Distinct gut microbial compositional and functional changes associated with impaired inhibitory control in patients with cirrhosis.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1953247},
pmid = {34346283},
issn = {1949-0984},
support = {I01 CX001076/CX/CSRD VA/United States ; R01 HS025412/HS/AHRQ HHS/United States ; R21 TR002024/TR/NCATS NIH HHS/United States ; R21 TR003095/TR/NCATS NIH HHS/United States ; },
mesh = {Aged ; *Gastrointestinal Microbiome ; Hepatic Encephalopathy/*etiology/*physiopathology ; Humans ; Liver Cirrhosis/*complications/*microbiology/*physiopathology ; Male ; Middle Aged ; Severity of Illness Index ; },
abstract = {Most cirrhosis etiologies, such as alcohol, hepatitis C, and obesity, involve behavior that require the loss of inhibitory control. Once cirrhosis develops, patients can also develop cognitive impairment due to minimal hepatic encephalopathy (MHE). Both processes could have distinct imprints on the gut-liver-brain axis. Determine the impact of inhibitory control versus traditional cirrhosis-related cognitive performance on gut microbial composition and function. Outpatients with cirrhosis underwent two tests for MHE: inhibitory control test (MHEICT, computerized associated with response inhibition) and psychometric hepatic encephalopathy score (MHEPHES, paper-pencil HE-specific associated with subcortical impairment) along with stool collection for metagenomics. MHEICT/not, MHEPHES/not, and discordant (positive on one test but negative on the other) were analyzed for demographics, bacterial species, and gut-brain modules (GBM) using multi-variable analyses. Ninety-seven patients [47 (49%) MHEPHES, 76 (78%) MHEICT, 41 discordant] were enrolled. MHEPHES/not: Cirrhosis severity was worse in MHEPHES without differences in alpha/beta diversity on bacterial species or GBMs. Pathobionts (Enterobacteriaceae) and γ-amino-butryic acid (GABA) synthesis GBM were higher in MHEPHES. MHEICT/not: We found similar cirrhosis severity and metagenomic alpha/beta diversity in MHEICT versus not. However, alpha/beta diversity of GBMs were different in MHEICT versus No-MHE patients. Alistipes ihumii, Prevotella copri, and Eubacterium spp. were higher, while Enterococcus spp. were uniquely lower in MHEICT versus no-MHE and discordant comparisons. GBMs belonging to tryptophan, menaquinone, GABA, glutamate, and short-chain fatty acid synthesis were also unique to MHEICT. Gut microbial signature of impaired inhibitory control, which is associated with addictive disorders that can lead to cirrhosis, is distinct from cirrhosis-related cognitive impairment.},
}
@article {pmid34264786,
year = {2021},
author = {Thänert, R and Thänert, A and Ou, J and Bajinting, A and Burnham, CD and Engelstad, HJ and Tecos, ME and Ndao, IM and Hall-Moore, C and Rouggly-Nickless, C and Carl, MA and Rubin, DC and Davidson, NO and Tarr, PI and Warner, BB and Dantas, G and Warner, BW},
title = {Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1940792},
pmid = {34264786},
issn = {1949-0984},
support = {U01 AI131342/AI/NIAID NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; },
mesh = {Adolescent ; Anti-Bacterial Agents/*therapeutic use ; Child ; Child, Preschool ; Cohort Studies ; Dysbiosis/*drug therapy/*etiology/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Missouri ; Sepsis/*drug therapy/*etiology ; Short Bowel Syndrome/*complications/microbiology ; },
abstract = {Surgical removal of the intestine, lifesaving in catastrophic gastrointestinal disorders of infancy, can result in a form of intestinal failure known as short bowel syndrome (SBS). Bloodstream infections (BSIs) are a major challenge in pediatric SBS management. BSIs require frequent antibiotic therapy, with ill-defined consequences for the gut microbiome and childhood health. Here, we combine serial stool collection, shotgun metagenomic sequencing, multivariate statistics and genome-resolved strain-tracking in a cohort of 19 patients with surgically-induced SBS to show that antibiotic-driven intestinal dysbiosis in SBS enriches for persistent intestinal colonization with BSI causative pathogens in SBS. Comparing the gut microbiome composition of SBS patients over the first 4 years of life to 19 age-matched term and 18 preterm controls, we find that SBS gut microbiota diversity and composition was persistently altered compared to controls. Commensals including Ruminococcus, Bifidobacterium, Eubacterium, and Clostridium species were depleted in SBS, while pathobionts (Enterococcus) were enriched. Integrating clinical covariates with gut microbiome composition in pediatric SBS, we identified dietary and antibiotic exposures as the main drivers of these alterations. Moreover, antibiotic resistance genes, specifically broad-spectrum efflux pumps, were at a higher abundance in SBS, while putatively beneficial microbiota functions, including amino acid and vitamin biosynthesis, were depleted. Moreover, using strain-tracking we found that the SBS gut microbiome harbors BSI causing pathogens, which can persist intestinally throughout the first years of life. The association between antibiotic-driven gut dysbiosis and enrichment of intestinal pathobionts isolated from BSI suggests that antibiotic treatment may predispose SBS patients to infection. Persistence of pathobionts and depletion of beneficial microbiota and functionalities in SBS highlights the need for microbiota-targeted interventions to prevent infection and facilitate intestinal adaptation.},
}
@article {pmid33815293,
year = {2021},
author = {Yuan, X and Chen, R and Zhang, Y and Lin, X and Yang, X and McCormick, KL},
title = {Gut Microbiota of Chinese Obese Children and Adolescents With and Without Insulin Resistance.},
journal = {Frontiers in endocrinology},
volume = {12},
number = {},
pages = {636272},
pmid = {33815293},
issn = {1664-2392},
mesh = {Adolescent ; Angiopoietin-Like Protein 4/*biosynthesis ; Bacteria/genetics/metabolism ; Child ; China/epidemiology ; Cross-Sectional Studies ; Cytokines/blood/metabolism ; Diet ; Feces ; Female ; *Gastrointestinal Microbiome ; Genomics ; Glucose/metabolism ; Humans ; *Insulin Resistance ; Male ; Metagenome ; Pediatric Obesity/*metabolism ; Principal Component Analysis ; RNA, Ribosomal, 16S/metabolism ; },
abstract = {Objective: The intestinal flora of gut microbiota in obese Chinese children and adolescents with and without insulin resistance (IR) was analyzed, as well as associations between the gut microbiota and two serum cytokines related to glucose metabolism, adropin and angiopoietin-like 4 (ANGPTL4).<br><br>Methods: Clinical data, fecal bacterial composition, glucose-related hormones, and serum adipokines (adropin and ANGPTL4) were analyzed in 65 Chinese children with exogenous obesity. The composition of the gut microbiota was determined by 16S rRNA-based metagenomics and IR was calculated using the homeostasis model assessment (HOMA).<br><br>Results: The 65 obese subjects were divided into two groups: insulin sensitive (IS) (n=40, 57.5% males) or IR (n=25, 60% males). Principal coordinates analysis revealed that the gut microbiota samples from the IS group clustered together and separated partly from the IR group (p=0.008). By Mann-Whitney U-test, at a phylum level, a reduction of Firmicutes and an increase of Bacteroidetes in the IR subjects was observed. LEfSe analysis revealed that IS subject, when compared to their IR counterparts, harbored members of the order Coriobacteriales, Turicibacterales, Pasteurellales and family Turicibacteraceae, that were significantly more abundant. In contrast, the IR subjects had members of family Peptococcaceae that were significantly more prevalent than the IS subjects (all p<0.05). Spearman's correlation analysis revealed that serum ANGPTL4 was positively associated with genus Bacteroides, Butyricimonas, and Alistipes, and adropin was positively associated with genus Anaerostipes and Alistipes, and negatively associated with genus Blautia (all p<0.05).<br><br>Conclusion: In obese children, the gut microbiome in IR subjects was significantly discordant from the IS subjects, and the abundance of some metabolism-related bacteria correlated with the serum concentrations of adropin and ANGPTL4. These observations infer that the gut microbiota may be involved in the regulation of glucose metabolism in obesity.},
}
@article {pmid33553973,
year = {2021},
author = {Bajaj, JS and Shamsaddini, A and Fagan, A and Sterling, RK and Gavis, E and Khoruts, A and Fuchs, M and Lee, H and Sikaroodi, M and Gillevet, PM},
title = {Fecal Microbiota Transplant in Cirrhosis Reduces Gut Microbial Antibiotic Resistance Genes: Analysis of Two Trials.},
journal = {Hepatology communications},
volume = {5},
number = {2},
pages = {258-271},
pmid = {33553973},
issn = {2471-254X},
support = {R21 TR002024/TR/NCATS NIH HHS/United States ; R21 TR003095/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Aged ; Anti-Bacterial Agents/administration &amp; dosage/*adverse effects ; *Drug Resistance, Microbial ; Fecal Microbiota Transplantation/*methods ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Lactulose/therapeutic use ; Liver Cirrhosis/pathology/*therapy ; Male ; Middle Aged ; Proton Pump Inhibitors/therapeutic use ; Rifaximin/therapeutic use ; Treatment Outcome ; Young Adult ; },
abstract = {Antibiotic resistance leads to poor outcomes in cirrhosis. Fecal microbiota transplant (FMT) is associated with reduction in antibiotic resistance gene (ARG) burden in patients without cirrhosis; however, the impact in cirrhosis is unclear. We aimed to study the effect of capsule and enema FMT on ARG abundance in fecal samples, which were collected during two published FMT trials in patients with cirrhosis on rifaximin, lactulose, and proton pump inhibitors. ARGs were identified using metagenomics and mapped against the Comprehensive Antibiotic Resistance Database. Changes in ARG abundance were studied within/between groups. The capsule FMT trial involved a one-time FMT or placebo capsule administration with stool collection at baseline and week 4 postintervention. Antibiotics+enema FMT included preprocedure antibiotics followed by FMT enema versus standard-of-care (SOC). Stool was collected at baseline, postantibiotics, and day 7/15 postintervention. Both trials included 20 patients each. There was no safety/infection signal linked to FMT. In the capsule trial, beta-lactamase (OXY/LEN) expression decreased post-FMT versus baseline. Compared to placebo, patients who were post-FMT had lower abundance of vancomycin (VanH), beta-lactamase (ACT), and rifamycin ARGs; the latter was associated with cognitive improvement. No changes were seen within patients treated with placebo. In the antibiotics+enema trial for postantibiotics at day 7 versus baseline, there was an increase in vancomycin and beta-lactamase ARGs, which decreased at day 15. However, quinolone resistance increased at day 15 versus baseline. Between SOC and FMT, day 7 had largely lower ARG (CfxA beta-lactamase, VanW, and VanX) that continued at day 15 (cepA beta-lactamase, VanW). No changes were seen within the SOC group. Conclusion: Despite differences in routes of administration and preintervention antibiotics, we found that ARG abundance is largely reduced after FMT compared to pre-FMT baseline and non-FMT groups in decompensated cirrhosis.},
}
@article {pmid34836316,
year = {2021},
author = {Enaud, R and Cambos, S and Viaud, E and Guichoux, E and Chancerel, E and Marighetto, A and Etchamendy, N and Clark, S and Mohammedi, K and Cota, D and Delhaes, L and Gatta-Cherifi, B},
title = {Gut Microbiota and Mycobiota Evolution Is Linked to Memory Improvement after Bariatric Surgery in Obese Patients: A Pilot Study.},
journal = {Nutrients},
volume = {13},
number = {11},
pages = {},
pmid = {34836316},
issn = {2072-6643},
mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/growth &amp; development ; *Bariatric Surgery ; Feces/microbiology ; Female ; Fungi/growth &amp; development ; *Gastrointestinal Microbiome ; Humans ; Male ; *Memory ; Middle Aged ; *Mycobiome ; Obesity, Morbid/microbiology/psychology/*surgery ; Pilot Projects ; Prospective Studies ; Young Adult ; },
abstract = {Patients with obesity are known to exhibit gut microbiota dysbiosis and memory deficits. Bariatric surgery (BS) is currently the most efficient anti-obesity treatment and may improve both gut dysbiosis and cognition. However, no study has investigated association between changes of gut microbiota and cognitive function after BS. We prospectively evaluated 13 obese patients on anthropometric data, memory functions, and gut microbiota-mycobiota before and six months after BS. The Rey Auditory Verbal Learning Test (AVLT) and the symbol span (SS) of the Weschler Memory Scale were used to assess verbal and working memory, respectively. Fecal microbiota and mycobiota were longitudinally analyzed by 16S and ITS2 rRNA sequencing respectively. AVLT and SS scores were significantly improved after BS (AVLT scores: 9.7 ± 1.7 vs. 11.2 ± 1.9, p = 0.02, and SS scores: 9.7 ± 23.0 vs. 11.6 ± 2.9, p = 0.05). An increase in bacterial alpha-diversity, and Ruminococcaceae, Prevotella, Agaricus, Rhodotorula, Dipodascus, Malassezia, and Mucor were significantly associated with AVLT score improvement after BS, while an increase in Prevotella and a decrease in Clostridium, Akkermansia,&amp;nbsp;Dipodascus and Candida were linked to SS scores improvement. We identified several changes in the microbial communities that differ according to the improvement of either the verbal or working memories, suggesting a complex gut-brain-axis that evolves after BS.},
}
@article {pmid34831411,
year = {2021},
author = {Schierova, D and Roubalova, R and Kolar, M and Stehlikova, Z and Rob, F and Jackova, Z and Coufal, S and Thon, T and Mihula, M and Modrak, M and Kverka, M and Bajer, L and Kostovcikova, K and Drastich, P and Hercogova, J and Novakova, M and Vasatko, M and Lukas, M and Tlaskalova-Hogenova, H and Jiraskova Zakostelska, Z},
title = {Fecal Microbiome Changes and Specific Anti-Bacterial Response in Patients with IBD during Anti-TNF Therapy.},
journal = {Cells},
volume = {10},
number = {11},
pages = {},
pmid = {34831411},
issn = {2073-4409},
support = {grant number NV18-09-00493.//Ministry of Health of the Czech Republic/ ; },
mesh = {Adult ; Antibodies/blood ; Biodiversity ; Case-Control Studies ; Feces/*microbiology ; Female ; Fungi/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Inflammatory Bowel Diseases/blood/*drug therapy/*microbiology/surgery ; Interleukin-17/metabolism ; Leukocytes, Mononuclear/metabolism ; Male ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Tumor Necrosis Factor Inhibitors/*therapeutic use ; },
abstract = {Inflammatory bowel diseases (IBD) are chronic disorders of the gastrointestinal tract that have been linked to microbiome dysbiosis and immune system dysregulation. We investigated the longitudinal effect of anti-TNF therapy on gut microbiota composition and specific immune response to commensals in IBD patients. The study included 52 patients tracked over 38 weeks of therapy and 37 healthy controls (HC). To characterize the diversity and composition of the gut microbiota, we used amplicon sequencing of the V3V4 region of 16S rRNA for the bacterial community and of the ITS1 region for the fungal community. We measured total antibody levels as well as specific antibodies against assorted gut commensals by ELISA. We found diversity differences between HC, Crohn's disease, and ulcerative colitis patients. The bacterial community of patients with IBD was more similar to HC at the study endpoint, suggesting a beneficial shift in the microbiome in response to treatment. We identified factors such as disease severity, localization, and surgical intervention that significantly contribute to the observed changes in the gut bacteriome. Furthermore, we revealed increased IgM levels against specific gut commensals after anti-TNF treatment. In summary, this study, with its longitudinal design, brings insights into the course of anti-TNF therapy in patients with IBD and correlates the bacterial diversity with disease severity in patients with ulcerative colitis (UC).},
}
@article {pmid34748542,
year = {2021},
author = {Robeson, MS and O'Rourke, DR and Kaehler, BD and Ziemski, M and Dillon, MR and Foster, JT and Bokulich, NA},
title = {RESCRIPt: Reproducible sequence taxonomy reference database management.},
journal = {PLoS computational biology},
volume = {17},
number = {11},
pages = {e1009581},
pmid = {34748542},
issn = {1553-7358},
mesh = {Animals ; Classification ; Computational Biology ; DNA Barcoding, Taxonomic ; *Database Management Systems ; Databases, Genetic/*statistics &amp; numerical data ; Databases, Nucleic Acid ; Genomics ; Humans ; Metagenome ; Metagenomics ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis ; *Software ; },
abstract = {Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a Python 3 software package and QIIME 2 plugin for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases. To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA and diet metabarcoding surveys (BOLD, GenBank), as well as for genome comparison. We show that bigger is not always better, and reference databases with standardized taxonomies and those that focus on type strains have quantitative advantages, though may not be appropriate for all use cases. Most databases appear to benefit from some curation (quality filtering), though sequence clustering appears detrimental to database quality. Finally, we demonstrate the breadth and extensibility of RESCRIPt for reproducible workflows with a comparison of global hepatitis genomes. RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research applications. RESCRIPt is released under a permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt.},
}
@article {pmid34634272,
year = {2022},
author = {Hu, Y and Liu, T and Chen, N and Feng, C},
title = {Changes in microbial community diversity, composition, and functions upon nitrate and Cr(VI) contaminated groundwater.},
journal = {Chemosphere},
volume = {288},
number = {Pt 2},
pages = {132476},
doi = {10.1016/j.chemosphere.2021.132476},
pmid = {34634272},
issn = {1879-1298},
mesh = {Chromium ; *Groundwater ; Metagenomics ; *Microbiota ; Nitrates ; },
abstract = {With the increasing occurrences of nitrate and Cr(VI) pollution globally, microbially driven pollutant reduction and its interaction effects were of growing interest. Despite the increasing number of experimental reports on the simultaneous reduction of nitrate and Cr(VI), a broad picture of the keystone species and metabolic differences in this process remained elusive. This study explored the changing of microorganisms with the introduction of Cr(VI)/NO3- through analyzing 242 samples from the NCBI database. The correlation between microbial abundance and environmental factors showed that, the types of energy substances and pollutants species in the environment had an impact on the diversity of microorganisms and community structure. The genus of Zoogloea, Candidatus Accumulibacter, and Candidatus Kapabacteria sp. 59-99 had the ability of denitrification, while genus of Alcaligenes, Kerstersia, Petrimonas, and Leucobacter showed effectively Cr(VI) resistance and reducing ability. Azoarcus, Pseudomonas, and Thauera were recognized as important candidates in the simultaneous reduction of nitrate and Cr(VI). Metagenomic predictions of these microorganisms using PICRUSt2 further highlighted the enrichment of Cr(VI)and nitrate reduction-related genes (such as chrA and norC). Special attention should therefore be paid to these bacteria in subsequent studies to evaluate their performance and mechanisms involved in simultaneous denitrification and chromium removal. The microbial co-occurrence network analysis conducted on this basis emphasized a strong association between community collaboration and pollution removal. Collectively, either site surveys or laboratory experiments, subsequent studies should focus on these microbial populations and the interspecific collaborations as they strongly influence the occurrence of simultaneous nitrate and Cr(VI) reduction.},
}
@article {pmid34626348,
year = {2021},
author = {Van Borm, S and Steensels, M and Mathijs, E and Vandenbussche, F and van den Berg, T and Lambrecht, B},
title = {Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples.},
journal = {Virus genes},
volume = {57},
number = {6},
pages = {529-540},
pmid = {34626348},
issn = {1572-994X},
support = {773830//horizon 2020 framework programme/ ; },
mesh = {Animals ; Chickens/*virology ; *Genomics ; Infectious bronchitis virus/*classification/*genetics/pathogenicity ; Poultry Diseases/virology ; Virome/*genetics ; },
abstract = {Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity.},
}
@article {pmid34562162,
year = {2021},
author = {de Fátima Silva Lopes, H and Tu, Z and Sumi, H and Furukawa, H and Yumoto, I},
title = {Indigofera tinctoria leaf powder as a promising additive to improve indigo fermentation prepared with sukumo (composted Polygonum tinctorium leaves).},
journal = {World journal of microbiology &amp; biotechnology},
volume = {37},
number = {10},
pages = {179},
pmid = {34562162},
issn = {1573-0972},
support = {G-2020-3-035//Institute for Fermentation, Osaka/ ; },
mesh = {Bacteria, Anaerobic/genetics ; Coloring Agents/chemistry ; *Fermentation ; High-Throughput Nucleotide Sequencing ; Indigo Carmine/chemistry ; *Indigofera/chemistry/microbiology ; Metagenomics ; Microbiota/genetics ; Plant Extracts/chemistry ; Plant Leaves/chemistry/microbiology ; *Polygonum/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Being insoluble in the oxidize form, indigo dye must be solubilized by reduction for it to penetrate textile. One of the procedures is the reduction by natural bacterial fermentation. Sukumo, composted leaves of Polygonum tinctorium, is a natural source of indigo in Japan. Although sukumo has an intrinsic bacterial seed, the onset of indigo reduction with this material may vary greatly. Certain additives improve indigo fermentation. Here, we studied the effects of Indigofera tinctoria leaf powder (LP) on the initiation of indigo reduction, bacterial community, redox potential (ORP), and dyeing intensity in the initial stages and in aged fermentation fluids prepared with sukumo. I. tinctoria LP markedly decreased ORP at day 1 and stabilised it during early fermentation. These effects could be explained by the phytochemicals present in I. tinctoria LP that act as oxygen scavengers and electron mediators. Using next generation sequencing results, we observed differences in the bacterial community in sukumo fermentation treated with I. tinctoria LP, which was not influenced by the bacterial community in I. tinctoria LP per se. The concomitant decrease in Bacillaceae and increase in Proteinivoraceae at the onset of fermentation, increase in the ratio of facultative to obligate anaerobes (F/O ratio), or the total abundance of facultative anaerobes (F) or obligate anaerobes (O) (designated F + O) are vital for the initiation and maintenance of indigo reduction. Hence, I. tinctoria LP improved early indigo reduction by decreasing the ORP and hasten the appropriate transitions in the bacterial community in sukumo fermentation.},
}
@article {pmid34539647,
year = {2021},
author = {Zhang, J and Tao, J and Gao, RN and Wei, ZY and He, YS and Ren, CY and Li, QC and Liu, YS and Wang, KW and Yang, G and Qian, C and Chen, JH},
title = {Cytotoxic T-Cell Trafficking Chemokine Profiles Correlate With Defined Mucosal Microbial Communities in Colorectal Cancer.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {715559},
pmid = {34539647},
issn = {1664-3224},
mesh = {Adult ; Aged ; Biomarkers ; CD8-Positive T-Lymphocytes/immunology/metabolism ; Chemokines/*metabolism ; Chemotaxis, Leukocyte/*immunology ; Colorectal Neoplasms/*etiology/*metabolism/pathology ; Computational Biology/methods ; Disease Progression ; Disease Susceptibility ; Female ; Fluorescent Antibody Technique ; Gastrointestinal Microbiome/*immunology ; Humans ; Immunohistochemistry ; Male ; Metagenome ; Metagenomics ; Middle Aged ; Neoplasm Grading ; Neoplasm Staging ; T-Lymphocytes, Cytotoxic/*immunology/*metabolism ; },
abstract = {The involvement of gut microbiota in T-cell trafficking into tumor tissue of colorectal cancer (CRC) remains to be further elucidated. The current study aimed to evaluate the expression of major cytotoxic T-cell trafficking chemokines (CTTCs) and chemokine-associated microbiota profiles in both tumor and adjacent normal tissues during CRC progression. We analyzed the expression of chemokine C-X-C motif ligands 9, 10, and 11 (CXCL9, CXCL10, and CXCL11), and C-C motif ligand 5 (CCL5), characterized gut mucosa-associated microbiota (MAM), and investigated their correlations in CRC patients. Our results showed that the expression of CXCL9, CXCL10, and CXCL11 was significantly higher in tumor than in adjacent normal tissues in 136 CRC patients. Notably, the high expression of CXCL9 in tumor tissues was associated with enhanced CD8+ T-cell infiltration and improved survival. Moreover, the MAM in tumor tissues showed reduction of microbial diversity and increase of oral bacteria. Microbial network analysis identified differences in microbial composition and structure between tumor and adjacent normal tissues. In addition, stronger associations between oral bacteria and other gut microbes were observed. Furthermore, the correlation analysis between the defined MAM and individual CTTCs showed that the CTTCs' correlated operational taxonomic units (OTUs) in tumor and adjacent normal tissues rarely overlap with each other. Notably, all the enriched OTUs were positively correlated with the CTTCs in either tumor or adjacent normal tissues. Our findings demonstrated stronger interactions between oral bacteria and gut microbes, and a shifted correlation pattern between MAM and major CTTCs in tumor tissues, underlining possible mechanisms of gut microbiota-host interaction in CRC.},
}
@article {pmid34489372,
year = {2021},
author = {Kim, S and Seo, H and Rahim, MA and Lee, S and Kim, YS and Song, HY},
title = {Changes in the Microbiome of Vaginal Fluid after Menopause in Korean Women.},
journal = {Journal of microbiology and biotechnology},
volume = {31},
number = {11},
pages = {1490-1500},
doi = {10.4014/jmb.2106.06022},
pmid = {34489372},
issn = {1738-8872},
mesh = {Adult ; Bacteria/classification ; Female ; Humans ; Metagenome ; *Microbiota ; Middle Aged ; *Postmenopause ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Vagina/*microbiology ; },
abstract = {Various microorganisms reside in the human vagina; the vaginal microbiome is closely linked to both vaginal and general health, and for this reason, microbiome studies of the vagina are an area of research. In this study, we analyzed the vaginal microbiome of women before and after menopause to further increase our understanding of the vaginal microbiome and its contribution to general health. We did a 16s rRNA gene-based metagenomic analysis on the vaginal fluids of 11 premenopausal and 19 postmenopausal women in Korea. We confirmed that the taxonomic composition was significantly different between the two groups. In postmenopausal women, species richness was significantly decreased, but species diversity was significantly increased. In particular, among the taxonomic components corresponding to all taxon ranks of the vaginal microbiome, a reduction in Lactobacillus taxa after menopause contributed the most to the difference between the two groups. In addition, we confirmed through metabolic analysis that the lactic-acid concentration was also decreased in the vaginal fluid of women after menopause. Our findings on the correlation between menopause and the microbiome could help diagnose menopause and enhance the prevention and treatment diseases related to menopause.},
}
@article {pmid34484230,
year = {2021},
author = {Que, Y and Cao, M and He, J and Zhang, Q and Chen, Q and Yan, C and Lin, A and Yang, L and Wu, Z and Zhu, D and Chen, F and Chen, Z and Xiao, C and Hou, K and Zhang, B},
title = {Gut Bacterial Characteristics of Patients With Type 2 Diabetes Mellitus and the Application Potential.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {722206},
pmid = {34484230},
issn = {1664-3224},
mesh = {Case-Control Studies ; Diabetes Mellitus, Type 2/*complications/metabolism ; Dysbiosis/*etiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Probiotics ; RNA, Ribosomal, 16S ; ROC Curve ; },
abstract = {Type 2 diabetes mellitus (T2DM) is a complex disorder comprehensively influenced by genetic and environmental risk, and research increasingly has indicated the role of microbial dysbiosis in T2DM pathogenesis. However, studies comparing the microbiome characteristics between T2DM and healthy controls have reported inconsistent results. To further identify and describe the characteristics of the intestinal flora of T2DM patients, we performed a systematic review and meta-analysis of stool microbial profiles to discern and describe microbial dysbiosis in T2DM and to explore heterogeneity among 7 studies (600 T2DM cases, 543 controls, 1143 samples in total). Using a random effects model and a fixed effects model, we observed significant differences in beta diversity, but not alpha diversity, between individuals with T2DM and controls. We identified various operational taxonomic unit (OTUs) and bacterial genera with significant odds ratios for T2DM. The T2DM signatures derived from a single study by stepwise feature selection could be applied in other studies. By training on multiple studies, we improved the detection accuracy and disease specificity for T2DM. We also discuss the relationship between T2DM-enriched or T2DM-depleted genera and probiotics and provide new ideas for diabetes prevention and improvement.},
}
@article {pmid34406857,
year = {2021},
author = {Taylor, LJ and Dothard, MI and Rubel, MA and Allen, AA and Hwang, Y and Roche, AM and Graham-Wooten, J and Fitzgerald, AS and Khatib, LA and Ranciaro, A and Thompson, SR and Beggs, WR and Campbell, MC and Mokone, GG and Mpoloka, SW and Fokunang, C and Njamnshi, AK and Mbunwe, E and Woldemeskel, D and Belay, G and Nyambo, T and Tishkoff, SA and Collman, RG and Bushman, FD},
title = {Redondovirus Diversity and Evolution on Global, Individual, and Molecular Scales.},
journal = {Journal of virology},
volume = {95},
number = {21},
pages = {e0081721},
pmid = {34406857},
issn = {1098-5514},
support = {T32 AI007532/AI/NIAID NIH HHS/United States ; 9299//Wenner-Gren Foundation (WGF)/ ; R33HL137063-S1//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; P30 AI045008/AI/NIAID NIH HHS/United States ; BCS-1540432//National Science Foundation (NSF)/ ; R33HL137063//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1-19-VSN-02//American Diabetes Association/ ; 5T32AI007532-18//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R35 GM134957/GM/NIGMS NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; T32AI007324//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R25 GM071745/GM/NIGMS NIH HHS/United States ; T32 AI007324/AI/NIAID NIH HHS/United States ; R25GM071745//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R35GM134957-01//HHS | National Institutes of Health (NIH)/ ; },
mesh = {Africa/epidemiology ; Biodiversity ; Critical Illness ; DNA Virus Infections/epidemiology/*virology ; DNA Viruses/*classification/*genetics/*metabolism ; DNA-Binding Proteins/metabolism ; Evolution, Molecular ; Genome, Viral ; Humans ; Metagenomics ; Mouth/*virology ; Periodontitis/virology ; Phylogeny ; Prevalence ; Respiratory System/*virology ; Rural Population ; Saliva/*virology ; United States/epidemiology ; Viral Proteins/metabolism ; },
abstract = {Redondoviridae is a newly established family of circular Rep-encoding single-stranded (CRESS) DNA viruses found in the human ororespiratory tract. Redondoviruses were previously found in ∼15% of respiratory specimens from U.S. urban subjects; levels were elevated in individuals with periodontitis or critical illness. Here, we report higher redondovirus prevalence in saliva samples: four rural African populations showed 61 to 82% prevalence, and an urban U.S. population showed 32% prevalence. Longitudinal, limiting-dilution single-genome sequencing revealed diverse strains of both redondovirus species (Brisavirus and Vientovirus) in single individuals, persistence over time, and evidence of intergenomic recombination. Computational analysis of viral genomes identified a recombination hot spot associated with a conserved potential DNA stem-loop structure. To assess the possible role of this site in recombination, we carried out in vitro studies which showed that this potential stem-loop was cleaved by the virus-encoded Rep protein. In addition, in reconstructed reactions, a Rep-DNA covalent intermediate was shown to mediate DNA strand transfer at this site. Thus, redondoviruses are highly prevalent in humans, found in individuals on multiple continents, heterogeneous even within individuals and encode a Rep protein implicated in facilitating recombination. IMPORTANCE Redondoviridae is a recently established family of DNA viruses predominantly found in the human respiratory tract and associated with multiple clinical conditions. In this study, we found high redondovirus prevalence in saliva from urban North American individuals and nonindustrialized African populations in Botswana, Cameroon, Ethiopia, and Tanzania. Individuals on both continents harbored both known redondovirus species. Global prevalence of both species suggests that redondoviruses have long been associated with humans but have remained undetected until recently due to their divergent genomes. By sequencing single redondovirus genomes in longitudinally sampled humans, we found that redondoviruses persisted over time within subjects and likely evolve by recombination. The Rep protein encoded by redondoviruses catalyzes multiple reactions in vitro, consistent with a role in mediating DNA replication and recombination. In summary, we identify high redondovirus prevalence in humans across multiple continents, longitudinal heterogeneity and persistence, and potential mechanisms of redondovirus evolution by recombination.},
}
@article {pmid34367180,
year = {2021},
author = {Lv, L and Jiang, H and Chen, X and Wang, Q and Wang, K and Ye, J and Li, Y and Fang, D and Lu, Y and Yang, L and Gu, S and Chen, J and Diao, H and Yan, R and Li, L},
title = {The Salivary Microbiota of Patients With Primary Biliary Cholangitis Is Distinctive and Pathogenic.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {713647},
pmid = {34367180},
issn = {1664-3224},
mesh = {Biomarkers ; Case-Control Studies ; Chemokines/metabolism ; Cytokines/metabolism ; Dysbiosis/*etiology ; Female ; *Host Microbial Interactions/immunology ; Humans ; Inflammation Mediators/metabolism ; Keratinocytes/metabolism ; Liver Cirrhosis, Biliary/*complications/diagnosis/etiology/metabolism ; Liver Function Tests ; Male ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Saliva/*microbiology ; },
abstract = {The role of host-microbiota interactions in primary biliary cholangitis (PBC) has received increased attention. However, the impact of PBC on the oral microbiota and contribution of the oral microbiota to PBC are unclear. In this study, thirty-nine PBC patients without other diseases and 37 healthy controls (HCs) were enrolled and tested for liver functions and haematological variables. Saliva specimens were collected before and after brushing, microbiota was determined using 16S rDNA sequencing, metabolomics was profiled using Gas Chromatography-Mass Spectrometer (GC-MS), 80 cytokines were assayed using biochips, and inflammation inducibility was evaluated using OKF6 keratinocytes and THP-1 macrophages. Finally, the effect of ultrasonic scaling on PBC was estimated. Compared with HCs, PBC saliva had enriched taxa such as Bacteroidetes, Campylobacter, Prevotella and Veillonella and depleted taxa such as Enterococcaceae, Granulicatella, Rothia and Streptococcus. PBC saliva also had enriched sCD163, enriched metabolites such as 2-aminomalonic acid and 1-dodecanol, and depleted metabolites such as dodecanoic acid and propylene glycol. sCD163, 4-hydroxybenzeneacetic acid and 2-aminomalonic acid were significantly correlated with salivary cytokines, bacteria and metabolites. Salivary Veillonellaceae members, 2-aminomalonic acid, and sCD163 were positively correlated with liver function indicators such as serum alkaline phosphatase (ALP), aspartate aminotransferase (AST) and alanine aminotransferase (ALT). PBC salivary microbes induced more soluble interleukin (IL)-6 receptor α (sIL-6Rα), sIL-6Rβ and tumour necrosis factor ligand superfamily (TNFSF)13B from OKF6 keratinocytes, and PBC salivary supernatant induced more IL-6, IL-10, granulocyte-macrophage colony-stimulating factor (GM-CSF), chemokine (C-C motif) ligand (CCL)13, C-X-C motif chemokine (CXC)L1 and CXCL16 from THP-1 macrophages. Toothbrushing significantly reduced the expression of inflammatory cytokines such as IL-1β, IL-8 and TNF-α and harmful metabolites such as cadaverine and putrescine in PBC but not HC saliva after P-value correction. The levels of ALP and bilirubin in PBC serum were decreased after ultrasonic scaling. Together, PBC patients show significant alterations in their salivary microbiota, likely representing one cause and treatment target of oral inflammation and worsening liver functions.},
}
@article {pmid34349022,
year = {2021},
author = {Lee, S and Sieradzki, ET and Nicolas, AM and Walker, RL and Firestone, MK and Hazard, C and Nicol, GW},
title = {Methane-derived carbon flows into host-virus networks at different trophic levels in soil.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {32},
pages = {},
pmid = {34349022},
issn = {1091-6490},
mesh = {Bacteria/genetics/metabolism/*virology ; Carbon/*metabolism ; Carbon Radioisotopes/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Viruses/*genetics ; Genome, Bacterial ; Genome, Viral ; Metagenomics ; Methane/chemistry/*metabolism ; Microbiota ; Soil/*chemistry ; Soil Microbiology ; },
abstract = {The concentration of atmospheric methane (CH4) continues to increase with microbial communities controlling soil-atmosphere fluxes. While there is substantial knowledge of the diversity and function of prokaryotes regulating CH4 production and consumption, their active interactions with viruses in soil have not been identified. Metagenomic sequencing of soil microbial communities enables identification of linkages between viruses and hosts. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active. In this study, we identified active interactions between individual host and virus populations in situ by following the transfer of assimilated carbon. Using DNA stable-isotope probing combined with metagenomic analyses, we characterized CH4-fueled microbial networks in acidic and neutral pH soils, specifically primary and secondary utilizers, together with the recent transfer of CH4-derived carbon to viruses. A total of 63% of viral contigs from replicated soil incubations contained homologs of genes present in known methylotrophic bacteria. Genomic sequences of 13C-enriched viruses were represented in over one-third of spacers in CRISPR arrays of multiple closely related Methylocystis populations and revealed differences in their history of viral interaction. Viruses infecting nonmethanotrophic methylotrophs and heterotrophic predatory bacteria were also identified through the analysis of shared homologous genes, demonstrating that carbon is transferred to a diverse range of viruses associated with CH4-fueled microbial food networks.},
}
@article {pmid34319574,
year = {2021},
author = {Cezar, RM and Vezzani, FM and Kaschuk, G and Balsanelli, E and de Souza, EM and Vargas, LK and Molin, R},
title = {Crop rotation reduces the frequency of anaerobic soil bacteria in Red Latosol of Brazil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {52},
number = {4},
pages = {2169-2177},
pmid = {34319574},
issn = {1678-4405},
mesh = {*Agriculture/methods ; Bacteria/genetics ; *Bacteria, Anaerobic/physiology ; *Biodiversity ; Brazil ; Crop Production ; Oxygen ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; },
abstract = {Crop diversity affects the processes of soil physical structuring and most likely provokes changes in the frequencies of soil microbial communities. The study was conducted for soil prokaryotic diversity sequencing 16S rDNA genes from a 25-year no-tillage experiment comprised of two crop systems: crop succession (Triticum aestivum-Glycine max) and rotation (Vicia sativa-Zea mays-Avena sativa-Glycine max-Triticum aestivum-Glycine max). The hypothesis was that a crop system with higher crop diversification (rotation) would affect the frequencies of prokaryotic taxa against a less diverse crop system (succession) altering the major soil functions guided by bacterial diversity. Soils in both crop systems were dominated by Proteobacteria (31%), Acidobacteria (23%), Actinobacteria (10%), and Gemmatimonadetes (7.2%), among other common copiotrophic soil bacteria. Crop systems did not affect the richness and diversity indexes of soil bacteria and soil archaea. However, the crop rotation system reduced only the frequencies of anaerobic metabolism bacteria Chloroacidobacteria, Holophagae, Spirochaetes, Euryarchaeota, and Crenarchaeota. It can be concluded that crop succession, a system that is poorer in root diversity over time, may have conditioned the soil to lower oxygen diffusion and built up ecological niches that suitable for anaerobic bacteria tolerating lower levels of oxygen. On the other hand, it appeared that crop rotation has restructured the soil over the years while enabling copiotrophic aerobic bacteria to dominate the soil ecosystem. The changes prompted by crop succession have implications for efficient soil organic matter decomposition, reduced greenhouse gas emissions, higher root activity, and overall soil productivity, which compromise to agriculture sustainability.},
}
@article {pmid34312252,
year = {2021},
author = {Ottoni, C and Borić, D and Cheronet, O and Sparacello, V and Dori, I and Coppa, A and Antonović, D and Vujević, D and Price, TD and Pinhasi, R and Cristiani, E},
title = {Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {32},
pages = {},
pmid = {34312252},
issn = {1091-6490},
mesh = {Agriculture/*history ; Bacteria/genetics ; Balkan Peninsula ; *DNA, Ancient ; Dental Calculus/chemistry/*genetics/*microbiology ; Drug Resistance, Microbial/genetics ; Europe ; History, Ancient ; History, Medieval ; Humans ; Microbiota/*genetics ; Phylogeny ; Plants/chemistry ; },
abstract = {Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.},
}
@article {pmid33299088,
year = {2021},
author = {Malard, F and Dore, J and Gaugler, B and Mohty, M},
title = {Introduction to host microbiome symbiosis in health and disease.},
journal = {Mucosal immunology},
volume = {14},
number = {3},
pages = {547-554},
pmid = {33299088},
issn = {1935-3456},
mesh = {Animals ; Dysbiosis/*therapy ; Host Microbial Interactions ; Humans ; Iatrogenic Disease/*prevention &amp; control ; Metagenomics ; Microbiota/*physiology ; Nutrition Therapy ; Precision Medicine ; Symbiosis ; },
abstract = {Humans share a core intestinal microbiome and yet human microbiome differs by genes, species, enterotypes (ecology), and gene count (microbial diversity). Achievement of microbiota metagenomic analysis has revealed that the microbiome gene count is a key stratifier of health in several immune disorders and clinical conditions. We review here the progress of the metagenomic pipeline analysis, and how this has allowed us to define the host-microbe symbiosis associated with a healthy status. The link between host-microbe symbiosis disruption, the so-called dysbiosis and chronic diseases or iatrogenic conditions is highlighted. Finally, opportunities to use microbiota modulation, with specific nutrients and/or live microbes, as a target for personalized nutrition and therapy for the maintenance, preservation, or restoration of host-microbe symbiosis are discussed.},
}
@article {pmid32835897,
year = {2021},
author = {Miyoshi, J and Lee, STM and Kennedy, M and Puertolas, M and Frith, M and Koval, JC and Miyoshi, S and Antonopoulos, DA and Leone, V and Chang, EB},
title = {Metagenomic Alterations in Gut Microbiota Precede and Predict Onset of Colitis in the IL10 Gene-Deficient Murine Model.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {11},
number = {2},
pages = {491-502},
doi = {10.1016/j.jcmgh.2020.08.008},
pmid = {32835897},
issn = {2352-345X},
support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; T32 DK007074/DK/NIDDK NIH HHS/United States ; T32 GM007281/GM/NIGMS NIH HHS/United States ; K01 DK111785/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/administration &amp; dosage ; Cefoperazone/administration &amp; dosage ; Colitis/*diagnosis/immunology/microbiology ; Disease Models, Animal ; Dysbiosis/chemically induced/*complications/immunology/microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Interleukin-10/*deficiency/genetics ; Intestinal Mucosa/immunology ; Male ; Metagenome ; Metagenomics ; Mice ; Mice, Knockout ; Prognosis ; },
abstract = {BACKGROUND &amp; AIMS: Inflammatory bowel diseases (IBD) are chronic inflammatory disorders where predictive biomarkers for the disease development and clinical course are sorely needed for development of prevention and early intervention strategies that can be implemented to improve clinical outcomes. Since gut microbiome alterations can reflect and/or contribute to impending host health changes, we examined whether gut microbiota metagenomic profiles would provide more robust measures for predicting disease outcomes in colitis-prone hosts.<br><br>METHODS: Using the interleukin (IL) 10 gene-deficient (IL10 KO) murine model where early life dysbiosis from antibiotic (cefoperozone [CPZ]) treated dams vertically transferred to pups increases risk for colitis later in life, we investigated temporal metagenomic profiles in the gut microbiota of post-weaning offspring and determined their relationship to eventual clinical outcomes.<br><br>RESULTS: Compared to controls, offspring acquiring maternal CPZ-induced dysbiosis exhibited a restructuring of intestinal microbial membership in both bacteriome and mycobiome that was associated with alterations in specific functional subsystems. Furthermore, among IL10 KO offspring from CPZ-treated dams, several functional subsystems, particularly nitrogen metabolism, diverged between mice that developed spontaneous colitis (CPZ-colitis) versus those that did not (CPZ-no-colitis) at a time point prior to eventual clinical outcome.<br><br>CONCLUSIONS: Our findings provide support that functional metagenomic profiling of gut microbes has potential and promise meriting further study for development of tools to assess risk and manage human IBD.},
}
@article {pmid34424926,
year = {2021},
author = {Zacho, CM and Bager, MA and Margaryan, A and Gravlund, P and Galatius, A and Rasmussen, AR and Allentoft, ME},
title = {Uncovering the genomic and metagenomic research potential in old ethanol-preserved snakes.},
journal = {PloS one},
volume = {16},
number = {8},
pages = {e0256353},
pmid = {34424926},
issn = {1932-6203},
mesh = {Biodiversity ; Formaldehyde ; *Metagenomics ; Phylogeny ; },
abstract = {Natural history museum collections worldwide represent a tremendous resource of information on past and present biodiversity. Fish, reptiles, amphibians and many invertebrate collections have often been preserved in ethanol for decades or centuries and our knowledge on the genomic and metagenomic research potential of such material is limited. Here, we use ancient DNA protocols, combined with shotgun sequencing to test the molecular preservation in liver, skin and bone tissue from five old (1842 to 1964) museum specimens of the common garter snake (Thamnophis sirtalis). When mapping reads to a T. sirtalis reference genome, we find that the DNA molecules are highly damaged with short average sequence lengths (38-64 bp) and high C-T deamination, ranging from 9% to 21% at the first position. Despite this, the samples displayed relatively high endogenous DNA content, ranging from 26% to 56%, revealing that genome-scale analyses are indeed possible from all specimens and tissues included here. Of the three tested types of tissue, bone shows marginally but significantly higher DNA quality in these metrics. Though at least one of the snakes had been exposed to formalin, neither the concentration nor the quality of the obtained DNA was affected. Lastly, we demonstrate that these specimens display a diverse and tissue-specific microbial genetic profile, thus offering authentic metagenomic data despite being submerged in ethanol for many years. Our results emphasize that historical museum collections continue to offer an invaluable source of information in the era of genomics.},
}
@article {pmid34906246,
year = {2021},
author = {Chaudhari, NM and Overholt, WA and Figueroa-Gonzalez, PA and Taubert, M and Bornemann, TLV and Probst, AJ and Hölzer, M and Marz, M and Küsel, K},
title = {The economical lifestyle of CPR bacteria in groundwater allows little preference for environmental drivers.},
journal = {Environmental microbiome},
volume = {16},
number = {1},
pages = {24},
pmid = {34906246},
issn = {2524-6372},
support = {SFB 1076 -Project Number 218627073//deutsche forschungsgemeinschaft/ ; FZT 118 - 202548816//deutsche forschungsgemeinschaft/ ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//deutsche forschungsgemeinschaft/ ; Nachwuchsgruppe Dr. Alexander Probst//ministerium für kultur und wissenschaft des landes nordrhein-westfalen/ ; },
abstract = {BACKGROUND: The highly diverse Cand. Patescibacteria are predicted to have minimal biosynthetic and metabolic pathways, which hinders understanding of how their populations differentiate in response to environmental drivers or host organisms. Their mechanisms employed to cope with oxidative stress are largely unknown. Here, we utilized genome-resolved metagenomics to investigate the adaptive genome repertoire of Patescibacteria in oxic and anoxic groundwaters, and to infer putative host ranges.<br><br>RESULTS: Within six groundwater wells, Cand. Patescibacteria was the most dominant (up to 79%) super-phylum across 32 metagenomes sequenced from DNA retained on 0.2 and 0.1 µm filters after sequential filtration. Of the reconstructed 1275 metagenome-assembled genomes (MAGs), 291 high-quality MAGs were classified as Cand. Patescibacteria. Cand. Paceibacteria and Cand. Microgenomates were enriched exclusively in the 0.1 µm fractions, whereas candidate division ABY1 and Cand. Gracilibacteria were enriched in the 0.2 µm fractions. On average, Patescibacteria enriched in the smaller 0.1 µm filter fractions had 22% smaller genomes, 13.4% lower replication measures, higher proportion of rod-shape determining proteins, and of genomic features suggesting type IV pili mediated cell-cell attachments. Near-surface wells harbored Patescibacteria with higher replication rates than anoxic downstream wells characterized by longer water residence time. Except prevalence of superoxide dismutase genes in Patescibacteria MAGs enriched in oxic groundwaters (83%), no major metabolic or phylogenetic differences were observed. The most abundant Patescibacteria MAG in oxic groundwater encoded a nitrate transporter, nitrite reductase, and F-type ATPase, suggesting an alternative energy conservation mechanism. Patescibacteria consistently co-occurred with one another or with members of phyla Nanoarchaeota, Bacteroidota, Nitrospirota, and Omnitrophota. Among the MAGs enriched in 0.2 µm fractions,, only 8% Patescibacteria showed highly significant one-to-one correlation, mostly with Omnitrophota. Motility and transport related genes in certain Patescibacteria were highly similar to genes from other phyla (Omnitrophota, Proteobacteria and Nanoarchaeota).<br><br>CONCLUSION: Other than genes to cope with oxidative stress, we found little genomic evidence for niche adaptation of Patescibacteria to oxic or anoxic groundwaters. Given that we could detect specific host preference only for a few MAGs, we speculate that the majority of Patescibacteria is able to attach multiple hosts just long enough to loot or exchange supplies.},
}
@article {pmid34905206,
year = {2022},
author = {Raza, A and Wu, Q},
title = {Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2400},
number = {},
pages = {225-243},
pmid = {34905206},
issn = {1940-6029},
abstract = {Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding of viral biodiversity associated with plant diseases. Deep sequencing combined with metagenomics is a powerful approach that has proven to be revolutionary in the last decade and involves the direct analysis of viral genomes present in a diseased tissue sample. This protocol describes the details of RNA extraction and purification from wild rice plant and their yield, RNA purity, and integrity assessment. As a final step, bioinformatics data analysis including demultiplexing, quality control, de novo transcriptome assembly, taxonomic allocation and read mapping following Illumina HiSeq small and total RNA sequencing are described. Furthermore, the total RNAs extraction protocol and an additional ribosomal rRNAs depletion step which are significantly important for viral genomes construction are provided.},
}
@article {pmid34878610,
year = {2021},
author = {Kumar, V and Kumar, S and Singh, D},
title = {Metagenomic insights into Himalayan glacial and kettle lake sediments revealed microbial community structure, function, and stress adaptation strategies.},
journal = {Extremophiles : life under extreme conditions},
volume = {26},
number = {1},
pages = {3},
pmid = {34878610},
issn = {1433-4909},
support = {MLP0143//CSIR-Institute of Himalayan Bioresource Technology/ ; },
mesh = {Geologic Sediments ; *Lakes ; Metagenome ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Glacial and kettle lakes in the high-altitude Himalayas are unique habitats with significant scope for microbial ecology. The present study provides insights into bacterial community structure and function of the sediments of two high-altitude lakes using 16S amplicon and whole-genome shotgun (WGS) metagenomics. Microbial communities in the sediments of Parvati kund (glacial lake) and Bhoot ground (kettle lake) majorly consist of bacteria and a small fraction of archaea and eukaryota. The bacterial population has an abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, Actinobacteria, Firmicutes, and Verrucomicrobia. Despite the common phyla, the sediments from each lake have a distinct distribution of bacterial and archaeal taxa. The analysis of the WGS metagenomes at the functional level provides a broad picture of microbial community metabolism of key elements and suggested chemotrophs as the major primary producers. In addition, the findings also revealed that polyhydroxyalkanoates (PHA) are a crucial stress adaptation molecule. The abundance of PHA metabolism in Alpha- and Betaproteobacteria and less representation in other bacterial and archaeal classes in both metagenomes was disclosed. The metagenomic insights provided an incisive view of the microbiome from Himalayan lake's sediments. It has also opened the scope for further bioprospection from virgin Himalayan niches.},
}
@article {pmid34872176,
year = {2022},
author = {Chen, X and Hu, X and Lu, Q and Yang, Y and Linghu, S and Zhang, X},
title = {Study on the differences in sludge toxicity and microbial community structure caused by catechol, resorcinol and hydroquinone with metagenomic analysis.},
journal = {Journal of environmental management},
volume = {302},
number = {Pt A},
pages = {114027},
doi = {10.1016/j.jenvman.2021.114027},
pmid = {34872176},
issn = {1095-8630},
mesh = {Bioreactors ; Catechols/toxicity ; Hydroquinones/toxicity ; *Microbiota ; Resorcinols/toxicity ; *Sewage ; },
abstract = {The aerobic biodegradation rate, organic toxicity and microbial community structure of activated sludge acclimated by catechol, resorcinol and hydroquinone were investigated, to study the relationship between microbial structure and sludge organic toxicity caused by phenolic compounds. At the stable operation stage, the degradation rates of the dihydroxy benzenes in a single sequencing batch reactor (SBR) cycle were followed the order: resorcinol (89.71%) > hydroquinone (85.64%) > catechol (59.62%). Sludge toxicity bioassay indicated that the toxicity of sludge was catechol (45.63%) > hydroquinone (40.28%) > resorcinol (38.15%). The accumulation of secondary metabolites such as 5-10 kDa tryptophan and tyrosine protein substances caused the differential sludge toxicity. Microbial metagenomic analysis showed that the toxicity of sludge was significantly related to the microbial community structure. Thauera, Azoarcus, Pseudomonas and other Proteobacteria formed in the sludge during acclimation. Catechol group had the least dominant bacteria and loop ring opening enzyme genes (catA, dmpB, dxnF, hapD) numbers. Therefore, the degradation of catechol was the most difficult than resorcinol and hydroquinone, resulting the highest sludge toxicity.},
}
@article {pmid34865800,
year = {2021},
author = {Zhang, Z and Han, Z and Wu, Y and Jiang, S and Ma, C and Zhang, Y and Zhang, J},
title = {Metagenomics assembled genome scale analysis revealed the microbial diversity and genetic polymorphism of Lactiplantibacillus plantarum in traditional fermented foods of Hainan, China.},
journal = {Food research international (Ottawa, Ont.)},
volume = {150},
number = {Pt A},
pages = {110785},
doi = {10.1016/j.foodres.2021.110785},
pmid = {34865800},
issn = {1873-7145},
mesh = {*Fermented Foods ; Food Microbiology ; Humans ; Metagenomics ; *Microbiota ; Polymorphism, Genetic ; },
abstract = {Exploring the microbiome in fermented foods and their effects on food quality and sustainability is beneficial to provide data support for understanding how they affects human physiology. Here, metagenomic sequencing and metagenomic assembled genomes (MAGs) were applied to appraise the microbial diversity of fermented Yucha (FYC) and fermented vegetables (FVE). The antibiotic resistance genes (ARGs) enrichment and genetic polymorphism of Lactiplantibacillus plantarum in fermented foods of different regions were compared. The results showed that Lactiplantibacillus plantarum was the dominant species in FYC, while Lactiplantibacillus fermentum in FVE occupied the dominant position. From 32 high-quality MAGs, the central differential Lactic acid bacteria were higher in FVE. By comparing the Lactiplantibacillus plantarum MAGs in Hainan and Other regions, we found that the total Single Nucleotide Polymorphisms of Lactiplantibacillus plantarum in Hainan were significantly higher than other areas. Six non-synonymous mutations were included in the primary differential mutation, especially TrkA family potassium uptake protein and MerR family transcriptional regulator, which may be related to the hypersaline environment and highest ARGs enrichment in Hainan. This research provides valuable insight into our understanding of the microbiome of fermented food. Meanwhile, the analysis of Lactiplantibacillus plantarum genetic polymorphism based on MAGs helps us understand this strain's evolutionary history.},
}
@article {pmid34844317,
year = {2022},
author = {Chen, S and Holyoak, M and Liu, H and Bao, H and Ma, Y and Dou, H and Jiang, G},
title = {Effects of spatially heterogeneous warming on gut microbiota, nutrition and gene flow of a heat-sensitive ungulate population.},
journal = {The Science of the total environment},
volume = {806},
number = {Pt 1},
pages = {150537},
doi = {10.1016/j.scitotenv.2021.150537},
pmid = {34844317},
issn = {1879-1026},
mesh = {Animals ; *Deer ; Ecosystem ; *Gastrointestinal Microbiome ; Gene Flow ; Hot Temperature ; },
abstract = {Effects of climate warming on trophic cascades are increasingly reported for large herbivores occupying northern latitudes. During the last 40 years, moose (Alces alces) in northeast China have lost nearly half of their historical distribution through their habitat shifting northwards. There are many possible causes of bottom-up and top-down effects of temperature and for moose in northeast China they are poorly understood. Of particular relevance are the effects of extrinsic environmental factors on gene flow, nutritional adaptions, and gut microbiota that occur as moose populations retreat northwards. We combined molecular biology, nutritional ecology and metagenomics to gain deeper mechanistic insights into the effects of temperature on moose populations. In this study, we revealed that the direction and intensity of gene flow is consistent with global warming driving retreats of moose populations. We interpret this as evidence for the northward movement of moose populations, with cooler northern populations receiving more immigrants and warmer southern populations supplying emigrants. Comparison across latitudes showed that warmer late spring temperatures were associated with plant community composition and facilitated related changes in moose protein and carbohydrate intake through altering forage availability, forage quality and diet composition. Furthermore, these nutrient shifts were accompanied by changes in gut microbial composition and functional pathways related to nutrient metabolism. This study provided insights into mechanisms driving effects of spatial heterogeneous warming on genetic, nutritional and physiological adaptions related to key demographic rates and patterns of survival of heat-sensitive ungulates along a latitude gradient. Understanding such changes helps to identify key habitat areas and plant species to ensure accurate assessment of population status and targeted management of moose populations.},
}
@article {pmid34824201,
year = {2021},
author = {Li, L and Solvi, C and Zhang, F and Qi, Z and Chittka, L and Zhao, W},
title = {Gut microbiome drives individual memory variation in bumblebees.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {6588},
pmid = {34824201},
issn = {2041-1723},
mesh = {Animals ; Bacteria/genetics/metabolism ; Bees/*microbiology/*physiology ; Gastrointestinal Microbiome/genetics/*physiology ; Glycerophospholipids/metabolism ; Individuality ; Lactobacillus/genetics/metabolism ; Memory, Long-Term/*physiology ; Metabolomics ; Metagenome ; *Metagenomics ; },
abstract = {The potential of the gut microbiome as a driver of individual cognitive differences in natural populations of animals remains unexplored. Here, using metagenomic sequencing of individual bumblebee hindguts, we find a positive correlation between the abundance of Lactobacillus Firm-5 cluster and memory retention on a visual discrimination task. Supplementation with the Firm-5 species Lactobacillus apis, but not other non-Firm-5 bacterial species, enhances bees' memory. Untargeted metabolomics after L. apis supplementation show increased LPA (14:0) glycerophospholipid in the haemolymph. Oral administration of the LPA increases long-term memory significantly. Based on our findings and metagenomic/metabolomic analyses, we propose a molecular pathway for this gut-brain interaction. Our results provide insights into proximate and ultimate causes of cognitive differences in natural bumblebee populations.},
}
@article {pmid34780902,
year = {2022},
author = {Innard, N and Chong, JPJ},
title = {The challenges of monitoring and manipulating anaerobic microbial communities.},
journal = {Bioresource technology},
volume = {344},
number = {Pt B},
pages = {126326},
doi = {10.1016/j.biortech.2021.126326},
pmid = {34780902},
issn = {1873-2976},
mesh = {Anaerobiosis ; Animals ; Biomass ; *Bioreactors ; *Microbiota ; },
abstract = {Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.},
}
@article {pmid34773153,
year = {2021},
author = {Kwon, YJ and Kwak, HJ and Lee, HK and Lim, HC and Jung, DH},
title = {Comparison of bacterial community profiles from large intestine specimens, rectal swabs, and stool samples.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {24},
pages = {9273-9284},
pmid = {34773153},
issn = {1432-0614},
mesh = {Bacteria/genetics ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rectum ; },
abstract = {The human gastrointestinal tract contains a complex and dynamic population of microorganisms, known as the gut microbiota. Although interest in the role of the gut microbiota in human health has increased in recent years, there remains no standard sampling protocol for analyzing these organisms. Here, we aimed to characterize the microbial composition of distinct segments of the large intestine and to determine whether rectal swabs are suitable for identifying colon microbiota. A total of 100 participants who underwent screening colonoscopy from October 2019 to October 2020 were included in this study. Large intestinal samples (ascending colon, descending colon, sigmoid colon, and rectum) were aspirated by colonoscopy. Rectal swabs were collected before colonoscopy, and stool samples were collected before patients began colonoscopy preparation. All samples were subjected to 16S ribosomal RNA gene sequencing. We identified differences in the number of phylum-level operational taxonomic units among large intestinal samples, rectal swabs, and stool. Five major phyla were detected in all samples (Firmicutes, Bacteroides, Proteobacteria, Actinobacteria, Fusobacteria), although their relative abundances varied. Notably, we found that the microbial compositions of rectal swabs were most similar to those of the sigmoid colon and rectum, whereas the microbiota in stool were relatively different than those from the large intestine and rectal swabs. Our results reveal the existence of microbial heterogeneity within different large intestinal compartments and further suggest that rectal swabs are an acceptable and practical tool for gut microbiota analysis. KEY POINTS: • Our findings highlight local microbiome variations within different regions of the large intestine. • Stool samples do not appear to fully recapitulate the gut microbiome. • Our data from a large population-based cohort indicate that rectal swabs can be used to study the gut microbiome.},
}
@article {pmid34756979,
year = {2022},
author = {Liu, L and Wang, F and Xu, S and Yan, Z and Ji, M},
title = {Long-term effect of fulvic acid amendment on the anammox biofilm system at 15 ℃: performance, microbial community and metagenomics analysis.},
journal = {Bioresource technology},
volume = {344},
number = {Pt B},
pages = {126234},
doi = {10.1016/j.biortech.2021.126234},
pmid = {34756979},
issn = {1873-2976},
mesh = {Anaerobic Ammonia Oxidation ; Anaerobiosis ; Benzopyrans ; Biofilms ; Bioreactors ; *Metagenomics ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; },
abstract = {The role of fulvic acid (FA) on the anammox system at 15 ℃ was investigated. After operation for 113 days, total inorganic nitrogen removal efficiency in FA amendment reactor achieved to 58.6% on average, higher than that of control group (42.1%). Anammox-related functional genes, i.e., hzo and hzs, also demonstrated higher expression level after introduction of FA. It was observed that Candidatus Kuenenia became more competitive than Candidatus Brocadia with the existence of FA at 15 ℃. Also, co-occurrence analysis showed that FA stimulated the complexity and interactive relationship of microbial communities in the anammox system. Metagenomics analysis revealed that FA introduction stimulated relative abundances of genes in central pathway of tricarboxylic acid cycle such as ACO, IDH, OGDH, SCS, FUM, and MDH. Meanwhile, metabolomics analysis revealed that metabolites related to amino sugar metabolic pathways (glucose 1-phosphate, UDP-D-glucuronate, UDP) and redox reactions (NAD+ and NADH) improved in the FA amendment reactor.},
}
@article {pmid34740587,
year = {2021},
author = {Corrêa, PS and Mendes, LW and Lemos, LN and Sampaio, ACK and Issakowicz, J and McManus, CM and Tsai, SM and Faciola, AP and Abdalla, AL and Louvandini, H},
title = {The effect of Haemonchus contortus and Trichostrongylus colubriforms infection on the ruminal microbiome of lambs.},
journal = {Experimental parasitology},
volume = {231},
number = {},
pages = {108175},
doi = {10.1016/j.exppara.2021.108175},
pmid = {34740587},
issn = {1090-2449},
mesh = {Animals ; Chromatography, Gas/methods/veterinary ; DNA/chemistry/isolation &amp; purification ; Flame Ionization/veterinary ; *Gastrointestinal Microbiome ; Haemonchiasis/complications/microbiology/*veterinary ; Metagenomics ; Methane/analysis/metabolism ; Purines/urine ; Real-Time Polymerase Chain Reaction/veterinary ; Rumen/*microbiology ; Sequence Analysis, DNA/veterinary ; Sheep ; Sheep Diseases/*microbiology/*parasitology ; Trichostrongyloidiasis/complications/microbiology/*veterinary ; },
abstract = {We evaluated Haemonchus contortus (HC) and Trichostrongylus colubriformis (TC) infection on the ruminal microbial community of Santa Ines lambs to better understand the pathophysiology of parasite infections and the interactions among gastrointestinal nematodes and gut resident microbiota. In this study, 18 six months of age lambs were maintained for 34 days in individual pens divided into three treatments that included animals infected with HC and TC, and control (infection-free). Haematological, ruminal parameter and microbial nitrogen absorbed by pune derivatives, as well as enteric methane emission (CH4), were analysed, and the rumen microbial taxonomic and functional profile assessed by shotgun metagenomics. The analysis showed that total protein, albumin, urea, and butyrate level were lower in animals infected by both parasites, while HC infection also decreased the haemoglobin level. Both infected groups (TC and HC) increased the enteric methane emission (CH4). TC and HC infections increased the diversity and richness of functional microbial genes. Most alterations in the rumen microbiome composition of infected groups are associated with the suppression of microbes involved in microbial homeostasis maintenance and expansion of the archaeal community in the infected animals. Infection led to an increased abundance of nitrogen, amino acid, protein, and energy metabolism genes. Overall, TC and HC infection increased the enteric methane emission, negatively affected taxon's responsible for maintenance de rumen homeostasis and modulated some important genes related to protein and energy metabolism.},
}
@article {pmid34710599,
year = {2022},
author = {Kim, H and Kang, S and Sang, BI},
title = {Metabolic cascade of complex organic wastes to medium-chain carboxylic acids: A review on the state-of-the-art multi-omics analysis for anaerobic chain elongation pathways.},
journal = {Bioresource technology},
volume = {344},
number = {Pt A},
pages = {126211},
doi = {10.1016/j.biortech.2021.126211},
pmid = {34710599},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Bioreactors ; Carboxylic Acids ; Fermentation ; *Microbiota ; },
abstract = {Medium-chain carboxylic acid (MCCA) production from organic wastes has attracted much attention because of their higher energy contents and diverse applications. Anaerobic reactor microbiomes are stable and resilient and have resulted in efficient performance during many years of operation for thousands of full-scale anaerobic digesters worldwide. The method underlying how the relevant microbial pathways contribute to elongate carbon chains in reactor microbiomes is important. In particular, the reverse β-oxidation pathway genes are critical to upgrading short-chain fermentation products to MCCAs via a chain elongation (CE) process. Diverse genomics and metagenomics studies have been conducted in various fields, ranging from intracellular metabolic pathways to metabolic cascades between different strains. This review covers taxonomic approach to culture processes depending on types of organic wastes and the deeper understanding of genome and metagenome-scale CE pathway construction, and the co-culture and multi-omics technology that should be addressed in future research.},
}
@article {pmid34685776,
year = {2021},
author = {Kameli, N and Becker, HEF and Welbers, T and Jonkers, DMAE and Penders, J and Savelkoul, P and Stassen, FR},
title = {Metagenomic Profiling of Fecal-Derived Bacterial Membrane Vesicles in Crohn's Disease Patients.},
journal = {Cells},
volume = {10},
number = {10},
pages = {},
pmid = {34685776},
issn = {2073-4409},
mesh = {Bacteria/*metabolism ; Biodiversity ; Cell Membrane/*metabolism ; Crohn Disease/*microbiology ; DNA, Bacterial/genetics ; Feces/*microbiology ; Humans ; *Metagenomics ; },
abstract = {BACKGROUND: In the past, many studies suggested a crucial role for dysbiosis of the gut microbiota in the etiology of Crohn's disease (CD). However, despite being important players in host-bacteria interaction, the role of bacterial membrane vesicles (MV) has been largely overlooked in the pathogenesis of CD. In this study, we addressed the composition of the bacterial and MV composition in fecal samples of CD patients and compared this to the composition in healthy individuals.<br><br>METHODS: Fecal samples from six healthy subjects (HC) in addition to twelve CD patients (six active, six remission) were analyzed in this study. Fecal bacterial membrane vesicles (fMVs) were isolated by a combination of ultrafiltration and size exclusion chromatography. DNA was obtained from the fMV fraction, the pellet of dissolved feces as bacterial DNA (bDNA), or directly from feces as fecal DNA (fDNA). The fMVs were characterized by nanoparticle tracking analysis and cryo-electron microscopy. Amplicon sequencing of 16s rRNA V4 hypervariable gene regions was conducted to assess microbial composition of all fractions.<br><br>RESULTS: Beta-diversity analysis showed that the microbial community structure of the fMVs was significantly different from the microbial profiles of the fDNA and bDNA. However, no differences were observed in microbial composition between fDNA and bDNA. The microbial richness of fMVs was significantly decreased in CD patients compared to HC, and even lower in active patients. Profiling of fDNA and bDNA demonstrated that Firmicutes was the most dominant phylum in these fractions, while in fMVs Bacteroidetes was dominant. In fMV, several families and genera belonging to Firmicutes and Proteobacteria were significantly altered in CD patients when compared to HC.<br><br>CONCLUSION: The microbial alterations of MVs in CD patients particularly in Firmicutes and Proteobacteria suggest a possible role of MVs in host-microbe symbiosis and induction or progression of inflammation in CD pathogenesis. Yet, the exact role for these fMV in the pathogenesis of the disease needs to be elucidated in future studies.},
}
@article {pmid34681921,
year = {2021},
author = {Lacroix, V and Cassard, A and Mas, E and Barreau, F},
title = {Multi-Omics Analysis of Gut Microbiota in Inflammatory Bowel Diseases: What Benefits for Diagnostic, Prognostic and Therapeutic Tools?.},
journal = {International journal of molecular sciences},
volume = {22},
number = {20},
pages = {},
pmid = {34681921},
issn = {1422-0067},
mesh = {Bacteria/*classification/isolation &amp; purification ; Disease Progression ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases/*microbiology ; Metagenomics/*methods ; Phylogeny ; Precision Medicine ; },
abstract = {Inflammatory bowel diseases (IBDs), which include Crohn's disease and ulcerative colitis, are multifactorial diseases that involve in particular a modification of the gut microbiota, known as dysbiosis. The initial sets of metataxonomic and metagenomic data first made it possible to approximate the microbiota profile in IBD. In addition, today the new 'omics' techniques have enabled us to draw up a functional and integrative map of the microbiota. The key concern in IBD is to develop biomarkers that allow us to assess the activity of the disease and predict the complications and progression, while also guiding the therapeutic care so as to develop personalized medicine. In this review, we present all of the latest discoveries on the microbiota provided by "omics" and we outline the benefits of these techniques in developing new diagnostic, prognostic and therapeutic tools.},
}
@article {pmid34673779,
year = {2021},
author = {Sugimoto, R and Nishimura, L and Nguyen, PT and Ito, J and Parrish, NF and Mori, H and Kurokawa, K and Nakaoka, H and Inoue, I},
title = {Comprehensive discovery of CRISPR-targeted terminally redundant sequences in the human gut metagenome: Viruses, plasmids, and more.},
journal = {PLoS computational biology},
volume = {17},
number = {10},
pages = {e1009428},
pmid = {34673779},
issn = {1553-7358},
mesh = {Archaea/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/*genetics ; Gastrointestinal Microbiome/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics ; Plasmids/*genetics ; Sequence Analysis, DNA ; Viruses/*genetics ; },
abstract = {Viruses are the most numerous biological entity, existing in all environments and infecting all cellular organisms. Compared with cellular life, the evolution and origin of viruses are poorly understood; viruses are enormously diverse, and most lack sequence similarity to cellular genes. To uncover viral sequences without relying on either reference viral sequences from databases or marker genes that characterize specific viral taxa, we developed an analysis pipeline for virus inference based on clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR is a prokaryotic nucleic acid restriction system that stores the memory of previous exposure. Our protocol can infer CRISPR-targeted sequences, including viruses, plasmids, and previously uncharacterized elements, and predict their hosts using unassembled short-read metagenomic sequencing data. By analyzing human gut metagenomic data, we extracted 11,391 terminally redundant CRISPR-targeted sequences, which are likely complete circular genomes. The sequences included 2,154 tailed-phage genomes, together with 257 complete crAssphage genomes, 11 genomes larger than 200 kilobases, 766 genomes of Microviridae species, 56 genomes of Inoviridae species, and 95 previously uncharacterized circular small genomes that have no reliably predicted protein-coding gene. We predicted the host(s) of approximately 70% of the discovered genomes at the taxonomic level of phylum by linking protospacers to taxonomically assigned CRISPR direct repeats. These results demonstrate that our protocol is efficient for de novo inference of CRISPR-targeted sequences and their host prediction.},
}
@article {pmid34637433,
year = {2021},
author = {Matsumoto, K and Sakami, T and Watanabe, T and Taniuchi, Y and Kuwata, A and Kakehi, S and Engkong, T and Igarashi, Y and Kinoshita, S and Asakawa, S and Hattori, M and Watabe, S and Ishino, Y and Kobayashi, T and Gojobori, T and Ikeo, K},
title = {Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters.},
journal = {PloS one},
volume = {16},
number = {10},
pages = {e0257862},
pmid = {34637433},
issn = {1932-6203},
mesh = {Bays/microbiology ; Chlorophyll A/metabolism ; Cyanobacteria/*genetics ; Japan ; *Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Phylogeny ; Phytoplankton/*genetics ; RNA, Ribosomal, 16S/genetics ; Salinity ; *Seasons ; Seawater/chemistry/*microbiology ; Temperature ; },
abstract = {The taxonomic compositions of marine prokaryotic communities are known to follow seasonal cycles, but functional metagenomic insights into this seasonality is still limited. We analyzed a total of 22 metagenomes collected at 11 time points over a 14-month period from two sites in Sendai Bay, Japan to obtain seasonal snapshots of predicted functional profiles of the non-cyanobacterial prokaryotic community. Along with taxonomic composition, functional gene composition varied seasonally and was related to chlorophyll a concentration, water temperature, and salinity. Spring phytoplankton bloom stimulated increased abundances of putative genes that encode enzymes in amino acid metabolism pathways. Several groups of functional genes, including those related to signal transduction and cellular communication, increased in abundance during the mid- to post-bloom period, which seemed to be associated with a particle-attached lifestyle. Alternatively, genes in carbon metabolism pathways were generally more abundant in the low chlorophyll a period than the bloom period. These results indicate that changes in trophic condition associated with seasonal phytoplankton succession altered the community function of prokaryotes. Our findings on seasonal changes of predicted function provide fundamental information for future research on the mechanisms that shape marine microbial communities.},
}
@article {pmid34606860,
year = {2022},
author = {Chen, G and Bai, R and Zhang, Y and Zhao, B and Xiao, Y},
title = {Application of metagenomics to biological wastewater treatment.},
journal = {The Science of the total environment},
volume = {807},
number = {Pt 1},
pages = {150737},
doi = {10.1016/j.scitotenv.2021.150737},
pmid = {34606860},
issn = {1879-1026},
mesh = {Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Metagenomics ; *Microbiota ; *Water Purification ; },
abstract = {Biological wastewater treatment is a process in which the microbial metabolism of complex communities transforms pollutants into low- or non-toxic products. Due to the absence of an in-depth understanding of the diversity and complexity of microbial communities, it is very likely to ignore the potential mechanisms of microbial community in wastewater treatment. Metagenomics is a technology based on molecular biology, in which massive gene sequences are obtained from environmental samples and analyzed by bioinformatics to determine the composition and function of a microbial community. Metagenomics can identify the state of microbes in their native environments more effectively than traditional molecular methods. This review summarizes the application of metagenomics to assess microbial communities in biological wastewater treatment, such as the biological removal of phosphorus and nitrogen by bacteria, the study of antibiotic resistance genes (ARGs), and the reduction of heavy metals by microbial communities, with an emphasis on the contribution of microbial diversity and metabolic diversity. Technical bottlenecks in the application of metagenomics to biological wastewater treatment are elucidated, and future research directions for metagenomics are proposed, among which the application of multi-omics will be an important research method for future biological wastewater treatment.},
}
@article {pmid34592929,
year = {2021},
author = {Shao, L and Liao, J and Qian, J and Chen, W and Fan, X},
title = {MetaGeneBank: a standardized database to study deep sequenced metagenomic data from human fecal specimen.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {263},
pmid = {34592929},
issn = {1471-2180},
mesh = {*Databases, Genetic ; Feces/*microbiology ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*instrumentation ; },
abstract = {BACKGROUND: Microbiome big data from population-scale cohorts holds the key to unleash the power of microbiomes to overcome critical challenges in disease control, treatment and precision medicine. However, variations introduced during data generation and processing limit the comparisons among independent studies in respect of interpretability. Although multiple databases have been constructed as platforms for data reuse, they are of limited value since only raw sequencing files are considered.<br><br>DESCRIPTION: Here, we present MetaGeneBank, a standardized database that provides details on sample collection and sequencing, and abundances of genes, microbiota and molecular functions for 4470 raw sequencing files (over 12 TB) collected from 16 studies covering over 10 types of diseases and 14 countries using a unified data-processing pipeline. The incorporation of tools that enable browsing and searching with descriptive attributes, gene sequences, microbiota and functions makes the database user-friendly. We found that the source of specimen contributes more than sequencing centers or platforms to the variations of microbiota. Special attention should be paid when re-analyzing sequencing files from different countries.<br><br>CONCLUSIONS: Collectively, MetaGeneBank provides a gateway to utilize the untapped potential of gut metagenomic data in helping fighting against human diseases. With the continuous updating of the database in terms of data volume, data types and sample types, MetaGeneBank would undoubtedly be the benchmarking database in the future in respect of data reuse, and would be valuable in translational science.},
}
@article {pmid34526611,
year = {2021},
author = {Garneau, JR and Legrand, V and Marbouty, M and Press, MO and Vik, DR and Fortier, LC and Sullivan, MB and Bikard, D and Monot, M},
title = {High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {18319},
pmid = {34526611},
issn = {2045-2322},
mesh = {Algorithms ; Bacteriophages/*genetics/physiology ; Computational Biology/methods ; Databases, Genetic ; *Genome, Viral ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Software ; *Viral Packaging Sequence ; *Virome ; Workflow ; },
abstract = {Viruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv .},
}
@article {pmid34526566,
year = {2021},
author = {Misra, N and Clavaud, C and Guinot, F and Bourokba, N and Nouveau, S and Mezzache, S and Palazzi, P and Appenzeller, BMR and Tenenhaus, A and Leung, MHY and Lee, PKH and Bastien, P and Aguilar, L and Cavusoglu, N},
title = {Multi-omics analysis to decipher the molecular link between chronic exposure to pollution and human skin dysfunction.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {18302},
pmid = {34526566},
issn = {2045-2322},
mesh = {*Biomarkers ; Disease Susceptibility ; Environmental Exposure/*adverse effects ; Environmental Pollution/*adverse effects ; *Genomics/methods ; Humans ; *Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Microbiota ; Skin/*metabolism/microbiology/pathology ; Skin Diseases/etiology/metabolism/pathology ; },
abstract = {Environmental pollution is composed of several factors, namely particulate matter (PM2.5, PM10), ozone and Ultra Violet (UV) rays among others and first and the most exposed tissue to these substances is the skin epidermis. It has been established that several skin disorders such as eczema, acne, lentigines and wrinkles are aggravated by exposure to atmospheric pollution. While pollutants can interact with skin surface, contamination of deep skin by ultrafine particles or Polycyclic aromatic hydrocarbons (PAH) might be explained by their presence in blood and hair cortex. Molecular mechanisms leading to skin dysfunction due to pollution exposure have been poorly explored in humans. In addition to various host skin components, cutaneous microbiome is another target of these environment aggressors and can actively contribute to visible clinical manifestation such as wrinkles and aging. The present study aimed to investigate the association between pollution exposure, skin microbiota, metabolites and skin clinical signs in women from two cities with different pollution levels. Untargeted metabolomics and targeted proteins were analyzed from D-Squame samples from healthy women (n = 67 per city), aged 25-45 years and living for at least 15 years in the Chinese cities of Baoding (used as a model of polluted area) and Dalian (control area with lower level of pollution). Additional samples by swabs were collected from the cheeks from the same population and microbiome was analysed using bacterial 16S rRNA as well as fungal ITS1 amplicon sequencing and metagenomics analysis. The level of exposure to pollution was assessed individually by the analysis of polycyclic aromatic hydrocarbons (PAH) and their metabolites in hair samples collected from each participant. All the participants of the study were assessed for the skin clinical parameters (acne, wrinkles, pigmented spots etc.). Women from the two cities (polluted and less polluted) showed distinct metabolic profiles and alterations in skin microbiome. Profiling data from 350 identified metabolites, 143 microbes and 39 PAH served to characterize biochemical events that correlate with pollution exposure. Finally, using multiblock data analysis methods, we obtained a potential molecular map consisting of multi-omics signatures that correlated with the presence of skin pigmentation dysfunction in individuals living in a polluted environment. Overall, these signatures point towards macromolecular alterations by pollution that could manifest as clinical sign of early skin pigmentation and/or other imperfections.},
}
@article {pmid34521917,
year = {2021},
author = {Leontidou, K and Vokou, D and Sandionigi, A and Bruno, A and Lazarina, M and De Groeve, J and Li, M and Varotto, C and Girardi, M and Casiraghi, M and Cristofori, A},
title = {Plant biodiversity assessment through pollen DNA metabarcoding in Natura 2000 habitats (Italian Alps).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {18226},
pmid = {34521917},
issn = {2045-2322},
mesh = {*Biodiversity ; DNA Barcoding, Taxonomic/*methods ; Genome, Plant ; Magnoliopsida/*classification/genetics/physiology ; Metagenome ; Metagenomics/*methods ; Pollen/*genetics ; },
abstract = {Monitoring biodiversity is of increasing importance in natural ecosystems. Metabarcoding can be used as a powerful molecular tool to complement traditional biodiversity monitoring, as total environmental DNA can be analyzed from complex samples containing DNA of different origin. The aim of this research was to demonstrate the potential of pollen DNA metabarcoding using the chloroplast trnL partial gene sequencing to characterize plant biodiversity. Collecting airborne biological particles with gravimetric Tauber traps in four Natura 2000 habitats within the Natural Park of Paneveggio Pale di San Martino (Italian Alps), at three-time intervals in 1 year, metabarcoding identified 68 taxa belonging to 32 local plant families. Metabarcoding could identify with finer taxonomic resolution almost all non-rare families found by conventional light microscopy concurrently applied. However, compared to microscopy quantitative results, Poaceae, Betulaceae, and Oleaceae were found to contribute to a lesser extent to the plant biodiversity and Pinaceae were more represented. Temporal changes detected by metabarcoding matched the features of each pollen season, as defined by aerobiological studies running in parallel, and spatial heterogeneity was revealed between sites. Our results showcase that pollen metabarcoding is a promising approach in detecting plant species composition which could provide support to continuous monitoring required in Natura 2000 habitats for biodiversity conservation.},
}
@article {pmid34518213,
year = {2021},
author = {Six, C and Ratin, M and Marie, D and Corre, E},
title = {Marine Synechococcus picocyanobacteria: Light utilization across latitudes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {38},
pages = {},
pmid = {34518213},
issn = {1091-6490},
mesh = {Adaptation, Physiological/genetics/physiology ; Bacterial Proteins/genetics ; Cold Temperature ; Ecosystem ; Ecotype ; Light ; Metagenome/genetics ; Metagenomics/methods ; Photosynthesis/genetics/physiology ; Seawater ; Synechococcus/*genetics/*physiology ; },
abstract = {The most ubiquitous cyanobacteria, Synechococcus, have colonized different marine thermal niches through the evolutionary specialization of lineages adapted to different ranges of temperature seawater. We used the strains of Synechococcus temperature ecotypes to study how light utilization has evolved in the function of temperature. The tropical Synechococcus (clade II) was unable to grow under 16 °C but, at temperatures >25 °C, induced very high growth rates that relied on a strong synthesis of the components of the photosynthetic machinery, leading to a large increase in photosystem cross-section and electron flux. By contrast, the Synechococcus adapted to subpolar habitats (clade I) grew more slowly but was able to cope with temperatures <10 °C. We show that growth at such temperatures was accompanied by a large increase of the photoprotection capacities using the orange carotenoid protein (OCP). Metagenomic analyzes revealed that Synechococcus natural communities show the highest prevalence of the ocp genes in low-temperature niches, whereas most tropical clade II Synechococcus have lost the gene. Moreover, bioinformatic analyzes suggested that the OCP variants of the two cold-adapted Synechococcus clades I and IV have undergone evolutionary convergence through the adaptation of the molecular flexibility. Our study points to an important role of temperature in the evolution of the OCP. We, furthermore, discuss the implications of the different metabolic cost of these physiological strategies on the competitiveness of Synechococcus in a warming ocean. This study can help improve the current hypotheses and models aimed at predicting the changes in ocean carbon fluxes in response to global warming.},
}
@article {pmid34508122,
year = {2021},
author = {Suriyaphol, P and Chiu, JKH and Yimpring, N and Tunsagool, P and Mhuantong, W and Chuanchuen, R and Bessarab, I and Williams, RBH and Ong, RT and Suriyaphol, G},
title = {Dynamics of the fecal microbiome and antimicrobial resistome in commercial piglets during the weaning period.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {18091},
pmid = {34508122},
issn = {2045-2322},
mesh = {Age Factors ; Animals ; Anti-Bacterial Agents/*pharmacology ; Biodiversity ; Feces/*microbiology ; Metagenome ; Metagenomics/methods ; Microbiota/*drug effects ; Swine ; *Weaning ; },
abstract = {This study aimed to characterize the alteration of the fecal microbiome and antimicrobial resistance (AMR) determinants in 24 piglets at day 3 pre-weaning (D. - 3), weaning day (D.0), days 3 (D.3) and 8 post-weaning (D.8), using whole-genome shotgun sequencing. Distinct clusters of microbiomes and AMR determinants were observed at D.8 when Prevotella (20.9%) was the major genus, whereas at D. - 3-D.3, Alistipes (6.9-12.7%) and Bacteroides (5.2-8.5%) were the major genera. Lactobacillus and Escherichia were notably observed at D. - 3 (1.2%) and D. - 3-D.3 (0.2-0.4%), respectively. For AMR, a distinct cluster of AMR determinants was observed at D.8, mainly conferring resistance to macrolide-lincosamide-streptogramin (mefA), β-lactam (cfxA6 and aci1) and phenicol (rlmN). In contrast, at D. - 3-D.3, a high abundance of determinants with aminoglycoside (AMG) (sat, aac(6')-aph(2''), aadA and acrF), β-lactam (fus-1, cepA and mrdA), multidrug resistance (MDR) (gadW, mdtE, emrA, evgS, tolC and mdtB), phenicol (catB4 and cmlA4), and sulfonamide patterns (sul3) was observed. Canonical correlation analysis (CCA) plot associated Escherichia coli with aac(6')-aph(2''), emrA, mdtB, catB4 and cmlA4 at D. - 3, D.0 and/or D.3 whereas at D.8 associations between Prevotella and mefA, cfxA6 and aci1 were identified. The weaning age and diet factor played an important role in the microbial community composition.},
}
@article {pmid34488552,
year = {2021},
author = {Chen, J and Wang, S and Shen, J and Hu, Q and Zhang, Y and Ma, D and Chai, K},
title = {Analysis of Gut Microbiota Composition in Lung Adenocarcinoma Patients with TCM Qi-Yin Deficiency.},
journal = {The American journal of Chinese medicine},
volume = {49},
number = {7},
pages = {1667-1682},
doi = {10.1142/S0192415X21500786},
pmid = {34488552},
issn = {1793-6853},
mesh = {Adenocarcinoma of Lung/*microbiology ; Adolescent ; Adult ; Aged ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Lung Neoplasms/*microbiology ; Medicine, Chinese Traditional ; Middle Aged ; Yin Deficiency/*microbiology ; Young Adult ; },
abstract = {In Lung adenocarcinoma (ADC), Qi-Yin deficiency syndrome (QY) is the most common Traditional Chinese medicine (TCM) syndrome. This study aimed to investigate the diversity and composition of gut microbiota in ADC patients with QY syndrome. 90 stool samples, including 30 healthy individuals (H), 30 ADC patients with QY syndrome, and 30 ADC patients with another syndrome (O) were collected. Then, 16s-RNA sequencing was used to analyze stool samples to clarify the structure of gut microbiota, and linear discriminant analysis (LDA) effect size (LEfSe) was applied to identify biomarkers for ADC with QY syndrome. Logistic regression analysis was performed to establish a diagnostic model for the diagnosis of QY syndrome in ADC patients, which was assessed with the AUC. Finally, 20 fecal samples (QY: 10; O: 10) were analyzed with Metagenomics to validate the diagnostic model. The [Formula: see text] diversity and [Formula: see text] diversity demonstrated that the structure of gut microbiota in the QY group was different from that of the H group and O group. In the QY group, the top 3 taxonomies at phylum level were Firmicutes, Bacteroidetes, and Proteobacteria, and at genus level were Faecalibacterium, Prevotella_9, and Bifidobacterium. LEfSe identified Prevotella_9 and Streptococcus might be the biomarkers for QY syndrome. A diagnostic model was constructed using those 2 genera with the AUC = 0.801, similar to the AUC based on Metagenomics (0.842). The structure of gut microbiota in ADC patients with QY syndrome was investigated, and a diagnostic model was developed for the diagnosis of QY syndrome in ADC patients, which provides a novel idea for the understanding and diagnosis of TCM syndrome.},
}
@article {pmid34426398,
year = {2021},
author = {Tomofuji, Y and Maeda, Y and Oguro-Igashira, E and Kishikawa, T and Yamamoto, K and Sonehara, K and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Yagita, M and Nii, T and Ohshima, S and Nakamura, S and Inohara, H and Takeda, K and Kumanogoh, A and Okada, Y},
title = {Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese.},
journal = {Annals of the rheumatic diseases},
volume = {80},
number = {12},
pages = {1575-1583},
pmid = {34426398},
issn = {1468-2060},
mesh = {Adult ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial/*genetics ; Genome-Wide Association Study ; Humans ; Japan ; Lupus Erythematosus, Systemic/genetics/*microbiology ; Male ; Metabolic Networks and Pathways/genetics ; *Metagenome ; Metagenomics ; Middle Aged ; Streptococcus anginosus/*genetics ; Streptococcus intermedius/*genetics ; },
abstract = {OBJECTIVE: Alteration of the gut microbiome has been linked to the pathogenesis of systemic lupus erythematosus (SLE). However, a comprehensive view of the gut microbiome in SLE and its interaction with the host remains to be revealed. This study aimed to reveal SLE-associated changes in the gut microbiome and its interaction with the host by a comprehensive metagenome-wide association study (MWAS) followed by integrative analysis.<br><br>METHODS: We performed a MWAS of SLE based on shotgun sequencing of the gut microbial DNA from Japanese individuals (N case=47, N control=203). We integrated the result of the MWAS with the genome-wide association study (GWAS) data and plasma metabolite data.<br><br>RESULTS: Via species level phylogenetic analysis, we identified and validated increases of Streptococcus intermedius and Streptococcus anginosus in the patients with SLE. Microbial gene analysis revealed increases of Streptococcus-derived genes including one involved in redox reaction. Additionally, microbial pathways related to sulfur metabolism and flagella assembly were altered in the patients with SLE. We identified an overlap in the enriched biological pathways between the metagenome and the germline genome by comparing the result of the MWAS and the GWAS of SLE (ie, MWAS-GWAS interaction). α-diversity and β-diversity analyses provided evidence of dysbiosis in the metagenome of the patients with SLE. Microbiome-metabolome association analysis identified positive dosage correlation of acylcarnitine with Streptococcus intermedius, an SLE-associated taxon.<br><br>CONCLUSION: Our MWAS followed by integrative analysis revealed SLE-associated changes in the gut microbiome and its interaction with the host, which contribute to our understanding of the relationship between the microbiome and SLE.},
}
@article {pmid34407871,
year = {2021},
author = {He, W and Chen, Y and Zhang, X and Peng, M and Xu, D and He, H and Gao, Y and Chen, J and Zhang, J and Li, Z and Chen, Q},
title = {Virome in adult Aedes albopictus captured during different seasons in Guangzhou City, China.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {415},
pmid = {34407871},
issn = {1756-3305},
support = {2018B020241002//Key-Area Research and Development Program of Guangdong Province/ ; },
mesh = {Aedes/classification/*virology ; Animals ; China ; Female ; Male ; Metagenomics/methods ; Mosquito Vectors/*virology ; *Seasons ; Virome/*genetics ; Viruses/classification/*genetics ; },
abstract = {BACKGROUND: The mosquito Aedes albopictus is an important vector for many pathogens. Understanding the virome in Ae. albopictus is critical for assessing the risk of disease transmission, implementation of vector control measures, and health system strengthening.<br><br>METHODS: In this study, viral metagenomic and PCR methods were used to reveal the virome in adult Ae. albopictus captured in different areas and during different seasons in Guangzhou, China.<br><br>RESULTS: The viral composition of adult Ae. albopictus varied mainly between seasons. Over 50 viral families were found, which were specific to vertebrates, invertebrates, plants, fungi, bacteria, and protozoa. In rural areas, Siphoviridae (6.5%) was the most common viral family harbored by mosquitoes captured during winter and spring, while Luteoviridae (1.1%) was the most common viral family harbored by mosquitoes captured during summer and autumn. Myoviridae (7.0% and 1.3%) was the most common viral family in mosquitoes captured in urban areas during all seasons. Hepatitis B virus (HBV) was detected by PCR in a female mosquito pool. The first near full-length HBV genome from Ae. albopictus was amplified, which showed a high level of similarity with human HBV genotype B sequences. Human parechovirus (HPeV) was detected in male and female mosquito pools, and the sequences were clustered with HPeV 1 and 3 sequences.<br><br>CONCLUSIONS: Large numbers of viral species were found in adult Ae. albopictus, including viruses from vertebrates, insects, and plants. The viral composition in Ae. albopictus mainly varied between seasons. Herein, we are the first to report the detection of HPeV and HBV in mosquitoes. This study not only provides valuable information for the control and prevention of mosquito-borne diseases, but it also demonstrates the feasibility of xenosurveillance.},
}
@article {pmid34400165,
year = {2022},
author = {Peña-Ocaña, BA and Ovando-Ovando, CI and Puente-Sánchez, F and Tamames, J and Servín-Garcidueñas, LE and González-Toril, E and Gutiérrez-Sarmiento, W and Jasso-Chávez, R and Ruíz-Valdiviezo, VM},
title = {Metagenomic and metabolic analyses of poly-extreme microbiome from an active crater volcano lake.},
journal = {Environmental research},
volume = {203},
number = {},
pages = {111862},
doi = {10.1016/j.envres.2021.111862},
pmid = {34400165},
issn = {1096-0953},
mesh = {Archaea/genetics ; Lakes ; Metagenome ; *Metagenomics ; *Microbiota ; Phylogeny ; },
abstract = {El Chichón volcano is one of the most active volcanoes in Mexico. Previous studies have described its poly-extreme conditions and its bacterial composition, although the functional features of the complete microbiome have not been characterized yet. By using metabarcoding analysis, metagenomics, metabolomics and enzymology techniques, the microbiome of the crater lake was characterized in this study. New information is provided on the taxonomic and functional diversity of the representative Archaea phyla, Crenarchaeota and Euryarchaeota, as well as those that are representative of Bacteria, Thermotogales and Aquificae. With culture of microbial consortia and with the genetic information collected from the natural environment sampling, metabolic interactions were identified between prokaryotes, which can withstand multiple extreme conditions. The existence of a close relationship between the biogeochemical cycles of carbon and sulfur in an active volcano has been proposed, while the relationship in the energy metabolism of thermoacidophilic bacteria and archaea in this multi-extreme environment was biochemically revealed for the first time. These findings contribute towards understanding microbial metabolism under extreme conditions, and provide potential knowledge pertaining to "microbial dark matter", which can be applied to biotechnological processes and evolutionary studies.},
}
@article {pmid34394092,
year = {2021},
author = {Doaré, E and Héry-Arnaud, G and Devauchelle-Pensec, V and Alegria, GC},
title = {Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren's Syndrome in a Systematic Review.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {699011},
pmid = {34394092},
issn = {1664-3224},
mesh = {*Control Groups ; *Dysbiosis ; Humans ; *Microbiota ; *Sjogren's Syndrome ; },
abstract = {Introduction: It has been hypothesized that gut and oral dysbiosis may contribute to the development of primary Sjögren's syndrome (pSS). The aim of this systematic review was to assemble available data regarding the oral and gut microbiota in pSS and to compare them to data from healthy individuals and patients with dry symptoms without a diagnosis of Sjögren's syndrome or lupus disease to identify dysbiosis and discuss the results.<br><br>Methodology: Using the PRISMA guidelines, we systematically reviewed studies that compared the oral and gut microbiota of Sjögren's patients and controls. The PubMed database and Google Scholar were searched.<br><br>Results: Two-hundred and eighty-nine studies were found, and 18 studies were included: 13 referred to the oral microbiota, 4 referred to the gut microbiota, and 1 referred to both anatomical sites. The most frequent controls were healthy volunteers and patients with sicca symptoms. The most common analysis method used was 16S-targeted metagenomics. The results were mostly heterogeneous, and the results regarding diversity were not always in accordance. Dysbiosis in pSS was not confirmed, and reduced salivary secretion seems to explain more microbial changes than the underlying disease.<br><br>Conclusion: These heterogeneous results might be explained by the lack of a standardized methodology at each step of the process and highlight the need for guidelines. Our review provides evidence that sicca patients seem to be more relevant than healthy subjects as a control group.},
}
@article {pmid34354708,
year = {2021},
author = {Wang, X and Yuan, X and Su, Y and Hu, J and Ji, Q and Fu, S and Li, R and Hu, L and Dai, C},
title = {Targeting Purinergic Receptor P2RX1 Modulates Intestinal Microbiota and Alleviates Inflammation in Colitis.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {696766},
pmid = {34354708},
issn = {1664-3224},
mesh = {Animals ; Antibodies, Neutralizing/*pharmacology ; Bacteria/*metabolism ; Benzenesulfonates/*pharmacology ; Colitis/immunology/metabolism/microbiology/*prevention &amp; control ; Colon/*drug effects/immunology/metabolism/microbiology ; Disease Models, Animal ; Drug Therapy, Combination ; Dysbiosis ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Mice, Knockout ; Purinergic P2X Receptor Antagonists/*pharmacology ; Receptors, Purinergic P2X1/genetics/*metabolism ; Signal Transduction ; Tumor Necrosis Factor Inhibitors/*pharmacology ; },
abstract = {Inflammatory bowel disease (IBD) remains one of the most prevalent gastrointestinal diseases worldwide. Purinergic signaling has emerged as a promising therapeutic target of inflammation-associated diseases. However, little is known about the specific roles of purinergic receptors in IBD. In the present study, expression profile of purinergic receptors was screened in the public Gene Expression Omnibus (GEO) datasets, and we found that expression of P2RX1 was significantly upregulated in inflamed colon tissues. Then, purinergic receptor P2RX1 was genetically ablated in the background of C57BL/6 mice, and dextran sulfate sodium (DSS) was used to induce mice colitis. RNA sequencing results of colon tissues showed that genetic knockout of P2RX1 suppressed the inflammation responses in DSS-induced mice colitis. Flow cytometry indicated that neutrophil infiltration was inhibited in P2RX1 ablated mice. 16S ribosomal DNA sequencing revealed major differences of intestinal microbiota between WT and P2RX1 ablated mice. Functional metagenomics prediction indicated that the indole alkaloid biogenesis pathway was upregulated in P2RX1 gene ablated mice. Further studies revealed that microbiota metabolites (indole alkaloid)-involved aryl hydrocarbon receptor (AhR)/IL-22 axis was associated with the beneficial effects of P2RX1 ablation. Finally, we found that a specific P2RX1 inhibitor succeeded to improve the therapeutic efficiency of anti-TNF-α therapy in DSS-induced mice colitis. Therefore, our study suggests that targeting purinergic receptor P2RX1 may provide novel therapeutic strategy for IBD.},
}
@article {pmid34256961,
year = {2021},
author = {Santiago-Rodriguez, TM and Hollister, EB},
title = {Multi 'omic data integration: A review of concepts, considerations, and approaches.},
journal = {Seminars in perinatology},
volume = {45},
number = {6},
pages = {151456},
doi = {10.1016/j.semperi.2021.151456},
pmid = {34256961},
issn = {1558-075X},
mesh = {*Genomics ; Humans ; Metabolomics ; *Microbiota ; Proteomics ; },
abstract = {The application of 'omic techniques including, but not limited to genomics/metagenomics, transcriptomics/meta-transcriptomics, proteomics/meta-proteomics, and metabolomics to generate multiple datasets from a single sample have facilitated hypothesis generation leading to the identification of biological, molecular and ecological functions and mechanisms, as well as associations and correlations. Despite their power and promise, a variety of challenges must be considered in the successful design and execution of a multi-omics study. In this review, various 'omic technologies applicable to single- and meta-organisms (i.e., host + microbiome) are described, and considerations for sample collection, storage and processing prior to data generation and analysis, as well as approaches to data storage, dissemination and analysis are discussed. Finally, case studies are included as examples of multi-omic applications providing novel insights and a more holistic understanding of biological processes.},
}
@article {pmid34253790,
year = {2021},
author = {Sawaswong, V and Praianantathavorn, K and Chanchaem, P and Khamwut, A and Kemthong, T and Hamada, Y and Malaivijitnond, S and Payungporn, S},
title = {Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14280},
pmid = {34253790},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; Body Weight ; Ecosystem ; Female ; Firmicutes/*metabolism ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Macaca/*microbiology/*physiology ; Male ; Metagenomics ; Microbiota ; Mouth Mucosa/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/metabolism ; Thailand ; Zoology ; },
abstract = {Long-tailed macaques (Macaca fascicularis), distributed in Southeast Asia, are generally used in biomedical research. At present, the expansion of human communities overlapping of macaques' natural habitat causes human-macaque conflicts. To mitigate this problem in Thailand, the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), was granted the permit to catch the surplus wild-born macaques and transfer them to the center. Based on the fact that the diets provided and the captive environments were different, their oral-gut microbiota should be altered. Thus, we investigated and compared the oral and fecal microbiome between wild-born macaques that lived in the natural habitats and those transferred to and reared in the NPRCT-CU for 1 year. The results from 16S rRNA high-throughput sequencing showed that the captive macaques had distinct oral-gut microbiota profiles and lower bacterial richness compared to those in wild macaques. The gut of wild macaques was dominated by Firmicutes which is probably associated with lipid absorption and storage. These results implicated the effects of captivity conditions on the microbiome that might contribute to crucial metabolic functions. Our study should be applied to the animal health care program, with respect to microbial functions, for non-human primates.},
}
@article {pmid34253606,
year = {2021},
author = {Leonard, MM and Valitutti, F and Karathia, H and Pujolassos, M and Kenyon, V and Fanelli, B and Troisi, J and Subramanian, P and Camhi, S and Colucci, A and Serena, G and Cucchiara, S and Trovato, CM and Malamisura, B and Francavilla, R and Elli, L and Hasan, NA and Zomorrodi, AR and Colwell, R and Fasano, A and , },
title = {Microbiome signatures of progression toward celiac disease onset in at-risk children in a longitudinal prospective cohort study.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {29},
pages = {},
pmid = {34253606},
issn = {1091-6490},
support = {F32 DK109620/DK/NIDDK NIH HHS/United States ; K23 DK122127/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; R01 DK104344/DK/NIDDK NIH HHS/United States ; },
mesh = {Autoimmunity ; Biomarkers/metabolism ; Celiac Disease/metabolism/*microbiology ; Child, Preschool ; Cross-Sectional Studies ; Female ; *Gastrointestinal Microbiome/genetics ; Host Microbial Interactions ; Humans ; Infant ; Inflammation ; Longitudinal Studies ; Male ; Metabolic Networks and Pathways ; Metabolome ; Metagenomics ; Prospective Studies ; },
abstract = {Other than exposure to gluten and genetic compatibility, the gut microbiome has been suggested to be involved in celiac disease (CD) pathogenesis by mediating interactions between gluten/environmental factors and the host immune system. However, to establish disease progression markers, it is essential to assess alterations in the gut microbiota before disease onset. Here, a prospective metagenomic analysis of the gut microbiota of infants at risk of CD was done to track shifts in the microbiota before CD development. We performed cross-sectional and longitudinal analyses of gut microbiota, functional pathways, and metabolites, starting from 18 mo before CD onset, in 10 infants who developed CD and 10 matched nonaffected infants. Cross-sectional analysis at CD onset identified altered abundance of six microbial strains and several metabolites between cases and controls but no change in microbial species or pathway abundance. Conversely, results of longitudinal analysis revealed several microbial species/strains/pathways/metabolites occurring in increased abundance and detected before CD onset. These had previously been linked to autoimmune and inflammatory conditions (e.g., Dialister invisus, Parabacteroides sp., Lachnospiraceae, tryptophan metabolism, and metabolites serine and threonine). Others occurred in decreased abundance before CD onset and are known to have anti-inflammatory effects (e.g., Streptococcus thermophilus, Faecalibacterium prausnitzii, and Clostridium clostridioforme). Additionally, we uncovered previously unreported microbes/pathways/metabolites (e.g., Porphyromonas sp., high mannose-type N-glycan biosynthesis, and serine) that point to CD-specific biomarkers. Our study establishes a road map for prospective longitudinal study designs to better understand the role of gut microbiota in disease pathogenesis and therapeutic targets to reestablish tolerance and/or prevent autoimmunity.},
}
@article {pmid34226407,
year = {2021},
author = {Wang, Y and Wang, C and Chen, Y and Chen, B and Guo, P and Cui, Z},
title = {Metagenomic Insight into Lignocellulose Degradation of the Thermophilic Microbial Consortium TMC7.},
journal = {Journal of microbiology and biotechnology},
volume = {31},
number = {8},
pages = {1123-1133},
doi = {10.4014/jmb.2106.06015},
pmid = {34226407},
issn = {1738-8872},
mesh = {Bacteria/classification/enzymology/genetics/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodegradation, Environmental ; Cellulose/metabolism ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; Microbial Consortia/*genetics ; Polysaccharides/metabolism ; },
abstract = {Biodegradation is the key process involved in natural lignocellulose biotransformation and utilization. Microbial consortia represent promising candidates for applications in lignocellulose conversion strategies for biofuel production; however, cooperation among the enzymes and the labor division of microbes in the microbial consortia remains unclear. In this study, metagenomic analysis was performed to reveal the community structure and extremozyme systems of a lignocellulolytic microbial consortium, TMC7. The taxonomic affiliation of TMC7 metagenome included members of the genera Ruminiclostridium (42.85%), Thermoanaerobacterium (18.41%), Geobacillus (10.44%), unclassified_f__Bacillaceae (7.48%), Aeribacillus (2.65%), Symbiobacterium (2.47%), Desulfotomaculum (2.33%), Caldibacillus (1.56%), Clostridium (1.26%), and others (10.55%). The carbohydrate-active enzyme annotation revealed that TMC7 encoded a broad array of enzymes responsible for cellulose and hemicellulose degradation. Ten glycoside hydrolases (GHs) endoglucanase, 4 GHs exoglucanase, and 6 GHs β-glucosidase were identified for cellulose degradation; 6 GHs endo-β-1,4-xylanase, 9 GHs β-xylosidase, and 3 GHs β-mannanase were identified for degradation of the hemicellulose main chain; 6 GHs arabinofuranosidase, 2 GHs α-mannosidase, 11 GHs galactosidase, 3 GHs α-rhamnosidase, and 4 GHs α-fucosidase were identified as xylan debranching enzymes. Furthermore, by introducing a factor named as the contribution coefficient, we found that Ruminiclostridium and Thermoanaerobacterium may be the dominant contributors, whereas Symbiobacterium and Desulfotomaculum may serve as "sugar cheaters" in lignocellulose degradation by TMC7. Our findings provide mechanistic profiles of an array of enzymes that degrade complex lignocellulosic biomass in the microbial consortium TMC7 and provide a promising approach for studying the potential contribution of microbes in microbial consortia.},
}
@article {pmid34215179,
year = {2021},
author = {Lebeaux, RM and Coker, MO and Dade, EF and Palys, TJ and Morrison, HG and Ross, BD and Baker, ER and Karagas, MR and Madan, JC and Hoen, AG},
title = {The infant gut resistome is associated with E. coli and early-life exposures.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {201},
pmid = {34215179},
issn = {1471-2180},
support = {P20 ES018175/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; T32 AI007519/AI/NIAID NIH HHS/United States ; R01 LM012723/LM/NLM NIH HHS/United States ; K01 LM011985/LM/NLM NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/*classification/*genetics ; Delivery, Obstetric/statistics &amp; numerical data ; Drug Resistance, Microbial/*genetics ; Environmental Exposure/statistics &amp; numerical data ; Escherichia coli/*physiology ; Feces/microbiology ; Feeding Methods/statistics &amp; numerical data ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Male ; Metagenomics ; },
abstract = {BACKGROUND: The human gut microbiome harbors a collection of bacterial antimicrobial resistance genes (ARGs) known as the resistome. The factors associated with establishment of the resistome in early life are not well understood. We investigated the early-life exposures and taxonomic signatures associated with resistome development over the first year of life in a large, prospective cohort in the United States. Shotgun metagenomic sequencing was used to profile both microbial composition and ARGs in stool samples collected at 6 weeks and 1 year of age from infants enrolled in the New Hampshire Birth Cohort Study. Negative binomial regression and statistical modeling were used to examine infant factors such as sex, delivery mode, feeding method, gestational age, antibiotic exposure, and infant gut microbiome composition in relation to the diversity and relative abundance of ARGs.<br><br>RESULTS: Metagenomic sequencing was performed on paired samples from 195 full term (at least 37 weeks' gestation) and 15 late preterm (33-36 weeks' gestation) infants. 6-week samples compared to 1-year samples had 4.37 times (95% CI: 3.54-5.39) the rate of harboring ARGs. The majority of ARGs that were at a greater relative abundance at 6 weeks (chi-squared p < 0.01) worked through the mechanism of antibiotic efflux. The overall relative abundance of the resistome was strongly correlated with Proteobacteria (Spearman correlation = 78.9%) and specifically Escherichia coli (62.2%) relative abundance in the gut microbiome. Among infant characteristics, delivery mode was most strongly associated with the diversity and relative abundance of ARGs. Infants born via cesarean delivery had a trend towards a higher risk of harboring unique ARGs [relative risk = 1.12 (95% CI: 0.97-1.29)] as well as having an increased risk for overall ARG relative abundance [relative risk = 1.43 (95% CI: 1.12-1.84)] at 1 year compared to infants born vaginally.<br><br>CONCLUSIONS: Our findings suggest that the developing infant gut resistome may be alterable by early-life exposures. Establishing the extent to which infant characteristics and early-life exposures impact the resistome can ultimately lead to interventions that decrease the transmission of ARGs and thus the risk of antibiotic resistant infections.},
}
@article {pmid34207804,
year = {2021},
author = {Hardouin, P and Chiron, R and Marchandin, H and Armengaud, J and Grenga, L},
title = {Metaproteomics to Decipher CF Host-Microbiota Interactions: Overview, Challenges and Future Perspectives.},
journal = {Genes},
volume = {12},
number = {6},
pages = {},
pmid = {34207804},
issn = {2073-4425},
mesh = {Animals ; Cystic Fibrosis/metabolism/*microbiology ; *Host-Pathogen Interactions ; Humans ; Metagenomics/*methods ; *Microbiota ; Proteome/genetics/metabolism ; Proteomics/*methods ; },
abstract = {Cystic fibrosis (CF) is a hereditary disease caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, triggering dysfunction of the anion channel in several organs including the lung and gut. The main cause of morbidity and mortality is chronic infection. The microbiota is now included among the additional factors that could contribute to the exacerbation of patient symptoms, to treatment outcome, and more generally to the phenotypic variability observed in CF patients. In recent years, various omics tools have started to shed new light on microbial communities associated with CF and host-microbiota interactions. In this context, proteomics targets the key effectors of the responses from organisms, and thus their phenotypes. Recent advances are promising in terms of gaining insights into the CF microbiota and its relation with the host. This review provides an overview of the contributions made by proteomics and metaproteomics to our knowledge of the complex host-microbiota partnership in CF. Considering the strengths and weaknesses of proteomics-based approaches in profiling the microbiota in the context of other diseases, we illustrate their potential and discuss possible strategies to overcome their limitations in monitoring both the respiratory and intestinal microbiota in sample from patients with CF.},
}
@article {pmid34126977,
year = {2021},
author = {Liu, ZZ and Liu, QH and Liu, Z and Tang, JW and Chua, EG and Li, F and Xiong, XS and Wang, MM and Wen, PB and Shi, XY and Xi, XY and Zhang, X and Wang, L},
title = {Ethanol extract of mulberry leaves partially restores the composition of intestinal microbiota and strengthens liver glycogen fragility in type 2 diabetic rats.},
journal = {BMC complementary medicine and therapies},
volume = {21},
number = {1},
pages = {172},
pmid = {34126977},
issn = {2662-7671},
support = {2020//Jiangsu Qing-Lan Project/ ; },
mesh = {Animals ; Diabetes Mellitus, Experimental/drug therapy ; Diabetes Mellitus, Type 2/*drug therapy ; Dysbiosis/prevention &amp; control ; Ethanol/chemistry ; Gastrointestinal Microbiome/*drug effects ; Liver Glycogen/*analysis ; Morus/*chemistry ; Plant Extracts/*pharmacology ; Plant Leaves/chemistry ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: Mulberry leaf as a traditional Chinese medicine is able to treat obesity, diabetes, and dyslipidemia. It is well known that diabetes leads to intestinal microbiota dysbiosis. It is also recently discovered that liver glycogen structure is impaired in diabetic animals. Since mulberry leaves are able to improve the diabetic conditions through reducing blood glucose level, it would be interesting to investigate whether they have any positive effects on intestinal microbiota and liver glycogen structure.<br><br>METHODS: In this study, we first determined the bioactive components of ethanol extract of mulberry leaves via high-performance liquid chromatography (HPLC) and liquid chromatography/mass spectrometry (LC/MS). Murine animal models were divided into three groups, normal Sprague-Dawley (SD) rats, high-fat diet (HFD) and streptozotocin (STZ) induced type 2 diabetic rats, and HFD/STZ-induced rats administered with ethanol extract of mulberry leaves (200 mg/kg/day). Composition of intestinal microbiota was analyzed via metagenomics by sequencing the V3-V4 region of 16S rDNAs. Liver glycogen structure was characterized through size exclusion chromatography (SEC). Both Student's t-test and Tukey's test were used for statistical analysis.<br><br>RESULTS: A group of type 2 diabetic rat models were successfully established. Intestinal microbiota analysis showed that ethanol extract of mulberry leaves could partially change intestinal microbiota back to normal conditions. In addition, liver glycogen was restored from fragile state to stable state through administration of ethanol extract of mulberry leaves.<br><br>CONCLUSIONS: This study confirms that the ethanol extract of mulberry leaves (MLE) ameliorates intestinal microbiota dysbiosis and strengthens liver glycogen fragility in diabetic rats. These finding can be helpful in discovering the novel therapeutic targets with the help of further investigations.},
}
@article {pmid34083435,
year = {2021},
author = {Tisza, MJ and Buck, CB},
title = {A catalog of tens of thousands of viruses from human metagenomes reveals hidden associations with chronic diseases.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {23},
pages = {},
pmid = {34083435},
issn = {1091-6490},
mesh = {Adolescent ; Adult ; CRISPR-Cas Systems ; Case-Control Studies ; *Chronic Disease ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA Viruses/genetics ; Data Management ; Genome, Viral ; Genomics ; Humans ; *Metagenome ; Metagenomics ; Microbiota ; Parkinson Disease ; Virome ; Viruses/*genetics ; Young Adult ; },
abstract = {Despite remarkable strides in microbiome research, the viral component of the microbiome has generally presented a more challenging target than the bacteriome. This gap persists, even though many thousands of shotgun sequencing runs from human metagenomic samples exist in public databases, and all of them encompass large amounts of viral sequence data. The lack of a comprehensive database for human-associated viruses has historically stymied efforts to interrogate the impact of the virome on human health. This study probes thousands of datasets to uncover sequences from over 45,000 unique virus taxa, with historically high per-genome completeness. Large publicly available case-control studies are reanalyzed, and over 2,200 strong virus-disease associations are found.},
}
@article {pmid34078289,
year = {2021},
author = {Moitinho-Silva, L and Wegener, M and May, S and Schrinner, F and Akhtar, A and Boysen, TJ and Schaeffer, E and Hansen, C and Schmidt, T and Rühlemann, MC and Hübenthal, M and Rausch, P and Kondakci, MT and Maetzler, W and Weidinger, S and Laudes, M and Süß, P and Schulte, D and Junker, R and Sommer, F and Weisser, B and Bang, C and Franke, A},
title = {Short-term physical exercise impacts on the human holobiont obtained by a randomised intervention study.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {162},
pmid = {34078289},
issn = {1471-2180},
support = {EXC2167//Deutsche Forschungsgemeinschaft/ ; FOR5042//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Adult ; Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Diet ; *Exercise ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {BACKGROUND: Human well-being has been linked to the composition and functional capacity of the intestinal microbiota. As regular exercise is known to improve human health, it is not surprising that exercise was previously described to positively modulate the gut microbiota, too. However, most previous studies mainly focused on either elite athletes or animal models. Thus, we conducted a randomised intervention study that focused on the effects of different types of training (endurance and strength) in previously physically inactive, healthy adults in comparison to controls that did not perform regular exercise. Overall study duration was ten weeks including six weeks of intervention period. In addition to 16S rRNA gene amplicon sequencing of longitudinally sampled faecal material of participants (six time points), detailed body composition measurements and analysis of blood samples (at baseline and after the intervention) were performed to obtain overall physiological changes within the intervention period. Activity tracker devices (wrist-band wearables) provided activity status and sleeping patterns of participants as well as exercise intensity and heart measurements.<br><br>RESULTS: Different biometric responses between endurance and strength activities were identified, such as a significant increase of lymphocytes and decrease of mean corpuscular haemoglobin concentration (MCHC) only within the strength intervention group. In the endurance group, we observed a significant reduction in hip circumference and an increase in physical working capacity (PWC). Though a large variation of microbiota changes were observed between individuals of the same group, we did not find specific collective alterations in the endurance nor the strength groups, arguing for microbiome variations specific to individuals, and therefore, were not captured in our analysis.<br><br>CONCLUSIONS: We could show that different types of exercise have distinct but moderate effects on the overall physiology of humans and very distinct microbial changes in the gut. The observed overall changes during the intervention highlight the importance of physical activity on well-being. Future studies should investigate the effect of exercise on a longer timescale, investigate different training intensities and consider high-resolution shotgun metagenomics technology.<br><br>TRIAL REGISTRATION: DRKS, DRKS00015873 . Registered 12 December 2018; Retrospectively registered.},
}
@article {pmid34077260,
year = {2021},
author = {Cornell, CR and Zhang, Y and Van Nostrand, JD and Wagle, P and Xiao, X and Zhou, J},
title = {Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils.},
journal = {mSphere},
volume = {6},
number = {3},
pages = {e0116020},
pmid = {34077260},
issn = {2379-5042},
mesh = {Crops, Agricultural/*virology ; *Grassland ; *Metagenome ; Metagenomics ; *Soil Microbiology ; Spatio-Temporal Analysis ; Virome/*genetics ; Viruses/*genetics ; },
abstract = {During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.},
}
@article {pmid34051731,
year = {2021},
author = {Kazantseva, J and Malv, E and Kaleda, A and Kallastu, A and Meikas, A},
title = {Optimisation of sample storage and DNA extraction for human gut microbiota studies​.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {158},
pmid = {34051731},
issn = {1471-2180},
support = {EU48667//Ettevõtluse Arendamise Sihtasutus/ ; },
mesh = {Bacteria/classification/*genetics/isolation &amp; purification ; DNA, Bacterial/genetics/*isolation &amp; purification ; Feces/microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics/*methods ; Preservation, Biological/*methods ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important.<br><br>RESULTS: Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution.<br><br>CONCLUSIONS: Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations.},
}
@article {pmid33847922,
year = {2021},
author = {Duan, M and Bau, T},
title = {Grassland fairy rings of Leucocalocybe mongolica represent the center of a rich soil microbial community.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {52},
number = {3},
pages = {1357-1369},
pmid = {33847922},
issn = {1678-4405},
mesh = {Agaricales/*growth &amp; development ; Bacteria/genetics ; China ; Fungi/genetics ; *Grassland ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Soil ; *Soil Microbiology ; },
abstract = {BACKGROUND: The ecological phenomenon of fungal fairy rings is usually found in grasslands and caused by the growth of specific fairy ring fungi in soil. The fairy rings are classified into three zones (DARK, DEAD, and OUT), and they have the potential to increase crop yield. Among these fairy rings, distinct characteristics of type I fairy rings can be seen in the rings formed by Leucocalocybe mongolica (LM). Our studies addressed changes in the soil microbial structure due to LM fairy rings to enhance understand of this ecological phenomenon.<br><br>METHODS: In the present study, we report the soil microbial analysis results (fungi and bacteria), including those of metabarcoding (16s rRNA, ITS), microbial quantity, and metagenomics surveys of soils collected from various fairy ring zones, of 6 LM fairy rings. All sampling sites cover the grasslands of Mongolian Plateau in China.<br><br>RESULTS: First, we found through metabarcoding surveys that the difference in microbial diversity is relatively less in bacteria and that the abundance of fairy ring fungi (LM) is relatively high in DEAD zones. We also identified eight bacterial and fungal families, including Sphingobacteriaceae and Sphingomonadaceae that were enriched within the soils of fairy ring zones. Second, we found that the abundance of soil bacteria in the DEAD zones is sharply increased along with the growth of fairy ring fungi (LM). Third, we found through shotgun sequencing that fairy ring-infected zones, DARK and DEAD, exhibit greater genetic diversity than OUT zones. Finally, we showed that the fairy ring ecosystem is the center for a rich grassland microbial community.<br><br>CONCLUSIONS: The reported data can improve our understanding of type I fairy rings and will be further insightful to the research on crop production.},
}
@article {pmid33839214,
year = {2021},
author = {Priya, P and Aneesh, B and Harikrishnan, K},
title = {Genomics as a potential tool to unravel the rhizosphere microbiome interactions on plant health.},
journal = {Journal of microbiological methods},
volume = {185},
number = {},
pages = {106215},
doi = {10.1016/j.mimet.2021.106215},
pmid = {33839214},
issn = {1872-8359},
mesh = {Agriculture/methods ; Crops, Agricultural ; Ecosystem ; Genomics/*methods ; Metagenomics ; *Microbial Interactions ; Microbiota/*genetics ; Plant Roots ; Proteomics ; *Rhizosphere ; Soil ; Soil Microbiology ; Transcriptome ; },
abstract = {Intense agricultural practices to meet rising food demands have caused ecosystem perturbations. For sustainable crop production, biological agents are gaining attention, but exploring their functional potential on a multi-layered complex ecosystem like the rhizosphere is challenging. This review explains the significance of genomics as a culture-independent molecular tool to understand the diversity and functional significance of the rhizosphere microbiome for sustainable agriculture. It discusses the recent significant studies in the rhizosphere environment carried out using evolving techniques like metagenomics, metatranscriptomics, and metaproteomics, their challenges, constraints infield application, and prospective solutions. The recent advances in techniques such as nanotechnology for the development of bioformulations and visualization techniques contemplating environmental safety were also discussed. The need for development of metagenomic data sets of regionally important crops, their plant microbial interactions and agricultural practices for narrowing down significant data from huge databases have been suggested. The role of taxonomical and functional diversity of soil microbiota in understanding soil suppression and part played by the microbial metabolites in the process have been analyzed and discussed in the context of 'omics' approach. 'Omics' studies have revealed important information about microbial diversity, their responses to various biotic and abiotic stimuli, and the physiology of disease suppression. This can be translated to crop sustainability and combinational approaches with advancing visualization and analysis methodologies fix the existing knowledge gap to a huge extend. With improved data processing and standardization of the methods, details of plant-microbe interactions can be successfully decoded to develop sustainable agricultural practices.},
}
@article {pmid33789570,
year = {2021},
author = {Loftus, M and Hassouneh, SA and Yooseph, S},
title = {Bacterial community structure alterations within the colorectal cancer gut microbiome.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {98},
pmid = {33789570},
issn = {1471-2180},
mesh = {Bacteria/classification/*genetics ; *Biodiversity ; Colorectal Neoplasms/*microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; },
abstract = {BACKGROUND: Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome.<br><br>RESULTS: By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome.<br><br>CONCLUSIONS: We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.},
}
@article {pmid33785357,
year = {2021},
author = {Biegert, G and El Alam, MB and Karpinets, T and Wu, X and Sims, TT and Yoshida-Court, K and Lynn, EJ and Yue, J and Medrano, AD and Petrosino, J and Mezzari, MP and Ajami, NJ and Solley, T and Ahmed-Kaddar, M and Klopp, AH and Colbert, LE},
title = {Diversity and composition of gut microbiome of cervical cancer patients: Do results of 16S rRNA sequencing and whole genome sequencing approaches align?.},
journal = {Journal of microbiological methods},
volume = {185},
number = {},
pages = {106213},
doi = {10.1016/j.mimet.2021.106213},
pmid = {33785357},
issn = {1872-8359},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; },
mesh = {Bacteria/genetics ; Biodiversity ; DNA, Bacterial ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; Microbiota/genetics ; Middle Aged ; RNA, Ribosomal, 16S/*genetics ; Uterine Cervical Neoplasms/*genetics ; Whole Genome Sequencing/*methods ; },
abstract = {BACKGROUND: Next generation sequencing has progressed rapidly, characterizing microbial communities beyond culture-based or biochemical techniques. 16S ribosomal RNA gene sequencing (16S) produces reliable taxonomic classifications and relative abundances, while shotgun metagenome sequencing (WMS) allows higher taxonomic and functional resolution at greater cost. The purpose of this study was to determine if 16S and WMS provide congruent information for our patient population from paired fecal microbiome samples.<br><br>RESULTS: Comparative indices were highly congruent between 16S and WMS. The most abundant genera for 16S and WMS data did not overlap. Overlap was observed at the Phylum level, as expected. However, relative abundances correlated poorly between the two methodologies (all P-value>0.05). Hierarchical clustering of both sequencing analyses identified overlapping enterotypes. Both approaches were in agreement with regard to demographic variables.<br><br>CONCLUSION: Diversity, evenness and richness are comparable when using 16S and WMS techniques, however relative abundances of individual genera are not. Clinical associations with diversity and evenness metrics were similarly identified with WMS or 16S.},
}
@article {pmid33773594,
year = {2021},
author = {Chan, SH and Ismail, MH and Tan, CH and Rice, SA and McDougald, D},
title = {Microbial predation accelerates granulation and modulates microbial community composition.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {91},
pmid = {33773594},
issn = {1471-2180},
mesh = {Bacteria/*metabolism ; Bacteriophages/*physiology ; *Ecosystem ; Eukaryota/*physiology ; *Microbiota ; },
abstract = {BACKGROUND: Bacterial communities are responsible for biological nutrient removal and flocculation in engineered systems such as activated floccular sludge. Predators such as bacteriophage and protozoa exert significant predation pressure and cause bacterial mortality within these communities. However, the roles of bacteriophage and protozoan predation in impacting granulation process remain limited. Recent studies hypothesised that protozoa, particularly sessile ciliates, could have an important role in granulation as these ciliates were often observed in high abundance on surfaces of granules. Bacteriophages were hypothesized to contribute to granular stability through bacteriophage-mediated extracellular DNA release by lysing bacterial cells. This current study investigated the bacteriophage and protozoan communities throughout the granulation process. In addition, the importance of protozoan predation during granulation was also determined through chemical killing of protozoa in the floccular sludge.<br><br>RESULTS: Four independent bioreactors seeded with activated floccular sludge were operated for aerobic granulation for 11 weeks. Changes in the phage, protozoa and bacterial communities were characterized throughout the granulation process. The filamentous phage, Inoviridae, increased in abundance at the initiation phase of granulation. However, the abundance shifted towards lytic phages during the maturation phase. In contrast, the abundance and diversity of protozoa decreased initially, possibly due to the reduction in settling time and subsequent washout. Upon the formation of granules, ciliated protozoa from the class Oligohymenophorea were the dominant group of protozoa based on metacommunity analysis. These protozoa had a strong, positive-correlation with the initial formation of compact aggregates prior to granule development. Furthermore, chemical inhibition of these ciliates in the floccular sludge delayed the initiation of granule formation. Analysis of the bacterial communities in the thiram treated sludge demonstrated that the recovery of 'Candidatus Accumulibacter' was positively correlated with the formation of compact aggregates and granules.<br><br>CONCLUSION: Predation by bacteriophage and protozoa were positively correlated with the formation of aerobic granules. Increases in Inoviridae abundance suggested that filamentous phages may promote the structural formation of granules. Initiation of granules formation was delayed due to an absence of protozoa after chemical treatment. The presence of 'Candidatus Accumulibacter' was necessary for the formation of granules in the absence of protozoa.},
}
@article {pmid33726974,
year = {2021},
author = {Dos Santos Bezerra, R and Bub, CB and Peronni, KC and de Figiueiredo Barros, BD and da Costa Lira, SM and Kutner, JM and Covas, DT and Kashima, S and Slavov, SN},
title = {Virome comparison of deferred blood donations obtained from different geographic regions in the Sao Paulo State, Brazil.},
journal = {Transfusion and apheresis science : official journal of the World Apheresis Association : official journal of the European Society for Haemapheresis},
volume = {60},
number = {3},
pages = {103106},
doi = {10.1016/j.transci.2021.103106},
pmid = {33726974},
issn = {1473-0502},
mesh = {Blood Donors/*statistics &amp; numerical data ; Brazil ; Humans ; Virome/*immunology ; },
abstract = {The virome composition of blood units deferred due to symptomatic disease of the donors reported after blood donation may reveal novel or unsuspected viral agents which may have impact in the area of hemotherapy. The objective of this study was to compare the virome of blood donations obtained from two distantly located blood collecting institutions in the Saqo Paulo State and deferred from use due to post donation illness reports (PDIR). Plasma samples with PDIR due to different symptoms were collected in two cities of the Sao Paulo State (Sao Paulo city, 28 samples and Ribeirao Preto city, 11 samples). The samples were assembled in pools and sequenced in Illumina NextSeq 550 sequencer. The obtained raw sequencing data was analyzed using bioinformatic pipeline aiming viral identification. Phylogenetic classification of the most important contigs was also performed. The virome composition of the plasma samples obtained in both cities was different. This was more pronounced for some specific anellovirus types and the human pegivirus-1 (HPgV-1) which were exclusively found among donations obtained from the city of Sao Paulo. On the other hand, in PDIR samples from Ribeirao Preto, Dengue -2 reads were more abundant compared to commensal viral representatives. The obtained virome findings show that the differential viral abundance is related to geographic localization and specific disease endemicity. The virome of PDIR samples may be used to more profoundly analyze the hypothetic transfusion threats in a given location.},
}
@article {pmid33723291,
year = {2021},
author = {Desbois, AC and Ciocan, D and Saadoun, D and Perlemuter, G and Cacoub, P},
title = {Specific microbiome profile in Takayasu's arteritis and giant cell arteritis.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {5926},
pmid = {33723291},
issn = {2045-2322},
mesh = {Aged ; Aged, 80 and over ; Biomarkers/blood ; Computational Biology/methods ; *Disease Susceptibility ; Female ; Giant Cell Arteritis/drug therapy/*etiology/metabolism/pathology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Sepsis/complications/microbiology ; Takayasu Arteritis/drug therapy/*etiology/metabolism/pathology ; },
abstract = {Recent studies have provided evidence of a close link between specific microbiota and inflammatory disorders. While the vessel wall microbiota has been recently described in large vessel vasculitis (LVV) and controls, the blood microbiome in these diseases has not been previously reported (LVV). We aimed to analyse the blood microbiome profile of LVV patients (Takayasu's arteritis [TAK], giant cell arteritis [GCA]) and healthy blood donors (HD). We studied the blood samples of 13 patients with TAK (20 samples), 9 patients with GCA (11 samples) and 15 HD patients. We assessed the blood microbiome profile by sequencing the 16S rDNA blood bacterial DNA. We used linear discriminant analysis (LDA) coupled with linear discriminant effect size measurement (LEfSe) to investigate the differences in the blood microbiome profile between TAK and GCA patients. An increase in the levels of Clostridia, Cytophagia and Deltaproteobacteria and a decrease in Bacilli at the class level were found in TAK patients compared with HD patients (LDA > 2, p < 0.05). Active TAK patients had significantly lower levels of Staphylococcus compared with inactive TAK patients. Samples of GCA patients had an increased abundance of Rhodococcus and an unidentified member of the Cytophagaceae family. Microbiota of TAK compared with GCA patients was found to show higher levels of Candidatus Aquiluna and Cloacibacterium (LDA > 2; p < 0.05). Differences highlighted in the blood microbiome were also associated with a shift of bacterial predicted metabolic functions in TAK in comparison with HD. Similar results were also found in patients with active versus inactive TAK. In conclusion, patients with TAK were found to present a specific blood microbiome profile in comparison with healthy donors and GCA subjects. Significant changes in the blood microbiome profiles of TAK patients were associated with specific metabolic functions.},
}
@article {pmid33723271,
year = {2021},
author = {Papa, G and Di Prisco, G and Spini, G and Puglisi, E and Negri, I},
title = {Acute and chronic effects of Titanium dioxide (TiO2) PM1 on honey bee gut microbiota under laboratory conditions.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {5946},
pmid = {33723271},
issn = {2045-2322},
mesh = {Animals ; *Bees ; Biodiversity ; Environmental Pollutants/*adverse effects ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; Particulate Matter/*adverse effects ; Titanium/*adverse effects/chemistry ; },
abstract = {Apis mellifera is an important provider of ecosystem services, and during flight and foraging behaviour is exposed to environmental pollutants including airborne particulate matter (PM). While exposure to insecticides, antibiotics, and herbicides may compromise bee health through alterations of the gut microbial community, no data are available on the impacts of PM on the bee microbiota. Here we tested the effects of ultrapure Titanium dioxide (TiO2) submicrometric PM (i.e., PM1, less than 1 µm in diameter) on the gut microbiota of adult bees. TiO2 PM1 is widely used as a filler and whitening agent in a range of manufactured objects, and ultrapure TiO2 PM1 is also a common food additive, even if it has been classified by the International Agency for Research on Cancer (IARC) as a possible human carcinogen in Group 2B. Due to its ubiquitous use, honey bees may be severely exposed to TiO2 ingestion through contaminated honey and pollen. Here, we demonstrated that acute and chronic oral administration of ultrapure TiO2 PM1 to adult bees alters the bee microbial community; therefore, airborne PM may represent a further risk factor for the honey bee health, promoting sublethal effects against the gut microbiota.},
}
@article {pmid33712656,
year = {2021},
author = {Kim, J and Park, KY and Park, HK and Hwang, HS and Seo, MR and Kim, B and Cho, Y and Rho, M and Pai, H},
title = {High fecal carriage of blaCTX-M, blaCMY-2, and plasmid-mediated quinolone resistance genes among healthy Korean people in a metagenomic analysis.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {5874},
pmid = {33712656},
issn = {2045-2322},
mesh = {Adult ; Alleles ; Drug Resistance, Multiple, Bacterial/*genetics ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome ; *Genes, Bacterial ; *Health ; Humans ; Male ; *Metagenomics ; Middle Aged ; Phenotype ; Plasmids/*genetics ; Quinolones/*pharmacology ; Republic of Korea ; beta-Lactamases/*genetics ; },
abstract = {To characterize the carriage of antibiotic resistance genes (ARGs) in the gut microbiome of healthy individuals. Fecal carriage of ARGs was investigated in 61 healthy individuals aged 30 to 59 years through whole metagenome sequencing of the gut microbiome and a targeted metagenomic approach. The number of ARGs in the gut microbiome was counted and normalized per million predicted genes (GPM). In the Korean population, the resistome ranged from 49.7 to 292.5 GPM (median 89.7). Based on the abundance of ARGs, the subjects were categorised into high (> 120 GPM), middle (60‒120 GPM), and low (< 60 GPM) ARG groups. Individuals in the high ARG group tended to visit hospitals more often (P = 0.065), particularly for upper respiratory tract infections (P = 0.066), and carried more blaCTX-M (P = 0.008). The targeted metagenome approach for bla and plasmid-mediated quinolone resistance (PMQR) genes revealed a high fecal carriage rate; 23% or 13.1% of the subjects carried blaCTX-M or blaCMY-2, respectively. Regarding PMQR genes, 59% of the subjects carried PMQR, and 83% of them harboured 2‒4 PMQR genes (qnrB 44.3%, qnrS 47.5% etc.). The presence of blaCTX-M correlated with ARG abundance in the gut resistome, whereas PMQR genes were irrelevant to other ARGs (P = 0.176). Fecal carriage of blaCTX-M and PMQR genes was broad and multiplexed among healthy individuals.},
}
@article {pmid33707503,
year = {2021},
author = {Andersen, D and Roager, HM and Zhang, L and Moll, JM and Frandsen, HL and Danneskiold-Samsøe, NB and Hansen, AK and Kristiansen, K and Licht, TR and Brix, S},
title = {Systems-wide effects of short-term feed deprivation in obese mice.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {5716},
pmid = {33707503},
issn = {2045-2322},
mesh = {Animals ; Bacteria/metabolism ; Butyric Acid/metabolism ; Cecum/metabolism ; Fermentation ; Gastrointestinal Microbiome ; Intra-Abdominal Fat/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Obese ; Multivariate Analysis ; Starvation/*pathology ; *Systems Biology ; Time Factors ; Uncoupling Protein 1/metabolism ; },
abstract = {While prolonged fasting induces significant metabolic changes in humans and mice, less is known about systems-wide metabolic changes in response to short-term feed deprivation, which is used in experimental animal studies prior to metabolic challenge tests. We here performed a systems biology-based investigation of connections between gut bacterial composition and function, inflammatory and metabolic parameters in the intestine, liver, visceral adipose tissue, blood and urine in high-fat fed, obese mice that were feed deprived up to 12 h. The systems-wide analysis revealed that feed deprivation linked to enhanced intestinal butyric acid production and expression of the gene encoding the pro-thermogenic uncoupling protein UCP1 in visceral adipose tissue of obese mice. Ucp1 expression was also positively associated with Il33 expression in ileum, colon and adipose tissue as well as with the abundance of colonic Porphyromonadaceae, the latter also correlating to cecal butyric acid levels. Collectively, the data highlighted presence of a multi-tiered system of inter-tissue communication involving intestinal, immune and metabolic functions which is affected by feed deprivation in obese mice, thus pointing to careful use of short-feed deprivation in metabolic studies using obese mice.},
}
@article {pmid33633264,
year = {2021},
author = {Staley, C and Halaweish, H and Graiziger, C and Hamilton, MJ and Kabage, AJ and Galdys, AL and Vaughn, BP and Vantanasiri, K and Suryanarayanan, R and Sadowsky, MJ and Khoruts, A},
title = {Lower endoscopic delivery of freeze-dried intestinal microbiota results in more rapid and efficient engraftment than oral administration.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4519},
pmid = {33633264},
issn = {2045-2322},
mesh = {Aged ; Aged, 80 and over ; Biodiversity ; Clostridium Infections/*microbiology/*therapy ; Disease Management ; Disease Susceptibility ; Fecal Microbiota Transplantation/*methods ; Female ; Freeze Drying ; Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Transanal Endoscopic Microsurgery/*methods ; Treatment Outcome ; },
abstract = {Fecal microbiota transplantation (FMT) is a highly effective treatment for recurrent Clostridioides difficile infection (rCDI). However, standardization of FMT products is essential for its broad implementation into clinical practice. We have developed an oral preparation of freeze-dried, encapsulated microbiota, which is ~ 80% clinically effective, but results in delayed engraftment of donor bacteria relative to administration via colonoscopy. Our objective was to measure the engraftment potential of freeze-dried microbiota without the complexity of variables associated with oral administration. We compared engraftment of identical preparations and doses of freeze-dried microbiota following colonoscopic (9 patients) versus oral administration (18 patients). Microbiota were characterized by sequencing of the 16S rRNA gene, and engraftment was determined using the SourceTracker algorithm. Oligotyping analysis was done to provide high-resolution patterns of microbiota engraftment. Colonoscopic FMT was associated with greater levels of donor engraftment within days following the procedure (ANOVA P = 0.035) and specific increases in the relative abundances of donor Lachnospiraceae, Bacteroidaceae, and Porphyromonadaceae (P ≤ 0.033). Lower relative abundances of Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae families were associated with clinical failures. These results suggest that further optimization of oral capsule FMT may improve its engraftment efficiency and clinical efficacy.},
}
@article {pmid33633172,
year = {2021},
author = {Carrieri, AP and Haiminen, N and Maudsley-Barton, S and Gardiner, LJ and Murphy, B and Mayes, AE and Paterson, S and Grimshaw, S and Winn, M and Shand, C and Hadjidoukas, P and Rowe, WPM and Hawkins, S and MacGuire-Flanagan, A and Tazzioli, J and Kenny, JG and Parida, L and Hoptroff, M and Pyzer-Knapp, EO},
title = {Explainable AI reveals changes in skin microbiome composition linked to phenotypic differences.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4565},
pmid = {33633172},
issn = {2045-2322},
mesh = {Adult ; Aged ; Aging ; *Artificial Intelligence ; *Biodiversity ; Computational Biology/methods ; Data Analysis ; Deep Learning ; Female ; Humans ; Male ; Menopause ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; *Phenotype ; Skin/*microbiology ; Smokers ; Young Adult ; },
abstract = {Alterations in the human microbiome have been observed in a variety of conditions such as asthma, gingivitis, dermatitis and cancer, and much remains to be learned about the links between the microbiome and human health. The fusion of artificial intelligence with rich microbiome datasets can offer an improved understanding of the microbiome's role in human health. To gain actionable insights it is essential to consider both the predictive power and the transparency of the models by providing explanations for the predictions. We combine the collection of leg skin microbiome samples from two healthy cohorts of women with the application of an explainable artificial intelligence (EAI) approach that provides accurate predictions of phenotypes with explanations. The explanations are expressed in terms of variations in the relative abundance of key microbes that drive the predictions. We predict skin hydration, subject's age, pre/post-menopausal status and smoking status from the leg skin microbiome. The changes in microbial composition linked to skin hydration can accelerate the development of personalized treatments for healthy skin, while those associated with age may offer insights into the skin aging process. The leg microbiome signatures associated with smoking and menopausal status are consistent with previous findings from oral/respiratory tract microbiomes and vaginal/gut microbiomes respectively. This suggests that easily accessible microbiome samples could be used to investigate health-related phenotypes, offering potential for non-invasive diagnosis and condition monitoring. Our EAI approach sets the stage for new work focused on understanding the complex relationships between microbial communities and phenotypes. Our approach can be applied to predict any condition from microbiome samples and has the potential to accelerate the development of microbiome-based personalized therapeutics and non-invasive diagnostics.},
}
@article {pmid33619300,
year = {2021},
author = {Reed, KJ and Kunz, IGZ and Scare, JA and Nielsen, MK and Turk, PJ and Coleman, RJ and Coleman, SJ},
title = {The pelvic flexure separates distinct microbial communities in the equine hindgut.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {4332},
pmid = {33619300},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; *Gastrointestinal Microbiome ; *Horses ; *Intestine, Large ; Metagenome ; Metagenomics/methods ; Pelvis/*anatomy &amp; histology ; },
abstract = {As hindgut fermenters, horses are especially dependent on the microbiota residing in their cecum and large intestines. Interactions between these microbial populations and the horse are critical for maintaining gut homeostasis, which supports proper digestion. The current project was motivated to determine if any features of the fecal microbiota are informative of the microbial communities from the cecum, ventral colon, or dorsal colon. Digesta from the cecum, ventral colon, dorsal colon and feces were collected from 6 yearling miniature horses. Microbial DNA was isolated and the microbiota from each sample was characterized by profiling the V4 region of the 16S rRNA. Principal coordinate analysis of the beta diversity results revealed significant (p = 0.0001; F = 5.2393) similarities between the microbial populations from cecal and ventral colon and the dorsal colon and fecal samples, however, there was little overlap between the proximal and distal ends of the hindgut. These distinct population structures observed in our results coincide with the pelvic flexure, which itself separates intestinal compartments with distinct roles in digestive physiology. An indicator species analysis confirmed the population differences, supported by the identification of several microbial families characteristic of the compartments upstream of the pelvic flexure that were not represented following it. Our data suggest that the fecal microbiota is not informative of the proximal hindgut but can provide insight into communities of the distal compartments. Further, our results suggest that the pelvic flexure might be an important anatomical landmark relative to the microbial communities in the equine large intestine.},
}
@article {pmid33589511,
year = {2021},
author = {Bi, Y and Tu, Y and Zhang, N and Wang, S and Zhang, F and Suen, G and Shao, D and Li, S and Diao, Q},
title = {Multiomics analysis reveals the presence of a microbiome in the gut of fetal lambs.},
journal = {Gut},
volume = {70},
number = {5},
pages = {853-864},
pmid = {33589511},
issn = {1468-3288},
mesh = {Animals ; Female ; Fetus/*metabolism/*microbiology ; Gastrointestinal Microbiome/*genetics ; Gene Expression Profiling ; Metabolomics ; Metagenomics ; Models, Animal ; Pregnancy ; Sheep/*genetics/*microbiology ; },
abstract = {OBJECTIVE: Microbial exposure is critical to neonatal and infant development, growth and immunity. However, whether a microbiome is present in the fetal gut prior to birth remains debated. In this study, lambs delivered by aseptic hysterectomy at full term were used as an animal model to investigate the presence of a microbiome in the prenatal gut using a multiomics approach.<br><br>DESIGN: Lambs were euthanised immediately after aseptic caesarean section and their cecal content and umbilical cord blood samples were aseptically acquired. Cecal content samples were assessed using metagenomic and metatranscriptomic sequencing to characterise any existing microbiome. Both sample types were analysed using metabolomics in order to detect microbial metabolites.<br><br>RESULTS: We detected a low-diversity and low-biomass microbiome in the prenatal fetal gut, which was mainly composed of bacteria belonging to the phyla Proteobacteria, Actinobacteria and Firmicutes. Escherichia coli was the most abundant species in the prenatal fetal gut. We also detected multiple microbial metabolites including short chain fatty acids, deoxynojirimycin, mitomycin and tobramycin, further indicating the presence of metabolically active microbiota. Additionally, bacteriophage phiX174 and Orf virus, as well as antibiotic resistance genes, were detected in the fetal gut, suggesting that bacteriophage, viruses and bacteria carrying antibiotic resistance genes can be transmitted from the mother to the fetus during the gestation period.<br><br>CONCLUSIONS: This study provides strong evidence that the prenatal gut harbours a microbiome and that microbial colonisation of the fetal gut commences in utero.},
}
@article {pmid33395552,
year = {2021},
author = {Zhu, Z and Cao, M and Wang, W and Zhang, L and Ma, T and Liu, G and Zhang, Y and Shang, Z and Chen, X and Shi, Y and Zhang, J},
title = {Exploring the Prevalence and Distribution Patterns of Antibiotic Resistance Genes in Bovine Gut Microbiota Using a Metagenomic Approach.},
journal = {Microbial drug resistance (Larchmont, N.Y.)},
volume = {27},
number = {7},
pages = {980-990},
doi = {10.1089/mdr.2020.0271},
pmid = {33395552},
issn = {1931-8448},
mesh = {Agriculture ; Animals ; Anti-Bacterial Agents/*pharmacology ; Cattle ; Drug Resistance, Microbial/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Genes, Bacterial/*genetics ; Metagenomics ; Polymorphism, Single Nucleotide ; },
abstract = {Antibiotic resistance genes (ARGs) have become recognized contaminants and pose a high public health risk. The animal gut microbiota is a reservoir of ARGs, but the knowledge of the origin and dissemination of ARGs remains unclear. In this study, we provide a comprehensive profile of ARGs and mobile genetic elements in the gut microbiota from 30 bovines to study the impact of modern antibiotics on resistance. A total of 42 ARG types were detected by annotating the metagenomic sequencing data from Comprehensive Antibiotic Resistance Database (CARD). We found that the diversity and abundance of ARGs in individual yaks were significantly lower than those in dairy and beef cattle (p < 0.0001). The results of heat map and single nucleotide polymorphism clustering suggest that ARGs from dairy and beef cattle are more similar, whereas those from yaks cluster separately. The long-term use of antibiotics may contribute to this difference, suggesting that antibiotic consumption is the main cause of ARG prevalence. Furthermore, abundant insertions were also found in this study, signifying a strong potential for horizontal transfer of ARGs among microbes, especially pathogens.},
}
@article {pmid33249136,
year = {2021},
author = {Kong, G and Ellul, S and Narayana, VK and Kanojia, K and Ha, HTT and Li, S and Renoir, T and Cao, KL and Hannan, AJ},
title = {An integrated metagenomics and metabolomics approach implicates the microbiota-gut-brain axis in the pathogenesis of Huntington's disease.},
journal = {Neurobiology of disease},
volume = {148},
number = {},
pages = {105199},
doi = {10.1016/j.nbd.2020.105199},
pmid = {33249136},
issn = {1095-953X},
mesh = {Animals ; *Asymptomatic Diseases ; Brain/*metabolism ; Chromatography, Liquid ; Disease Models, Animal ; Disease Progression ; Dysbiosis/*metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*metabolism/microbiology ; Huntington Disease/*metabolism/microbiology ; Mass Spectrometry ; *Metabolomics ; *Metagenomics ; Mice ; Mice, Transgenic ; },
abstract = {BACKGROUND: Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder with onset and severity of symptoms influenced by various environmental factors. Recent discoveries have highlighted the importance of the gastrointestinal microbiome in mediating the gut-brain-axis bidirectional communication via circulating factors. Using shotgun sequencing, we investigated the gut microbiome composition in the R6/1 transgenic mouse model of HD from 4 to 12 weeks of age (early adolescent through to adult stages). Targeted metabolomics was also performed on the blood plasma of these mice (n = 9 per group) at 12 weeks of age to investigate potential effects of gut dysbiosis on the plasma metabolome profile.<br><br>RESULTS: Modelled time profiles of each species, KEGG Orthologs and bacterial genes, revealed heightened volatility in the R6/1 mice, indicating potential early effects of the HD mutation in the gut. In addition to gut dysbiosis in R6/1 mice at 12 weeks of age, gut microbiome function was perturbed. In particular, the butanoate metabolism pathway was elevated, suggesting increased production of the protective SCFA, butyrate, in the gut. No significant alterations were found in the plasma butyrate and propionate levels in the R6/1 mice at 12 weeks of age. The statistical integration of the metagenomics and metabolomics unraveled several Bacteroides species that were negatively correlated with ATP and pipecolic acid in the plasma.<br><br>CONCLUSIONS: The present study revealed the instability of the HD gut microbiome during the pre-motor symptomatic stage of the disease which may have dire consequences on the host's health. Perturbation of the HD gut microbiome function prior to significant cognitive and motor dysfunction suggest the potential role of the gut in modulating the pathogenesis of HD, potentially via specific altered plasma metabolites which mediate gut-brain signaling.},
}
@article {pmid33239396,
year = {2021},
author = {Baker, JL and Morton, JT and Dinis, M and Alvarez, R and Tran, NC and Knight, R and Edlund, A},
title = {Deep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules.},
journal = {Genome research},
volume = {31},
number = {1},
pages = {64-74},
pmid = {33239396},
issn = {1549-5469},
support = {F32 DE026947/DE/NIDCR NIH HHS/United States ; K99 DE029228/DE/NIDCR NIH HHS/United States ; R00 DE024543/DE/NIDCR NIH HHS/United States ; },
mesh = {Bacteria ; *Dental Caries ; Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; Humans ; *Metagenomics ; *Microbiota/genetics ; },
abstract = {Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host cytokines and chemokines were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. Forty-two of these species had no genomes in public repositories, thereby representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria. Saccharibacteria are understood to be obligate epibionts, which are dependent on host bacteria. These data suggest that the various Saccharibacteria clades may rely on their hosts for highly distinct metabolic requirements, which would have significant evolutionary and ecological implications. Across the study group, Rothia, Neisseria, and Haemophilus spp. were associated with good dental health, whereas Prevotella spp., Streptococcus mutans, and Human herpesvirus 4 (Epstein-Barr virus [EBV]) were more prevalent in children with caries. Finally, 10 of the host immunological markers were significantly elevated in the caries group, and co-occurrence analysis provided an atlas of potential relationships between microbes and host immunological molecules. Overall, this study illustrated the oral microbiome at an unprecedented resolution and contributed several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.},
}
@article {pmid34896510,
year = {2021},
author = {Zhou, L and Xu, P and Gong, J and Huang, S and Chen, W and Fu, B and Zhao, Z and Huang, X},
title = {Metagenomic profiles of the resistome in subtropical estuaries: Co-occurrence patterns, indicative genes, and driving factors.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {152263},
doi = {10.1016/j.scitotenv.2021.152263},
pmid = {34896510},
issn = {1879-1026},
abstract = {Estuaries are resistome hotspots owing to resistome accumulation and propagation at these locations from surrounding rivers, yet the large-scale biogeographic pattern of resistome, especially biocide and metal resistance genes (BMRGs) and its driving mechanisms in estuarine waters remains to be elucidated. Here, a metagenomics-based approach was firstly used to investigate resistome and mobilome profiles in waters from 30 subtropical estuaries, South China. The Pearl River estuaries had a higher diversity and abundance of antibiotic resistance genes (ARGs), BMRGs, and mobile genetic elements (MGEs) when compared with estuaries from east and west regions. Genes resistant to multiple antibiotics, metals, and biocides were the most abundant gene types in the resistome. The abundance of MGEs (e.g., intI1, IS91, and tnpA) was highly associated with the total abundance of resistance genes, suggesting their utility as potential indicators for quantitative estimations of the resistome contamination. Further, MGEs contributed more than bacterial communities in shaping the resistome in subtropical estuaries. Physicochemical factors (e.g., pH) regulated MGE composition and stochastic assembly, which mediated the co-selection of ARGs and BMRGs via horizontal gene transfer. Our findings have important implications and provide a reference on the management of ARGs and BMRGs in subtropical estuarine ecosystems.},
}
@article {pmid34890483,
year = {2021},
author = {Shen, Z and Wang, F and Liang, Y and Li, Y and Liu, Q and Liu, F},
title = {Diversity and functions of microbes in surface sediments under heavy metal pollution of western Chaohu Lake.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/lam.13627},
pmid = {34890483},
issn = {1472-765X},
abstract = {Heavy metal pollution is a global concern. Targeting at the surface sediments in western Chaohu Lake and using metagenome sequencing, we probed into the mechanism how microbes adapted to heavy-metal-polluted sediments under natural conditions. It was found the heavy metal pollution intensity of the three typical sampling places ranked as estuary of Nanfeihe River (NFH) > Zhongmiao Town (HZ) > Hongshizui (HSZ). Totally 129 phyla, 2631 genera and 12989 species were detected in the sediment samples, and HSZ, HZ and NFH had 35, 51 and 67 exclusive genera, respectively. The bacterial biomass and virus quantity from NFH accounted for 22.84% and 70.69% of total quantities, respectively, and the microbial community compositions in NFH were also different from those in HSZ and HZ. Metagenomics sequencing and functional gene annotation showed NFH contained many functional genes related to nucleic acid transport and metabolism, ribosome structures and biological origin, replication recombining and repair and inorganic ion transport and metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested the sediments from NFH were rich in enzymes correlated with heavy metal transport and reduction. Our findings offer some scientific basis for Chaohu Lake control and microbe resource utilization.},
}
@article {pmid34881191,
year = {2021},
author = {Afolayan, AO and Biagi, E and Rampelli, S and Candela, M and Brigidi, P and Turroni, S and Ayeni, FA},
title = {The Gut Microbiota of an Individual Varies With Intercontinental Four-Month Stay Between Italy and Nigeria: A Pilot Study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {725769},
pmid = {34881191},
issn = {2235-2988},
abstract = {Despite well-established knowledge of the role of diet and the geographic effect on the gut microbiota of human populations, the temporal dynamics of the individual microbiota profile across changes associated with intercontinental short residence are still far from being understood. This pilot study sought to provide insights into the trajectory of the gut microbiota of an individual during a two-month stay in Italy and a subsequent two-month stay in Nigeria, by 16S rRNA gene sequencing and inferred metagenomics. The gut microbiota underwent massive but temporary changes, both taxonomically and based on predicted functionality. The faecal microbiota associated with the short stay in Italy progressively lost diversity and showed a dominance of Firmicutes, while after returning to Nigeria, the microbial community quickly regained the typical profile, in terms of biodiversity and bacterial signatures of traditional lifestyle, i.e., Prevotella and Treponema. Predicted pathways involved in glycolysis, fermentation and N-acetylneuraminate degradation were enriched during the subsequent two-month stay in Nigeria, whereas pathways associated with amino acid and peptidoglycan synthesis and maturation became over-represented during short stay in Italy. Our findings stress the plasticity of the individual gut microbiota even during a short-term travel, with loss/gain of taxonomic and functional features that mirror those of the gut microbiota of indigenous people dwelling therein.},
}
@article {pmid34875513,
year = {2021},
author = {Iasakov, TR and Kanapatskiy, TA and Toshchakov, SV and Korzhenkov, AA and Ulyanova, MO and Pimenov, NV},
title = {The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation.},
journal = {Marine environmental research},
volume = {173},
number = {},
pages = {105533},
doi = {10.1016/j.marenvres.2021.105533},
pmid = {34875513},
issn = {1879-0291},
abstract = {Pockmarks are important "pumps", which are believed to play a significant role in the global methane cycling and harboring a unique assemblage of very diverse prokaryotes. This study reports the results of massive sequencing of the 16S rRNA gene V4 hypervariable regions for the samples from thirteen pockmark horizons (the Baltic Sea) collected at depths from 0 to 280 cm below seafloor (cmbsf) and the rates of microbially mediated anaerobic oxidation of methane (AOM) and sulfate reduction (SR). Altogether, 76 bacterial and 12 archaeal phyla were identified, 23 of which were candidate divisions. Of the total obtained in the pockmark sequences, 84.3% of them were classified as Bacteria and 12.4% as Archaea; 3.3% of the sequences were assigned to unknown operational taxonomic units (OTUs). Members of the phyla Planctomycetota, Chloroflexota, Desulfobacterota, Caldatribacteriota, Acidobacteriota and Proteobacteria predominated across all horizons, comprising 58.5% of the total prokaryotic community. These phyla showed different types of patterns of relative abundance. Analysis of AOM-SR-mediated prokaryotes abundance and biogeochemical measurements revealed that ANME-2a-2b subcluster was predominant in sulfate-rich upper horizons (including sulfate-methane transition zone (SMTZ)) and together with sulfate-reducing bacterial group SEEP-SRB1 had a primary role in AOM coupled to SR. At deeper sulfate-depleted horizons ANME-2a-2b shifted to ANME-1a and ANME-1b which alone mediated AOM or switch to methanogenic metabolism. Shifting of the ANME subclusters depending on depth reflect a tendency for niche separation in these groups. It was shown that the abundance of Caldatribacteriota and organohalide-respiring Dehalococcoidia (Chloroflexota) exhibited a strong correlation with AOM rates. This is the first detailed study of depth profiles of prokaryotic diversity, patterns of relative abundance, and ANME niche separation in the Baltic Sea pockmark microbiomes sheds light on assembly of prokaryotes in a pockmark.},
}
@article {pmid34867834,
year = {2021},
author = {Thomas, P and Sahu, PK},
title = {Vertical Transmission of Diverse Cultivation-Recalcitrant Endophytic Bacteria Elucidated Using Watermelon Seed Embryos.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {635810},
pmid = {34867834},
issn = {1664-302X},
abstract = {Seed transmission of endophytic microorganisms is a growing research area in plant biology and microbiology. We employed cultivation versus cultivation-independent approaches on excised embryos from watermelon seeds (6-12 months in storage) and on embryo-derived in vitro seedlings (EIVS) to assess the vertical transmission of endophytic bacteria. Surface-disinfected watermelon seeds bore abundant residual bacteria in the testa and perisperm tissues, predominantly Bacillus spp. propounding the essentiality of excluding all non-embryonic tissues for vertical transmission studies. Tissue homogenates from re-disinfected seed embryos displayed no cultivable bacteria during the 1-week monitoring. Bright-field live microscopy revealed abundant bacteria in tissue homogenates and in embryo sections as intracellular motile particles. Confocal imaging on embryo sections after SYTO-9 staining and eubacterial fluorescent in situ hybridization (FISH) endorsed enormous bacterial colonization. Quantitative Insights Into Microbial Ecology (QIIME)-based 16S rRNA V3-V4 taxonomic profiling excluding the preponderant chloroplast and mitochondrial sequences revealed a high bacterial diversity in watermelon seed embryos mainly Firmicutes barring spore formers followed by Proteobacteria, Bacteroidetes, and Actinobacteria, and other minor phyla. Embryo-base (comprising the radicle plus plumule parts) and embryo-cotyledon parts differed in bacterial profiles with the abundance of Firmicutes in the former and Proteobacteria dominance in the latter. EIVS displayed a higher bacterial diversity over seed embryos indicating the activation from the dormant stage of more organisms in seedlings or their better amenability to DNA techniques. It also indicated embryo-to-seedling bacterial transmission, varying taxonomic abundances for seed embryos and seedlings, and differing phylogenic profiles for root, hypocotyl, and cotyledon/shoot-tip tissues. Investigations on different watermelon cultivars confirmed the embryo transmission of diverse cultivation recalcitrant endophytic bacteria. Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes formed the core phyla across different cultivars with 80-90% similarity at genus to phylum levels. Conversely, freshly harvested seeds displayed a dominance of Proteobacteria. The findings revealed that dicot seeds such as in different watermelon cultivars come packaged with abundant and diverse vertical and seedling-transmissible cultivation recalcitrant endophytic bacteria with significant implications for plant biology.},
}
@article {pmid34864203,
year = {2021},
author = {Maran, MIJ and Davis G, DJ},
title = {Benefits of merging paired-end reads before pre-processing environmental metagenomics data.},
journal = {Marine genomics},
volume = {61},
number = {},
pages = {100914},
doi = {10.1016/j.margen.2021.100914},
pmid = {34864203},
issn = {1876-7478},
abstract = {BACKGROUND: High throughput sequencing of environmental DNA has applications in biodiversity monitoring, taxa abundance estimation, understanding the dynamics of community ecology, and marine species studies and conservation. Environmental DNA, especially, marine eDNA, has a fast degradation rate. Aside from the good quality reads, the data could have a significant number of reads that fall slightly below the default PHRED quality threshold of 30 on sequencing. For quality control, trimming methods are employed, which generally precede the merging of the read pairs. However, in the case of eDNA, a significant percentage of reads within the acceptable quality score range are also dropped.<br><br>METHODS: To infer the ideal merge tool that is sensitive to eDNA, two Hiseq paired-end eDNA datasets were utilized to study the merging by the tools - FLASH (Fast Length Adjustment of SHort reads), PANDAseq, COPE, BBMerge, and VSEARCH without preprocessing. We assessed these tools on the following parameters: Time taken to process, the quality, and the number of merged reads. Trimmomatic, a widely-used preprocessing tool, was also assessed by preprocessing the datasets at different parameters for the two approaches of preprocessing: Sliding Window and Maximum Information. The preprocessed read pairs were then merged using the ideal merge tool identified earlier.<br><br>RESULTS: FLASH is the most efficient merge tool balancing data conservation, quality of reads, and processing time. We compared Trimmomatic's two quality trimming options with increasing strictness with FLASH's direct merge. The raw reads processed with Trimmomatic then merged, yielded a significant drop in reads compared to the direct merge. An average of 29% of reads was dropped when directly merged with FLASH. Maximum Information option resulted in 30.7% to 68.05% read loss with lowest and highest stringency parameters, respectively. The Sliding Window approach conserves approximately 10% more reads at a PHRED score of 25 set as the threshold for a window of size 4. The lowered PHRED cut off conserves about 50% of the reads that could potentially be informative. We noted no significant reduction of data while optimizing the number of reads read in a window with the ideal quality (Q) score.<br><br>CONCLUSIONS: Losing reads can negatively impact the downstream processing of the environmental data, especially for sequence alignment studies. The quality trim-first-merge-later approach can significantly decrease the number of reads conserved. However, direct merging of pair-end reads using FLASH conserved more than 60% of the reads. Therefore, direct merging of the paired-end reads can prevent potential removal of informative reads that do not comply by the trimming tool's strict checks. FLASH to be an efficient tool in conserving reads while carrying out quality trimming in moderation. Overall, our results show that merging paired-end reads of eDNA data before trimming can conserve more reads.},
}
@article {pmid34828970,
year = {2021},
author = {Barbieri, F and Tabanelli, G and Montanari, C and Dall'Osso, N and Šimat, V and Smole Možina, S and Baños, A and Özogul, F and Bassi, D and Fontana, C and Gardini, F},
title = {Mediterranean Spontaneously Fermented Sausages: Spotlight on Microbiological and Quality Features to Exploit Their Bacterial Biodiversity.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {11},
pages = {},
pmid = {34828970},
issn = {2304-8158},
support = {Project ID 1467//PRIMA programme (supported by the European Union H2020 programme)/ ; },
abstract = {The wide array of spontaneously fermented sausages of the Mediterranean area can represent a reservoir of microbial biodiversity and can be an important source of new technological and functional strains able to preserve product properties, counteracting the impoverishment of their organoleptic typical features due to the introduction of commercial starter cultures. We analysed 15 artisanal salamis from Italy, Spain, Croatia and Slovenia to evaluate the microbiota composition, through culture-dependent and culture-independent techniques (i.e., metagenomic analysis), chemical-physical features, biogenic amines and aroma profile. The final pH varied according to origin and procedures (e.g., higher pH in Italian samples due to long ripening and mold growth). Lactic acid bacteria (LAB) and coagulase-negative cocci (CNC) were the dominant population, with highest LAB counts in Croatian and Italian samples. Metagenomic analysis showed high variability in qualitative and quantitative microbial composition: among LAB, Latilactobacillus sakei was the dominant species, but Companilactobacillus spp. was present in high amounts (45-55% of the total ASVs) in some Spanish sausages. Among staphylococci, S. epidermidis, S. equorum, S. saprophyticus, S. succinus and S. xylosus were detected. As far as biogenic amines, tyramine was always present, while histamine was found only in two Spanish samples. These results can valorize the bacterial genetic heritage present in Mediterranean products, to find new candidates of autochthonous starter cultures or bioprotective agents.},
}
@article {pmid34828362,
year = {2021},
author = {Lach, J and Jęcz, P and Strapagiel, D and Matera-Witkiewicz, A and Stączek, P},
title = {The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools.},
journal = {Genes},
volume = {12},
number = {11},
pages = {},
pmid = {34828362},
issn = {2073-4425},
abstract = {Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.},
}
@article {pmid34827957,
year = {2021},
author = {Benmazouz, I and Jokimäki, J and Lengyel, S and Juhász, L and Kaisanlahti-Jokimäki, ML and Kardos, G and Paládi, P and Kövér, L},
title = {Corvids in Urban Environments: A Systematic Global Literature Review.},
journal = {Animals : an open access journal from MDPI},
volume = {11},
number = {11},
pages = {},
pmid = {34827957},
issn = {2076-2615},
support = {SH-00355-004/2019//Stipendium Hungaricum program/ ; NKFIH-OTKA K134391//National Research, Development, and Innovation Office of Hungary/ ; },
abstract = {Urbanization is one of the most prevalent drivers of biodiversity loss, yet few taxonomic groups are remarkably successful at adapting to urban environments. We systematically surveyed the global literature on the effects of urbanization on species of family Corvidae (crows, choughs, jackdaws, jays, magpies, nutcrackers, ravens, rooks, treepies) to assess the occurrence of corvids in urban environments and the factors affecting their success. We found a total of 424 primary research articles, and the number of articles has increased exponentially since the 1970s. Most studies were carried out in cities of Europe and North America (45.5% and 31.4%, respectively) and were directed on a single species (75.2). We found that 30 corvid species (23% of 133 total) regularly occur in urban environments. The majority (72%) of the studies reported positive effects of urbanization on corvids, with 85% of studies detecting population increases and 64% of studies detecting higher breeding success with urbanization. Of the factors proposed to explain corvids' success (availability of nesting sites and food sources, low predation and persecution), food availability coupled with diet shifts emerged as the most important factors promoting Corvidae to live in urban settings. The breeding of corvids in urban environments was further associated with earlier nesting, similar or larger clutches, lower hatching but higher fledging success, reduced home range size and limited territoriality, increased tolerance towards humans and increasing frequency of conflicts with humans. Despite geographic and taxonomic biases in our literature sample, our review indicates that corvids show both flexibility in resource use and behavioral plasticity that enable them to exploit novel resources for nesting and feeding. Corvids can thus be urban exploiters of the large-scale modifications of ecosystems caused by urbanization.},
}
@article {pmid34818799,
year = {2022},
author = {Hernández-Álvarez, C and García-Oliva, F and Cruz-Ortega, R and Romero, MF and Barajas, HR and Piñero, D and Alcaraz, LD},
title = {Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations.},
journal = {The Science of the total environment},
volume = {805},
number = {},
pages = {150136},
doi = {10.1016/j.scitotenv.2021.150136},
pmid = {34818799},
issn = {1879-1026},
mesh = {*Cucurbita ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Plant Roots ; RNA, Ribosomal, 16S ; *Rhizobiaceae ; Rhizosphere ; Soil Microbiology ; Streptomyces ; },
abstract = {Arid zones contain a diverse set of microbes capable of survival under dry conditions, some of which can form relationships with plants under drought stress conditions to improve plant health. We studied squash (Cucurbita pepo L.) root microbiome under historically arid and humid sites, both in situ and performing a common garden experiment. Plants were grown in soils from sites with different drought levels, using in situ collected soils as the microbial source. We described and analyzed bacterial diversity by 16S rRNA gene sequencing (N = 48) from the soil, rhizosphere, and endosphere. Proteobacteria were the most abundant phylum present in humid and arid samples, while Actinobacteriota abundance was higher in arid ones. The β-diversity analyses showed split microbiomes between arid and humid microbiomes, and aridity and soil pH levels could explain it. These differences between humid and arid microbiomes were maintained in the common garden experiment, showing that it is possible to transplant in situ diversity to the greenhouse. We detected a total of 1009 bacterial genera; 199 exclusively associated with roots under arid conditions. By 16S and shotgun metagenomics, we identified dry-associated taxa such as Cellvibrio, Ensifer adhaerens, and Streptomyces flavovariabilis. With shotgun metagenomic sequencing of rhizospheres (N = 6), we identified 2969 protein families in the squash core metagenome and found an increased number of exclusively protein families from arid (924) than humid samples (158). We found arid conditions enriched genes involved in protein degradation and folding, oxidative stress, compatible solute synthesis, and ion pumps associated with osmotic regulation. Plant phenotyping allowed us to correlate bacterial communities with plant growth. Our study revealed that it is possible to evaluate microbiome diversity ex-situ and identify critical species and genes involved in plant-microbe interactions in historically arid locations.},
}
@article {pmid34818790,
year = {2022},
author = {Soto, DF and Franzetti, A and Gómez, I and Huovinen, P},
title = {Functional filtering and random processes affect the assembly of microbial communities of snow algae blooms at Maritime Antarctic.},
journal = {The Science of the total environment},
volume = {805},
number = {},
pages = {150305},
doi = {10.1016/j.scitotenv.2021.150305},
pmid = {34818790},
issn = {1879-1026},
mesh = {Antarctic Regions ; Bacteria/genetics ; Eutrophication ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The increasing temperatures at the West Antarctic Peninsula (Maritime Antarctic) could lead to a higher occurrence of snow algal blooms which are ubiquitous events that change the snow coloration, reducing albedo and in turn exacerbating melting. However, there is a limited understanding of snow algae blooms biodiversity, composition, and their functional profiles, especially in one of the world's areas most affected by climate change. In this study we used 16S rRNA and 18S rRNA metabarcoding, and shotgun metagenomics to assess the diversity, composition, and functional potential of the snow algae blooms bacterial and eukaryotic communities at three different sites of Maritime Antarctic, between different colors of the algae blooms and between seasonal and semi-permanent snowfields. We tested the hypothesis that the functional potential of snow algae blooms is conserved despite a changing taxonomic composition. Furthermore, we determined taxonomic co-occurrence patterns of bacteria and eukaryotes and assessed the potential for the exchange of metabolites among bacterial taxa. Here, we tested the prediction that there are co-occurring taxa within snow algae whose biotic interactions are marked by the exchange of metabolites. Our results show that the composition of snow algae blooms vary significantly among sites. For instance, a higher abundance of fungi and protists were detected in Fildes Peninsula compared with Doumer Island and O'Higgins. Likewise, the composition varied between snow colors and snow types. However, the functional potential varied only among sampling sites with a higher abundance of genes involved in tolerance to environmental stress at O'Higgins. Co-occurrence patterns of dominant bacterial genera such as Pedobacter, Polaromonas, Flavobacterium and Hymenobacter were recorded, contrasting the absence of co-occurring patterns displayed by Chlamydomonadales algae with other eukaryotes. Finally, genome-scale metabolic models revealed that bacteria within snow algae blooms likely compete for resources instead of forming cooperative communities.},
}
@article {pmid34795298,
year = {2021},
author = {Armstrong, AJS and Parmar, V and Blaser, MJ},
title = {Assessing saliva microbiome collection and processing methods.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {81},
pmid = {34795298},
issn = {2055-5008},
support = {R01 AI158911/AI/NIAID NIH HHS/United States ; },
mesh = {Adult ; Bacteria/genetics ; COVID-19/genetics ; DNA/genetics ; DNA, Bacterial/genetics ; Female ; Humans ; Male ; Metagenome/genetics ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2/pathogenicity ; Saliva/*microbiology ; Sequence Analysis, DNA/methods ; },
abstract = {The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.},
}
@article {pmid34778105,
year = {2021},
author = {Pang, L and Wang, Y and Ye, Y and Zhou, Y and Zhi, Q and Lin, H},
title = {Metagenomic Analysis of Dental Plaque on Pit and Fissure Sites With and Without Caries Among Adolescents.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {740981},
pmid = {34778105},
issn = {2235-2988},
mesh = {Adolescent ; Biofilms ; *Dental Caries ; Dental Caries Susceptibility ; *Dental Plaque ; Humans ; Metagenomics ; *Microbiota ; },
abstract = {Caries is one of the most prevalent infectious diseases worldwide and is driven by the dysbiosis of dental biofilms adhering to tooth surfaces. The pits and fissured surfaces are the most susceptible sites of caries. However, information on the taxonomic composition and functional characteristics of the plaque microbiota in the pit and fissure sites is very limited. This study aimed to use metagenomic sequencing analyses to investigate the relationship between the plaque microbiome in the pit and fissure site and caries in adolescents. A total of 20 adolescents with active pit and fissure surface caries were involved as well as 20 age-matched, caries-free teenagers for control tests. Plaque samples were collected from the pit and fissure site and were subjected to metagenomic analyses, in which the microbial communities were investigated. Our results showed that the microbiota diversity was similar between those two groups. At the species level, the relative abundances of A. gerencseriae, P. acidifaciens, P. multisaccharivorax, S. oralis, S. mutans, and P. denticolens were higher in the caries-active group. N. elongata, C. hominis, and A. johnsonii were relatively more abundant in the caries-free groups. Functional analysis suggested that the metabolic pathway was the most abundant pathway, and the functional traits of the level 2 pathways included amino acid metabolism, metabolism of cofactors, and vitamins and carbohydrate metabolism. Our results also revealed that the caries group displayed several alterations in metabolic pathways, including enriched functions in carbohydrate digestion and absorption. This study suggested that in addition to the specific anatomical structures of the pit and fissured surfaces, the fundamental differences in the plaque microbiome may also be related to the susceptibility of pit and fissure caries.},
}
@article {pmid34760716,
year = {2021},
author = {Xie, J and Cho, H and Lin, BM and Pillai, M and Heimisdottir, LH and Bandyopadhyay, D and Zou, F and Roach, J and Divaris, K and Wu, D},
title = {Improved Metabolite Prediction Using Microbiome Data-Based Elastic Net Models.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {734416},
pmid = {34760716},
issn = {2235-2988},
support = {U01 DE025046/DE/NIDCR NIH HHS/United States ; P30 CA016059/CA/NCI NIH HHS/United States ; T15 LM012500/LM/NLM NIH HHS/United States ; },
mesh = {Child ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics ; Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {Microbiome data are becoming increasingly available in large health cohorts, yet metabolomics data are still scant. While many studies generate microbiome data, they lack matched metabolomics data or have considerable missing proportions of metabolites. Since metabolomics is key to understanding microbial and general biological activities, the possibility of imputing individual metabolites or inferring metabolomics pathways from microbial taxonomy or metagenomics is intriguing. Importantly, current metabolomics profiling methods such as the HMP Unified Metabolic Analysis Network (HUMAnN) have unknown accuracy and are limited in their ability to predict individual metabolites. To address this gap, we developed a novel metabolite prediction method, and we present its application and evaluation in an oral microbiome study. The new method for predicting metabolites using microbiome data (ENVIM) is based on the elastic net model (ENM). ENVIM introduces an extra step to ENM to consider variable importance (VI) scores, and thus, achieves better prediction power. We investigate the metabolite prediction performance of ENVIM using metagenomic and metatranscriptomic data in a supragingival biofilm multi-omics dataset of 289 children ages 3-5 who were participants of a community-based study of early childhood oral health (ZOE 2.0) in North Carolina, United States. We further validate ENVIM in two additional publicly available multi-omics datasets generated from studies of gut health. We select gene family sets based on variable importance scores and modify the existing ENM strategy used in the MelonnPan prediction software to accommodate the unique features of microbiome and metabolome data. We evaluate metagenomic and metatranscriptomic predictors and compare the prediction performance of ENVIM to the standard ENM employed in MelonnPan. The newly developed ENVIM method showed superior metabolite predictive accuracy than MelonnPan when trained with metatranscriptomics data only, metagenomics data only, or both. Better metabolite prediction is achieved in the gut microbiome compared with the oral microbiome setting. We report the best-predictable compounds in all these three datasets from two different body sites. For example, the metabolites trehalose, maltose, stachyose, and ribose are all well predicted by the supragingival microbiome.},
}
@article {pmid34758191,
year = {2021},
author = {Briscoe, AG and Nichols, S and Hartikainen, H and Knipe, H and Foster, R and Green, AJ and Okamura, B and Bass, D},
title = {High-Throughput Sequencing of faeces provides evidence for dispersal of parasites and pathogens by migratory waterbirds.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13548},
pmid = {34758191},
issn = {1755-0998},
abstract = {Examination of faecal material has demonstrated how a broad range of organisms are distributed by bird movements. Such research has largely focused on dispersal of plant seeds by frugivores and of freshwater organisms by waterbirds. However, with few exceptions (e.g. avian influenza, Ebola virus), there is a dearth of evidence for transport of parasites and pathogens. High-throughput sequencing methods now provide a powerful means of addressing this knowledge gap by elucidating faecal contents in unprecedented detail. We collected faeces excreted by a range of migratory waterbirds in south-west Spain and pooled faecal DNA to create libraries reflective of feeding behavior. We created sets of libraries using high-throughput metagenomic and amplicon sequencing. For the latter we employed two sets of primers to broadly target the V4 region of the 18S rRNA gene (one set amplifying the region across all eukaryotes, the other excluding amplification of metazoans). Libraries revealed a wide diversity of eukaryotes, including parasites of the faecal producers themselves, parasites of food items, or those incidentally ingested. We also detected novel microbial eukaryotic taxa and found that parasite assemblage profiles were relatively distinct. Comparing the performance of the methods used supports their joint use for future studies of diversity and abundance. Because viable stages of many parasites are likely to be present in faeces, our results suggest significant levels of bird-mediated dispersal of parasites (both from avian and other hosts). Our methods revealed much hidden biodiversity, and allowed identification of the individuals who produced the faecal samples to species level, facilitating the study of interaction networks.},
}
@article {pmid34743174,
year = {2021},
author = {Sakoula, D and Smith, GJ and Frank, J and Mesman, RJ and Kop, LFM and Blom, P and Jetten, MSM and van Kessel, MAHJ and Lücker, S},
title = {Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {34743174},
issn = {1751-7370},
support = {339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; SIAM 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; SIAM 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 016.Veni.192.062//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 339880//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)/ ; },
abstract = {The advance of metagenomics in combination with intricate cultivation approaches has facilitated the discovery of novel ammonia-, methane-, and other short-chain alkane-oxidizing microorganisms, indicating that our understanding of the microbial biodiversity within the biogeochemical nitrogen and carbon cycles still is incomplete. The in situ detection and phylogenetic identification of novel ammonia- and alkane-oxidizing bacteria remain challenging due to their naturally low abundances and difficulties in obtaining new isolates from complex samples. Here, we describe an activity-based protein profiling protocol allowing cultivation-independent unveiling of ammonia- and alkane-oxidizing bacteria. In this protocol, 1,7-octadiyne is used as a bifunctional enzyme probe that, in combination with a highly specific alkyne-azide cycloaddition reaction, enables the fluorescent or biotin labeling of cells harboring active ammonia and alkane monooxygenases. Biotinylation of these enzymes in combination with immunogold labeling revealed the subcellular localization of the tagged proteins, which corroborated expected enzyme targets in model strains. In addition, fluorescent labeling of cells harboring active ammonia or alkane monooxygenases provided a direct link of these functional lifestyles to phylogenetic identification when combined with fluorescence in situ hybridization. Furthermore, we show that this activity-based labeling protocol can be successfully coupled with fluorescence-activated cell sorting for the enrichment of nitrifiers and alkane-oxidizing bacteria from complex environmental samples, enabling the recovery of high-quality metagenome-assembled genomes. In conclusion, this study demonstrates a novel, functional tagging technique for the reliable detection, identification, and enrichment of ammonia- and alkane-oxidizing bacteria present in complex microbial communities.},
}
@article {pmid34715437,
year = {2021},
author = {Lugli, GA and Calvete-Torre, I and Alessandri, G and Milani, C and Turroni, F and Laiolo, P and Ossiprandi, MC and Margolles, A and Ruiz, L and Ventura, M},
title = {Phylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov.},
journal = {Systematic and applied microbiology},
volume = {44},
number = {6},
pages = {126273},
doi = {10.1016/j.syapm.2021.126273},
pmid = {34715437},
issn = {1618-0984},
mesh = {Animals ; Bacterial Typing Techniques ; Base Composition ; *Bifidobacterium/genetics ; DNA, Bacterial/genetics ; *Fatty Acids ; Feces ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Ten Bifidobacterium strains, i.e., 6T3, 64T4, 79T10, 80T4, 81T8, 82T1, 82T10, 82T18, 82T24, and 82T25, were isolated from mantled guereza (Colobus guereza), Sumatran orangutan (Pongo abeli), silvery marmoset (Mico argentatus), golden lion tamarin (Leontopithecus rosalia), pied tamarin (Saguinus bicolor), and common pheasant (Phaisanus colchinus). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic, and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on the core genome sequences revealed that isolated strains exhibit close phylogenetic relatedness with Bifidobacterium genus members belonging to the Bifidobacterium bifidum, Bifidobacterium longum, Bifidobacterium pullorum, and Bifidobacterium tissieri phylogenetic groups. Phenotypic characterization and genotyping based on the genome sequences clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, B. phasiani sp. nov. (6T3 = LMG 32224T = DSM 112544T), B. pongonis sp. nov. (64T4 = LMG 32281T = DSM 112547T), B. saguinibicoloris sp. nov. (79T10 = LMG 32232T = DSM 112543T), B. colobi sp. nov. (80T4 = LMG 32225T = DSM 112552T), B. simiiventris sp. nov. (81T8 = LMG 32226T = DSM 112549T), B. santillanense sp. nov. (82T1 = LMG 32284T = DSM 112550T), B. miconis sp. nov. (82T10 = LMG 32282T = DSM 112551T), B. amazonense sp. nov. (82T18 = LMG 32297T = DSM 112548T), pluvialisilvae sp. nov. (82T24 = LMG 32229T = DSM 112545T), and B. miconisargentati sp. nov. (82T25 = LMG 32283T = DSM 112546T) are proposed as novel Bifidobacterium species.},
}
@article {pmid34714225,
year = {2021},
author = {Lu, X and Hua, X and Wang, Y and Zhang, D and Jiang, S and Yang, S and Wang, X and Shen, Q and Zhou, T and Lin, Z and Zhang, W and Cui, L},
title = {Comparison of gut viral communities in diarrhoea and healthy dairy calves.},
journal = {The Journal of general virology},
volume = {102},
number = {10},
pages = {},
doi = {10.1099/jgv.0.001663},
pmid = {34714225},
issn = {1465-2099},
mesh = {Animals ; Caliciviridae/classification/genetics/isolation &amp; purification ; Cattle/*virology ; Cattle Diseases/*virology ; DNA Viruses/classification/genetics/isolation &amp; purification ; Dairying ; Diarrhea/*veterinary/virology ; Feces/virology ; Genome, Viral ; Intestines/*virology ; Mamastrovirus/classification/genetics/isolation &amp; purification ; Metagenomics ; Phylogeny ; *Virome ; },
abstract = {Calf diarrhoea has been a major cause of economic losses in the global dairy industry. Many factors, including multiple pathogen infections, can directly or indirectly cause calf diarrhoea. This study compared the faecal virome between 15 healthy calves and 15 calves with diarrhoea. Significantly lower diversity of viruses was found in samples from animals with diarrhoea than those in the healthy ones, and this feature may also be related to the age of the calves. Viruses belonging to the families Astroviridae and Caliciviridae that may cause diarrhoea in dairy calves have been characterized, which revealed that reads of caliciviruses and astroviruses in diarrhoea calves were much higher than those in healthy calves. Five complete genomic sequences closely related to Smacoviridae have been identified, which may participate in the regulation of the gut virus community ecology of healthy hosts together with bacteriophages. This research provides a theoretical basis for further understanding of known or potential enteric pathogens related to calf diarrhoea.},
}
@article {pmid34710422,
year = {2021},
author = {DeBofsky, A and Xie, Y and Challis, JK and Ankley, PJ and Brinkmann, M and Jones, PD and Giesy, JP},
title = {16S rRNA metabarcoding unearths responses of rare gut microbiome of fathead minnows exposed to benzo[a]pyrene.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {151060},
doi = {10.1016/j.scitotenv.2021.151060},
pmid = {34710422},
issn = {1879-1026},
abstract = {Activities of gut microbiomes are often overlooked in assessments of ecotoxicological effects of environmental contaminants. Effects of the polycyclic aromatic hydrocarbon, benzo[a]pyrene (BaP) on active gut microbiomes of juvenile fathead minnows (Pimephales promelas) were investigated. Fish were exposed for two weeks, to concentrations of 0, 1, 10, 100, or 1000 μg BaP g-1 in the diet. The active gut microbiome was characterized using 16S rRNA metabarcoding to determine its response to dietary exposure of BaP. BaP reduced alpha-diversity at the greatest exposure concentrations. Additionally, exposure to BaP altered community composition of active microbiome and resulted in differential proportion of taxa associated with hydrocarbon degradation and fish health. Neighborhood selection networks of active microbiomes were not reduced with greater concentrations of BaP, which suggests ecological resistance and/or resilience of gut microbiota. The active gut microbiome had a similar overall biodiversity as that of the genomic gut microbiota, but had a distinct composition from that of the 16S rDNA profile. Responses of alpha- and beta-diversities of the active microbiome to BaP exposure were consistent with that of genomic microbiomes. Normalized activity of microbiome via the ratio of rRNA to rDNA abundance revealed rare taxa that became active or dormant due to exposure to BaP. These differences highlight the need to assess both 16S rDNA and rRNA metabarcoding to fully derive bacterial compositional changes resulting from exposure to contaminants.},
}
@article {pmid34704805,
year = {2021},
author = {Tarracchini, C and Milani, C and Longhi, G and Fontana, F and Mancabelli, L and Pintus, R and Lugli, GA and Alessandri, G and Anzalone, R and Viappiani, A and Turroni, F and Mussap, M and Dessì, A and Cesare Marincola, F and Noto, A and De Magistris, A and Vincent, M and Bernasconi, S and Picaud, JC and Fanos, V and Ventura, M},
title = {Unraveling the Microbiome of Necrotizing Enterocolitis: Insights in Novel Microbial and Metabolomic Biomarkers.},
journal = {Microbiology spectrum},
volume = {9},
number = {2},
pages = {e0117621},
pmid = {34704805},
issn = {2165-0497},
abstract = {Necrotizing enterocolitis (NEC) is among the most relevant gastrointestinal diseases affecting mostly prematurely born infants with low birth weight. While intestinal dysbiosis has been proposed as one of the possible factors involved in NEC pathogenesis, the role of the gut microbiota remains poorly understood. In this study, the gut microbiota of preterm infants was explored to highlight differences in the composition between infants affected by NEC and infants prior to NEC development. A large-scale gut microbiome analysis was performed, including 47 shotgun sequencing data sets generated in the framework of this study, along with 124 retrieved from publicly available repositories. Meta-analysis led to the identification of preterm community state types (PT-CSTs), which recur in healthy controls and NEC infants. Such analyses revealed an overgrowth of a range of opportunistic microbial species accompanying the loss of gut microbial biodiversity in NEC subjects. Moreover, longitudinal insights into preterm infants prior to NEC development indicated Clostridium neonatale and Clostridium perfringens species as potential biomarkers for predictive early diagnosis of this disease. Furthermore, functional investigation of the enzymatic reaction profiles associated with pre-NEC condition suggested DL-lactate as a putative metabolic biomarker for early detection of NEC onset. IMPORTANCE Necrotizing enterocolitis (NEC) is a severe gastrointestinal disease occurring predominantly in premature infants whose etiology is still not fully understood. In this study, the analysis of infant fecal samples through shotgun metagenomics approaches revealed a marked reduction of the intestinal (bio)diversity and an overgrowth of (opportunistic) pathogens associated with the NEC development. In particular, dissection of the infant's gut microbiome before NEC diagnosis highlighted the potential involvement of Clostridium genus members in the progression of NEC. Remarkably, our analyses highlighted a gastrointestinal DL-lactate accumulation among NEC patients that might represent a novel potential functional biomarker for the early diagnosis of NEC.},
}
@article {pmid34696369,
year = {2021},
author = {Hasiów-Jaroszewska, B and Boezen, D and Zwart, MP},
title = {Metagenomic Studies of Viruses in Weeds and Wild Plants: A Powerful Approach to Characterise Variable Virus Communities.},
journal = {Viruses},
volume = {13},
number = {10},
pages = {},
pmid = {34696369},
issn = {1999-4915},
support = {2017/25/B/NZ9/01715//Narodowe Centrum Nauki/ ; },
abstract = {High throughput sequencing (HTS) has revolutionised virus detection and discovery, allowing for the untargeted characterisation of whole viromes. Viral metagenomics studies have demonstrated the ubiquity of virus infection - often in the absence of disease symptoms - and tend to discover many novel viruses, highlighting the small fraction of virus biodiversity described to date. The majority of the studies using high-throughput sequencing to characterise plant viromes have focused on economically important crops, and only a small number of studies have considered weeds and wild plants. Characterising the viromes of wild plants is highly relevant, as these plants can affect disease dynamics in crops, often by acting as viral reservoirs. Moreover, the viruses in unmanaged systems may also have important effects on wild plant populations and communities. Here, we review metagenomic studies on weeds and wild plants to show the benefits and limitations of this approach and identify knowledge gaps. We consider key genomics developments that are likely to benefit the field in the near future. Although only a small number of HTS studies have been performed on weeds and wild plants, these studies have already discovered many novel viruses, demonstrated unexpected trends in virus distributions, and highlighted the potential of metagenomics as an approach.},
}
@article {pmid34695305,
year = {2021},
author = {Carasso, S and Fishman, B and Lask, LS and Shochat, T and Geva-Zatorsky, N and Tauber, E},
title = {Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {35},
number = {11},
pages = {e22011},
doi = {10.1096/fj.202100857RR},
pmid = {34695305},
issn = {1530-6860},
mesh = {Adult ; *Circadian Rhythm ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Surveys and Questionnaires ; Young Adult ; },
abstract = {Patterns of diurnal activity differ substantially between individuals, with early risers and late sleepers being examples of opposite chronotypes. Growing evidence suggests that the late chronotype significantly impacts the risk of developing mood disorders, obesity, diabetes, and other chronic diseases. Despite the vast potential of utilizing chronotype information for precision medicine, those factors that shape chronotypes remain poorly understood. Here, we assessed whether the various chronotypes are associated with different gut microbiome compositions. Using metagenomic sequencing analysis, we established a distinct signature associated with chronotype based on two bacterial genera, Alistipes (elevated in "larks") and Lachnospira (elevated in "owls"). We identified three metabolic pathways associated with the early chronotype, and linked distinct dietary patterns with different chronotypes. Our work demonstrates an association between the gut microbiome and chronotype and may represent the first step towards developing dietary interventions aimed at ameliorating the deleterious health correlates of the late chronotype.},
}
@article {pmid34693622,
year = {2021},
author = {Sun, H and Liu, J and Tan, S and Zheng, Y and Wang, X and Liang, J and Todd, JD and Zhang, XH},
title = {Spatiotemporal distribution of bacterial dimethylsulfoniopropionate producing and catabolic genes in the Changjiang Estuary.},
journal = {Environmental microbiology},
volume = {23},
number = {11},
pages = {7073-7092},
doi = {10.1111/1462-2920.15813},
pmid = {34693622},
issn = {1462-2920},
support = {2016YFA0601303//National Key Research and Development Program of China/ ; 41730530//National Natural Science Foundation of China/ ; 91751202//National Natural Science Foundation of China/ ; NE/P012671//Natural Environment Research Council UK Standard grants/ ; NE/S001352//Natural Environment Research Council UK Standard grants/ ; },
abstract = {The osmolyte dimethylsulfoniopropionate (DMSP) is produced in petagram amounts by marine microorganisms. Estuaries provide natural gradients in salinity and nutrients, factors known to regulate DMSP production; yet there have been no molecular studies of DMSP production and cycling across these gradients. Here, we study the abundance, distribution and transcription of key DMSP synthesis (e.g. dsyB and mmtN) and catabolic (e.g. dddP and dmdA) genes along the salinity gradient of the Changjiang Estuary. DMSP levels did not correlate with Chl a across the salinity gradient. In contrast, DMSP concentration, abundance of bacterial DMSP producers and their dsyB and mmtN transcripts were lowest in the freshwater samples and increased abruptly with salinity in the transitional and seawater samples. Metagenomics analysis suggests bacterial DMSP-producers were more abundant than their algal equivalents and were more prominent in summer than winter samples. Bacterial DMSP catabolic genes and their transcripts followed the same trend of being greatly enhanced in transitional and seawater samples with higher DMSP levels than freshwater samples. DMSP cleavage was likely the dominant catabolic pathway, with DMSP lyase genes being ~4.3-fold more abundant than the demethylase gene dmdA. This is an exemplar study for future research on microbial DMSP cycling in estuary environments.},
}
@article {pmid34693512,
year = {2021},
author = {G Giske, C and Allander, T and Fröding, I and Ininbergs, K and Mölling, P and Engstrand, L and Albert, J},
title = {[Precision diagnostics in clinical microbiology].},
journal = {Lakartidningen},
volume = {118},
number = {},
pages = {},
pmid = {34693512},
issn = {1652-7518},
mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; },
abstract = {Genomic methods have had a major impact in clinical microbiology in the last decades. Microbial genomes are relatively small and therefore easier to characterise than human genomes. In both bacteriology and in virology, genomic methods have largely been used for molecular epidemiology, but also for molecular resistance testing of microorganisms. Targeted sequencing of predefined or isolated microorganisms was initially a dominant method but has gradually been supplemented with metagenomic diagnostics. Metagenomics aims at mapping all microorganisms - pathogenic as well as apathogenic - in a sample without determining in advance which agent(s) the analysis is targeting. Finally, there is also an increasing interest in mapping the significance of the microbiome, i.e. normal flora, both in health and disease.},
}
@article {pmid34693062,
year = {2021},
author = {Lahlali, R and Ibrahim, DSS and Belabess, Z and Kadir Roni, MZ and Radouane, N and Vicente, CSL and Menéndez, E and Mokrini, F and Barka, EA and Galvão de Melo E Mota, M and Peng, G},
title = {High-throughput molecular technologies for unraveling the mystery of soil microbial community: challenges and future prospects.},
journal = {Heliyon},
volume = {7},
number = {10},
pages = {e08142},
pmid = {34693062},
issn = {2405-8440},
abstract = {Soil microbial communities play a crucial role in soil fertility, sustainability, and plant health. However, intensive agriculture with increasing chemical inputs and changing environments have influenced native soil microbial communities. Approaches have been developed to study the structure, diversity, and activity of soil microbes to better understand the biology and plant-microbe interactions in soils. Unfortunately, a good understanding of soil microbial community remains a challenge due to the complexity of community composition, interactions of the soil environment, and limitations of technologies, especially related to the functionality of some taxa rarely detected using conventional techniques. Culture-based methods have been shown unable and sometimes are biased for assessing soil microbial communities. To gain further knowledge, culture-independent methods relying on direct analysis of nucleic acids, proteins, and lipids are worth exploring. In recent years, metagenomics, metaproteomics, metatranscriptomics, and proteogenomics have been increasingly used in studying microbial ecology. In this review, we examined the importance of microbial community to soil quality, the mystery of rhizosphere and plant-microbe interactions, and the biodiversity and multi-trophic interactions that influence the soil structure and functionality. The impact of the cropping system and climate change on the soil microbial community was also explored. Importantly, progresses in molecular biology, especially in the development of high-throughput biotechnological tools, were extensively assessed for potential uses to decipher the diversity and dynamics of soil microbial communities, with the highlighted advantages/limitations.},
}
@article {pmid34684657,
year = {2021},
author = {Hossain, F and Majumder, S and David, J and Bunnell, BA and Miele, L},
title = {Obesity Modulates the Gut Microbiome in Triple-Negative Breast Cancer.},
journal = {Nutrients},
volume = {13},
number = {10},
pages = {},
pmid = {34684657},
issn = {2072-6643},
mesh = {Analysis of Variance ; Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Mice ; Obesity/*complications/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, RNA ; Triple Negative Breast Neoplasms/*complications/*microbiology ; },
abstract = {Triple-negative breast cancer (TNBC) is an aggressive, molecularly heterogeneous subtype of breast cancer. Obesity is associated with increased incidence and worse prognosis in TNBC through various potential mechanisms. Recent evidence suggests that the gut microbiome plays a central role in the progression of cancer, and that imbalances or dysbiosis in the population of commensal microbiota can lead to inflammation and contribute to tumor progression. Obesity is characterized by low-grade inflammation, and gut dysbiosis is associated with obesity, chronic inflammation, and failure of cancer immunotherapy. However, the debate on what constitutes a "healthy" gut microbiome is ongoing, and the connection among the gut microbiome, obesity, and TNBC has not yet been addressed. This study aims to characterize the role of obesity in modulating the gut microbiome in a syngeneic mouse model of TNBC. 16S rRNA sequencing and metagenomic analyses were performed to analyze and annotate genus and taxonomic profiles. Our results suggest that obesity decreases alpha diversity in the gut microbiome. Metagenomic analysis revealed that obesity was the only significant factor explaining the similarity of the bacterial communities according to their taxonomic profiles. In contrast to the analysis of taxonomic profiles, the analysis of variation of functional profiles suggested that obesity status, tumor presence, and the obesity-tumor interaction were significant in explaining the variation of profiles, with obesity having the strongest correlation. The presence of tumor modified the profiles to a greater extent in obese than in lean animals. Further research is warranted to understand the impact of the gut microbiome on TNBC progression and immunotherapy.},
}
@article {pmid34684459,
year = {2021},
author = {Ahrens, AP and Culpepper, T and Saldivar, B and Anton, S and Stoll, S and Handberg, EM and Xu, K and Pepine, C and Triplett, EW and Aggarwal, M},
title = {A Six-Day, Lifestyle-Based Immersion Program Mitigates Cardiovascular Risk Factors and Induces Shifts in Gut Microbiota, Specifically Lachnospiraceae, Ruminococcaceae, Faecalibacterium prausnitzii: A Pilot Study.},
journal = {Nutrients},
volume = {13},
number = {10},
pages = {},
pmid = {34684459},
issn = {2072-6643},
support = {N/A//Whole Foods, Inc./ ; },
mesh = {Adult ; Biodiversity ; Biomarkers ; Body Weights and Measures ; *Diet ; Disease Susceptibility ; Faecalibacterium prausnitzii ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; *Heart Disease Risk Factors ; Humans ; *Life Style ; Male ; Metagenomics/methods ; Middle Aged ; Pilot Projects ; Ruminococcus ; },
abstract = {Cardiovascular disease (CVD) prevalence remains elevated globally. We have previously shown that a one-week lifestyle "immersion program" leads to clinical improvements and sustained improvements in quality of life in moderate to high atherosclerotic CVD (ASCVD) risk individuals. In a subsequent year of this similarly modeled immersion program, we again collected markers of cardiovascular health and, additionally, evaluated intestinal microbiome composition. ASCVD risk volunteers (n = 73) completed the one-week "immersion program" involving nutrition (100% plant-based foods), stress management education, and exercise. Anthropometric measurements and CVD risk factors were compared at baseline and post intervention. A subgroup (n = 22) provided stool, which we analyzed with 16S rRNA sequencing. We assessed abundance changes within-person, correlated the abundance shifts with clinical changes, and inferred functional pathways using PICRUSt. Reductions in blood pressure, total cholesterol, and triglycerides, were observed without reduction in weight. Significant increases in butyrate producers were detected, including Lachnospiraceae and Oscillospirales. Within-person, significant shifts in relative abundance (RA) occurred, e.g., increased Lachnospiraceae (+58.8% RA, p = 0.0002), Ruminococcaceae (+82.1%, p = 0.0003), Faecalibacterium prausnitzii (+54.5%, p = 0.002), and diversification and richness. Microbiota changes significantly correlated with body mass index (BMI), blood pressure (BP), cholesterol, high-sensitivity C-reactive protein (hsCRP), glucose, and trimethylamine N-oxide (TMAO) changes. Pairwise decreases were inferred in microbial genes corresponding to cancer, metabolic disease, and amino acid metabolism. This brief lifestyle-based intervention improved lipids and BP and enhanced known butyrate producers, without significant weight loss. These results demonstrate a promising non-pharmacological preventative strategy for improving cardiovascular health.},
}
@article {pmid34671161,
year = {2021},
author = {Wang, Y and Pedersen, MW and Alsos, IG and De Sanctis, B and Racimo, F and Prohaska, A and Coissac, E and Owens, HL and Merkel, MKF and Fernandez-Guerra, A and Rouillard, A and Lammers, Y and Alberti, A and Denoeud, F and Money, D and Ruter, AH and McColl, H and Larsen, NK and Cherezova, AA and Edwards, ME and Fedorov, GB and Haile, J and Orlando, L and Vinner, L and Korneliussen, TS and Beilman, DW and Bjørk, AA and Cao, J and Dockter, C and Esdale, J and Gusarova, G and Kjeldsen, KK and Mangerud, J and Rasic, JT and Skadhauge, B and Svendsen, JI and Tikhonov, A and Wincker, P and Xing, Y and Zhang, Y and Froese, DG and Rahbek, C and Nogues, DB and Holden, PB and Edwards, NR and Durbin, R and Meltzer, DJ and Kjær, KH and Möller, P and Willerslev, E},
title = {Late Quaternary dynamics of Arctic biota from ancient environmental genomics.},
journal = {Nature},
volume = {600},
number = {7887},
pages = {86-92},
pmid = {34671161},
issn = {1476-4687},
support = {207492/WT_/Wellcome Trust/United Kingdom ; 069906/WT_/Wellcome Trust/United Kingdom ; WT220023/WT_/Wellcome Trust/United Kingdom ; /ERC_/European Research Council/International ; },
abstract = {During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.},
}
@article {pmid34669745,
year = {2021},
author = {Essigmann, HT and Hoffman, KL and Petrosino, JF and Jun, G and Aguilar, D and Hanis, CL and DuPont, HL and Brown, EL},
title = {The impact of the Th17:Treg axis on the IgA-Biome across the glycemic spectrum.},
journal = {PloS one},
volume = {16},
number = {10},
pages = {e0258812},
pmid = {34669745},
issn = {1932-6203},
support = {R01 DK116378/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Diabetes Mellitus, Type 2/*immunology/microbiology ; Epigenesis, Genetic ; Female ; Gastrointestinal Microbiome ; Humans ; Immunoglobulin A, Secretory/*metabolism ; Male ; Mexican Americans ; Middle Aged ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; T-Lymphocytes, Regulatory/*immunology ; Th17 Cells/*immunology ; },
abstract = {Secretory IgA (SIgA) is released into mucosal surfaces where its function extends beyond that of host defense to include the shaping of resident microbial communities by mediating exclusion/inclusion of respective microbes and regulating bacterial gene expression. In this capacity, SIgA acts as the fulcrum on which host immunity and the health of the microbiota are balanced. We recently completed an analysis of the gut and salivary IgA-Biomes (16S rDNA sequencing of SIgA-coated/uncoated bacteria) in Mexican-American adults that identified IgA-Biome differences across the glycemic spectrum. As Th17:Treg ratio imbalances are associated with gut microbiome dysbiosis and chronic inflammatory conditions such as type 2 diabetes, the present study extends our prior work by examining the impact of Th17:Treg ratios (pro-inflammatory:anti-inflammatory T-cell ratios) and the SIgA response (Th17:Treg-SIgA axis) in shaping microbial communities. Examining the impact of Th17:Treg ratios (determined by epigenetic qPCR lymphocyte subset quantification) on the IgA-Biome across diabetes phenotypes identified a proportional relationship between Th17:Treg ratios and alpha diversity in the stool IgA-Biome of those with dysglycemia, significant changes in community composition of the stool and salivary microbiomes across glycemic profiles, and genera preferentially abundant by T-cell inflammatory phenotype. This is the first study to associate epigenetically quantified Th17:Treg ratios with both the larger and SIgA-fractionated microbiome, assess these associations in the context of a chronic inflammatory disease, and offers a novel frame through which to evaluate mucosal microbiomes in the context of host responses and inflammation.},
}
@article {pmid34665113,
year = {2021},
author = {Cassir, N and Belkacemi, S and Ballouche, M and Khelaifia, S and La Scola, B},
title = {Evaluation of Culture Top transport systems for assessing the bacterial diversity of microbiota by culturomics as compared to a routine transport system.},
journal = {Journal of medical microbiology},
volume = {70},
number = {10},
pages = {},
doi = {10.1099/jmm.0.001411},
pmid = {34665113},
issn = {1473-5644},
mesh = {Bacteria/*isolation &amp; purification ; *Culture Media ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; Specimen Handling/*methods ; },
abstract = {In recent years, metagenomics and then culturomics, which consists of the multiplication of media and culture conditions and the rapid identification of all bacterial colonies, have generated renewed interest in the human microbiota, and diseases associated with modifications in its composition in particular. The sample transport media included in diverse swab transport systems and the storage conditions are among the factors that influence the results of the culturomics. In this study, we compared the results of culturomics from paired skin, oral and rectal swabs from intensive care unit (ICU) patients using Culture Top sample transport medium as compared to our routine one. From 152 clinical samples, we were able to isolate and identify 45 600 colonies, belonging to 338 different bacterial species. The transport system Culture Top identified 282 different bacterial species, while 244 were identified by our routine system. Of these, 188 different bacterial species were commonly identified using both transport systems, while 94 (27.8 %) and 56 (16.5 %) were only identified using Culture Top and our routine system, respectively (P<0.001), but there was no significant difference in bacterial diversity at the genus or phylum level, or in terms of their type of respiration and cell wall. In conclusion, the Culture Top transport system appears to be complementary to our routine system, although it seems slightly superior in terms of isolated bacterial species.},
}
@article {pmid34663463,
year = {2021},
author = {Trubl, G and Kimbrel, JA and Liquet-Gonzalez, J and Nuccio, EE and Weber, PK and Pett-Ridge, J and Jansson, JK and Waldrop, MP and Blazewicz, SJ},
title = {Active virus-host interactions at sub-freezing temperatures in Arctic peat soil.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {208},
pmid = {34663463},
issn = {2049-2618},
mesh = {Freezing ; *Microbiota ; *Soil ; Soil Microbiology ; Temperature ; },
abstract = {BACKGROUND: Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures).<br><br>RESULTS: We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients.<br><br>CONCLUSIONS: Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.},
}
@article {pmid34653444,
year = {2021},
author = {Chimetto Tonon, LA and Rua, C and Crnkovic, CM and Bernardi, DI and Pires Junior, OR and Haddad, CFB and Pedrosa, CSG and Souza, LRQ and Rehen, SK and de Azevedo, GPR and Thompson, CC and Thompson, FL and Berlinck, RGS},
title = {Microbiome associated with the tetrodotoxin-bearing anuran Brachycephalus pitanga.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {203},
number = {},
pages = {139-146},
doi = {10.1016/j.toxicon.2021.10.002},
pmid = {34653444},
issn = {1879-3150},
mesh = {Animals ; Anura ; Bacteria ; *Eugenia ; *Microbiota ; Tetrodotoxin/toxicity ; },
abstract = {The genus Brachycephalus includes small species of aposematic anurans known as microendemic, occurring in the mountains of the Atlantic Forest. Brachycephalus ephippium, B. nodoterga and B. pernix have been reported to contain the neurotoxin tetrodotoxin in skin and viscera. The biological conservation of several Brachycephalus species is currently threatened by climate change, deforestation, and the pandemic caused by the fungus Batrachochytrium dendrobatidis (Bd). Despite the well-known importance of amphibians' associated bacteria in the defensive role against pathogens, there is still a poor understanding of amphibian microbiome composition. The present study investigated the composition of B. pitanga microbial community and the presence of TTX in the host and in cultures of bacterial isolates, using a combination of metagenomics, bacterial culture isolation, mass spectrometry and metabolomic analyses. Results of culture-dependent and -independent analyses characterized the microbial communities associated with the skin and viscera of B. pitanga. Mass spectrometry analysis indicated the presence of TTX in host tissues, while bacterial production of TTX was not observed under the experimental conditions used in this investigation. This is the first report confirming the occurrence of TTX in B. pitanga.},
}
@article {pmid34649602,
year = {2021},
author = {Liu, L and Wang, Y and Yang, Y and Wang, D and Cheng, SH and Zheng, C and Zhang, T},
title = {Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {205},
pmid = {34649602},
issn = {2049-2618},
mesh = {Genome, Bacterial/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; *Sewage ; },
abstract = {BACKGROUND: Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain unresolved when leveraging error-prone long reads to characterize high-complexity metagenomes, for instance, complete/high-quality genome reconstruction from highly complex systems.<br><br>RESULTS: Here, we developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly (HCBHA) approach that capitalizes on a hybrid (error-prone long reads and high-accuracy short reads) sequencing strategy to reconstruct (near-) complete genomes from highly complex metagenomes. Using the HCBHA approach, we first phase short and long reads from the highly complex metagenomic dataset into different candidate bacterial haplotypes, then perform hybrid assembly of each bacterial genome individually. We reconstructed 557 metagenome-assembled genomes (MAGs) with an average N50 of 574 Kb from a deeply sequenced, highly complex activated sludge (AS) metagenome. These high-contiguity MAGs contained 14 closed genomes and 111 high-quality (HQ) MAGs including full-length rRNA operons, which accounted for 61.1% of the microbial community. Leveraging the near-complete genomes, we also profiled the metabolic potential of the AS microbiome and identified 2153 biosynthetic gene clusters (BGCs) encoded within the recovered AS MAGs.<br><br>CONCLUSION: Our results established the feasibility of an iterative haplotype-resolved HCBHA approach to reconstruct (near-) complete genomes from highly complex ecosystems, providing new insights into "complete metagenomics". The retrieved high-contiguity MAGs illustrated that various biosynthetic gene clusters (BGCs) were harbored in the AS microbiome. The high diversity of BGCs highlights the potential to discover new natural products biosynthesized by the AS microbial community, aside from the traditional function (e.g., organic carbon and nitrogen removal) in wastewater treatment. Video Abstract.},
}
@article {pmid34641974,
year = {2021},
author = {Muller, E and Algavi, YM and Borenstein, E},
title = {A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {203},
pmid = {34641974},
issn = {2049-2618},
support = {U19 AG057377/AG/NIA NIH HHS/United States ; U19AG057377/NH/NIH HHS/United States ; R01DK095869/NH/NIH HHS/United States ; },
mesh = {Bile Acids and Salts ; Dysbiosis ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics ; *Microbiota ; },
abstract = {BACKGROUND: Microbiome-metabolome studies of the human gut have been gaining popularity in recent years, mostly due to accumulating evidence of the interplay between gut microbes, metabolites, and host health. Statistical and machine learning-based methods have been widely applied to analyze such paired microbiome-metabolome data, in the hope of identifying metabolites that are governed by the composition of the microbiome. Such metabolites can be likely modulated by microbiome-based interventions, offering a route for promoting gut metabolic health. Yet, to date, it remains unclear whether findings of microbially associated metabolites in any single study carry over to other studies or cohorts, and how robust and universal are microbiome-metabolites links.<br><br>RESULTS: In this study, we addressed this challenge by performing a comprehensive meta-analysis to identify human gut metabolites that can be predicted based on the composition of the gut microbiome across multiple studies. We term such metabolites "robustly well-predicted". To this end, we processed data from 1733 samples from 10 independent human gut microbiome-metabolome studies, focusing initially on healthy subjects, and implemented a machine learning pipeline to predict metabolite levels in each dataset based on the composition of the microbiome. Comparing the predictability of each metabolite across datasets, we found 97 robustly well-predicted metabolites. These include metabolites involved in important microbial pathways such as bile acid transformations and polyamines metabolism. Importantly, however, other metabolites exhibited large variation in predictability across datasets, suggesting a cohort- or study-specific relationship between the microbiome and the metabolite. Comparing taxonomic contributors to different models, we found that some robustly well-predicted metabolites were predicted by markedly different sets of taxa across datasets, suggesting that some microbially associated metabolites may be governed by different members of the microbiome in different cohorts. We finally examined whether models trained on a control group of a given study successfully predicted the metabolite's level in the disease group of the same study, identifying several metabolites where the model was not transferable, indicating a shift in microbial metabolism in disease-associated dysbiosis.<br><br>CONCLUSIONS: Combined, our findings provide a better understanding of the link between the microbiome and metabolites and allow researchers to put identified microbially associated metabolites within the context of other studies. Video abstract.},
}
@article {pmid34641955,
year = {2021},
author = {Arikawa, K and Ide, K and Kogawa, M and Saeki, T and Yoda, T and Endoh, T and Matsuhashi, A and Takeyama, H and Hosokawa, M},
title = {Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {202},
pmid = {34641955},
issn = {2049-2618},
mesh = {Genome, Microbial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Obtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. Despite improvements in bioinformatic approaches to generate curated metagenome-assembled genomes (MAGs), existing metagenome binners obtain population consensus genomes but they are nowhere comparable to genomes sequenced from isolates in terms of strain level resolution. Here, we present a framework for the integration of single-cell genomics and metagenomics, referred to as single-cell (sc) metagenomics, to reconstruct strain-resolved genomes from microbial communities at once.<br><br>RESULTS: Our sc-metagenomics integration framework, termed SMAGLinker, uses single-cell amplified genomes (SAGs) generated using microfluidic technology as binning guides and integrates them with metagenome-assembled genomes (MAGs) to recover improved draft genomes. We compared sc-metagenomics with the metagenomics-alone approach using conventional metagenome binners. The sc-metagenomics approach showed precise contig binning and higher recovery rates (>97%) of rRNA and plasmids than conventional metagenomics in genome reconstruction from the cell mock community. In human microbiota samples, sc-metagenomics recovered the largest number of genomes with a total of 103 gut microbial genomes (21 HQ, with 65 showing >90% completeness) and 45 skin microbial genomes (10 HQ, with 40 showing >90% completeness), respectively. Conventional metagenomics recovered one Staphylococcus hominis genome, whereas sc-metagenomics recovered two S. hominis genomes from identical skin microbiota sample. Single-cell sequencing revealed that these S. hominis genomes were derived from two distinct strains harboring specifically different plasmids. We found that all conventional S. hominis MAGs had a substantial lack or excess of genome sequences and contamination from other Staphylococcus species (S. epidermidis).<br><br>CONCLUSIONS: SMAGLinker enabled us to obtain strain-resolved genomes in the mock community and human microbiota samples by assigning metagenomic sequences correctly and covering both highly conserved genes such as rRNA genes and unique extrachromosomal elements, including plasmids. SMAGLinker will provide HQ genomes that are difficult to obtain using metagenomics alone and will facilitate the understanding of microbial ecosystems by elucidating detailed metabolic pathways and horizontal gene transfer networks. SMAGLinker is available at https://github.com/kojiari/smaglinker . Video abstract.},
}
@article {pmid34638954,
year = {2021},
author = {Khalyfa, A and Qiao, Z and Raju, M and Shyu, CR and Coghill, L and Ericsson, A and Gozal, D},
title = {Monocarboxylate Transporter-2 Expression Restricts Tumor Growth in a Murine Model of Lung Cancer: A Multi-Omic Analysis.},
journal = {International journal of molecular sciences},
volume = {22},
number = {19},
pages = {},
pmid = {34638954},
issn = {1422-0067},
mesh = {Animals ; Antineoplastic Agents, Hormonal/therapeutic use ; Carcinogenesis/genetics/*metabolism ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/genetics ; Gene Expression Regulation, Neoplastic ; Gene Knockout Techniques ; Gene Regulatory Networks ; Lung Neoplasms/drug therapy/genetics/*metabolism/*pathology ; Male ; Metabolome/genetics ; Metabolomics/methods ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Monocarboxylic Acid Transporters/genetics/*metabolism ; Neoplasm Invasiveness/genetics ; RNA, Ribosomal, 16S ; RNA-Seq ; Tamoxifen/therapeutic use ; Treatment Outcome ; Tumor Burden/drug effects/*genetics ; Tumor-Associated Macrophages/immunology/metabolism ; },
abstract = {Monocarboxylate transporter 2 (MCT2) is a major high-affinity pyruvate transporter encoded by the SLC16A7 gene, and is associated with glucose metabolism and cancer. Changes in the gut microbiota and host immune system are associated with many diseases, including cancer. Using conditionally expressed MCT2 in mice and the TC1 lung carcinoma model, we examined the effects of MCT2 on lung cancer tumor growth and local invasion, while also evaluating potential effects on fecal microbiome, plasma metabolome, and bulk RNA-sequencing of tumor macrophages. Conditional MCT2 mice were generated in our laboratory using MCT2loxP mouse intercrossed with mCre-Tg mouse to generate MCT2loxP/loxP; Cre+ mouse (MCT2 KO). Male MCT2 KO mice (8 weeks old) were treated with tamoxifen (0.18 mg/g BW) KO or vehicle (CO), and then injected with mouse lung carcinoma TC1 cells (10 × 105/mouse) in the left flank. Body weight, tumor size and weight, and local tumor invasion were assessed. Fecal DNA samples were extracted using PowerFecal kits and bacterial 16S rRNA amplicons were also performed. Fecal and plasma samples were used for GC-MS Polar, as well as non-targeted UHPLC-MS/MS, and tumor-associated macrophages (TAMs) were subjected to bulk RNAseq. Tamoxifen-treated MCT2 KO mice showed significantly higher tumor weight and size, as well as evidence of local invasion beyond the capsule compared with the controls. PCoA and hierarchical clustering analyses of the fecal and plasma metabolomics, as well as microbiota, revealed a distinct separation between the two groups. KO TAMs showed distinct metabolic pathways including the Acetyl-coA metabolic process, activation of immune response, b-cell activation and differentiation, cAMP-mediated signaling, glucose and glutamate processes, and T-cell differentiation and response to oxidative stress. Multi-Omic approaches reveal a substantial role for MCT2 in the host response to TC1 lung carcinoma that may involve alterations in the gut and systemic metabolome, along with TAM-related metabolic pathway. These findings provide initial opportunities for potential delineation of oncometabolic immunomodulatory therapeutic approaches.},
}
@article {pmid34635053,
year = {2021},
author = {Bao, L and Zhang, C and Lyu, J and Yan, C and Cao, R and Pan, M and Li, Y},
title = {Beware of pharyngeal Fusobacterium nucleatum in COVID-19.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {277},
pmid = {34635053},
issn = {1471-2180},
mesh = {Adult ; Biomarkers/analysis ; COVID-19/*microbiology/virology ; Carrier State/microbiology ; Coinfection/microbiology/virology ; Dysbiosis ; Feces/*microbiology ; Female ; Fusobacterium Infections/*microbiology/virology ; Fusobacterium nucleatum/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Microbiota ; Middle Aged ; Pharynx/*microbiology/virology ; Sex Factors ; },
abstract = {BACKGROUND: Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker of gut eubiosis/dysbiosis to some extent. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: Pharyngeal F. n was significantly increased in COVID-19 patients, and it was higher in male than female patients. Increased abundance of pharyngeal F. n was associated with a higher risk of a positive SARS-CoV-2 test (adjusted OR = 1.32, 95% CI = 1.06 ~ 1.65, P < 0.05). A classifier to distinguish COVID-19 patients from the healthy controls based on the pharyngeal F. n was constructed and achieved an area under the curve (AUC) of 0.843 (95% CI = 0.688 ~ 0.940, P < 0.001). However, the level of fecal F. n and fecal F. p remained unaltered between groups. Besides, mNGS showed that the pharyngeal swabs of COVID-19 patients were dominated by opportunistic pathogens.<br><br>CONCLUSIONS: Pharyngeal but not fecal F. n was significantly increased in COVID-19 patients, clinicians should pay careful attention to potential coinfection. Pharyngeal F. n may serve as a promising candidate indicator for COVID-19.},
}
@article {pmid34634462,
year = {2022},
author = {Orellana, E and Guerrero, LD and Davies-Sala, C and Altina, M and Pontiggia, RM and Erijman, L},
title = {Extracellular hydrolytic potential drives microbiome shifts during anaerobic co-digestion of sewage sludge and food waste.},
journal = {Bioresource technology},
volume = {343},
number = {},
pages = {126102},
doi = {10.1016/j.biortech.2021.126102},
pmid = {34634462},
issn = {1873-2976},
mesh = {Anaerobiosis ; Bioreactors ; Digestion ; Food ; Methane ; *Microbiota ; *Refuse Disposal ; Sewage ; },
abstract = {Bacterial community structure and dynamics in anaerobic digesters are primarily influenced by feedstock composition. It is therefore important to unveil microbial traits that explain microbiome variations in response to substrate changes. Here, gene and genome-centric metagenomics were used to examine microbiome dynamics in four laboratory-scale reactors, in which sewage sludge was co-digested with increasing amounts of food waste. A co-occurrence network revealed microbiome shifts in response to changes in substrate composition and concentration. Food waste concentration correlated with extracellular enzymes and metagenome-assembled genomes (MAGs) involved in the degradation of complex carbohydrates commonly found in fruits and plant cell walls as well as with the abundance of hydrolytic MAGs. A key role was attributed to Proteiniphillum for being the only bacteria that encoded the complete pectin degradation pathway. These results suggest that changes of feedstock composition establish new microbial niches for bacteria with the capacity to degrade newly added substrates.},
}
@article {pmid34622635,
year = {2021},
author = {Xu, Z and Chen, X and Wei, Y and Zhang, Q and Ji, X},
title = {[Metagenomic analysis of the diversity of microbes in the Napahai plateau wetland and their carbon and nitrogen metabolisms].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {37},
number = {9},
pages = {3276-3292},
doi = {10.13345/j.cjb.200658},
pmid = {34622635},
issn = {1872-2075},
mesh = {*Carbon ; Ecosystem ; Metagenomics ; Nitrogen ; Soil Microbiology ; *Wetlands ; },
abstract = {Due to the special geographical location and the complex ecosystem types, plateau wetlands play important ecological roles in water supply, greenhouse gas regulation and biodiversity preservation. Napahai plateau wetland is a special wetland type with low latitude and high altitude, and its microbial diversity was rarely studied. The diversity of microbial communities in the Napahai plateau wetland was analyzed using metagenomics method. Among the microbes detected, 184 phyla, 3 262 genera and 24 260 species belong to the bacterial domain, 13 phyla and 32 genera belong to the archaeal domain, and 13 phyla and 47 genera belong to the fungal domain. Significant differences in species diversity between soil and water were observed. Acidobacteria, Proteobacteria and Actinobacteria were dominant phyla in soil, while Proteobacteria and Bacteroides were dominant phyla in water. Since the carbon and nitrogen metabolism genes were abundant, the pathways of carbon fixation and nitrogen metabolism were analyzed. Calvin cycle, reductive tricarboxylic acid cycle and 3-hydroxypropionic acid cycle were the main carbon fixation pathways, while Proteobacteria, Chloroflexi, and Crenarchaeota were the main carbon-fixing bacteria group. As for the nitrogen cycle, nitrogen fixation and dissimilatory nitrate reduction were dominant in water, while nitrification and denitrification were dominant in soil. Proteobacteria, Nitrospirae, Verrucomicrobia, Actinobacteria, Thaumarchaeota and Euryarchaeota contributed to the nitrogen cycle. The study on microbial diversity of Napahai plateau wetlands provides new knowledge for the comprehensive management and protection of wetland environment in China.},
}
@article {pmid34621696,
year = {2021},
author = {Belstrøm, D and Constancias, F and Markvart, M and Sikora, M and Sørensen, CE and Givskov, M},
title = {Transcriptional Activity of Predominant Streptococcus Species at Multiple Oral Sites Associate With Periodontal Status.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {752664},
pmid = {34621696},
issn = {2235-2988},
mesh = {Humans ; Metagenome ; Metagenomics ; *Microbiota ; Saliva ; Streptococcus/genetics ; },
abstract = {Background: Streptococcus species are predominant members of the oral microbiota in both health and diseased conditions. The purpose of the present study was to explore if different ecological characteristics, such as oxygen availability and presence of periodontitis, associates with transcriptional activity of predominant members of genus Streptococcus. We tested the hypothesis that genetically closely related Streptococcus species express different transcriptional activities in samples collected from environments with critically different ecological conditions determined by site and inflammatory status.<br><br>Methods: Metagenomic and metatranscriptomic data was retrieved from 66 oral samples, subgingival plaque (n=22), tongue scrapings (n=22) and stimulated saliva (n=22) collected from patients with periodontitis (n=11) and orally healthy individuals (n=11). Species-specific transcriptional activity was computed as Log2(RNA/DNA), and transcriptional activity of predominant Streptococcus species was compared between multiple samples collected from different sites in the same individual, and between individuals with different oral health status.<br><br>Results: The predominant Streptococcus species were identified with a site-specific colonization pattern of the tongue and the subgingival plaque. A total of 11, 4 and 2 pathways expressed by S. parasanguinis, S. infantis and S. salivarius, respectively, were recorded with significantly higher transcriptional activity in saliva than in tongue biofilm in healthy individuals. In addition, 18 pathways, including pathways involved in synthesis of peptidoglycan, amino acid biosynthesis, glycolysis and purine nucleotide biosynthesis expressed by S. parasanguinis and 3 pathways expressed by S. salivarius were identified with significantly less transcriptional activity in patients with periodontitis.<br><br>Conclusion: Data from the present study significantly demonstrates the association of site-specific ecological conditions and presence of periodontitis with transcriptional activity of the predominant Streptococcus species of the oral microbiota. In particular, pathways expressed by S. parasanguinis being involved in peptidoglycan, amino acid biosynthesis, glycolysis, and purine nucleotide biosynthesis were identified to be significantly associated with oral site and/or inflammation status.},
}
@article {pmid34601036,
year = {2022},
author = {Tripathi, S and Purchase, D and Al-Rashed, S and Chandra, R},
title = {Microbial community dynamics and their relationships with organic and metal pollutants of sugarcane molasses-based distillery wastewater sludge.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {292},
number = {Pt A},
pages = {118267},
doi = {10.1016/j.envpol.2021.118267},
pmid = {34601036},
issn = {1873-6424},
mesh = {*Environmental Pollutants ; *Microbiota ; Molasses ; *Saccharum ; Sewage ; Waste Disposal, Fluid ; Waste Water ; },
abstract = {Distillery sludge is a major source of aquatic pollution, but little is known about their microbial community and their association with the organic and metal pollutants. Sugarcane molasses-based distillery is an important industry in India, although the waste is usually treated prior to disposal, the treatment is often inadequate. The adverse effects of the organic and metal pollutants in sugarcane molasses-based distillery sludge on the microbial biodiversity and abundance in the disposal site have not been elucidated. This study aims to address this gap of knowledge. Samples were collected from the discharge point, 1 and 2 km downstream (D1, D2, and D3, respectively) of a sugarcane distillery in Uttar Pradesh, India, and their physico-chemical properties characterised. Using QIIME, taxonomic assignment for the V3 and V4 hypervariable regions of 16 S rRNA was performed. The phyla Proteobacteria (28-39%), Firmicutes (20-28%), Bacteriodetes (9-10%), Actinobacteria (5-10%), Tenericutes (1-9%) and Patescibacteria (2%) were the predominant bacteria in all three sites. Euryechaeota, were detected in sites D1 and D2 (1-2%) but absent in D3. Spirochaetes (5%), Sinergistetes (2%) and Cloacimonetes (1%) were only detected in samples from site D1. Shannon, Simpson, Chao1, and Observed-species indices indicated that site D1 (10.18, 0.0013, 36706.55 and 45653.84, respectively) has higher bacterial diversity and richness than D2 (6.66, 0.0001, 25987.71 and 49655.89, respectively) and D3 (8.31, 0.002, 30345.53 and 30654.88, respectively), suggesting the organic and metal pollutants provided the stressors to favour the survival of microbial community that can biodegrade and detoxify them in the distillery sludge. This study confirmed that the treatment of the distillery waste was not sufficiently effective and provided new metagenomic information on its impact on the surrounding microbial community. It also offered new insights into potential bioremediation candidates.},
}
@article {pmid34600010,
year = {2022},
author = {Su, H and Yuan, P and Lei, H and Zhang, L and Deng, D and Zhang, L and Chen, X},
title = {Long-term chronic exposure to di-(2-ethylhexyl)-phthalate induces obesity via disruption of host lipid metabolism and gut microbiota in mice.},
journal = {Chemosphere},
volume = {287},
number = {Pt 4},
pages = {132414},
doi = {10.1016/j.chemosphere.2021.132414},
pmid = {34600010},
issn = {1879-1298},
mesh = {Animals ; *Diethylhexyl Phthalate/toxicity ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Mice ; Obesity/chemically induced ; Phthalic Acids ; RNA, Ribosomal, 16S/metabolism ; },
abstract = {BACKGROUND: Numerous epidemiological findings have shown that di-(2-ethylhexyl)-phthalate (DEHP), one of industrial plasticizers with endocrine-disrupting properties, positively contributes to high incidence of obesity. However, potential pathogenesis of dietary DEHP exposure-induced obesity remains largely unknown.<br><br>METHODS: Chronic DEHP exposure at different doses (0.05 and 5 mg/kg body weight) to mice had been continuously lasted for 14 weeks through the diet. A combination of targeted quantitative metabolomics (LC/GC-MS) with global 1H NMR-based metabolic profiling to explore the effects of dietary DEHP exposure with different doses on host lipid metabolism of mice. Metagenomics (16S rRNA gene sequencing) was also employed to examine the alterations of gut microbiota composition in the cecal contents of mice after dietary DEHP exposure.<br><br>RESULTS: Dietary exposure to DEHP at both doses induced weight gain and hepatic lipogenesis of mice by promoting the uptake of fatty acids and disrupting phospholipids and choline metabolism. Dietary DEHP exposure altered the gut microbiota community with disruption of intestinal morphology and reduction of Firmicutes to Bacteroidetes ratio in the cecal contents of mice. Furthermore, DEHP exposure activated gut microbiota fermentation process producing excess short chain fatty acids of mice.<br><br>CONCLUSION: These findings provide systematic evidence that long-term chronic DEHP exposure induces obesity through disruption of host lipid metabolism and gut microbiota in mice, which not only confirm the epidemiological results, but also expand our understanding of metabolic diseases caused by environmental pollutants exposure.},
}
@article {pmid34589441,
year = {2021},
author = {Ding, L and Liu, Y and Wu, X and Wu, M and Luo, X and Ouyang, H and Xia, J and Liu, X and Ding, T},
title = {Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {708827},
pmid = {34589441},
issn = {2235-2988},
mesh = {Ascomycota ; Bronchoalveolar Lavage Fluid ; Haemophilus parainfluenzae ; Humans ; Kluyveromyces ; Lung ; Metagenomics ; *Microbiota ; *Mycobacterium tuberculosis/genetics ; Staphylococcus aureus ; *Tuberculosis/microbiology ; },
abstract = {Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.},
}
@article {pmid34586399,
year = {2021},
author = {Kiguchi, Y and Nishijima, S and Kumar, N and Hattori, M and Suda, W},
title = {Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {28},
number = {6},
pages = {},
pmid = {34586399},
issn = {1756-1663},
support = {19gm0010003h0204//Leading Advanced Projects for Medical Innovation (LEAP)/ ; },
mesh = {Algorithms ; Biomass ; Chimera ; DNA ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Sequence Analysis, DNA ; *Virome ; },
abstract = {The human gut bacteriophage community (phageome) plays an important role in the host's health and disease; however, the entire structure is poorly understood, partly owing to the generation of many incomplete genomes in conventional short-read metagenomics. Here, we show long-read metagenomics of amplified DNA of low-biomass phageomes with multiple displacement amplification (MDA), involving the development of a novel bioinformatics tool, split amplified chimeric read algorithm (SACRA), that efficiently pre-processed numerous chimeric reads generated through MDA. Using five samples, SACRA markedly reduced the average chimera ratio from 72% to 1.5% in PacBio reads with an average length of 1.8 kb. De novo assembly of chimera-less PacBio long reads reconstructed contigs of ≥5 kb with an average proportion of 27%, which was 1% in contigs from MiSeq short reads, thereby dramatically improving contig length and genome completeness. Comparison of PacBio and MiSeq contigs found MiSeq contig fragmentations frequently near local repeats and hypervariable regions in the phage genomes, and those caused by multiple homologous phage genomes coexisting in the community. We also developed a reference-independent method to assess the completeness of the linear phage genomes. Overall, we established a SACRA-coupled long-read metagenomics robust to highly diverse gut phageomes, identifying high-quality circular and linear phage genomes with adequate sequence quantity.},
}
@article {pmid34583815,
year = {2021},
author = {Vad, J and Barnhill, KA and Kazanidis, G and Roberts, JM},
title = {Human impacts on deep-sea sponge grounds: Applying environmental omics to monitoring.},
journal = {Advances in marine biology},
volume = {89},
number = {},
pages = {53-78},
doi = {10.1016/bs.amb.2021.08.004},
pmid = {34583815},
issn = {2162-5875},
mesh = {Animals ; Biodiversity ; *Ecosystem ; Environmental Monitoring ; Human Activities ; Humans ; *Porifera ; Seawater ; },
abstract = {Sponges (Phylum Porifera) are the oldest extant Metazoans. In the deep sea, sponges can occur at high densities forming habitats known as sponge grounds. Sponge grounds can extend over large areas of up to hundreds of km2 and are biodiversity hotspots. However, as human activities, including deep-water hydrocarbon extraction, continue to expand into areas harbouring sponge grounds, understanding how anthropogenic impacts affect sponges and the ecosystem services they provide at multiple biological scales (community, individual and (sub)cellular levels) is key for achieving sustainable management. This chapter (1) provides an update to the chapter of Advances in Marine Biology Volume 79 entitled "Potential Impacts of Offshore Oil and Gas Activities on Deep-Sea Sponges and the Habitats They Form" and (2) discusses the use of omics as a future tool for deep-sea ecosystem monitoring. While metagenomics and (meta)transcriptomics studies have contributed to improve our understanding of sponge biology in recent years, metabolomics analysis has mostly been used to identify natural products. The sponge metabolome, therefore, remains vastly unknown despite the fact that the metabolome is a key link between the genotype and phenotype, giving us a unique new insight to how key components of an ecosystem are functioning. As the fraction of the metabolome released into the seawater, the sponge exometabolome has only just started to be characterised in comparative environmental metabolomic studies. Yet, the sponge exometabolome constitute a unique opportunity for the identification of biomarkers of sponge health as compounds can be measured in seawater, bypassing the need for physical samples which can still be difficult to collect in the deep sea. Within sponge grounds, the characterisation of a shared sponge exometabolome could lead to the identification of biomarkers of ecosystem functioning and overall health. Challenges remain in establishing omics approaches in environmental monitoring but constant technological advances and reduction in costs means these techniques will become widely available in the future.},
}
@article {pmid34579474,
year = {2021},
author = {Smulders, L and Benítez, E and Moreno, B and López-García, Á and Pozo, MJ and Ferrero, V and de la Peña, E and Alcalá Herrera, R},
title = {Tomato Domestication Affects Potential Functional Molecular Pathways of Root-Associated Soil Bacteria.},
journal = {Plants (Basel, Switzerland)},
volume = {10},
number = {9},
pages = {},
pmid = {34579474},
issn = {2223-7747},
support = {765290//Horizon 2020 Framework Programme/ ; },
abstract = {While it has been well evidenced that plant domestication affects the structure of the root-associated microbiome, there is a poor understanding of how domestication-mediated differences between rhizosphere microorganisms functionally affect microbial ecosystem services. In this study, we explore how domestication influenced functional assembly patterns of bacterial communities in the root-associated soil of 27 tomato accessions through a transect of evolution, from plant ancestors to landraces to modern cultivars. Based on molecular analysis, functional profiles were predicted and co-occurrence networks were constructed based on the identification of co-presences of functional units in the tomato root-associated microbiome. The results revealed differences in eight metabolic pathway categories and highlighted the influence of the host genotype on the potential functions of soil bacterial communities. In general, wild tomatoes differed from modern cultivars and tomato landraces which showed similar values, although all ancestral functional characteristics have been conserved across time. We also found that certain functional groups tended to be more evolutionarily conserved in bacterial communities associated with tomato landraces than those of modern varieties. We hypothesize that the capacity of soil bacteria to provide ecosystem services is affected by agronomic practices linked to the domestication process, particularly those related to the preservation of soil organic matter.},
}
@article {pmid34579036,
year = {2021},
author = {Chiou, WC and Chang, BH and Tien, HH and Cai, YL and Fan, YC and Chen, WJ and Chu, HF and Chen, YH and Huang, C},
title = {Synbiotic Intervention with an Adlay-Based Prebiotic and Probiotics Improved Diet-Induced Metabolic Disturbance in Mice by Modulation of the Gut Microbiota.},
journal = {Nutrients},
volume = {13},
number = {9},
pages = {},
pmid = {34579036},
issn = {2072-6643},
support = {MOST 110-2628-B-A49A-501 -//Ministry of Science and Technology, Taiwan/ ; },
mesh = {Adipose Tissue ; Animal Feed/analysis ; Animals ; Bacteria/classification/genetics ; Body Weight ; Diet, High-Fat/*adverse effects ; Dysbiosis/*chemically induced ; Dyslipidemias ; Gastrointestinal Microbiome/*drug effects ; Insulin Resistance ; Male ; Mice ; Obesity/chemically induced ; *Prebiotics ; *Probiotics ; *Synbiotics ; },
abstract = {Metabolic syndrome and its associated conditions, such as obesity and type 2 diabetes mellitus (T2DM), are a major public health issue in modern societies. Dietary interventions, including microbiota-directed foods which effectively modulate the gut microbiome, may influence the regulation of obesity and associated comorbidities. Although research on probiotics and prebiotics has been conducted extensively in recent years, diets with the use of synbiotics remain relatively unexplored. Here, we investigated the effects of a novel synbiotic intervention, consisting of an adlay seed extrusion cooked (ASEC)-based prebiotic and probiotic (Lactobacillus paracasei and Bacillus coagulans) on metabolic disorders and microbial dysbiosis in high-fat diet (HFD)-induced obese mice. The ASEC-based synbiotic intervention helped improve HFD-induced body weight gain, hyperlipidemia, impaired glucose tolerance, insulin resistance, and inflammation of the adipose and liver tissues. In addition, data from fecal metagenomics indicated that the ASEC-based synbiotic intervention fostered reconstitution of gut bacterial diversity and composition in HFD-induced obese mice. In particular, the ASEC-based synbiotic intervention increased the relative abundance of families Ruminococcaceae and Muribaculaceae and order Bacteroidales and reduced that of families Lactobacillaceae, Erysipelotrichaceae, and Streptococcaceae in HFD-induced obese mice. Collectively, our results suggest that delayed dietary intervention with the novel ASEC-based synbiotic ameliorates HFD-induced obesity, metabolic disorders, and dysbiosis.},
}
@article {pmid34576010,
year = {2021},
author = {Pistone, D and Meroni, G and Panelli, S and D'Auria, E and Acunzo, M and Pasala, AR and Zuccotti, GV and Bandi, C and Drago, L},
title = {A Journey on the Skin Microbiome: Pitfalls and Opportunities.},
journal = {International journal of molecular sciences},
volume = {22},
number = {18},
pages = {},
pmid = {34576010},
issn = {1422-0067},
mesh = {Dysbiosis/*microbiology/therapy ; Humans ; Metagenomics/methods ; *Microbiota ; Probiotics/therapeutic use ; Skin/*microbiology ; Skin Diseases/*microbiology/therapy ; },
abstract = {The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.},
}
@article {pmid34571998,
year = {2021},
author = {Chang, CJ and Zhang, J and Tsai, YL and Chen, CB and Lu, CW and Huo, YP and Liou, HM and Ji, C and Chung, WH},
title = {Compositional Features of Distinct Microbiota Base on Serum Extracellular Vesicle Metagenomics Analysis in Moderate to Severe Psoriasis Patients.},
journal = {Cells},
volume = {10},
number = {9},
pages = {},
pmid = {34571998},
issn = {2073-4409},
mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/genetics ; Dysbiosis/microbiology ; Extracellular Vesicles/*microbiology ; Female ; Humans ; Male ; Metagenomics/methods ; Microbiota/*genetics ; Middle Aged ; Psoriasis/*microbiology ; Skin/microbiology ; Young Adult ; },
abstract = {The bacterial microbiota in the skin and intestine of patients with psoriasis were different compared with that of healthy individuals. However, the presence of a distinct blood microbiome in patients with psoriasis is yet to be investigated. In this study, we investigated the differences in bacterial communities in plasma-derived extracellular vesicles (EVs) between patients with moderate to severe psoriasis (PSOs) and healthy controls (HCs). The plasma EVs from the PSO (PASI > 10) (n = 20) and HC (n = 8) groups were obtained via a series of centrifugations, and patterns were examined and confirmed using transmission electron microscopy (TEM) and EV-specific markers. The taxonomic composition of the microbiota was determined by using full-length 16S ribosomal RNA gene sequencing. The PSO group had lower bacterial diversity and richness compared with HC group. Principal coordinate analysis (PCoA)-based clustering was used to assess diversity and validated dysbiosis for both groups. Differences at the level of amplicon sequence variant (ASV) were observed, suggesting alterations in specific ASVs according to health conditions. The HC group had higher levels of the phylum Firmicutes and Fusobacteria than in the PSO group. The order Lactobacillales, family Brucellaceae, genera Streptococcus, and species Kingella oralis and Aquabacterium parvum were highly abundant in the HC group compared with the PSO group. Conversely, the order Bacillales and the genera Staphylococcus and Sphihgomonas, as well as Ralstonia insidiosa, were more abundant in the PSO group. We further predicted the microbiota functional capacities, which revealed significant differences between the PSO and HC groups. In addition to previous studies on microbiome changes in the skin and gut, we demonstrated compositional differences in the microbe-derived EVs in the plasma of PSO patients. Plasma EVs could be an indicator for assessing the composition of the microbiome of PSO patients.},
}
@article {pmid34568090,
year = {2021},
author = {Yu, J and Zhang, H and Chen, L and Ruan, Y and Chen, Y and Liu, Q},
title = {Disease-Associated Gut Microbiota Reduces the Profile of Secondary Bile Acids in Pediatric Nonalcoholic Fatty Liver Disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {698852},
pmid = {34568090},
issn = {2235-2988},
mesh = {Bile Acids and Salts ; Child ; Chromatography, Liquid ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Non-alcoholic Fatty Liver Disease ; Tandem Mass Spectrometry ; },
abstract = {Children with nonalcoholic fatty liver disease (NAFLD) display an altered gut microbiota compared with healthy children. However, little is known about the fecal bile acid profiles and their association with gut microbiota dysbiosis in pediatric NAFLD. A total of 68 children were enrolled in this study, including 32 NAFLD patients and 36 healthy children. Fecal samples were collected and analyzed by metagenomic sequencing to determine the changes in the gut microbiota of children with NAFLD, and an ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) system was used to quantify the concentrations of primary and secondary bile acids. The associations between the gut microbiota and concentrations of primary and secondary bile acids in the fecal samples were then analyzed. We found that children with NAFLD exhibited reduced levels of secondary bile acids and alterations in bile acid biotransforming-related bacteria in the feces. Notably, the decrease in Eubacterium and Ruminococcaceae bacteria, which express bile salt hydrolase and 7α-dehydroxylase, was significantly positively correlated with the level of fecal lithocholic acid (LCA). However, the level of fecal LCA was negatively associated with the abundance of the potential pathogen Escherichia coli that was enriched in children with NAFLD. Pediatric NAFLD is characterized by an altered profile of gut microbiota and fecal bile acids. This study demonstrates that the disease-associated gut microbiota is linked with decreased concentrations of secondary bile acids in the feces. The disease-associated gut microbiota likely inhibits the conversion of primary to secondary bile acids.},
}
@article {pmid34568084,
year = {2021},
author = {Oh, KY and Lee, S and Lee, MS and Lee, MJ and Shim, E and Hwang, YH and Ha, JG and Yang, YS and Hwang, IT and Park, JS},
title = {Composition of Vaginal Microbiota in Pregnant Women With Aerobic Vaginitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {677648},
pmid = {34568084},
issn = {2235-2988},
mesh = {Case-Control Studies ; Dysbiosis ; Female ; Humans ; *Microbiota ; Pregnancy ; Pregnant Women ; Vagina ; *Vaginitis ; },
abstract = {Vaginal dysbiosis, such as bacterial vaginosis (BV) and aerobic vaginitis (AV), is an important cause of premature birth in pregnant women. However, there is very little research on vaginal microbial distribution in AV compared to that in BV. This study aimed to analyze the composition of the vaginal microbiota of pregnant women with AV using microbial community analysis and identify the causative organism using each criterion of the AV scoring system. Also, we compared the quantification of aerobic bacteria using quantitative polymerase chain reaction (qPCR) and their relative abundances (RA) using metagenomics. This prospective case-control study included 228 pregnant Korean women from our previous study. A wet mount test was conducted on 159 women to diagnose AV using the AV scoring system. Vaginal samples were analyzed using metagenomics, Gram staining for Nugent score determination, conventional culture, and qPCR for Staphylococcus spp., Streptococcus spp., and Enterobacteriaceae. The relative abundances (RAs) of eleven species showed significant differences among the three groups (Normal flora (NF), mild AV, and moderate AV). Three species including Lactobacillus crispatus were significantly lower in the AV groups than in the NF group, while eight species were higher in the AV groups, particularly moderate AV. The decrease in the RA of L. crispatus was common in three criteria of the AV scoring system (Lactobacillary, WBC, and background flora grades), while it did not show a significant difference among the three grade groups of the toxic leukocyte criterion. Also, the RAs of anaerobes, such as Gardnerella and Megasphaera, were higher in the AV groups, particularly moderate AV, while the RAs of aerobes were very low (RA < 0.01). Therefore, qPCR was performed for aerobes (Staphylococcus spp., Streptococcus spp., and Enterobacteriaceae); however, their quantification did not show a higher level in the AV groups when compared to that in the NF group. Therefore, AV might be affected by the RA of Lactobacillus spp. and the main anaerobes, such as Gardnerella spp. Activation of leukocytes under specific conditions might convert them to toxic leukocytes, despite high levels of L. crispatus. Thus, the pathogenesis of AV can be evaluated under such conditions.},
}
@article {pmid34559138,
year = {2021},
author = {Tanaka, T and Matsuno, Y and Torisu, T and Shibata, H and Hirano, A and Umeno, J and Kawasaki, K and Fujioka, S and Fuyuno, Y and Moriyama, T and Esaki, M and Kitazono, T},
title = {Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma.},
journal = {Medicine},
volume = {100},
number = {38},
pages = {e27287},
doi = {10.1097/MD.0000000000027287},
pmid = {34559138},
issn = {1536-5964},
mesh = {Aged ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Gastric Mucosa/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Lymphoma, B-Cell, Marginal Zone/*microbiology ; Male ; Metagenomics ; Middle Aged ; Stomach Neoplasms/*microbiology ; },
abstract = {ABSTRACT: To investigate the mucosal microbiota in the stomach of patients with Helicobacter pylori-negative mucosa-associated lymphoid tissue (MALT) lymphoma by means of metagenomic analysis.Although some gastric MALT lymphomas are associated with the presence of H. pylori, other gastric MALT lymphomas occur independently of H. pylori infection. The pathogenesis of H. pylori-negative MALT lymphoma remains unclear.Mucosal biopsy specimens were collected from the gastric body from 33 MALT lymphoma patients with gastric lesions, including both H. pylori-infection naïve patients and posteradication patients, as well as 27 control participants without H. pylori infection or cancer. Subsequently, the samples were subjected to 16S rRNA gene sequencing. Quantitative insights into microbial ecology, linear discriminant analysis effect size, and phylogenetic investigation of communities by reconstruction of unobserved states softwares were used to analyze the participants' microbiota.H. pylori-negative MALT lymphoma patients had significantly lower alpha diversity (P = .04), compared with control participants. Significant differences were evident in the microbial composition (P = .04), as determined by comparison of beta diversity between the 2 groups. Taxonomic composition analysis indicated that the genera Burkholderia and Sphingomonas were significantly more abundant in MALT lymphoma patients, while the genera Prevotella and Veillonella were less abundant. Functional microbiota prediction showed that the predicted gene pathways "replication and repair," "translation," and "nucleotide metabolism" were downregulated in MALT lymphoma patients.H. pylori-negative MALT lymphoma patients exhibited altered gastric mucosal microbial compositions, suggesting that altered microbiota might be involved in the pathogenesis of H. pylori-negative MALT lymphoma.},
}
@article {pmid34555741,
year = {2021},
author = {McDaniel, EA and Wahl, SA and Ishii, S and Pinto, A and Ziels, R and Nielsen, PH and McMahon, KD and Williams, RBH},
title = {Prospects for multi-omics in the microbial ecology of water engineering.},
journal = {Water research},
volume = {205},
number = {},
pages = {117608},
doi = {10.1016/j.watres.2021.117608},
pmid = {34555741},
issn = {1879-2448},
mesh = {Bioreactors ; Metagenomics ; *Microbiota ; Sewage ; *Water ; },
abstract = {Advances in high-throughput sequencing technologies and bioinformatics approaches over almost the last three decades have substantially increased our ability to explore microorganisms and their functions - including those that have yet to be cultivated in pure isolation. Genome-resolved metagenomic approaches have enabled linking powerful functional predictions to specific taxonomical groups with increasing fidelity. Additionally, related developments in both whole community gene expression surveys and metabolite profiling have permitted for direct surveys of community-scale functions in specific environmental settings. These advances have allowed for a shift in microbiome science away from descriptive studies and towards mechanistic and predictive frameworks for designing and harnessing microbial communities for desired beneficial outcomes. Water engineers, microbiologists, and microbial ecologists studying activated sludge, anaerobic digestion, and drinking water distribution systems have applied various (meta)omics techniques for connecting microbial community dynamics and physiologies to overall process parameters and system performance. However, the rapid pace at which new omics-based approaches are developed can appear daunting to those looking to apply these state-of-the-art practices for the first time. Here, we review how modern genome-resolved metagenomic approaches have been applied to a variety of water engineering applications from lab-scale bioreactors to full-scale systems. We describe integrated omics analysis across engineered water systems and the foundations for pairing these insights with modeling approaches. Lastly, we summarize emerging omics-based technologies that we believe will be powerful tools for water engineering applications. Overall, we provide a framework for microbial ecologists specializing in water engineering to apply cutting-edge omics approaches to their research questions to achieve novel functional insights. Successful adoption of predictive frameworks in engineered water systems could enable more economically and environmentally sustainable bioprocesses as demand for water and energy resources increases.},
}
@article {pmid34548111,
year = {2021},
author = {Wang, L and Huang, G and Hou, R and Qi, D and Wu, Q and Nie, Y and Zuo, Z and Ma, R and Zhou, W and Ma, Y and Hu, Y and Yang, Z and Yan, L and Wei, F},
title = {Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {192},
pmid = {34548111},
issn = {2049-2618},
mesh = {Animals ; Diet ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Ursidae ; },
abstract = {BACKGROUND: Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap.<br><br>RESULTS: Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species.<br><br>CONCLUSIONS: Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.},
}
@article {pmid34545840,
year = {2021},
author = {Dery, KJ and Kupiec-Weglinski, JW and Dong, TS},
title = {The human microbiome in transplantation: the past, present, and future.},
journal = {Current opinion in organ transplantation},
volume = {26},
number = {6},
pages = {595-602},
doi = {10.1097/MOT.0000000000000922},
pmid = {34545840},
issn = {1531-7013},
mesh = {High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota ; },
abstract = {PURPOSE OF REVIEW: Over the past 20 years, DNA sequencing technology has transformed human microbiome research from identity characterizations to metagenomics approaches that reveal how microbials correlate with human health and disease. New studies are showing unprecedented opportunity for deep characterization of the human microbial ecosystem, with benefits to the field of organ transplantation.<br><br>RECENT FINDINGS: In the present review, we focus on past milestones of human-associated microbiota research, paying homage to microbiota pioneers. We highlight the role of sequencing efforts to provide insights beyond taxonomic identification. Recent advances in microbiome technology is now integrating high-throughput datasets, giving rise to multi'omics - a comprehensive assessment modeling dynamic biologic networks. Studies that show benefits and mechanisms in peritransplant antibiotic (Abx)-conditioned recipients are reviewed. We describe how next-generation microbial sequencing has the potential to combine with new technologies like phage therapy (PT) to translate into life-saving therapeutics.<br><br>SUMMARY: The study of the microbiome is advancing the field of transplantation by enhancing our knowledge of precision medicine. Sequencing technology has allowed the use of the microbiome as a biomarker to risk stratify patients. Further research is needed to better understand how microbiomes shape transplantation outcomes while informing immune cell - tissue crosstalk platforms.},
}
@article {pmid34544379,
year = {2021},
author = {Zhang, W and Liang, Y and Zheng, K and Gu, C and Liu, Y and Wang, Z and Zhang, X and Shao, H and Jiang, Y and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Zhang, Y and McMinn, A and Wang, M},
title = {Characterization and genomic analysis of the first Oceanospirillum phage, vB_OliS_GJ44, representing a novel siphoviral cluster.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {675},
pmid = {34544379},
issn = {1471-2164},
mesh = {*Bacteriophages/genetics ; DNA, Viral/genetics ; Genome, Viral ; Genomics ; Phylogeny ; *Siphoviridae/genetics ; },
abstract = {BACKGROUND: Marine bacteriophages play key roles in the community structure of microorganisms, biogeochemical cycles, and the mediation of genetic diversity through horizontal gene transfer. Recently, traditional isolation methods, complemented by high-throughput sequencing metagenomics technology, have greatly increased our understanding of the diversity of bacteriophages. Oceanospirillum, within the order Oceanospirillales, are important symbiotic marine bacteria associated with hydrocarbon degradation and algal blooms, especially in polar regions. However, until now there has been no isolate of an Oceanospirillum bacteriophage, and so details of their metagenome has remained unknown.<br><br>RESULTS: Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. The recombinant module was highly adapted to the host, according to the tetranucleotides correlations. Genomic and morphological analyses identified vB_OliS_GJ44 as a siphovirus, however, due to the distant evolutionary relationship with any other known siphovirus, it is proposed that this virus could be classified as the type phage of a new Oceanospirivirus genus within the Siphoviridae family. vB_OliS_GJ44 showed synteny with six uncultured phages, which supports its representation in uncultured environmental viral contigs from metagenomics. Homologs of several vB_OliS_GJ44 genes have mostly been found in marine metagenomes, suggesting the prevalence of this phage genus in the oceans.<br><br>CONCLUSIONS: These results describe the first Oceanospirillum phage, vB_OliS_GJ44, that represents a novel viral cluster and exhibits interesting genetic features related to phage-host interactions and evolution. Thus, we propose a new viral genus Oceanospirivirus within the Siphoviridae family to reconcile this cluster, with vB_OliS_GJ44 as a representative member.},
}
@article {pmid34537552,
year = {2021},
author = {Jia, J and Liang, C and Wu, X and Xiong, L and Bao, P and Chen, Q and Yan, P},
title = {Effect of high proportion concentrate dietary on Ashdan Yak jejunal barrier and microbial function in cold season.},
journal = {Research in veterinary science},
volume = {140},
number = {},
pages = {259-267},
doi = {10.1016/j.rvsc.2021.09.010},
pmid = {34537552},
issn = {1532-2661},
mesh = {Animals ; Cattle ; Diet/veterinary ; Digestion ; *Jejunum ; Male ; *Microbiota ; Seasons ; },
abstract = {The intestinal health of ruminants plays a vital role in absorbing and metabolizing nutrients. In order to explore the jejunal barrier and microbiota dysfunction of Ashdan yaks, animals were fed with a high proportion of concentrated feeds in cold season. In present study, twelve Ashdan male yaks were arbitrarily separated into two categories, namely FF and CF. Compositional and functional differences in their jejunum barrier and microbiota between the FF and CF yaks were compared using metagenomics and proteomics methods. The results showed that the activity of jejunum digestive protease and microbe metabolite of forage-fed yaks were more conducive to healthy cultivation than the concentrate-fed yaks. 57 differentially expressed proteins (DEPs) were recognized using label-free MS, those could conclude to 2 principal classes: structural proteins and inflammatory factors, and 14 proteins were relatively active in those principal classes. Firmicutes were the dominant bacterial phylum in the jejunum microbiota of both the forage-fed group (24.33%) and concentrate-fed group (23.16%). As compared to forage-fed group, the concentrate-fed group showed enhanced alpha diversity and reduced beta diversity of the jejunal microbiota. The long-term high-proportion concentrate feeding inhibited the growth of Actinobacteria, Proteo-bacteria, Ascomycota, Bacteroidetes and stimulated the growth of Streptophyta, Cyanobacteria, Fusobacteria and Chlamydiae. The concentrate-fed group showed increase in the abundance of immune system process, along with decrease in the metabolic process, especially the binding process. Interestingly, the proteomics and metagenomics results were both inclined to the enrichment of jejunum mechanical barrier and inflammatory response. Overall, the study suggested that the long-term high-proportion concentrate feeding affected the expressions of specific jejunum proteins and composition of microbiota, which damaged the jejunum barrier and the function of microbiota in yaks.},
}
@article {pmid34537163,
year = {2021},
author = {Castillo-Álvarez, F and Pérez-Matute, P and Oteo, JA and Marzo-Sola, ME},
title = {The influence of interferon β-1b on gut microbiota composition in patients with multiple sclerosis.},
journal = {Neurologia (Barcelona, Spain)},
volume = {36},
number = {7},
pages = {495-503},
doi = {10.1016/j.nrleng.2020.05.006},
pmid = {34537163},
issn = {2173-5808},
mesh = {Cross-Sectional Studies ; Feces ; *Gastrointestinal Microbiome ; Humans ; Interferon beta-1b/*therapeutic use ; *Multiple Sclerosis/drug therapy ; Prevotella ; },
abstract = {INTRODUCTION: The association between gut microbiota and animal models of multiple sclerosis has been well established; however, studies in humans are scarce.<br><br>METHODS: We performed a descriptive, cross-sectional study comparing the relative composition of gut microbiota in 30 patients with multiple sclerosis (15 treated with interferon β-1b, 15 not receiving this treatment) and 14 healthy controls using next generation sequencing.<br><br>RESULTS: Patients with multiple sclerosis and controls showed differences in the proportion of Euryarchaeota, Firmicutes, Proteobacteria, Actinobacteria, and Lentisphaerae phyla and in 17 bacterial species. More specifically, we found significant differences in the proportion of Firmicutes, Actinobacteria, and Lentisphaerae and 6 bacteria species between controls and untreated patients; however, these differences disappeared when compared with treated patients. Untreated patients showed a significant reduction in the proportion of Prevotella copri compared to controls, while the bacteria was significantly more abundant in patients treated with interferon β-1b than in untreated patients, with levels resembling those observed in the healthy control group.<br><br>CONCLUSION: We observed differences in gut microbiota composition between patients with multiple sclerosis and controls, and between patients treated and not treated with interferon β-1b. In most cases, no differences were observed between treated patients and healthy controls, particularly for P. copri levels. This suggests that the clinical improvements observed in patients with multiple sclerosis receiving interferon β-1b may result from the effect of the drug on gut microbiota. Longitudinal and functional studies are necessary to establish a causal relationship.},
}
@article {pmid34530224,
year = {2021},
author = {Kim, DD and Wan, L and Cao, X and Klisarova, D and Gerdzhikov, D and Zhou, Y and Song, C and Yoon, S},
title = {Metagenomic insights into co-proliferation of Vibrio spp. and dinoflagellates Prorocentrum during a spring algal bloom in the coastal East China Sea.},
journal = {Water research},
volume = {204},
number = {},
pages = {117625},
doi = {10.1016/j.watres.2021.117625},
pmid = {34530224},
issn = {1879-2448},
mesh = {Cell Proliferation ; *Dinoflagellida/genetics ; Harmful Algal Bloom ; *Microbiota ; *Vibrio ; },
abstract = {Coastal harmful algal blooms (HABs), commonly termed 'red tides', have severe undesirable consequences to the marine ecosystems and local fishery and tourism industries. Increase in nitrogen and/or phosphorus loading is often regarded as the major culprits of increasing frequency and intensity of the coastal HAB; however, fundamental understanding is lacking as to the causes and mechanism of bloom formation despite decades of intensive investigation. In this study, we interrogated the prokaryotic microbiomes of surface water samples collected at two neighboring segments of East China Sea that contrast greatly in terms of the intensity and frequency of Prorocentrum-dominated HAB. Mantel tests identified significant correlations between the structural and functional composition of the microbiomes and the physicochemical state and the algal biomass density of the surface seawater, implying the possibility that prokaryotic microbiota may play key roles in the coastal HAB. A conspicuous feature of the microbiomes at the sites characterized with high trophic state index and eukaryotic algal cell counts was disproportionate proliferation of Vibrio spp., and their complete domination of the functional genes attributable to the dissimilatory nitrate reduction to ammonia (DNRA) pathway substantially enriched at these sites. The genes attributed to phosphorus uptake function were significantly enriched at these sites, presumably due to the Pi-deficiency induced by algal growth; however, the profiles of the phosphorus mineralization genes lacked consistency, barring any conclusive evidence with regard to contribution of prokaryotic microbiota to phosphorus bioavailability. The results of the co-occurrence network analysis performed with the core prokaryotic microbiome supported that the observed proliferation of Vibrio and HAB may be causally associated. The findings of this study suggest a previously unidentified association between Vibrio proliferation and the Prorocentrum-dominated HAB in the subtropical East China Sea, and opens a discussion regarding a theoretically unlikely, but still possible, involvement of Vibrio-mediated DNRA in Vibrio-Prorocentrum symbiosis. Further experimental substantiation of this supposed symbiotic mechanism may prove crucial in understanding the dynamics of explosive local algal growth in the region during spring algal blooms.},
}
@article {pmid34526096,
year = {2021},
author = {Gao, M and Xiong, C and Gao, C and Tsui, CKM and Wang, MM and Zhou, X and Zhang, AM and Cai, L},
title = {Disease-induced changes in plant microbiome assembly and functional adaptation.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {187},
pmid = {34526096},
issn = {2049-2618},
mesh = {Bacteria/genetics ; *Microbiota/genetics ; Plant Roots ; Rhizosphere ; *Soil Microbiology ; },
abstract = {BACKGROUND: The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes.<br><br>RESULTS: The amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants.<br><br>CONCLUSIONS: Together, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture. Video abstract.},
}
@article {pmid34523982,
year = {2021},
author = {Guan, H and Pu, Y and Liu, C and Lou, T and Tan, S and Kong, M and Sun, Z and Mei, Z and Qi, Q and Quan, Z and Zhao, G and Zheng, Y},
title = {Comparison of Fecal Collection Methods on Variation in Gut Metagenomics and Untargeted Metabolomics.},
journal = {mSphere},
volume = {6},
number = {5},
pages = {e0063621},
pmid = {34523982},
issn = {2379-5042},
abstract = {Integrative analysis of high-quality metagenomics and metabolomics data from fecal samples provides novel clues for the mechanism underpinning gut microbe-human interactions. However, data regarding the influence of fecal collection methods on both metagenomics and metabolomics are sparse. Six fecal collection methods (the gold standard [GS] [i.e., immediate freezing at -80°C with no solution], 95% ethanol, RNAlater, OMNIgene Gut, fecal occult blood test [FOBT] cards, and Microlution) were used to collect 88 fecal samples from eight healthy volunteers for whole-genome shotgun sequencing (WGSS) and untargeted metabolomic profiling. Metrics assessed included the abundances of predominant phyla and α- and β-diversity at the species, gene, and pathway levels. Intraclass correlation coefficients (ICCs) were calculated for microbes and metabolites to estimate (i) stability (day 4 versus day 0 within each method), (ii) concordance (day 0 for each method versus the GS), and (iii) reliability (day 4 for each method versus the GS). For the top 4 phyla and microbial diversity metrics at the species, gene, and pathway levels, generally high stability and reliability were observed for most methods except for 95% ethanol; similar concordances were seen for different methods. For metabolomics data, 95% ethanol showed the highest stability, concordance, and reliability (median ICCs = 0.71, 0.71, and 0.65, respectively). Taken together, OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles. We recommend using separate collecting methods for gut metagenomic sequencing and fecal metabolomic profiling in large population studies. IMPORTANCE The choice of fecal collection method is essential for studying gut microbe-human interactions in large-scale population-based research. In this study, we examined the effects of fecal collection methods and storage time at ambient temperature on variations in the gut microbiome community composition; microbial diversity metrics at the species, gene, and pathway levels; antibiotic resistance genes; and metabolome profiling. Our findings suggest using different fecal sample collection methods for different data generation purposes. OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles.},
}
@article {pmid34519857,
year = {2021},
author = {Zhu, HZ and Jiang, MZ and Zhou, N and Jiang, CY and Liu, SJ},
title = {Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {19},
pages = {7517-7528},
pmid = {34519857},
issn = {1432-0614},
support = {NSFC grant no. 31861133002//National Natural Science Foundation of China/ ; },
mesh = {Beijing ; *Metagenomics ; *Microbiota ; },
abstract = {Aquatic and wetland systems are widely used for landscapes and water regeneration. Microbiomes and submerged macrophytes (hydrophytes) play essential roles in conversions of organic and inorganic compounds in those ecosystems. The systems were extensively investigated for microbial diversities and compositions. However, little is known about how hydrophytes recruited diverse microbiota and affected functional zonation in aquatic systems. To address this issue, epiphytic leaf and root, sediment, and surrounding water samples were collected from the dragon-shape aquatic system in Beijing Olympic Park. Metagenomic DNAs were extracted and subjected to sequencing. Results showed that epiphytic leaf and root microbiomes and metabolic marker genes were remarkably different from that of surrounding environment. Twenty indicator bacterial genera for epiphytic microbiomes were identified and 50 metabolic marker genes were applied to evaluate the function of epiphytic leaf and root, water, and sediment microbiomes. Co-occurrence analysis revealed highly modularized pattern of metabolic marker genes and indicator bacterial genera related to metabolic functions. These results suggested that hydrophytes shaped microbiomes and drove functional zonation in aquatic systems. KEY POINTS: • Microbiomes of hydrophytes and their surrounding environments were investigated. • Twenty indicator bacterial genera highly specific to epiphytic biofilms were identified. • Epiphytes recruited unique microbiomes and drove functional zonation in aquatic systems.},
}
@article {pmid34512604,
year = {2021},
author = {Liu, Y and Zheng, K and Liu, B and Liang, Y and You, S and Zhang, W and Zhang, X and Jie, Y and Shao, H and Jiang, Y and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M},
title = {Characterization and Genomic Analysis of Marinobacter Phage vB_MalS-PS3, Representing a New Lambda-Like Temperate Siphoviral Genus Infecting Algae-Associated Bacteria.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {726074},
pmid = {34512604},
issn = {1664-302X},
abstract = {Marinobacter is the abundant and important algal-associated and hydrocarbon biodegradation bacteria in the ocean. However, little knowledge about their phages has been reported. Here, a novel siphovirus, vB_MalS-PS3, infecting Marinobacter algicola DG893(T), was isolated from the surface waters of the western Pacific Ocean. Transmission electron microscopy (TEM) indicated that vB_MalS-PS3 has the morphology of siphoviruses. VB_MalS-PS3 was stable from -20 to 55°C, and with the latent and rise periods of about 80 and 10 min, respectively. The genome sequence of VB_MalS-PS3 contains a linear, double-strand 42,168-bp DNA molecule with a G + C content of 56.23% and 54 putative open reading frames (ORFs). Nineteen conserved domains were predicted by BLASTp in NCBI. We found that vB_MalS-PS3 represent an understudied viral group with only one known isolate. The phylogenetic tree based on the amino acid sequences of whole genomes revealed that vB_MalS-PS3 has a distant evolutionary relationship with other siphoviruses, and can be grouped into a novel viral genus cluster with six uncultured assembled viral genomes from metagenomics, named here as Marinovirus. This study of the Marinobacter phage vB_MalS-PS3 genome enriched the genetic database of marine bacteriophages, in addition, will provide useful information for further research on the interaction between Marinobacter phages and their hosts, and their relationship with algal blooms and hydrocarbon biodegradation in the ocean.},
}
@article {pmid34508085,
year = {2021},
author = {Bramble, MS and Vashist, N and Ko, A and Priya, S and Musasa, C and Mathieu, A and Spencer, A and Lupamba Kasendue, M and Mamona Dilufwasayo, P and Karume, K and Nsibu, J and Manya, H and Uy, MNA and Colwell, B and Boivin, M and Mayambu, JPB and Okitundu, D and Droit, A and Mumba Ngoyi, D and Blekhman, R and Tshala-Katumbay, D and Vilain, E},
title = {The gut microbiome in konzo.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {5371},
pmid = {34508085},
issn = {2041-1723},
support = {D43 TW009343/TW/FIC NIH HHS/United States ; R01 ES019841/ES/NIEHS NIH HHS/United States ; },
mesh = {Child ; Democratic Republic of the Congo/epidemiology ; Disease Susceptibility/*microbiology ; Feces/microbiology ; *Feeding Behavior ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Manihot/*adverse effects/chemistry ; Metagenomics ; Motor Neuron Disease/epidemiology/*microbiology ; Nitriles/adverse effects ; },
abstract = {Konzo, a distinct upper motor neuron disease associated with a cyanogenic diet and chronic malnutrition, predominately affects children and women of childbearing age in sub-Saharan Africa. While the exact biological mechanisms that cause this disease have largely remained elusive, host-genetics and environmental components such as the gut microbiome have been implicated. Using a large study population of 180 individuals from the Democratic Republic of the Congo, where konzo is most frequent, we investigate how the structure of the gut microbiome varied across geographical contexts, as well as provide the first insight into the gut flora of children affected with this debilitating disease using shotgun metagenomic sequencing. Our findings indicate that the gut microbiome structure is highly variable depending on region of sampling, but most interestingly, we identify unique enrichments of bacterial species and functional pathways that potentially modulate the susceptibility of konzo in prone regions of the Congo.},
}
@article {pmid34507779,
year = {2021},
author = {Jia, Y and Niu, CT and Xu, X and Zheng, FY and Liu, CF and Wang, JJ and Lu, ZM and Xu, ZH and Li, Q},
title = {Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {148},
number = {},
pages = {110533},
doi = {10.1016/j.foodres.2021.110533},
pmid = {34507779},
issn = {1873-7145},
mesh = {Fermentation ; *Fermented Foods ; *Microbiota ; Staphylococcus ; *Vicia faba ; },
abstract = {Although the microbial diversity and structure in bean-based fermented foods have been widely studied, systematic studies on functional microbiota and mechanism of community forms in multi-microbial fermentation systems were still lacking. In this work, the metabolic pathway and functional potential of microbial community in broad bean paste (BBP) were investigated by metagenomics approach, and Staphylococcus, Bacillus, Weissella, Aspergillus and Zygosaccharomyces were found to be the potential predominant populations responsible for substrate alteration and flavor biosynthesis. Among them, Staphylococcus was the most abundant and widespread functional microbe, and closely related Staphylococcus species were diverse and ubiquitously distributed, with the opportunistic pathogen S. gallinarum being the most abundant Staphylococcus specie isolated from BBP. To explain the dominance status of S. gallinarum and species distributions of Staphylococcus genus, we tested the effects of abiotic and biotic factors on three Staphylococcus species using a tractable BBP model, demonstrating that adaptation to environmental conditions (environmental parameters and other functional microbes) led to the dominant position and species coexistence of Staphylococcus, and congeneric competition among Staphylococcus species further shaped ecological distributions of closely related Staphylococcus species. In general, this work revealed the metabolic potential of microbial community and distribution mechanism of Staphylococcus species during BBP fermentation, which could help traditional factories to more precisely control the safety and quality of bean-based fermented foods.},
}
@article {pmid34507766,
year = {2021},
author = {Liu, D and Zhang, C and Zhang, J and Xin, X and Liao, X},
title = {Metagenomics reveals the formation mechanism of flavor metabolites during the spontaneous fermentation of potherb mustard (Brassica juncea var. multiceps).},
journal = {Food research international (Ottawa, Ont.)},
volume = {148},
number = {},
pages = {110622},
doi = {10.1016/j.foodres.2021.110622},
pmid = {34507766},
issn = {1873-7145},
mesh = {Fermentation ; *Lactobacillales/genetics ; Metagenomics ; *Microbiota ; Mustard Plant/genetics ; },
abstract = {Fermented vegetable flavors are closely associated with microbial metabolism. Here, shifts in flavor metabolites and their correlations to the structure and function of fermentative microbial communities were explored during the spontaneous fermentation process of potherb mustard (Brassica juncea var. multiceps), a traditionally fermented vegetable from China. Halophilic bacteria (HAB, i.e., Halomonas, Salinivibrio, and Vibrio) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) became highly abundant after potherb mustard fermentation. Further, HAB and LAB abundances exhibited significant, positive correlations with metabolites important in fermented potherb mustard flavoring (e.g., organic acids, amino acids, alcohols, aldehydes, and nitriles). Metagenomic analysis indicated that Halomonas, Salinivibrio, Weissella, and Lactobacillus-related genera were likely actively engaged in pyruvate metabolism (ko00620) and citrate cycle (TCA cycle, ko00020), leading to higher lactic and acetic acid concentrations, along with lower pH, which would affect levels of volatile isothiocyanates and nitriles that contribute to flavoring of fermented potherb mustard. Further, HAB and LAB were the primary populations inferred to be responsible for amino acid and fatty acid metabolism in addition to the biosynthesis of numerous volatile flavor compounds. This study highlights the predominance and importance of LAB and HAB during spontaneous fermentation of potherb mustard and provides new insights into their roles in this process.},
}
@article {pmid34498139,
year = {2021},
author = {Xu, X and Ran, X and Tang, J and Pradhan, S and Dai, Y and Zhuang, K and Ran, Y},
title = {Skin Microbiota in Non-inflammatory and Inflammatory Lesions of Acne Vulgaris: The Underlying Changes within the Pilosebaceous Unit.},
journal = {Mycopathologia},
volume = {186},
number = {6},
pages = {863-869},
pmid = {34498139},
issn = {1573-0832},
support = {ZYJC18033//1.3.5 project for disciplines of excellence/ ; HXYS19003//HX-Academician project (HXYS19003) of West China Hospital, Sichuan University/ ; 81773343//National Natural Science Foundation of China/ ; },
mesh = {*Acne Vulgaris ; Adolescent ; Adult ; Humans ; Malassezia ; Male ; *Microbiota ; Propionibacterium acnes ; Skin ; Young Adult ; },
abstract = {Acne vulgaris is a common chronic inflammatory skin disease of the pilosebaceous unit. Clinical manifestations include seborrhea, non-inflammatory lesions, inflammatory lesions, or scar formation. Fourteen eligible participants of either sex, aged 18-28 years old, with mild to moderate acne lesions, were recruited in this observational study. The contents of 10 pilosebaceous units of non-inflammatory (comedones) and inflammatory lesions (papules and pustules) were collected from each participant's face and examined by amplicon metagenomics sequencing and real-time Polymerase Chain Reaction (PCR). Male participants, participants with a higher body mass index (BMI) than normal, and participants younger than 20 years old, were revealed to have a higher proportion of Malassezia in their non-inflammatory lesions than that in inflammatory lesions. There was an increased abundance of Malassezia restricta (M. restricta) and Cutibacterium acnes (C. acnes) in the non-inflammatory group. Correlation analysis indicated that Staphylococcus epidermidis (S. epidermidis) and M. restricta have similar proliferation trends with C. acnes during the transformation from non-inflammatory to inflammatory lesions. M. restricta probably involve in the microecological balance within the pilosebaceous unit.},
}
@article {pmid34495150,
year = {2021},
author = {Can-Herrera, LA and Gutierrez-Canul, CD and Dzul-Cervantes, MAA and Pacheco-Salazar, OF and Chi-Cortez, JD and Carbonell, LS},
title = {Identification by molecular techniques of halophilic bacteria producing important enzymes from pristine area in Campeche, Mexico.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {83},
number = {},
pages = {e246038},
doi = {10.1590/1519-6984.246038},
pmid = {34495150},
issn = {1678-4375},
mesh = {*Archaea ; Bacteria/genetics ; Mexico ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Isla Arena is located in the coordinate 20° 70´ N - 90° 45´ W, from Campeche, Mexico. In these estuaries, the ocean mixes with fresh water, and ecosystems are concentrated where petenes and pink flamingos proliferate. Crustaceans and mollusks abound in the sea. Despite its enormous marine wealth, there are no studies carried out on which halophilic microorganisms are present in these waters. In this work, the diversity and structure of the microbial community was investigated through a metagenomics approach and corroborated for sequencing of 16S rRNA genes. It was found that the phylum Fimicutes predominates with more than 50%, in almost the same proportion of the class Bacilli and with almost 41% of relative abundance of the order Bacillales. The sequencing results showed that one of the samples presented a high percentage of similarity (99.75%) using the Nucleotide BLAST program with a peculiar microorganism: Bacillus subtilis. This microorganism is one of the best characterized bacteria among the gram-positive ones. Our results demonstrate that B. subtilis can be an efficient source of proteases, lipases and cellulases, from halophilic microbial communities located in poorly explored areas.},
}
@article {pmid34490138,
year = {2021},
author = {Lyu, X and Zheng, H and Wang, X and Zhang, H and Gao, L and Xun, Z and Zhang, Q and He, X and Hua, H and Yan, Z and Chen, F},
title = {Oral Microbiota Composition and Function Changes During Chronic Erythematous Candidiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {691092},
pmid = {34490138},
issn = {2235-2988},
mesh = {*Candidiasis, Oral ; Humans ; Metagenomics ; *Microbiota ; *Micrococcaceae ; },
abstract = {Oral microbiota is constantly changing with the host state, whereas the oral microbiome of chronic erythematous candidiasis remains poorly understood. The aim of this study was to compare oral microbial signatures and functional profiling between chronic erythematous candidiasis and healthy subjects. Using shotgun metagenomic sequencing, we analyzed the microbiome in 12 chronic erythematous candidiasis, 12 healthy subjects, and 2 chronic erythematous candidiasis cured by antifungal therapy. We found that the salivary microbiota of chronic erythematous candidiasis was significantly different from that of healthy subjects. Among them, Rothia mucilaginosa and Streptococcus mitis were the most abundant disease-enriched species (Mann-Whitney U-test, P < 0.05). In addition, co-occurrence network analysis showed that C. albicans formed densely connected modules with oral bacterial species and was mainly positive connected to Streptococcus species. Furthermore, we investigated the functional potentials of the microbiome and identified a set of microbial marker genes associated with chronic erythematous candidiasis. Some of these genes enriching in chronic erythematous candidiasis are involved in eukaryotic ribosome, putative glutamine transport system, and cytochrome bc1 complex respiratory unit. Altogether, this study revealed the changes of oral microbial composition, the co-occurrence between C. albicans and oral bacteria, as well as the changes of microbial marker genes during chronic erythematous candidiasis, which provides evidence of oral microbiome as a target for the treatment and prevention of chronic erythematous candidiasis.},
}
@article {pmid34484688,
year = {2021},
author = {Mehta, S and Crane, M and Leith, E and Batut, B and Hiltemann, S and Arntzen, MØ and Kunath, BJ and Pope, PB and Delogu, F and Sajulga, R and Kumar, P and Johnson, JE and Griffin, TJ and Jagtap, PD},
title = {ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework.},
journal = {F1000Research},
volume = {10},
number = {},
pages = {103},
pmid = {34484688},
issn = {2046-1402},
support = {U24 CA199347/CA/NCI NIH HHS/United States ; },
mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Workflow ; },
abstract = {The Earth Microbiome Project (EMP) aided in understanding the role of microbial communities and the influence of collective genetic material (the 'microbiome') and microbial diversity patterns across the habitats of our planet. With the evolution of new sequencing technologies, researchers can now investigate the microbiome and map its influence on the environment and human health. Advances in bioinformatics methods for next-generation sequencing (NGS) data analysis have helped researchers to gain an in-depth knowledge about the taxonomic and genetic composition of microbial communities. Metagenomic-based methods have been the most commonly used approaches for microbiome analysis; however, it primarily extracts information about taxonomic composition and genetic potential of the microbiome under study, lacking quantification of the gene products (RNA and proteins). On the other hand, metatranscriptomics, the study of a microbial community's RNA expression, can reveal the dynamic gene expression of individual microbial populations and the community as a whole, ultimately providing information about the active pathways in the microbiome. In order to address the analysis of NGS data, the ASaiM analysis framework was previously developed and made available via the Galaxy platform. Although developed for both metagenomics and metatranscriptomics, the original publication demonstrated the use of ASaiM only for metagenomics, while thorough testing for metatranscriptomics data was lacking. In the current study, we have focused on validating and optimizing the tools within ASaiM for metatranscriptomics data. As a result, we deliver a robust workflow that will enable researchers to understand dynamic functional response of the microbiome in a wide variety of metatranscriptomics studies. This improved and optimized ASaiM-metatranscriptomics (ASaiM-MT) workflow is publicly available via the ASaiM framework, documented and supported with training material so that users can interrogate and characterize metatranscriptomic data, as part of larger meta-omic studies of microbiomes.},
}
@article {pmid34481302,
year = {2021},
author = {Aguinaga, OE and White, KN and Dean, AP and Pittman, JK},
title = {Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {290},
number = {},
pages = {118064},
doi = {10.1016/j.envpol.2021.118064},
pmid = {34481302},
issn = {1873-6424},
mesh = {Acids ; *Microbiota ; Mining ; Water Quality ; *Wetlands ; },
abstract = {Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.},
}
@article {pmid34472853,
year = {2021},
author = {Wu, X and Chauhan, A and Layton, AC and Lau Vetter, MCY and Stackhouse, BT and Williams, DE and Whyte, L and Pfiffner, SM and Onstott, TC and Vishnivetskaya, TA},
title = {Comparative Metagenomics of the Active Layer and Permafrost from Low-Carbon Soil in the Canadian High Arctic.},
journal = {Environmental science &amp; technology},
volume = {55},
number = {18},
pages = {12683-12693},
doi = {10.1021/acs.est.1c00802},
pmid = {34472853},
issn = {1520-5851},
mesh = {Arctic Regions ; Canada ; Carbon ; Metagenomics ; *Permafrost ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; },
abstract = {Approximately 87% of the Arctic consists of low-organic carbon mineral soil, but knowledge of microbial activity in low-carbon permafrost (PF) and active layer soils remains limited. This study investigated the taxonomic composition and genetic potential of microbial communities at contrasting depths of the active layer (5, 35, and 65 cm below surface, bls) and PF (80 cm bls). We showed microbial communities in PF to be taxonomically and functionally different from those in the active layer. 16S rRNA gene sequence analysis revealed higher biodiversity in the active layer than in PF, and biodiversity decreased significantly with depth. The reconstructed 91 metagenome-assembled genomes showed that PF was dominated by heterotrophic, fermenting Bacteroidota using nitrite as their main electron acceptor. Prevalent microbes identified in the active layer belonged to bacterial taxa, gaining energy via aerobic respiration. Gene abundance in metagenomes revealed enrichment of genes encoding the plant-derived polysaccharide degradation and metabolism of nitrate and sulfate in PF, whereas genes encoding methane/ammonia oxidation, cold-shock protein, and two-component systems were generally more abundant in the active layer, particularly at 5 cm bls. The results of this study deepen our understanding of the low-carbon Arctic soil microbiome and improve prediction of the impacts of thawing PF.},
}
@article {pmid34469192,
year = {2021},
author = {Gao, C and Xia, J and Zhou, X and Liang, Y and Jiang, Y and Wang, M and Shao, H and Shi, X and Guo, C and He, H and Wang, H and He, J and Hu, D and Wang, X and Zhao, J and Zhang, YZ and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Suttle, CA and Wang, M},
title = {Viral Characteristics of the Warm Atlantic and Cold Arctic Water Masses in the Nordic Seas.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {22},
pages = {e0116021},
pmid = {34469192},
issn = {1098-5336},
abstract = {Nordic Seas are the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean with complex water masses, experiencing an abrupt climate change. Though knowledge of the marine virosphere has expanded rapidly, the diversity of viruses and their relationships with host cells and water masses in the Nordic Seas remain to be fully revealed. Here, we establish the Nordic Sea DNA virome (NSV) data set of 55,315 viral contigs including 1,478 unique viral populations from seven stations influenced by both the warm Atlantic and cold Arctic water masses. Caudovirales dominated in the seven NSVs, especially in the warm Atlantic waters. The major giant nucleocytoplasmic large DNA viruses (NCLDVs) contributed a significant proportion of the classified viral contigs in the NSVs (32.2%), especially in the cold Arctic waters (44.9%). The distribution patterns of Caudovirales and NCLDVs were a reflection of the community structure of their hosts in the corresponding water masses and currents. Latitude, pH, and flow speed were found to be key factors influencing the microbial communities and coinfluencing the variation of viral communities. Network analysis illustrated the tight coupling between the variation of viral communities and microbial communities in the Nordic Seas. This study suggests a probable linkage between viromes, host cells, and surface water masses from both the cool Arctic and warm Atlantic Oceans. IMPORTANCE This is a systematic study of Nordic Sea viromes using metagenomic analysis. The viral diversity, community structure, and their relationships with host cells and the complex water masses from both the cool Arctic and the warm Atlantic oceans were illustrated. The NCLDVs and Caudovirales are proposed as the viral characteristics of the cold Arctic and warm Atlantic waters, respectively. This study provides an important background for the viromes in the subarctic seas connecting the Arctic Ocean and North Atlantic Ocean and sheds light on their responses to abrupt climate change in the future.},
}
@article {pmid34468193,
year = {2021},
author = {Nagy-Szakal, D and Couto-Rodriguez, M and Wells, HL and Barrows, JE and Debieu, M and Butcher, K and Chen, S and Berki, A and Hager, C and Boorstein, RJ and Taylor, MK and Jonsson, CB and Mason, CE and O'Hara, NB},
title = {Targeted Hybridization Capture of SARS-CoV-2 and Metagenomics Enables Genetic Variant Discovery and Nasal Microbiome Insights.},
journal = {Microbiology spectrum},
volume = {9},
number = {2},
pages = {e0019721},
pmid = {34468193},
issn = {2165-0497},
mesh = {Anti-Bacterial Agents/pharmacology ; COVID-19/pathology ; Drug Resistance, Bacterial/genetics ; Genetic Variation/*genetics ; Genome, Viral/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Limit of Detection ; Macrolides/pharmacology ; Metagenomics/methods ; Microbiota/*genetics ; Nasopharynx/*microbiology ; RNA, Viral/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; SARS-CoV-2/*genetics/isolation &amp; purification ; },
abstract = {The emergence of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic variants that may alter viral fitness highlights the urgency of widespread next-generation sequencing (NGS) surveillance. To profile genetic variants of the entire SARS-CoV-2 genome, we developed and clinically validated a hybridization capture SARS-CoV-2 NGS assay, integrating novel methods for panel design using double-stranded DNA (dsDNA) biotin-labeled probes, and built accompanying software. This test is the first hybrid capture-based NGS assay given Food and Drug Administration (FDA) emergency use authorization for detection of the SARS-CoV-2 virus. The positive and negative percent agreement (PPA and NPA, respectively) were defined in comparison to the results for an orthogonal real-time reverse transcription polymerase chain reaction (RT-PCR) assay (PPA and NPA, 96.7 and 100%, respectively). The limit of detection was established to be 800 copies/ml with an average fold enrichment of 46,791. Furthermore, utilizing the research-use-only analysis to profile the variants, we identified 55 novel mutations, including 11 in the functionally important spike protein. Finally, we profiled the full nasopharyngeal microbiome using metagenomics and found overrepresentation of 7 taxa and evidence of macrolide resistance in SARS-CoV-2-positive patients. This hybrid capture NGS assay, coupled with optimized software, is a powerful approach to detect and comprehensively map SARS-CoV-2 genetic variants for tracking viral evolution and guiding vaccine updates. IMPORTANCE This is the first FDA emergency-use-authorized hybridization capture-based next-generation sequencing (NGS) assay to detect the SARS-CoV-2 genome. Viral metagenomics and the novel hybrid capture NGS-based assay, along with its research-use-only analysis, can provide important genetic insights into SARS-CoV-2 and other emerging pathogens and improve surveillance and early detection, potentially preventing or mitigating new outbreaks. Better understanding of the continuously evolving SARS-CoV-2 viral genome and the impact of genetic variants may provide individual risk stratification, precision therapeutic options, improved molecular diagnostics, and population-based therapeutic solutions.},
}
@article {pmid34465900,
year = {2021},
author = {Sulaiman, I and Chung, M and Angel, L and Tsay, JJ and Wu, BG and Yeung, ST and Krolikowski, K and Li, Y and Duerr, R and Schluger, R and Thannickal, SA and Koide, A and Rafeq, S and Barnett, C and Postelnicu, R and Wang, C and Banakis, S and Pérez-Pérez, L and Shen, G and Jour, G and Meyn, P and Carpenito, J and Liu, X and Ji, K and Collazo, D and Labarbiera, A and Amoroso, N and Brosnahan, S and Mukherjee, V and Kaufman, D and Bakker, J and Lubinsky, A and Pradhan, D and Sterman, DH and Weiden, M and Heguy, A and Evans, L and Uyeki, TM and Clemente, JC and de Wit, E and Schmidt, AM and Shopsin, B and Desvignes, L and Wang, C and Li, H and Zhang, B and Forst, CV and Koide, S and Stapleford, KA and Khanna, KM and Ghedin, E and Segal, LN},
title = {Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome.},
journal = {Nature microbiology},
volume = {6},
number = {10},
pages = {1245-1258},
pmid = {34465900},
issn = {2058-5276},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK110014/DK/NIDDK NIH HHS/United States ; R01 AI143861/AI/NIAID NIH HHS/United States ; R01 HL125816/HL/NHLBI NIH HHS/United States ; R21 AI158997/AI/NIAID NIH HHS/United States ; R01 AI140754/AI/NIAID NIH HHS/United States ; R37 CA244775/CA/NCI NIH HHS/United States ; R01 AI137336/AI/NIAID NIH HHS/United States ; P20 CA252728/CA/NCI NIH HHS/United States ; },
mesh = {Adaptive Immunity ; Adult ; Aged ; Bacteria/classification/genetics/isolation &amp; purification ; Bacterial Load ; Bronchoalveolar Lavage Fluid/immunology/*microbiology/virology ; COVID-19/immunology/microbiology/mortality/*therapy ; Critical Illness ; Female ; Hospitalization ; Humans ; Immunity, Innate ; Male ; Microbiota ; Middle Aged ; Odds Ratio ; Prognosis ; Prospective Studies ; *Respiration, Artificial ; Respiratory System/immunology/microbiology/virology ; SARS-CoV-2/immunology/*pathogenicity ; Viral Load ; },
abstract = {Respiratory failure is associated with increased mortality in COVID-19 patients. There are no validated lower airway biomarkers to predict clinical outcome. We investigated whether bacterial respiratory infections were associated with poor clinical outcome of COVID-19 in a prospective, observational cohort of 589 critically ill adults, all of whom required mechanical ventilation. For a subset of 142 patients who underwent bronchoscopy, we quantified SARS-CoV-2 viral load, analysed the lower respiratory tract microbiome using metagenomics and metatranscriptomics and profiled the host immune response. Acquisition of a hospital-acquired respiratory pathogen was not associated with fatal outcome. Poor clinical outcome was associated with lower airway enrichment with an oral commensal (Mycoplasma salivarium). Increased SARS-CoV-2 abundance, low anti-SARS-CoV-2 antibody response and a distinct host transcriptome profile of the lower airways were most predictive of mortality. Our data provide evidence that secondary respiratory infections do not drive mortality in COVID-19 and clinical management strategies should prioritize reducing viral replication and maximizing host responses to SARS-CoV-2.},
}
@article {pmid34465175,
year = {2021},
author = {Zhang, Y and Thompson, KN and Branck, T and Yan Yan, and Nguyen, LH and Franzosa, EA and Huttenhower, C},
title = {Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling.},
journal = {Annual review of biomedical data science},
volume = {4},
number = {},
pages = {279-311},
doi = {10.1146/annurev-biodatasci-031121-103035},
pmid = {34465175},
issn = {2574-3414},
support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; R39789/VAC_/Versus Arthritis/United Kingdom ; C10674/A27140/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {Host Microbial Interactions ; Humans ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, RNA ; Transcriptome ; },
abstract = {Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.},
}
@article {pmid34458157,
year = {2021},
author = {Chen, J and Li, H and Hird, SM and Chen, MH and Xu, W and Maas, K and Cong, X},
title = {Sex Differences in Gut Microbial Development of Preterm Infant Twins in Early Life: A Longitudinal Analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {671074},
pmid = {34458157},
issn = {2235-2988},
support = {K23 NR014674/NR/NINR NIH HHS/United States ; R01 NR016928/NR/NINR NIH HHS/United States ; },
mesh = {Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Longitudinal Studies ; Male ; Phylogeny ; *Sex Characteristics ; *Twins ; },
abstract = {Infant gut microbiota plays a vital role in immune response, mediates neurobehavioral development and health maintenance. Studies of twins' gut microbiota found that gut microbiota composition and diversity tend to be mature and stable with increasing postnatal age (PNA). Preterm infant gut microbiome shifts dramatically when they were staying in the neonatal intensive care unit (NICU). Compositions and shifting characteristics of gut microbiota among neonatal preterm twins and triplets during their early life are still unknown, which impedes a better understanding of the mechanism underpinning neurobehavioral development and precise intervention/health of preterm neonates. This longitudinal cohort study used a twins/triplets design to investigate the interaction of genetic (e.g., male vs. female) and environmental factors influencing the development of the gut microbiome in early life. We included 39 preterm infants, 12 were Female twins/triplets (Female T/T) including 3 twins pairs and 2 triplets, 12 were male twins (Male T) including 6 twins pairs, and 15 were mixed-sex twins/triplets (Mix T/T) including 6 twins pairs and 1 triplet (8 females and 7 males) during the first four weeks of NICU stay. Weekly gut microbiota patterns between females and males were compared by linear discriminant analysis (LDA) effect size (LEfSe). Metagenomics function of gut microbiota was predicted by using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Weekly function (KEGG pathways) differences between females and males were detected by using Statistical Analysis of Metagenomic Profiles (STAMP). Results found that female pairs and male pairs were significantly different in gut microbiome diversity, compositions, and predicted metabolic profiles, importantly, females and males were also significantly dissimilar within their co-twin/triplet pairs of the mixed-sex group, infants of co-twins/triplets shared more similar features than un-related infants from different twins' pair. Future research developing personalized interventions for vulnerable high-risk infants should consider sex, and the interaction of sex and environmental factors.},
}
@article {pmid34454634,
year = {2021},
author = {Gupta, CL and Blum, SE and Kattusamy, K and Daniel, T and Druyan, S and Shapira, R and Krifucks, O and Zhu, YG and Zhou, XY and Su, JQ and Cytryn, E},
title = {Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {178},
pmid = {34454634},
issn = {2049-2618},
mesh = {Animals ; Anti-Bacterial Agents/*therapeutic use ; *Chickens ; Cloaca/microbiology ; *Drug Resistance, Bacterial/genetics ; Escherichia coli ; Longitudinal Studies ; *Microbiota ; Staphylococcus aureus ; },
abstract = {BACKGROUND: Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae).<br><br>RESULTS: Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28-76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified.<br><br>CONCLUSIONS: Within a "farm-to-fork, one health" perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment. Video Abstract.},
}
@article {pmid34446773,
year = {2021},
author = {Kobiyama, A and Rashid, J and Reza, MS and Ikeda, Y and Yamada, Y and Kudo, T and Mizusawa, N and Yanagisawa, S and Ikeda, D and Sato, S and Ogata, T and Ikeo, K and Kaga, S and Watanabe, S and Naiki, K and Kaga, Y and Segawa, S and Tada, Y and Musashi, T and Mineta, K and Gojobori, T and Watabe, S},
title = {Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {17277},
pmid = {34446773},
issn = {2045-2322},
mesh = {Bacteria/classification/genetics ; Bays/*microbiology ; Cyanobacteria/classification/genetics ; Ecosystem ; Geography ; Japan ; Metagenomics/*methods ; Microbiota/*genetics ; Oxygen/metabolism ; Population Dynamics ; Salinity ; *Seasons ; Seawater/chemistry/*microbiology ; Temperature ; Whole Genome Sequencing/methods ; },
abstract = {Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.},
}
@article {pmid34444993,
year = {2021},
author = {Tso, L and Bonham, KS and Fishbein, A and Rowland, S and Klepac-Ceraj, V},
title = {Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes.},
journal = {Nutrients},
volume = {13},
number = {8},
pages = {},
pmid = {34444993},
issn = {2072-6643},
support = {UG3 OD023313/GF/NIH HHS/United States ; },
mesh = {Bacterial Proteins/classification/genetics ; *Bifidobacterium longum/genetics/metabolism ; Breast Feeding ; Cohort Studies ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial/genetics ; Humans ; Infant ; Infant, Newborn ; Milk, Human/*chemistry ; Oligosaccharides/*metabolism ; },
abstract = {Bifidobacterium longum subsp. infantis (B. infantis) is one of a few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis. All three organisms are classified in the same species group but only B. infantis can metabolize human milk oligosaccharides (HMOs). We compared HMO-metabolizing genes across different Bifidobacterium genomes and developed B. infantis-specific primers to determine if the genes alone or the primers can be used to quickly characterize B. infantis. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, tested for its prevalence in infant gut metagenomes, and validated the results using the B. infantis-specific primers. We observed that only 15 of 203 (7.4%) children under 2 years old from a cohort of US children harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.},
}
@article {pmid34444797,
year = {2021},
author = {Barber, C and Mego, M and Sabater, C and Vallejo, F and Bendezu, RA and Masihy, M and Guarner, F and Espín, JC and Margolles, A and Azpiroz, F},
title = {Differential Effects of Western and Mediterranean-Type Diets on Gut Microbiota: A Metagenomics and Metabolomics Approach.},
journal = {Nutrients},
volume = {13},
number = {8},
pages = {},
pmid = {34444797},
issn = {2072-6643},
support = {SAF 2016-76648-R//Ministerio de Economía y Competitividad/ ; PID2019-103914RB-I00//Ministerio de Ciencia e Innovacion/ ; AGL2016-78311-R//Ministerio de Ciencia e Innovación/ ; FJC2019-042125-I//Ministerio de Ciencia e Innovación/ ; },
mesh = {Adolescent ; Adult ; Biodiversity ; Colon ; Cross-Over Studies ; *Diet, Mediterranean ; *Diet, Western ; Feces/microbiology ; Flatulence ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; *Metagenomics ; Surveys and Questionnaires ; Young Adult ; },
abstract = {Our aim was to determine the effect of diet on gut microbiota, digestive function and sensations, using an integrated clinical, metagenomics and metabolomics approach. We conducted a cross-over, randomised study on the effects of a Western-type diet versus a fibre-enriched Mediterranean diet. In 20 healthy men, each diet was administered for 2 weeks preceded by a 2-week washout diet. The following outcomes were recorded: (a) number of anal gas evacuations; (b) digestive sensations; (c) volume of gas evacuated after a probe meal; (d) colonic content by magnetic resonance imaging; (e) gut microbiota taxonomy and metabolic functions by shotgun sequencing of faecal samples; (f) urinary metabolites using untargeted metabolomics. As compared to a Western diet, the Mediterranean diet was associated with (i) higher number of anal gas evacuations, (ii) sensation of flatulence and borborygmi, (iii) larger volume of gas after the meal and (iv) larger colonic content. Despite the relatively little difference in microbiota composition between both diets, microbial metabolism differed substantially, as shown by urinary metabolite profiles and the abundance of microbial metabolic pathways. The effects of the diet were less evident in individuals with robust microbiotas (higher beta-diversity). To conclude, healthy individuals tolerate dietary changes with minor microbial modifications at the composition level but with remarkable variation in microbial metabolism.},
}
@article {pmid34444679,
year = {2021},
author = {Juárez-Fernández, M and Román-Sagüillo, S and Porras, D and García-Mediavilla, MV and Linares, P and Ballesteros-Pomar, MD and Urioste-Fondo, A and Álvarez-Cuenllas, B and González-Gallego, J and Sánchez-Campos, S and Jorquera, F and Nistal, E},
title = {Long-Term Effects of Bariatric Surgery on Gut Microbiota Composition and Faecal Metabolome Related to Obesity Remission.},
journal = {Nutrients},
volume = {13},
number = {8},
pages = {},
pmid = {34444679},
issn = {2072-6643},
support = {BFU2017-87960-R//Ministerio de Economía y Competitividad/ ; GRS1888/A/18//Junta de Castilla y León/ ; },
mesh = {*Bariatric Surgery ; DNA/analysis ; Fatty Acids, Volatile/analysis ; Feces/*chemistry/microbiology ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; *Metabolome ; Metagenomics ; Obesity, Morbid/*microbiology/*surgery ; Weight Loss ; },
abstract = {Obesity is one of the main worldwide public health concerns whose clinical management demands new therapeutic approaches. Bariatric surgery is the most efficient treatment when other therapies have previously failed. Due to the role of gut microbiota in obesity development, the knowledge of the link between bariatric surgery and gut microbiota could elucidate new mechanistic approaches. This study aims to evaluate the long-term effects of bariatric surgery in the faecal metagenome and metabolome of patients with severe obesity. Faecal and blood samples were collected before and four years after the intervention from patients with severe obesity. Biochemical, metagenomic and metabolomic analyses were performed and faecal short-chain fatty acids were measured. Bariatric surgery improved the obesity-related status of patients and significantly reshaped gut microbiota composition. Moreover, this procedure was associated with a specific metabolome profile characterized by a reduction in energetic and amino acid metabolism. Acetate, butyrate and propionate showed a significant reduction with bariatric surgery. Finally, correlation analysis suggested the existence of a long-term compositional and functional gut microbiota profile associated with the intervention. In conclusion, bariatric surgery triggered long-lasting effects on gut microbiota composition and faecal metabolome that could be associated with the remission of obesity.},
}
@article {pmid34433845,
year = {2021},
author = {Hasrat, R and Kool, J and de Steenhuijsen Piters, WAA and Chu, MLJN and Kuiling, S and Groot, JA and van Logchem, EM and Fuentes, S and Franz, E and Bogaert, D and Bosch, T},
title = {Benchmarking laboratory processes to characterise low-biomass respiratory microbiota.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {17148},
pmid = {34433845},
issn = {2045-2322},
mesh = {Benchmarking/*methods ; Biomass ; Humans ; Metagenomics/methods/standards ; *Microbiota ; Polymerase Chain Reaction/methods/standards ; RNA, Ribosomal, 16S/genetics ; Reagent Kits, Diagnostic/*standards ; Respiratory Mucosa/*microbiology ; Saliva/microbiology ; },
abstract = {The low biomass of respiratory samples makes it difficult to accurately characterise the microbial community composition. PCR conditions and contaminating microbial DNA can alter the biological profile. The objective of this study was to benchmark the currently available laboratory protocols to accurately analyse the microbial community of low biomass samples. To study the effect of PCR conditions on the microbial community profile, we amplified the 16S rRNA gene of respiratory samples using various bacterial loads and different number of PCR cycles. Libraries were purified by gel electrophoresis or AMPure XP and sequenced by V2 or V3 MiSeq reagent kits by Illumina sequencing. The positive control was diluted in different solvents. PCR conditions had no significant influence on the microbial community profile of low biomass samples. Purification methods and MiSeq reagent kits provided nearly similar microbiota profiles (paired Bray-Curtis dissimilarity median: 0.03 and 0.05, respectively). While profiles of positive controls were significantly influenced by the type of dilution solvent, the theoretical profile of the Zymo mock was most accurately analysed when the Zymo mock was diluted in elution buffer (difference compared to the theoretical Zymo mock: 21.6% for elution buffer, 29.2% for Milli-Q, and 79.6% for DNA/RNA shield). Microbiota profiles of DNA blanks formed a distinct cluster compared to low biomass samples, demonstrating that low biomass samples can accurately be distinguished from DNA blanks. In summary, to accurately characterise the microbial community composition we recommend 1. amplification of the obtained microbial DNA with 30 PCR cycles, 2. purifying amplicon pools by two consecutive AMPure XP steps and 3. sequence the pooled amplicons by V3 MiSeq reagent kit. The benchmarked standardized laboratory workflow presented here ensures comparability of results within and between low biomass microbiome studies.},
}
@article {pmid34418978,
year = {2021},
author = {Christiansen, H and Heindler, FM and Hellemans, B and Jossart, Q and Pasotti, F and Robert, H and Verheye, M and Danis, B and Kochzius, M and Leliaert, F and Moreau, C and Patel, T and Van de Putte, AP and Vanreusel, A and Volckaert, FAM and Schön, I},
title = {Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {625},
pmid = {34418978},
issn = {1471-2164},
mesh = {Animals ; Genome ; Genomics ; Humans ; *Metagenomics ; *Research Design ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Genome-wide data are invaluable to characterize differentiation and adaptation of natural populations. Reduced representation sequencing (RRS) subsamples a genome repeatedly across many individuals. However, RRS requires careful optimization and fine-tuning to deliver high marker density while being cost-efficient. The number of genomic fragments created through restriction enzyme digestion and the sequencing library setup must match to achieve sufficient sequencing coverage per locus. Here, we present a workflow based on published information and computational and experimental procedures to investigate and streamline the applicability of RRS.<br><br>RESULTS: In an iterative process genome size estimates, restriction enzymes and size selection windows were tested and scaled in six classes of Antarctic animals (Ostracoda, Malacostraca, Bivalvia, Asteroidea, Actinopterygii, Aves). Achieving high marker density would be expensive in amphipods, the malacostracan target taxon, due to the large genome size. We propose alternative approaches such as mitogenome or target capture sequencing for this group. Pilot libraries were sequenced for all other target taxa. Ostracods, bivalves, sea stars, and fish showed overall good coverage and marker numbers for downstream population genomic analyses. In contrast, the bird test library produced low coverage and few polymorphic loci, likely due to degraded DNA.<br><br>CONCLUSIONS: Prior testing and optimization are important to identify which groups are amenable for RRS and where alternative methods may currently offer better cost-benefit ratios. The steps outlined here are easy to follow for other non-model taxa with little genomic resources, thus stimulating efficient resource use for the many pressing research questions in molecular ecology.},
}
@article {pmid34418463,
year = {2021},
author = {Brookes, ZLS and Belfield, LA and Ashworth, A and Casas-Agustench, P and Raja, M and Pollard, AJ and Bescos, R},
title = {Effects of chlorhexidine mouthwash on the oral microbiome.},
journal = {Journal of dentistry},
volume = {113},
number = {},
pages = {103768},
doi = {10.1016/j.jdent.2021.103768},
pmid = {34418463},
issn = {1879-176X},
mesh = {*Chlorhexidine/pharmacology ; *Microbiota ; Mouth ; Mouthwashes ; Nitrates ; },
abstract = {INTRODUCTION/OBJECTIVES: Chlorhexidine (CHX) is a commonly used mouthwash with potent anti-microbial effects useful for the management of oral disease. However, we are moving away from the view of simply 'killing' bacteria, towards managing oral microbial ecosystems (oral microbiome), as an integrated system, to promote oral and systemic health. Here, we aimed to review the effects of CHX mouthwash on the balance of microbial communities in the mouth in vivo in oral health and disease.<br><br>SOURCES AND STUDY SECTION: The hierarchy of evidence was applied, with systematic reviews and randomised controlled trials consulted where available and case controlled studies being described thereafter. Search terms for each subject category were entered into MEDLINE, PubMed, Google Scholar and the Cochrane database. Focussing on metagenomics studies provides unique overview of the oral microbiome as an integrated system.<br><br>DATA: Evidence was limited, but several next generation sequencing case-controlled studies suggested that in an integrated system, CHX may cause a shift towards lower bacterial diversity and abundance, in particular nitrate-reducing bacteria in vivo. CHX also appeared to alter salivary pH, lactate, nitrate and nitrite concentrations in saliva. Evidence regarding the effects of CHX on the oral microbiome during oral disease is still emerging.<br><br>CONCLUSIONS: CHX alters the composition the oral microbiome. However, as CHX use remains widespread in dentistry to manage oral disease, urgent research using metagenomics studies of microbial communities in vivo are still needed to determine CHX mouthwash is 'good', 'bad' or otherwise for bacteria, in the context of oral and systemic health.},
}
@article {pmid34415303,
year = {2021},
author = {Li, H and Zhao, C and Yang, Y and Zhou, Z and Qi, J and Li, C},
title = {The Influence of Gut Microbiota on the Fecundity of Henosepilachna vigintioctopunctata (Coleoptera: Coccinellidae).},
journal = {Journal of insect science (Online)},
volume = {21},
number = {4},
pages = {},
pmid = {34415303},
issn = {1536-2442},
support = {31572010//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Bacteria/isolation &amp; purification ; *Coleoptera/microbiology/physiology ; DNA, Bacterial ; Diet ; Female ; *Fertility ; Gastrointestinal Microbiome/*genetics ; Lipid Metabolism ; Male ; Metagenomics ; Ovary/growth &amp; development ; Pest Control ; RNA, Ribosomal, 16S ; Testis/growth &amp; development ; },
abstract = {The gut microbiota of insects usually plays an important role in the development and reproduction of their hosts. The fecundity of Henosepilachna vigintioctopunctata (Fabricius) varies greatly when they develop on different host plants. Whether and how the gut microbiota regulates the fecundity of H. vigintioctopunctata was unknown. To address this question, we used 16S rRNA sequencing to analyze the gut microbiomes of H. vigintioctopunctata adults fed on two host plant species (Solanum nigrum and Solanum melongena) and one artificial diet. The development of the ovaries and testes was also examined. Our results revealed that the diversity and abundance of gut microorganisms varied significantly in insects reared on different diets. The gut microbiota of H. vigintioctopunctata raised on the two host plants was similar, with Proteobacteria being the dominant phylum in both groups, whereas Firmicutes was the dominant phylum in the group reared on the artificial diet. The predominant microbiota in the S. nigrum group were Acinetobacter soli and Acinetobacter ursingii (Acinetobacter, Moraxellaceae); Moraxella osloensis (Enhydrobacter, Moraxellaceae); and Empedobacter brevis (Empedobacter, Weeksellaceae). The microbiota in this group are associated with high lipid metabolism. In addition, the beetles' ovaries and testes were more highly developed in the S. nigrum group than in the other two groups. These findings provide valuable information for elucidating the complex roles the gut microbiota play in the fecundity of H. vigintioctopunctata, and may also contribute to developing future novel control strategies involving this economically important pest.},
}
@article {pmid34411585,
year = {2021},
author = {Didion, EM and Sabree, ZL and Kenyon, L and Nine, G and Hagan, RW and Osman, S and Benoit, JB},
title = {Microbiome reduction prevents lipid accumulation during early diapause in the northern house mosquito, Culex pipiens pipiens.},
journal = {Journal of insect physiology},
volume = {134},
number = {},
pages = {104295},
pmid = {34411585},
issn = {1879-1611},
support = {R01 AI148551/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/genetics/isolation &amp; purification ; Carbohydrate Metabolism ; Culex/metabolism/*microbiology/physiology ; *Diapause, Insect ; Female ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Host Microbial Interactions ; Insect Proteins/metabolism ; *Lipid Metabolism ; Metagenomics/methods ; Microbiota ; RNA, Ribosomal, 16S ; Real-Time Polymerase Chain Reaction/methods ; },
abstract = {The mosquito microbiome is critical to multiple facets of their biology, including larval development and disease transmission. For mosquitoes that reside in temperate regions, periods of diapause are critical to overwintering survival, but how the microbiome impacts this state is unknown. In this study, we compared the midgut microbial communities of diapausing and non-diapausing Culex pipiens and assessed how a reduced midgut microbiome influences diapause preparation. High community variability was found within and between non-diapausing and diapausing individuals, but no specific diapause-based microbiome was noted. Emergence of adult, diapausing mosquitoes under sterile conditions generated low bacterial load (LBL) lines with nearly a 1000-fold reduction in bacteria levels. This reduction in bacterial content resulted in significantly lower survival of diapausing females after two weeks, indicating acquisition of the microbiome in adult females is critical for survival throughout diapause. LBL diapausing females had high carbohydrate levels, but did not accumulate lipid reserves, suggesting an inability to process ingested sugars necessary for diapause-associated lipid accumulation. Expression patterns of select genes associated with mosquito lipid metabolism during diapause showed no significant differences between LBL and control lines, suggesting transcriptional changes may not underlie impaired lipid accumulation. Overall, a diverse, adult-acquired microbiome is critical for diapause in C. pipiens to process sugar reserves and accumulate lipids that are necessary to survive prolonged overwintering.},
}
@article {pmid34408730,
year = {2021},
author = {Xue, CX and Lin, H and Zhu, XY and Liu, J and Zhang, Y and Rowley, G and Todd, JD and Li, M and Zhang, XH},
title = {DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {698286},
pmid = {34408730},
issn = {1664-302X},
abstract = {Metagenomics and metatranscriptomics are powerful methods to uncover key micro-organisms and processes driving biogeochemical cycling in natural ecosystems. Databases dedicated to depicting biogeochemical pathways (for example, metabolism of dimethylsulfoniopropionate (DMSP), which is an abundant organosulfur compound) from metagenomic/metatranscriptomic data are rarely seen. Additionally, a recognized normalization model to estimate the relative abundance and environmental importance of pathways from metagenomic and metatranscriptomic data has not been organized to date. These limitations impact the ability to accurately relate key microbial-driven biogeochemical processes to differences in environmental conditions. Thus, an easy-to-use, specialized tool that infers and visually compares the potential for biogeochemical processes, including DMSP cycling, is urgently required. To solve these issues, we developed DiTing, a tool wrapper to infer and compare biogeochemical pathways among a set of given metagenomic or metatranscriptomic reads in one step, based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and a manually created DMSP cycling gene database. Accurate and specific formulae for over 100 pathways were developed to calculate their relative abundance. Output reports detail the relative abundance of biogeochemical pathways in both text and graphical format. DiTing was applied to simulated metagenomic data and resulted in consistent genetic features of simulated benchmark genomic data. Subsequently, when applied to natural metagenomic and metatranscriptomic data from hydrothermal vents and the Tara Ocean project, the functional profiles predicted by DiTing were correlated with environmental condition changes. DiTing can now be confidently applied to wider metagenomic and metatranscriptomic datasets, and it is available at https://github.com/xuechunxu/DiTing.},
}
@article {pmid34407780,
year = {2021},
author = {Kværner, AS and Birkeland, E and Bucher-Johannessen, C and Vinberg, E and Nordby, JI and Kangas, H and Bemanian, V and Ellonen, P and Botteri, E and Natvig, E and Rognes, T and Hovig, E and Lyle, R and Ambur, OH and de Vos, WM and Bultman, S and Hjartåker, A and Landberg, R and Song, M and Blix, HS and Ursin, G and Randel, KR and de Lange, T and Hoff, G and Holme, Ø and Berstad, P and Rounge, TB},
title = {The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants.},
journal = {BMC cancer},
volume = {21},
number = {1},
pages = {930},
pmid = {34407780},
issn = {1471-2407},
mesh = {Aged ; Case-Control Studies ; Colonoscopy ; Colorectal Neoplasms/*diagnosis/epidemiology/microbiology ; Early Detection of Cancer/*methods ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Incidence ; *Life Style ; Male ; Middle Aged ; Norway/epidemiology ; Occult Blood ; Prognosis ; Prospective Studies ; ROC Curve ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) screening reduces CRC incidence and mortality. However, current screening methods are either hampered by invasiveness or suboptimal performance, limiting their effectiveness as primary screening methods. To aid in the development of a non-invasive screening test with improved sensitivity and specificity, we have initiated a prospective biomarker study (CRCbiome), nested within a large randomized CRC screening trial in Norway. We aim to develop a microbiome-based classification algorithm to identify advanced colorectal lesions in screening participants testing positive for an immunochemical fecal occult blood test (FIT). We will also examine interactions with host factors, diet, lifestyle and prescription drugs. The prospective nature of the study also enables the analysis of changes in the gut microbiome following the removal of precancerous lesions.<br><br>METHODS: The CRCbiome study recruits participants enrolled in the Bowel Cancer Screening in Norway (BCSN) study, a randomized trial initiated in 2012 comparing once-only sigmoidoscopy to repeated biennial FIT, where women and men aged 50-74 years at study entry are invited to participate. Since 2017, participants randomized to FIT screening with a positive test result have been invited to join the CRCbiome study. Self-reported diet, lifestyle and demographic data are collected prior to colonoscopy after the positive FIT-test (baseline). Screening data, including colonoscopy findings are obtained from the BCSN database. Fecal samples for gut microbiome analyses are collected both before and 2 and 12 months after colonoscopy. Samples are analyzed using metagenome sequencing, with taxonomy profiles, and gene and pathway content as primary measures. CRCbiome data will also be linked to national registries to obtain information on prescription histories and cancer relevant outcomes occurring during the 10 year follow-up period.<br><br>DISCUSSION: The CRCbiome study will increase our understanding of how the gut microbiome, in combination with lifestyle and environmental factors, influences the early stages of colorectal carcinogenesis. This knowledge will be crucial to develop microbiome-based screening tools for CRC. By evaluating biomarker performance in a screening setting, using samples from the target population, the generalizability of the findings to future screening cohorts is likely to be high.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01538550 .},
}
@article {pmid34405262,
year = {2021},
author = {Ghosh, S and Pramanik, S},
title = {Structural diversity, functional aspects and future therapeutic applications of human gut microbiome.},
journal = {Archives of microbiology},
volume = {203},
number = {9},
pages = {5281-5308},
pmid = {34405262},
issn = {1432-072X},
support = {BT/PR31826BIC/101/1211/2019//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {*Cyanobacteria ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; },
abstract = {The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.},
}
@article {pmid34393020,
year = {2021},
author = {Robertson, RC and Church, JA and Edens, TJ and Mutasa, K and Min Geum, H and Baharmand, I and Gill, SK and Ntozini, R and Chasekwa, B and Carr, L and Majo, FD and Kirkpatrick, BD and Lee, B and Moulton, LH and Humphrey, JH and Prendergast, AJ and Manges, AR and , },
title = {The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants.},
journal = {Vaccine},
volume = {39},
number = {38},
pages = {5391-5400},
pmid = {34393020},
issn = {1873-2518},
support = {203905/Z/16/Z//Wellcome Trust/United Kingdom ; 206455/Z/17/Z//Wellcome Trust/United Kingdom ; 093768/Z/10/Z//Wellcome Trust/United Kingdom ; 108065/Z/15/Z//Wellcome Trust/United Kingdom ; R01 HD060338/HD/NICHD NIH HHS/United States ; },
mesh = {Antibodies, Viral ; *Gastrointestinal Microbiome ; Humans ; Immunogenicity, Vaccine ; Immunoglobulin A ; Infant ; *Rotavirus/genetics ; *Rotavirus Infections/prevention &amp; control ; *Rotavirus Vaccines ; },
abstract = {BACKGROUND: Oral rotavirus vaccine (RVV) immunogenicity is considerably lower in low- versus high-income populations; however, the mechanisms underlying this remain unclear. Previous evidence suggests that the gut microbiota may contribute to differences in oral vaccine efficacy.<br><br>METHODS: We performed whole metagenome shotgun sequencing on stool samples and measured anti-rotavirus immunoglobulin A in plasma samples from a subset of infants enrolled in a cluster randomized 2 × 2 factorial trial of improved water, sanitation and hygiene and infant feeding in rural Zimbabwe (SHINE trial: NCT01824940). We examined taxonomic microbiome composition and functional metagenome features using random forest models, differential abundance testing and regression analyses to explored associations with RVV immunogenicity.<br><br>RESULTS: Among 158 infants with stool samples and anti-rotavirus IgA titres, 34 were RVV seroconverters. The median age at stool collection was 43 days (IQR: 35-68), corresponding to a median of 4 days before the first RVV dose. The infant microbiome was dominated by Bifidobacterium longum. The gut microbiome differed significantly between early (≤42 days) and later samples (>42 days) however, we observed no meaningful differences in alpha diversity, beta diversity, species composition or functional metagenomic features by RVV seroconversion status. Bacteroides thetaiotaomicron was the only species associated with anti-rotavirus IgA titre. Random forest models poorly classified seroconversion status by both composition and functional microbiome variables.<br><br>CONCLUSIONS: RVV immunogenicity is low in this rural Zimbabwean setting, however it was not associated with the composition or function of the early-life gut microbiome in this study. Further research is warranted to examine the mechanisms of poor oral RVV efficacy in low-income countries.},
}
@article {pmid34389047,
year = {2021},
author = {Xiong, C and Singh, BK and He, JZ and Han, YL and Li, PP and Wan, LH and Meng, GZ and Liu, SY and Wang, JT and Wu, CF and Ge, AH and Zhang, LM},
title = {Plant developmental stage drives the differentiation in ecological role of the maize microbiome.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {171},
pmid = {34389047},
issn = {2049-2618},
mesh = {Bacteria/genetics ; Fungi/genetics ; *Microbiota/genetics ; Plant Roots ; *Zea mays ; },
abstract = {BACKGROUND: Plants live with diverse microbial communities which profoundly affect multiple facets of host performance, but if and how host development impacts the assembly, functions and microbial interactions of crop microbiomes are poorly understood. Here we examined both bacterial and fungal communities across soils, epiphytic and endophytic niches of leaf and root, and plastic leaf of fake plant (representing environment-originating microbes) at three developmental stages of maize at two contrasting sites, and further explored the potential function of phylloplane microbiomes based on metagenomics.<br><br>RESULTS: Our results suggested that plant developmental stage had a much stronger influence on the microbial diversity, composition and interkingdom networks in plant compartments than in soils, with the strongest effect in the phylloplane. Phylloplane microbiomes were co-shaped by both plant growth and seasonal environmental factors, with the air (represented by fake plants) as its important source. Further, we found that bacterial communities in plant compartments were more strongly driven by deterministic processes at the early stage but a similar pattern was for fungal communities at the late stage. Moreover, bacterial taxa played a more important role in microbial interkingdom network and crop yield prediction at the early stage, while fungal taxa did so at the late stage. Metagenomic analyses further indicated that phylloplane microbiomes possessed higher functional diversity at the early stage than the late stage, with functional genes related to nutrient provision enriched at the early stage and N assimilation and C degradation enriched at the late stage. Coincidently, more abundant beneficial bacterial taxa like Actinobacteria, Burkholderiaceae and Rhizobiaceae in plant microbiomes were observed at the early stage, but more saprophytic fungi at the late stage.<br><br>CONCLUSIONS: Our results suggest that host developmental stage profoundly influences plant microbiome assembly and functions, and the bacterial and fungal microbiomes take a differentiated ecological role at different stages of plant development. This study provides empirical evidence for host exerting strong effect on plant microbiomes by deterministic selection during plant growth and development. These findings have implications for the development of future tools to manipulate microbiome for sustainable increase in primary productivity. Video Abstract.},
}
@article {pmid34387940,
year = {2021},
author = {Ruscheweyh, HJ and Milanese, A and Paoli, L and Sintsova, A and Mende, DR and Zeller, G and Sunagawa, S},
title = {mOTUs: Profiling Taxonomic Composition, Transcriptional Activity and Strain Populations of Microbial Communities.},
journal = {Current protocols},
volume = {1},
number = {8},
pages = {e218},
doi = {10.1002/cpz1.218},
pmid = {34387940},
issn = {2691-1299},
mesh = {Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; Software ; },
abstract = {The mOTU profiler, or mOTUs for short, is a software tool that enables the profiling of microbial communities in terms of their taxonomic composition, relative abundance of metabolically active members, and diversity of strain populations. To this end, it maintains a database of single-copy phylogenetic marker gene sequences, which are used as a reference to which short read metagenomic and metatranscriptomic reads are mapped for the identification and quantification of microbial taxa. Here, we describe the most common use cases of the mOTU profiler in two basic protocols. Additional supporting protocols provide information on its installation and in-depth guidance on adjusting its settings for increasing or decreasing the stringency with which taxa are detected and quantified, as well as for customizing the output file format. Guidelines for understanding the profiling results are provided, along with additional information on unique features, methodological details, and the development history of the tool. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Metagenomic and metatranscriptomic mOTU profiling Basic Protocol 2: Metagenomic SNV profiling Support Protocol 1: Installing mOTUs Support Protocol 2: Profiling pipeline-step by step Support Protocol 3: The mOTUs profiling routine using advanced parameters Support Protocol 4: Metagenomic SNV calling: advanced parameters.},
}
@article {pmid34385112,
year = {2021},
author = {Puthusseri, RM and Nair, HP and Johny, TK and Bhat, SG},
title = {Insights into the response of mangrove sediment microbiomes to heavy metal pollution: Ecological risk assessment and metagenomics perspectives.},
journal = {Journal of environmental management},
volume = {298},
number = {},
pages = {113492},
doi = {10.1016/j.jenvman.2021.113492},
pmid = {34385112},
issn = {1095-8630},
mesh = {Environmental Monitoring ; Geologic Sediments ; Metagenomics ; *Metals, Heavy/analysis ; *Microbiota/genetics ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; Wetlands ; },
abstract = {Rapid urbanisation and ensuing anthropogenic pollution lead to an escalated occurrence of heavy metals and metal-resistant bacteria in the soil ecosystem. Mangrove ecosystems are particularly vulnerable to heavy metal bioaccumulation and often act as metal sinks of the coastal areas. As a consequence, the microbial population in mangrove sediments develop multifarious metal tolerance mechanisms to combat metal toxicity. In this context, metagenomic investigation of two mangroves, viz. Mangalavanam and Puthuvypin from the heavily populated metropolitan city, Cochin (Central Kerala, India) was undertaken to discern the metal resistance functions and taxonomic diversity of the microbial consortia. Estimation of heavy metal content using Inductively Coupled Plasma Atomic Emission Spectrometer (ICP-MS) identified the abundance of zinc, chromium, nickel copper, lead, arsenic, and cadmium in the mangrove sediments. Ecological risk index values indicated high cadmium contamination of the two estuarine samples. Whole metagenome shotgun sequencing of the Central Kerala mangroves and comparative analysis with mangrove metal resistomes from other geographical regions revealed the prevalence of cobalt-zinc-cadmium resistance and preponderance of Proteobacteria in all the datasets. Cation efflux system protein CusA constituted the majority of the reads at the function level. Comparative analysis of taxonomy identified the dominance of Anaeromyxobacter, Geobacter, Pseudomonas, Candidatus Solibacter, and Pelobacter in the mangrove datasets. Non-metric multidimensional scaling analysis of the metal resistance genes depicted strong geographical clustering of the function and composition of metal resistant bacteria, suggesting a strong innate resilience of microbiome towards anthropogenic perturbations. More robust studies with intensive sampling will enhance our understanding of the occurrence, interactions, and functions of microbial heavy metal resistome in mangrove ecosystems.},
}
@article {pmid34384948,
year = {2021},
author = {Li, W and Gao, J and Zhuang, JL and Yao, GJ and Zhang, X and Liu, YD and Liu, QK and Shapleigh, JP and Ma, L},
title = {Metagenomics and metatranscriptomics uncover the microbial community associated with high S0 production in a denitrifying desulfurization granular sludge reactor.},
journal = {Water research},
volume = {203},
number = {},
pages = {117505},
doi = {10.1016/j.watres.2021.117505},
pmid = {34384948},
issn = {1879-2448},
mesh = {Bioreactors ; Denitrification ; Metagenomics ; *Microbiota ; Nitrates ; Oxidation-Reduction ; *Sewage ; Sulfides ; },
abstract = {The denitrification desulfurization process is a promising technology for elemental sulfur (S0) production from sulfide containing wastewater. However, the microbial community associated with high S0 production still is not well studied. This study describes an efficient denitrification S0 production bioreactor based on inoculation with anaerobic granular sludge. At an optimal S/N molar ratio of 7:2, 80 % of the influent sulfide was transformed to high quality elemental sulfur with a purity of 92.5% while the total inorganic nitrogen removal efficiency was stable at ∼80%. Metatranscriptomic analysis found that community expression of the gene encoding the sulfide-quinone reductase (SQR) was 10-fold greater than that of the flavocytochrome-c sulfide dehydrogenase subunit B (fccB). Moreover, the expression level of SQR was also significantly higher than the Dsr gene encoding for dissimilatory sulfate reductase, which encodes a critical S0 oxidation enzyme. Metagenomic binning analysis confirmed that sulfide-oxidizing bacteria (SOB) utilizing SQR were common in the community and most likely accounted for high S0 production. An unexpected enrichment in methanogens and high expression activity of bacteria carrying out Stickland fermentation as well as in other bacteria with reduced genomes indicated a complex community supporting stable sulfide oxidation to S0, likely aiding in performance stability. This study establishes this treatment approach as an alternative biotechnology for sulfide containing wastewater treatment and sheds light on the microbial interactions associated with high S0 production.},
}
@article {pmid34381036,
year = {2021},
author = {Stražar, M and Temba, GS and Vlamakis, H and Kullaya, VI and Lyamuya, F and Mmbaga, BT and Joosten, LAB and van der Ven, AJAM and Netea, MG and de Mast, Q and Xavier, RJ},
title = {Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {4845},
pmid = {34381036},
issn = {2041-1723},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Arginine/metabolism ; Bacteria/immunology/isolation &amp; purification/metabolism ; Cytokines/*immunology ; Diet ; Female ; Gastrointestinal Microbiome/immunology/*physiology ; Histidine/metabolism ; Humans ; Immunomodulation ; Male ; Metabolic Networks and Pathways ; Metabolome/immunology ; *Rural Population ; Socioeconomic Factors ; Tanzania ; *Urban Population ; Urbanization ; },
abstract = {The human gut microbiota is increasingly recognized as an important factor in modulating innate and adaptive immunity through release of ligands and metabolites that translocate into circulation. Urbanizing African populations harbor large intestinal diversity due to a range of lifestyles, providing the necessary variation to gauge immunomodulatory factors. Here, we uncover a gradient of intestinal microbial compositions from rural through urban Tanzanian, towards European samples, manifested both in relative abundance and genomic variation observed in stool metagenomics. The rural population shows increased Bacteroidetes, led by Prevotella copri, but also presence of fungi. Measured ex vivo cytokine responses were significantly associated with 34 immunomodulatory microbes, which have a larger impact on circulating metabolites than non-significant microbes. Pathway effects on cytokines, notably TNF-α and IFN-γ, differential metabolome analysis and enzyme copy number enrichment converge on histidine and arginine metabolism as potential immunomodulatory pathways mediated by Bifidobacterium longum and Akkermansia muciniphila.},
}
@article {pmid34380279,
year = {2021},
author = {Liang, H and Wang, F and Mu, R and Huang, J and Zhao, R and Li, X and Yu, K and Li, B},
title = {Metagenomics analysis revealing the occurrence of antibiotic resistome in salt lakes.},
journal = {The Science of the total environment},
volume = {790},
number = {},
pages = {148262},
doi = {10.1016/j.scitotenv.2021.148262},
pmid = {34380279},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Lakes ; *Metagenomics ; *Microbiota ; },
abstract = {Although antimicrobial resistance genes (ARGs) in dozens of environments have been well documented, the distribution of ARGs in salt lake ecosystems has been less intensively investigated. In this study, the broad-spectrum ARG profiles, microbial community composition and the comprehensive associations between microbiome and antimicrobial resistome in four salt lakes were investigated using a metagenomic approach. A total of 175 ARG subtypes affiliated with 19 ARG types were detected, and ARGs conferring resistance to multidrug, bacitracin, and macrolide-lincosamide-streptogramin (MLS) accounted for 71.2% of the total ARG abundance. However, the abundance of ARGs significantly decreased with the increasing salinity in the lakes. Both ARG profiles and microbial community structure presented remarkable discrepancies in different lakes, as well as in different sample types. Microbes such as genera Azoarcus, Aeromonas, Pseudomonas, and Kocuria, significantly co-occurred with multiple ARGs, indicating that these bacteria are potential ARG hosts in salt lake ecosystems. Collectively, this work provides new insights into the occurrence and distribution of ARGs in salt lake ecosystems.},
}
@article {pmid34378990,
year = {2021},
author = {Murphy, SMC and Bautista, MA and Cramm, MA and Hubert, CRJ},
title = {Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {20},
pages = {e0080021},
pmid = {34378990},
issn = {1098-5336},
support = {//Alberta Innovates - Technology Futures (AITF)/ ; //ArcticNet/ ; //Association of Canadian Universities for Northern Studies (ACUNS)/ ; //Genome Alberta/ ; //Genome Canada (Génome Canada)/ ; //Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Marine Environmental Observation Prediction and Response Network (MEOPAR)/ ; //W. Garfield Weston Foundation/ ; },
mesh = {Adaptation, Physiological ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Cold Temperature ; Geologic Sediments/*microbiology ; Hydrocarbons/metabolism ; *Microbiota/genetics ; Newfoundland and Labrador ; Petroleum/*metabolism ; Petroleum Pollution ; RNA, Ribosomal, 16S/genetics ; Water Pollutants/*metabolism ; },
abstract = {Oil spills in the subarctic marine environment off the coast of Labrador, Canada, are increasingly likely due to potential oil production and increases in ship traffic in the region. To understand the microbiome response and how nutrient biostimulation promotes biodegradation of oil spills in this cold marine setting, marine sediment microcosms amended with diesel or crude oil were incubated at in situ temperature (4°C) for several weeks. Sequencing of 16S rRNA genes following these spill simulations revealed decreased microbial diversity and enrichment of putative hydrocarbonoclastic bacteria that differed depending on the petroleum product. Metagenomic sequencing revealed that the genus Paraperlucidibaca harbors previously unrecognized capabilities for alkane biodegradation, which were also observed in Cycloclasticus. Genomic and amplicon sequencing together suggest that Oleispira and Thalassolituus degraded alkanes from diesel, while Zhongshania and the novel PGZG01 lineage contributed to crude oil alkane biodegradation. Greater losses in PAHs from crude oil than from diesel were consistent with Marinobacter, Pseudomonas_D, and Amphritea genomes exhibiting aromatic hydrocarbon biodegradation potential. Biostimulation with nitrogen and phosphorus (4.67 mM NH4Cl and 1.47 mM KH2PO4) was effective at enhancing n-alkane and PAH degradation following low-concentration (0.1% [vol/vol]) diesel and crude oil amendments, while at higher concentrations (1% [vol/vol]) only n-alkanes in diesel were consumed, suggesting toxicity induced by compounds in unrefined crude oil. Biostimulation allowed for a more rapid shift in the microbial community in response to petroleum amendments, more than doubling the rates of CO2 increase during the first few weeks of incubation. IMPORTANCE Increases in transportation of diesel and crude oil in the Labrador Sea will pose a significant threat to remote benthic and shoreline environments, where coastal communities and wildlife are particularly vulnerable to oil spill contaminants. Whereas marine microbiology has not been incorporated into environmental assessments in the Labrador Sea, there is a growing demand for microbial biodiversity evaluations given the pronounced impact of climate change in this region. Benthic microbial communities are important to consider given that a fraction of spilled oil typically sinks such that its biodegradation occurs at the seafloor, where novel taxa with previously unrecognized potential to degrade hydrocarbons were discovered in this work. Understanding how cold-adapted microbiomes catalyze hydrocarbon degradation at low in situ temperature is crucial in the Labrador Sea, which remains relatively cold throughout the year.},
}
@article {pmid34378953,
year = {2021},
author = {Casar, CP and Momper, LM and Kruger, BR and Osburn, MR},
title = {Iron-Fueled Life in the Continental Subsurface: Deep Mine Microbial Observatory, South Dakota, USA.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {20},
pages = {e0083221},
pmid = {34378953},
issn = {1098-5336},
support = {80NSSC18K1267/NASA/NASA/United States ; NNH14ZDA001N//National Aeronautics and Space Administration (NASA)/ ; },
mesh = {Bacteria ; Geological Phenomena ; Iron/*metabolism ; Metagenome ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S ; South Dakota ; },
abstract = {Iron-bearing minerals are key components of the Earth's crust and potentially critical energy sources for subsurface microbial life. The Deep Mine Microbial Observatory (DeMMO) is situated in a range of iron-rich lithologies, and fracture fluids here reach concentrations as high as 8.84 mg/liter. Iron cycling is likely an important process, given the high concentrations of iron in fracture fluids and detection of putative iron-cycling taxa via marker gene surveys. However, a previous metagenomic survey detected no iron cycling potential at two DeMMO localities. Here, we revisited the potential for iron cycling at DeMMO using a new metagenomic data set including all DeMMO sites and FeGenie, a new annotation pipeline that is optimized for the detection of iron cycling genes. We annotated functional genes from whole metagenomic assemblies and metagenome-assembled genomes and characterized putative iron cycling pathways and taxa in the context of local geochemical conditions and available metabolic energy estimated from thermodynamic models. We reannotated previous metagenomic data, revealing iron cycling potential that was previously missed. Across both metagenomic data sets, we found that not only is there genetic potential for iron cycling at DeMMO, but also, iron is likely an important source of energy across the system. In response to the dramatic differences we observed between annotation approaches, we recommend the use of optimized pipelines where the detection of iron cycling genes is a major goal. IMPORTANCE We investigated iron cycling potential among microbial communities inhabiting iron-rich fracture fluids to a depth of 1.5 km in the continental crust. A previous study found no iron cycling potential in the communities despite the iron-rich nature of the system. A new tool for detecting iron cycling genes was recently published, which we used on a new data set. We combined this with a number of other approaches to get a holistic view of metabolic strategies across the communities, revealing iron cycling to be an important process here. In addition, we used the tool on the data from the previous study, revealing previously missed iron cycling potential. Iron is common in continental crust; thus, our findings are likely not unique to our study site. Our new view of important metabolic strategies underscores the importance of choosing optimized tools for detecting the potential for metabolisms like iron cycling that may otherwise be missed.},
}
@article {pmid34375790,
year = {2021},
author = {Pan, Y and Zheng, X and Xiang, Y},
title = {Structure-function elucidation of a microbial consortium in degrading rice straw and producing acetic and butyric acids via metagenome combining 16S rDNA sequencing.},
journal = {Bioresource technology},
volume = {340},
number = {},
pages = {125709},
doi = {10.1016/j.biortech.2021.125709},
pmid = {34375790},
issn = {1873-2976},
mesh = {Butyrates ; DNA, Ribosomal ; Fermentation ; Lignin/metabolism ; Metagenome ; *Microbial Consortia ; *Oryza/metabolism ; },
abstract = {The characterized microbial consortium can efficiently degrade rice straw to produce acetic and butyric acids in high yields. The rice straw lost 86.9% in weight and degradation rates of hemicellulose, cellulose, and lignin attained were 97.1%, 86.4% and 70.3% within 12 days, respectively. During biodegradation via fermentation of rice straw, average concentrations of acetic and butyric acids reached 1570 mg/L and 1270 mg/L, accounting for 47.2% and 35.4% of the total volatile fatty acids, respectively. The consortium mainly composed of Prevotella, Cellulosilyticum, Pseudomonas, Clostridium and Ruminococcaceae, etc. Metagenomic analyses indicated that glycoside hydrolases (GHs) were the largest enzyme group with a relative abundance of 54.5%. Various lignocellulose degrading enzymes were identified in the top 30 abundant GHs, and were primarily distributed in the dominant genera (Prevotella, Cellulosilyticum and Clostridium). These results provide a new route for the commercial recycling of rice straw to produce organic acids.},
}
@article {pmid34372602,
year = {2021},
author = {Zakham, F and Albalawi, AE and Alanazi, AD and Truong Nguyen, P and Alouffi, AS and Alaoui, A and Sironen, T and Smura, T and Vapalahti, O},
title = {Viral RNA Metagenomics of Hyalomma Ticks Collected from Dromedary Camels in Makkah Province, Saudi Arabia.},
journal = {Viruses},
volume = {13},
number = {7},
pages = {},
pmid = {34372602},
issn = {1999-4915},
mesh = {Animals ; Camelus ; Humans ; Metagenomics/*methods ; RNA, Viral/*genetics ; Saudi Arabia ; Tick-Borne Diseases/prevention &amp; control/*virology ; Ticks/*virology ; Virome/*genetics ; Viruses/classification/*genetics/isolation &amp; purification ; },
abstract = {Arthropod-borne infections are a medical and economic threat to humans and livestock. Over the last three decades, several unprecedented viral outbreaks have been recorded in the Western part of the Arabian Peninsula. However, little is known about the circulation and diversity of arthropod-borne viruses in this region. To prepare for new outbreaks of vector-borne diseases, it is important to detect which viruses circulate in each vector population. In this study, we used a metagenomics approach to characterize the RNA virome of ticks infesting dromedary camels (Camelus dromedaries) in Makkah province, Saudi Arabia. Two hundred ticks of species Hyalomma dromedarii (n = 196) and Hyalomma impeltatum (n = 4) were collected from the Alkhurma district in Jeddah and Al-Taif city. Virome analysis showed the presence of several tick-specific viruses and tick-borne viruses associated with severe illness in humans. Some were identified for the first time in the Arabian Peninsula. The human disease-associated viruses detected included Crimean Congo Hemorrhagic fever virus and Tamdy virus (family Nairoviridae), Guertu virus (family Phenuiviridae), and a novel coltivirus that shares similarities with Tarumizu virus, Tai forest reovirus and Kundal virus (family Reoviridae). Furthermore, Alkhurma hemorrhagic virus (Flaviviridae) was detected in two tick pools by specific qPCR. In addition, tick-specific viruses in families Phenuiviridae (phleboviruses), Iflaviridae, Chuviridae, Totiviridae and Flaviviridae (Pestivirus) were detected. The presence of human pathogenetic viruses warrants further efforts in tick surveillance, xenosurveillence, vector control, and sero-epidemiological investigations in human and animal populations to predict, contain and mitigate future outbreaks in the region.},
}
@article {pmid34371435,
year = {2021},
author = {Balasubramanian, VK and Joseph Maran, MI and Ramteke, D and Vijaykumar, DS and Kottarathail Rajendran, A and Ramachandran, P and Ramachandran, R},
title = {Environmental DNA reveals aquatic biodiversity of an urban backwater area, southeast coast of India.},
journal = {Marine pollution bulletin},
volume = {171},
number = {},
pages = {112786},
doi = {10.1016/j.marpolbul.2021.112786},
pmid = {34371435},
issn = {1879-3363},
mesh = {Biodiversity ; DNA Barcoding, Taxonomic ; *DNA, Environmental ; Ecosystem ; Environmental Monitoring ; Humans ; India ; },
abstract = {Strong conservation management needs comprehensive data on biodiversity. Rapid methods that document aquatic biodiversity or assess the health condition of an ecosystem remain scarce. Herein, we have performed a metagenomics study on environmental DNA (eDNA) collected from an urban backwater area - Muttukadu, located in the southeast coast of India. Shotgun metagenomics approach using Illumina®NextSeq500 sequencing yielded 88.4 million raw reads. The processed data was assigned as 80% prokaryotes, 0.4% eukaryotes, ~2% viruses, and ~17% remain unknown. This approach has the potential to identify small micro-eukaryote, unseen species from both estuarine and marine environments. We have identified 156 eukaryote organisms represented from 21 phyla and 112 families, including those that are of conservational significance and ecological importance. Furthermore, our data also demonstrated the presence of pathogenic microorganisms due to sewage mixing with the backwaters. Given its sensitivity, we suggest this approach for an initial assessment of biodiversity structure in an ecosystem for the biomonitoring program.},
}
@article {pmid34367134,
year = {2021},
author = {Hetemäki, I and Jian, C and Laakso, S and Mäkitie, O and Pajari, AM and de Vos, WM and Arstila, TP and Salonen, A},
title = {Fecal Bacteria Implicated in Biofilm Production Are Enriched and Associate to Gastrointestinal Symptoms in Patients With APECED - A Pilot Study.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {668219},
pmid = {34367134},
issn = {1664-3224},
mesh = {Adult ; Aged ; Antibodies, Fungal/metabolism ; Bacteria/genetics/*growth &amp; development/immunology/metabolism ; Biofilms/*growth &amp; development ; Case-Control Studies ; Dysbiosis ; Feces/*microbiology ; Female ; Finland ; Gastrointestinal Diseases/diagnosis/immunology/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Genetic Predisposition to Disease ; Host-Pathogen Interactions ; Humans ; Immunoglobulin G/metabolism ; Intestines/*microbiology ; Lipopolysaccharides/metabolism ; Male ; Metagenome ; Middle Aged ; *Mutation ; Pilot Projects ; Polyendocrinopathies, Autoimmune/complications/diagnosis/genetics/immunology ; Saccharomyces cerevisiae/genetics/immunology ; Transcription Factors/*genetics ; Young Adult ; },
abstract = {Backgrounds and Aims: APECED is a rare autoimmune disease caused by mutations in the Autoimmune Regulator gene. A significant proportion of patients also have gastrointestinal symptoms, including malabsorption, chronic diarrhea, and obstipation. The pathological background of the gastrointestinal symptoms remains incompletely understood and involves multiple factors, with autoimmunity being the most common underlying cause. Patients with APECED have increased immune responses against gut commensals. Our objective was to evaluate whether the intestinal microbiota composition, predicted functions or fungal abundance differ between Finnish patients with APECED and healthy controls, and whether these associate to the patients' clinical phenotype and gastrointestinal symptoms.<br><br>Methods: DNA was isolated from fecal samples from 15 patients with APECED (median age 46.4 years) together with 15 samples from body mass index matched healthy controls. DNA samples were subjected to analysis of the gut microbiota using 16S rRNA gene amplicon sequencing, imputed metagenomics using the PICRUSt2 algorithm, and quantitative PCR for fungi. Extensive correlations of the microbiota with patient characteristics were determined.<br><br>Results: Analysis of gut microbiota indicated that both alpha- and beta-diversity were altered in patients with APECED compared to healthy controls. The fraction of Faecalibacterium was reduced in patients with APECED while that of Atopobium spp. and several gram-negative genera previously implicated in biofilm formation, e.g. Veillonella, Prevotella, Megasphaera and Heamophilus, were increased in parallel to lipopolysaccharide (LPS) synthesis in imputed metagenomics. The differences in gut microbiota were linked to patient characteristics, especially the presence of anti-Saccharomyces cerevisiae antibodies (ASCA) and severity of gastrointestinal symptoms.<br><br>Conclusions: Gut microbiota of patients with APECED is altered and enriched with predominantly gram-negative bacterial taxa that may promote biofilm formation and lead to increased exposure to LPS in the patients. The most pronounced alterations in the microbiota were associated with more severe gastrointestinal symptoms.},
}
@article {pmid34362459,
year = {2021},
author = {Roth-Schulze, AJ and Penno, MAS and Ngui, KM and Oakey, H and Bandala-Sanchez, E and Smith, AD and Allnutt, TR and Thomson, RL and Vuillermin, PJ and Craig, ME and Rawlinson, WD and Davis, EA and Harris, M and Soldatos, G and Colman, PG and Wentworth, JM and Haynes, A and Barry, SC and Sinnott, RO and Morahan, G and Bediaga, NG and Smyth, GK and Papenfuss, AT and Couper, JJ and Harrison, LC and , },
title = {Type 1 diabetes in pregnancy is associated with distinct changes in the composition and function of the gut microbiome.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {167},
pmid = {34362459},
issn = {2049-2618},
mesh = {*Diabetes Mellitus, Type 1/microbiology ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Intestines ; Metagenome ; Pregnancy ; Pregnancy in Diabetics/*microbiology ; },
abstract = {BACKGROUND: The gut microbiome changes in response to a range of environmental conditions, life events and disease states. Pregnancy is a natural life event that involves major physiological adaptation yet studies of the microbiome in pregnancy are limited and their findings inconsistent. Pregnancy with type 1 diabetes (T1D) is associated with increased maternal and fetal risks but the gut microbiome in this context has not been characterized. By whole metagenome sequencing (WMS), we defined the taxonomic composition and function of the gut bacterial microbiome across 70 pregnancies, 36 in women with T1D.<br><br>RESULTS: Women with and without T1D exhibited compositional and functional changes in the gut microbiome across pregnancy. Profiles in women with T1D were distinct, with an increase in bacteria that produce lipopolysaccharides and a decrease in those that produce short-chain fatty acids, especially in the third trimester. In addition, women with T1D had elevated concentrations of fecal calprotectin, a marker of intestinal inflammation, and serum intestinal fatty acid-binding protein (I-FABP), a marker of intestinal epithelial damage.<br><br>CONCLUSIONS: Women with T1D exhibit a shift towards a more pro-inflammatory gut microbiome during pregnancy, associated with evidence of intestinal inflammation. These changes could contribute to the increased risk of pregnancy complications in women with T1D and are potentially modifiable by dietary means. Video abstract.},
}
@article {pmid34361900,
year = {2021},
author = {Panaiotov, S and Hodzhev, Y and Tsafarova, B and Tolchkov, V and Kalfin, R},
title = {Culturable and Non-Culturable Blood Microbiota of Healthy Individuals.},
journal = {Microorganisms},
volume = {9},
number = {7},
pages = {},
pmid = {34361900},
issn = {2076-2607},
support = {DN-01-4/16.12.2016//Bulgarian National Science Fund/ ; KP-06-DV/10-21.12.2019//Bulgarian National Science Fund/ ; },
abstract = {Next-generation sequencing (NGS) and metagenomics revolutionized our capacity for analysis and identification of the microbial communities in complex samples. The existence of a blood microbiome in healthy individuals has been confirmed by sequencing, but some researchers suspect that this is a cell-free circulating DNA in blood, while others have had isolated a limited number of bacterial and fungal species by culture. It is not clear what part of the blood microbiota could be resuscitated and cultured. Here, we quantitatively measured the culturable part of blood microbiota of healthy individuals by testing a medium supplemented with a high concentration of vitamin K (1 mg/mL) and culturing at 43 °C for 24 h. We applied targeted sequencing of 16S rDNA and internal transcribed spacer (ITS) markers on cultured and non-cultured blood samples from 28 healthy individuals. Dominant bacterial phyla among non-cultured samples were Proteobacteria 92.97%, Firmicutes 2.18%, Actinobacteria 1.74% and Planctomycetes 1.55%, while among cultured samples Proteobacteria were 47.83%, Firmicutes 25.85%, Actinobacteria 16.42%, Bacteroidetes 3.48%, Cyanobacteria 2.74%, and Fusobacteria 1.53%. Fungi phyla Basidiomycota, Ascomycota, and unidentified fungi were 65.08%, 17.72%, and 17.2% respectively among non-cultured samples, while among cultured samples they were 58.08%, 21.72%, and 20.2% respectively. In cultured and non-cultured samples we identified 241 OTUs belonging to 40 bacterial orders comprising 66 families and 105 genera. Fungal biodiversity accounted for 272 OTUs distributed in 61 orders, 105 families, and 133 genera. Bacterial orders that remained non-cultured, compared to blood microbiota isolated from fresh blood collection, were Sphingomonadales, Rhizobiales, and Rhodospirillales. Species of orders Bacillales, Lactobacillales, and Corynebacteriales showed the best cultivability. Fungi orders Tremellales, Polyporales, and Filobasidiales were mostly unculturable. Species of fungi orders Pleosporales, Saccharomycetales, and Helotiales were among the culturable ones. In this study, we quantified the capacity of a specific medium applied for culturing of blood microbiota in healthy individuals. Other culturing conditions and media should be tested for optimization and better characterization of blood microbiota in healthy and diseased individuals.},
}
@article {pmid34356622,
year = {2021},
author = {Torrell, H and Cereto-Massagué, A and Kazakova, P and García, L and Palacios, H and Canela, N},
title = {Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization.},
journal = {Biomolecules},
volume = {11},
number = {7},
pages = {},
pmid = {34356622},
issn = {2218-273X},
mesh = {*Bacteria/classification/genetics/growth &amp; development ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Male ; RNA, Bacterial/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {BACKGROUND: The human intestinal microbiome plays a central role in overall health status, especially in early life stages. 16S rRNA amplicon sequencing is used to profile its taxonomic composition; however, multiomic approaches have been proposed as the most accurate methods for study of the complexity of the gut microbiota. In this study, we propose an optimized method for bacterial diversity analysis that we validated and complemented with metabolomics by analyzing fecal samples.<br><br>METHODS: Forty-eight different analytical combinations regarding (1) 16S rRNA variable region sequencing, (2) a feature selection approach, and (3) taxonomy assignment methods were tested. A total of 18 infant fecal samples grouped depending on the type of feeding were analyzed by the proposed 16S rRNA workflow and by metabolomic analysis.<br><br>RESULTS: The results showed that the sole use of V4 region sequencing with ASV identification and VSEARCH for taxonomy assignment produced the most accurate results. The application of this workflow showed clear differences between fecal samples according to the type of feeding, which correlated with changes in the fecal metabolic profile.<br><br>CONCLUSION: A multiomic approach using real fecal samples from 18 infants with different types of feeding demonstrated the effectiveness of the proposed 16S rRNA-amplicon sequencing workflow.},
}
@article {pmid34352595,
year = {2021},
author = {Lin, W and Djukovic, A and Mathur, D and Xavier, JB},
title = {Listening in on the conversation between the human gut microbiome and its host.},
journal = {Current opinion in microbiology},
volume = {63},
number = {},
pages = {150-157},
doi = {10.1016/j.mib.2021.07.009},
pmid = {34352595},
issn = {1879-0364},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; },
abstract = {The gut microbiome is an ecosystem. Natural selection favored microbes fit for the gut, which can utilize and convert molecules produced by the host for their own benefit. But natural selection also favored the host's mechanisms to sense and respond to the microbial ecosystem for its own benefit. We can listen in on the host-microbiome 'conversation' in the simultaneous responses of the microbiome and the host to strong perturbations. In laboratory animals a perturbation can be done for research; in human patients a perturbation can be caused by disease or therapy. Advances in metagenomics, metabolomics and computation amplify our means to listen in on the conversation between the gut microbiome and its host.},
}
@article {pmid34352239,
year = {2021},
author = {Frizzera, A and Bojko, J and Cremonte, F and Vázquez, N},
title = {Symbionts of invasive and native crabs, in Argentina: The most recently invaded area on the Southwestern Atlantic coastline.},
journal = {Journal of invertebrate pathology},
volume = {184},
number = {},
pages = {107650},
doi = {10.1016/j.jip.2021.107650},
pmid = {34352239},
issn = {1096-0805},
mesh = {Animals ; Argentina ; Brachyura/*parasitology/*physiology ; *Host-Parasite Interactions ; Introduced Species ; *Symbiosis ; Trematoda/*physiology ; },
abstract = {Biological invasions have the capacity to introduce non-native parasites. This study aimed to determine whether the invasive green crab population, Carcinus spp., on the Southwestern Atlantic coast of Argentina harbours any symbionts, and whether these may spillover or spillback between native crabs, Cyrtograpsus altimanus and C. angulatus. Macroscopy, histology, and molecular analyses of some parasites were used to describe and compare their diversity across the three species of crab. We also evaluated the susceptibility of invasive Carcinus spp. to a native digenean, Maritrema madrynense, via experimental infections (exposure and cohabitation). Our results revealed that the green crab pathobiome included similar symbiotic groups to native crabs. This included putative viral, bacterial, and protozoan parasites. Haplosporidium-like observations were recorded in all crab species, and a single green crab was found to be parasitized by an Agmasoma-like microsporidium. Metagenomic analysis of one individual revealed additional symbiotic diversity (46 bacteria, 5 eukaryotic species). The green crabs were infected by more microparasite taxa than the native crabs (5:3). Wild populations of Carcinus spp. were free of metazoan parasites and are shown not to be susceptible to M. madryense under experimental conditions. Our results suggest a reduction/escape of macroparasites (trematode Maritrema madrynense; acanthocephalan Profilicollis chasmagnathi) in invasive Carcinus spp. compared to their native competitors.},
}
@article {pmid34351018,
year = {2021},
author = {Paul, LJ and Ericsson, AC and Andrews, FM and Keowen, ML and Morales Yniguez, F and Garza, F and Banse, HE},
title = {Gastric microbiome in horses with and without equine glandular gastric disease.},
journal = {Journal of veterinary internal medicine},
volume = {35},
number = {5},
pages = {2458-2464},
pmid = {34351018},
issn = {1939-1676},
support = {//LSU Equine Health Studies Program Charles V. Cusimano Grant/ ; },
mesh = {Animals ; Gastric Mucosa ; *Gastrointestinal Microbiome ; *Horse Diseases ; Horses ; RNA, Ribosomal, 16S/genetics ; *Stomach Diseases/veterinary ; *Stomach Ulcer/veterinary ; },
abstract = {BACKGROUND: The role of the gastric microbiome in development or persistence of equine glandular gastric disease (EGGD) remains to be investigated.<br><br>HYPOTHESIS/OBJECTIVES: The objective was to characterize the glandular mucosal and gastric fluid microbiomes of horses with and without EGGD. It was hypothesized that differences in the mucosal microbiome are associated with EGGD.<br><br>ANIMALS: Twenty-four horses were enrolled.<br><br>METHODS: Gastroscopy was performed and EGGD scores recorded (score 0, n = 6; score 1, n = 8; score ≥2, n = 10). Gastric fluid and pinch biopsies of healthy glandular mucosa and EGGD lesions were collected via gastroscope. 16S rRNA amplicon sequencing of the gastric fluid and glandular mucosal biopsies was performed. Relationships between gastric fluid and mucosal microbial community composition were evaluated among EGGD score groups (EGGD 0-BX, EGGD 1-BX, EGGD ≥2-BX) and among endoscopic appearances: controls from horses without EGGD and normal areas, hyperemic areas, and lesions from horses with EGGD.<br><br>RESULTS: Microbial community structure of mucosal biopsies differed among EGGD score groups (Jaccard similarity index; P = .009). Principal coordinate analysis showed separate clusters for EGGD 0-BX and EGGD ≥2-BX.<br><br>A modest difference was detected in the community structure of the gastric glandular mucosal microbiome in association with EGGD score.},
}
@article {pmid34346741,
year = {2021},
author = {Breitkreuz, C and Heintz-Buschart, A and Buscot, F and Wahdan, SFM and Tarkka, M and Reitz, T},
title = {Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils.},
journal = {Microbiology spectrum},
volume = {9},
number = {1},
pages = {e0027821},
pmid = {34346741},
issn = {2165-0497},
abstract = {Computational approaches that link bacterial 16S rRNA gene amplicon data to functional genes based on prokaryotic reference genomes have emerged. This study aims to validate or refute the applicability of the functional gene prediction tools for assessment and comparison of community functionality among experimental treatments, inducing either fast or slow responses in rhizosphere microbial community composition and function. Rhizosphere samples of wheat and barley were collected in two consecutive years at active and mature growth phases from organic and conventional farming plots with ambient or future-climate treatments of the Global Change Experimental Facility. Bacterial community composition was determined by 16S rRNA gene amplicon sequencing, and the activities of five extracellular enzymes involved in carbon (β-glucosidases, cellobiohydrolase, and xylosidase), nitrogen (N-acetylglucosaminidase), and phosphorus (acid phosphatase) cycles were determined. Structural community data were used to predict functional patterns of the rhizosphere communities using Tax4Fun and PanFP. Subsequently, the predictions were compared with the measured activities. Despite the fact that different treatments mainly drove either community composition (plant growth phase) or measured enzyme activities (farming system), the predictions mirrored patterns in the treatments in a qualitative but not quantitative way. Most of the discrepancies between measured and predicted values resulted from plant growth stages (fast community response), followed by farming management and climate (slower community response). Thus, our results suggest the applicability of the prediction tools for comparative investigations of soil community functionality in less-dynamic environmental systems. IMPORTANCE Linking soil microbial community structure to its functionality, which is important for maintaining health and services of an ecosystem, is still challenging. Besides great advances in structural community analysis, functional equivalents, such as metagenomics and metatranscriptomics, are still time and cost intensive. Recent computational approaches (Tax4Fun and PanFP) aim to predict functions from structural community data based on reference genomes. Although the usability of these tools has been confirmed with metagenomic data, a comparison between predicted and measured functions is so far missing. Thus, this study comprises an expansive reality test on the performance of these tools under different environmental conditions, including relevant global change factors (land use and climate). The work provides a valuable validation of the applicability of the prediction tools for comparison of soil community functions across different sufficiently established soil ecosystems and suggest their usability to unravel the broad spectrum of functions provided by a given community structure.},
}
@article {pmid34344959,
year = {2021},
author = {Rouchka, EC and Chariker, JH and Alejandro, B and Adcock, RS and Singhal, R and Ramirez, J and Palmer, KE and Lasnik, AB and Carrico, R and Arnold, FW and Furmanek, S and Zhang, M and Wolf, LA and Waigel, S and Zacharias, W and Bordon, J and Chung, D},
title = {Induction of interferon response by high viral loads at early stage infection may protect against severe outcomes in COVID-19 patients.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15715},
pmid = {34344959},
issn = {2045-2322},
support = {P20 GM103436/GM/NIGMS NIH HHS/United States ; },
mesh = {Adult ; Aged ; COVID-19/*pathology/virology ; Dysbiosis/etiology ; Female ; Humans ; Interferons/*metabolism ; Male ; Metagenomics ; Microbiota/genetics ; Middle Aged ; Nasopharynx/virology ; RNA, Viral/analysis ; Real-Time Polymerase Chain Reaction ; Respiratory System/microbiology/virology ; SARS-CoV-2/*genetics/isolation &amp; purification ; Severity of Illness Index ; Transcriptome ; Up-Regulation ; Viral Load ; },
abstract = {Key elements for viral pathogenesis include viral strains, viral load, co-infection, and host responses. Several studies analyzing these factors in the function of disease severity of have been published; however, no studies have shown how all of these factors interplay within a defined cohort. To address this important question, we sought to understand how these four key components interplay in a cohort of COVID-19 patients. We determined the viral loads and gene expression using high throughput sequencing and various virological methods. We found that viral loads in the upper respiratory tract in COVID-19 patients at an early phase of infection vary widely. While the majority of nasopharyngeal (NP) samples have a viral load lower than the limit of detection of infectious viruses, there are samples with an extraordinary amount of SARS-CoV-2 RNA and a high viral titer. No specific viral factors were identified that are associated with high viral loads. Host gene expression analysis showed that viral loads were strongly correlated with cellular antiviral responses. Interestingly, however, COVID-19 patients who experience mild symptoms have a higher viral load than those with severe complications, indicating that naso-pharyngeal viral load may not be a key factor of the clinical outcomes of COVID-19. The metagenomics analysis revealed that the microflora in the upper respiratory tract of COVID-19 patients with high viral loads were dominated by SARS-CoV-2, with a high degree of dysbiosis. Finally, we found a strong inverse correlation between upregulation of interferon responses and disease severity. Overall our study suggests that a high viral load in the upper respiratory tract may not be a critical factor for severe symptoms; rather, dampened antiviral responses may be a critical factor for a severe outcome from the infection.},
}
@article {pmid34341379,
year = {2021},
author = {Bel Lassen, P and Belda, E and Prifti, E and Dao, MC and Specque, F and Henegar, C and Rinaldi, L and Wang, X and Kennedy, SP and Zucker, JD and Calame, W and Lamarche, B and Claus, SP and Clément, K},
title = {Protein supplementation during an energy-restricted diet induces visceral fat loss and gut microbiota amino acid metabolism activation: a randomized trial.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15620},
pmid = {34341379},
issn = {2045-2322},
mesh = {Adult ; *Caloric Restriction ; Double-Blind Method ; *Gastrointestinal Microbiome ; Humans ; Intra-Abdominal Fat ; Male ; *Metagenomics ; Weight Loss ; },
abstract = {Interactions between diet and gut microbiota are critical regulators of energy metabolism. The effects of fibre intake have been deeply studied but little is known about the impact of proteins. Here, we investigated the effects of high protein supplementation (Investigational Product, IP) in a double blind, randomised placebo-controled intervention study (NCT01755104) where 107 participants received the IP or an isocaloric normoproteic comparator (CP) alongside a mild caloric restriction. Gut microbiota profiles were explored in a patient subset (n = 53) using shotgun metagenomic sequencing. Visceral fat decreased in both groups (IP group: - 20.8 ± 23.2 cm2; CP group: - 14.5 ± 24.3 cm2) with a greater reduction (p < 0.05) with the IP supplementation in the Per Protocol population. Microbial diversity increased in individuals with a baseline low gene count (p < 0.05). The decrease in weight, fat mass and visceral fat mass significantly correlated with the increase in microbial diversity (p < 0.05). Protein supplementation had little effects on bacteria composition but major differences were seen at functional level. Protein supplementation stimulated bacterial amino acid metabolism (90% amino-acid synthesis functions enriched with IP versus 13% in CP group (p < 0.01)). Protein supplementation alongside a mild energy restriction induces visceral fat mass loss and an activation of gut microbiota amino-acid metabolism.Clinical trial registration: NCT01755104 (24/12/2012). https://clinicaltrials.gov/ct2/show/record/NCT01755104?term=NCT01755104&amp;draw=2&amp;rank=1 .},
}
@article {pmid34336713,
year = {2021},
author = {Caddey, B and De Buck, J},
title = {Meta-Analysis of Bovine Digital Dermatitis Microbiota Reveals Distinct Microbial Community Structures Associated With Lesions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {685861},
pmid = {34336713},
issn = {2235-2988},
mesh = {Animals ; Cattle ; *Cattle Diseases ; *Digital Dermatitis ; Metagenomics ; *Microbiota ; Treponema/genetics ; },
abstract = {Bovine digital dermatitis (DD) is a significant cause of infectious lameness and economic losses in cattle production across the world. There is a lack of a consensus across different 16S metagenomic studies on DD-associated bacteria that may be potential pathogens of the disease. The goal of this meta-analysis was to identify a consistent group of DD-associated bacteria in individual DD lesions across studies, regardless of experimental design choices including sample collection and preparation, hypervariable region sequenced, and sequencing platform. A total of 6 studies were included in this meta-analysis. Raw sequences and metadata were identified on the NCBI sequence read archive and European nucleotide archive. Bacterial community structures were investigated between normal skin and DD skin samples. Random forest models were generated to classify DD status based on microbial composition, and to identify taxa that best differentiate DD status. Among all samples, members of Treponema, Mycoplasma, Porphyromonas, and Fusobacterium were consistently identified in the majority of DD lesions, and were the best genera at differentiating DD lesions from normal skin. Individual study and 16S hypervariable region sequenced had significant influence on final DD lesion microbial composition (P < 0.05). These findings indicate that members of Treponema, Mycoplasma, Porphyromonas, and/or Fusobacterium may have significant roles in DD pathogenesis, and should be studied further in respect to elucidating DD etiopathogenic mechanisms and developing more effective treatment and mitigation strategies.},
}
@article {pmid34332366,
year = {2021},
author = {Font-Verdera, F and Liébana, R and Aldeguer-Riquelme, B and Gangloff, V and Santos, F and Viver, T and Rosselló-Móra, R},
title = {Inverted microbial community stratification and spatial-temporal stability in hypersaline anaerobic sediments from the S'Avall solar salterns.},
journal = {Systematic and applied microbiology},
volume = {44},
number = {5},
pages = {126231},
doi = {10.1016/j.syapm.2021.126231},
pmid = {34332366},
issn = {1618-0984},
mesh = {Anaerobiosis ; *Archaea/classification/metabolism ; *Bacteria/classification/metabolism ; Geologic Sediments ; Methane ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; Spatio-Temporal Analysis ; },
abstract = {The anaerobic hypersaline sediments of an ephemeral pond from the S'Avall solar salterns constituted an excellent study system because of their easy accessibility, as well as the analogy of their microbial assemblages with some known deep-sea hypersaline anaerobic brines. By means of shotgun metagenomics and 16S rRNA gene amplicon sequencing, the microbial composition of the sediment was shown to be stable in time and space. The communities were formed by prokaryote representatives with a clear inferred anaerobic metabolism, mainly related to the methane, sulfur and nitrate cycles. The most conspicuous finding was the inverted nature of the vertical stratification. Contrarily to what could be expected, a methanogenic archaeal metabolism was found to dominate in the upper layers, whereas Bacteria with fermentative and anaerobic respiration metabolisms increased with depth. We could demonstrate the methanogenic nature of the members of candidate lineages DHVE2 and MSBL1, which were present in high abundance in this system, and described, for the first time, viruses infecting these lineages. Members of the putatively active aerobic genera Salinibacter and Halorubrum were detected especially in the deepest layers for which we hypothesize that either oxygen could be sporadically available, or they could perform anaerobic metabolisms. We also report a novel repertoire of virus species thriving in these sediments, which had special relevance because of their lysogenic lifestyles.},
}
@article {pmid34330336,
year = {2021},
author = {Hiseni, P and Rudi, K and Wilson, RC and Hegge, FT and Snipen, L},
title = {HumGut: a comprehensive human gut prokaryotic genomes collection filtered by metagenome data.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {165},
pmid = {34330336},
issn = {2049-2618},
mesh = {*Gastrointestinal Microbiome/genetics ; Genome, Human ; Humans ; *Metagenome ; Metagenomics ; },
abstract = {BACKGROUND: A major bottleneck in the use of metagenome sequencing for human gut microbiome studies has been the lack of a comprehensive genome collection to be used as a reference database. Several recent efforts have been made to re-construct genomes from human gut metagenome data, resulting in a huge increase in the number of relevant genomes. In this work, we aimed to create a collection of the most prevalent healthy human gut prokaryotic genomes, to be used as a reference database, including both MAGs from the human gut and ordinary RefSeq genomes.<br><br>RESULTS: We screened > 5,700 healthy human gut metagenomes for the containment of > 490,000 publicly available prokaryotic genomes sourced from RefSeq and the recently announced UHGG collection. This resulted in a pool of > 381,000 genomes that were subsequently scored and ranked based on their prevalence in the healthy human metagenomes. The genomes were then clustered at a 97.5% sequence identity resolution, and cluster representatives (30,691 in total) were retained to comprise the HumGut collection. Using the Kraken2 software for classification, we find superior performance in the assignment of metagenomic reads, classifying on average 94.5% of the reads in a metagenome, as opposed to 86% with UHGG and 44% when using standard Kraken2 database. A coarser HumGut collection, consisting of genomes dereplicated at 95% sequence identity-similar to UHGG, classified 88.25% of the reads. HumGut, half the size of standard Kraken2 database and directly comparable to the UHGG size, outperforms them both.<br><br>CONCLUSIONS: The HumGut collection contains > 30,000 genomes clustered at a 97.5% sequence identity resolution and ranked by human gut prevalence. We demonstrate how metagenomes from IBD-patients map equally well to this collection, indicating this reference is relevant also for studies well outside the metagenome reference set used to obtain HumGut. All data and metadata, as well as helpful code, are available at http://arken.nmbu.no/~larssn/humgut/ . Video Abstract.},
}
@article {pmid34329005,
year = {2021},
author = {Li, J and Jia, C and Lu, Q and Hungate, BA and Dijkstra, P and Wang, S and Wu, C and Chen, S and Li, D and Shim, H},
title = {Mechanistic insights into the success of xenobiotic degraders resolved from metagenomes of microbial enrichment cultures.},
journal = {Journal of hazardous materials},
volume = {418},
number = {},
pages = {126384},
doi = {10.1016/j.jhazmat.2021.126384},
pmid = {34329005},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Xenobiotics ; },
abstract = {Even though microbial communities can be more effective at degrading xenobiotics than cultured micro-organisms, yet little is known about the microbial strategies that underpin xenobiotic biodegradation by microbial communities. Here, we employ metagenomic community sequencing to explore the mechanisms that drive the development of 49 xenobiotic-degrading microbial communities, which were enriched from 7 contaminated soils or sediments with a range of xenobiotic compounds. We show that multiple microbial strategies likely drive the development of xenobiotic degrading communities, notably (i) presence of genes encoding catabolic enzymes to degrade xenobiotics; (ii) presence of genes encoding efflux pumps; (iii) auxiliary catabolic genes on plasmids; and (iv) positive interactions dominate microbial communities with efficient degradation. Overall, the integrated analyses of microbial ecological strategies advance our understanding of microbial processes driving the biodegradation of xenobiotics and promote the design of bioremediation systems.},
}
@article {pmid34328924,
year = {2021},
author = {Fu, X and Ou, Z and Zhang, M and Meng, Y and Li, Y and Chen, Q and Jiang, J and Zhang, X and Norbäck, D and Zhao, Z and Sun, Y},
title = {Classroom microbiome, functional pathways and sick-building syndrome (SBS) in urban and rural schools - Potential roles of indoor microbial amino acids and vitamin metabolites.},
journal = {The Science of the total environment},
volume = {795},
number = {},
pages = {148879},
doi = {10.1016/j.scitotenv.2021.148879},
pmid = {34328924},
issn = {1879-1026},
mesh = {*Air Pollution, Indoor/analysis ; Amino Acids ; *Asthma ; Humans ; *Microbiota ; Propionibacteriaceae ; Schools ; *Sick Building Syndrome ; Vitamins ; },
abstract = {Sick building symptoms (SBS) are defined as non-specific symptoms related to indoor exposures, including mucosal symptoms in eye, nose, throat, and skin, and general symptoms as headache and tiredness. Indoor microbial composition is associated with SBS symptoms, but the impact of microbial functional genes and potential metabolic products has not been characterized. We conducted a shotgun microbial metagenomic sequencing for vacuum dust collected in urban and rural schools in Shanxi province, China. SBS symptoms in students were surveyed, and microbial taxa and functional pathways related to the symptoms were identified using a multi-level linear regression model. SBS symptoms were common in students, and the prevalence of ocular and throat symptoms, headache, and tiredness was higher in urban than in rural areas (p < 0.05). A significant higher microbial α-diversity was found in rural areas than in urban areas (Chao1, p = 0.001; ACE, p = 0.002). Also, significant variation in microbial taxonomic and functional composition (β-diversity) was observed between urban and rural areas (p < 0.005). Five potential risk Actinobacteria species were associated with SBS symptoms (p < 0.01); students in the classrooms with a higher abundance of an unclassified Geodermatophilaceae, Geodermatophilus, Fridmanniella luteola, Microlunatus phosphovorus and Mycetocola reported more nasal and throat symptoms and tiredness. Students with a higher abundance of an unclassified flavobacteriaceae reported fewer throat symptoms and tiredness. The abundance of microbial metabolic pathways related to the synthesis of B vitamins (biotin and folate), gamma-aminobutyric acid (GABA), short-chain fatty acids (SCFAs), and peptidoglycan and were protectively (negatively) associated with SBS symptoms (FDR < 0.05). The result is consistent with human microbiota studies, which reported that these microbial products are extensively involved in immunological processes and anti-inflammatory effects. This is the first study to report the functional potential of the indoor microbiome and the occurrence of SBS, providing new insights into the potential etiologic mechanisms in chronic inflammatory diseases.},
}
@article {pmid34325201,
year = {2021},
author = {Wang, M and Sun, Y and Zeng, Z and Wang, Z},
title = {Metagenomics of wastewater phageome identifies an extensively cored antibiotic resistome in a swine feedlot water treatment environment.},
journal = {Ecotoxicology and environmental safety},
volume = {222},
number = {},
pages = {112552},
doi = {10.1016/j.ecoenv.2021.112552},
pmid = {34325201},
issn = {1090-2414},
mesh = {Animals ; Anti-Bacterial Agents ; Genes, Bacterial ; *Metagenomics ; Swine ; Virome ; Waste Water ; *Water Purification ; },
abstract = {Huge number of antibiotic resistance genes (ARGs) have been widely detected in phage genomes from anthropogenic environment or animal farms, whereas little is known about the dynamic changes of phage contribution to resistance under a feedlot wastewater treatment facility (WTF) pressure. Here, a metagenomics method was used to characterize the sewage phageome and identifies the antibiotic resistome. The results showed that the phage families of Siphoviridae, Myoviridae, and Podoviridae were always the most dominant. Analysis of ARGs carried by bacterial and phages showed that MLS and tetracycline resistance genes always had the highest abundances and the other ARG types also have a fixed hierarchy, showing that there is no significant change in overall ARGs abundance distribution. However, an extensively cored antibiotic resistome were specifically identified in aerobic environment. ARGs encoding ribosomal protection proteins, especially for the ARG subtypes lsaE, tet44, tetM, tetP, macB, MdlB and rpoB2, were more inclined to be selected by phages, suggesting that a more refined mechanism, such as specialized transduction and lateral transduction, was probably involved. In all, these results suggest that monitoring of dynamic changes of phage contribution to resistance should be given more attention and ARGs-carrying phage management should focus on using technologies for controlling cored ARGs rather than only the overall distribution of ARGs in phages.},
}
@article {pmid34312531,
year = {2021},
author = {Wippel, K and Tao, K and Niu, Y and Zgadzaj, R and Kiel, N and Guan, R and Dahms, E and Zhang, P and Jensen, DB and Logemann, E and Radutoiu, S and Schulze-Lefert, P and Garrido-Oter, R},
title = {Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota.},
journal = {Nature microbiology},
volume = {6},
number = {9},
pages = {1150-1162},
pmid = {34312531},
issn = {2058-5276},
mesh = {Arabidopsis/microbiology/*physiology ; Bacteria/classification/genetics/*isolation &amp; purification ; Bacterial Physiological Phenomena ; Lotus/microbiology/*physiology ; *Microbiota ; Plant Roots/*microbiology/physiology ; Soil Microbiology ; *Symbiosis ; },
abstract = {Roots of different plant species are colonized by bacterial communities, that are distinct even when hosts share the same habitat. It remains unclear to what extent the host actively selects these communities and whether commensals are adapted to a specific plant species. To address this question, we assembled a sequence-indexed bacterial culture collection from roots and nodules of Lotus japonicus that contains representatives of most species previously identified using metagenomics. We analysed taxonomically paired synthetic communities from L. japonicus and Arabidopsis thaliana in a multi-species gnotobiotic system and detected signatures of host preference among commensal bacteria in a community context, but not in mono-associations. Sequential inoculation experiments revealed priority effects during root microbiota assembly, where established communities are resilient to invasion by latecomers, and that host preference of commensal bacteria confers a competitive advantage in their cognate host. Our findings show that host preference in commensal bacteria from diverse taxonomic groups is associated with their invasiveness into standing root-associated communities.},
}
@article {pmid34302348,
year = {2021},
author = {Dong, X and Zhang, C and Li, W and Weng, S and Song, W and Li, J and Wang, Y},
title = {Functional diversity of microbial communities in inactive seafloor sulfide deposits.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {8},
pages = {},
doi = {10.1093/femsec/fiab108},
pmid = {34302348},
issn = {1574-6941},
mesh = {Bacteria/genetics ; *Hydrothermal Vents ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfides ; },
abstract = {The seafloor sulfide structures of inactive vents are known to host abundant and diverse microorganisms potentially supported by mineralogy of sulfides. However, little is known about the diversity and distribution of microbial functions. Here, we used genome-resolved metagenomics to predict microbial metabolic functions and the contribution of horizontal gene transfer to the functionality of microorganisms inhabiting several hydrothermally inactive seafloor deposits among globally distributed deep-sea vent fields. Despite of geographically distant vent fields, similar microbial community patterns were observed with the dominance of Gammaproteobacteria, Bacteroidota and previously overlooked Candidatus Patescibacteria. Metabolically flexible Gammaproteobacteria are major potential primary producers utilizing mainly sulfur, iron and hydrogen as electron donors coupled with oxygen and nitrate respiration for chemolithoautotrophic growth. In addition to heterotrophic microorganisms like free-living Bacteroidota, Ca. Patescibacteria potentially perform fermentative recycling of organic carbon. Finally, we provided evidence that many functional genes that are central to energy metabolism have been laterally transferred among members within the community and largely within the same class. Taken together, these findings shed light on microbial ecology and evolution in inactive seafloor sulfide deposits after the cessation of hydrothermal activities.},
}
@article {pmid34301347,
year = {2021},
author = {Gerb, SA and Dashek, RJ and Ericsson, AC and Griffin, R and Franklin, CL},
title = {The Effects of Ketamine on the Gut Microbiome on CD1 Mice.},
journal = {Comparative medicine},
volume = {71},
number = {4},
pages = {295-301},
pmid = {34301347},
issn = {1532-0820},
support = {T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; },
mesh = {Animals ; Feces ; Female ; *Gastrointestinal Microbiome ; *Ketamine/pharmacology ; Mice ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; },
abstract = {The intestinal microbiota of an organism can significantly alter outcome data in otherwise identical experiments. Occasionally, animals may require sedation or anesthesia for scientific or health-related purposes, and certain anesthetics, such as ketamine, can profoundly affect the gastrointestinal system. While many factors can alter the gut microbiome (GM), the effects of anesthetics on the composition or diversity of the GM have not been established. The goal of the current study was to determine whether daily administration of ketamine would significantly alter the microbiome of CD1 mice. To achieve this goal, female CD1 mice received daily injections of ketamine HCl (100 mg/kg) or the equivalent volume of 0.9% saline for 10 consecutive days. Fecal samples were collected before the first administration and 24 h after the final dose of either ketamine or saline. Samples were analyzed by 16S rRNA sequencing to identify changes between groups in diversity or composition of GM. The study found no significant changes to the GM after serial ketamine administration when treated mice were housed with controls. Therefore, ketamine administration is unlikely to alter the GM of a CD1 mouse and should not serve be a confounding factor in reproducibility of research.},
}
@article {pmid34299675,
year = {2021},
author = {Su Mun, L and Wye Lum, S and Kong Yuiin Sze, G and Hock Yoong, C and Ching Yung, K and Kah Lok, L and Gopinath, D},
title = {Association of Microbiome with Oral Squamous Cell Carcinoma: A Systematic Review of the Metagenomic Studies.},
journal = {International journal of environmental research and public health},
volume = {18},
number = {14},
pages = {},
pmid = {34299675},
issn = {1660-4601},
mesh = {*Carcinoma, Squamous Cell ; *Head and Neck Neoplasms ; Humans ; Metagenomics ; *Microbiota ; *Mouth Neoplasms ; Squamous Cell Carcinoma of Head and Neck ; },
abstract = {The past decade has witnessed a surge in epidemiological studies that have explored the relationship between the oral microbiome and oral cancer. Owing to the diversity of the published data, a comprehensive systematic overview of the currently available evidence is critical. This review summarises the current evidence on the metagenomic studies on the oral microbiome in oral cancer. A systematic search was conducted in Medline and Embase databases to identify original studies examining the differences in the oral microbiome of oral cancer cases and controls. A total of twenty-six studies were identified that reported differences in microbial abundance between oral squamous cell carcinoma (OSCC) and controls. Although almost all the studies identified microbial dysbiosis to be associated with oral cancer, the detailed qualitative analysis did not reveal the presence/abundance of any individual bacteria or a consortium to be consistently enriched in OSCC samples across the studies. Interestingly, few studies reported a surge of periodontopathogenic taxa, especially Fusobacteria, whereas others demonstrated a depletion of commensal taxa Streptococci. Considerable heterogeneity could be identified in the parameters used for designing the studies as well as reporting the microbial data. If microbiome data needs to be translated in the future, to complement the clinical parameters for diagnosis and prognosis of oral cancer, further studies with the integration of clinical variables, adequate statistical power, reproducible methods, and models are required.},
}
@article {pmid34294835,
year = {2021},
author = {Wingfield, B and Lapsley, C and McDowell, A and Miliotis, G and McLafferty, M and O'Neill, SM and Coleman, S and McGinnity, TM and Bjourson, AJ and Murray, EK},
title = {Variations in the oral microbiome are associated with depression in young adults.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15009},
pmid = {34294835},
issn = {2045-2322},
mesh = {Adolescent ; Adult ; Age Factors ; Bacteria/genetics ; *Biodiversity ; Case-Control Studies ; Depression/diagnosis/*etiology ; Female ; *Host Microbial Interactions ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mouth/*microbiology ; Saliva/microbiology ; Young Adult ; },
abstract = {A growing body of evidence supports an important role for alterations in the brain-gut-microbiome axis in the aetiology of depression and other psychiatric disorders. The potential role of the oral microbiome in mental health has received little attention, even though it is one of the most diverse microbiomes in the body and oral dysbiosis has been linked to systemic diseases with an underlying inflammatory aetiology. This study examines the structure and composition of the salivary microbiome for the first time in young adults who met the DSM-IV criteria for depression (n = 40) and matched controls (n = 43) using 16S rRNA gene-based next generation sequencing. Subtle but significant differences in alpha and beta diversity of the salivary microbiome were observed, with clear separation of depressed and healthy control cohorts into distinct clusters. A total of 21 bacterial taxa were found to be differentially abundant in the depressed cohort, including increased Neisseria spp. and Prevotella nigrescens, while 19 taxa had a decreased abundance. In this preliminary study we have shown that the composition of the oral microbiome is associated with depression in young adults. Further studies are now warranted, particuarly investigations into whether such shifts play any role in the underling aetiology of depression.},
}
@article {pmid34294810,
year = {2021},
author = {Verspecht, T and Van Holm, W and Boon, N and Bernaerts, K and Daep, CA and Zayed, N and Quirynen, M and Teughels, W},
title = {Comparison of the modulatory effects of three structurally similar potential prebiotic substrates on an in vitro multi-species oral biofilm.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15033},
pmid = {34294810},
issn = {2045-2322},
mesh = {Biodiversity ; *Biofilms/drug effects/growth &amp; development ; Host Microbial Interactions ; Metagenome ; Metagenomics/methods ; Microbiota ; Mouth/*microbiology ; Prebiotics/*administration &amp; dosage ; Virulence/genetics ; },
abstract = {Previous research identified potential prebiotic substrates for oral health like the structural analogues N-acetyl-D-mannosamine (NADM) and N-acetyl-D-glucosamine (NADG). The main hypothesis of the current study was twofold. Firstly, it was hypothesized that the modulatory effects of NADM are not limited to changes in multi-species oral biofilm composition, but also include effects on metabolism, virulence, and inflammatory potential. Secondly, the presence and orientation of their N-acetyl group could play a role. Therefore, a comparison was made between the effects of NADM, NADG and D-(+)-mannose on multi-species oral biofilms. Besides a beneficial compositional shift, NADM-treated biofilms also showed an altered metabolism, a reduced virulence and a decreased inflammatory potential. At a substrate concentration of 1 M, these effects were pronounced for all biofilm aspects, whereas at ~ 0.05 M (1%(w/v)) only the effects on virulence were pronounced. When comparing between substrates, both the presence and orientation of the N-acetyl group played a role. However, this was generally only at 1 M and dependent on the biofilm aspect. Overall, NADM was found to have different effects at two concentrations that beneficially modulate in vitro multi-species oral biofilm composition, metabolism, virulence and inflammatory potential. The presence and orientation of the N-acetyl group influenced these effects.},
}
@article {pmid34294783,
year = {2021},
author = {Zhong, H and Zhang, J and Li, F and Chen, J},
title = {Gut microbial communities associated with phenotypically divergent populations of the striped stem borer Chilo suppressalis (Walker, 1863).},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {15010},
pmid = {34294783},
issn = {2045-2322},
mesh = {Animals ; *Biodiversity ; Computational Biology/methods ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/methods ; Moths/*microbiology ; Oryza/parasitology ; Plant Diseases ; RNA, Ribosomal, 16S ; },
abstract = {Chilo suppressalis (Walker, 1863) is a serious stem borer of rice and water-oat plants, and has phenotypically diverged into rice and water-oat populations. Insect gut microbiota plays an important role in the host life and understanding the dynamics of this complicated ecosystem may improve its biological control. The effect of diet and gut compartments on the gut microflora of divergent populations of C. suppressalis is not fully clear. Herein, we characterized the gut microbiota of C. suppressalis populations fed on two hosts (i.e., water-oats fruit pulps and rice seedlings), by sequencing the V3-V4 hypervariable region of the 16S rRNA gene using the Illumina MiSeq platform. Gut bacterial communities showed variation in relative abundance among C. suppressalis populations fed on water-oats fruit pulps or rice seedlings. Proteobacteria and Firmicutes became the predominant phyla, and Enterobacteriaceae, Enterococcaceae and Halomonadaceae were the predominant family in all C. suppressalis populations. The highest bacteria diversity was found in the midgut of the rice population fed on water-oat fruit pulps. Bacterial communities in the midgut were more diverse than those in the hindgut. The bacterial genera distribution showed great differences due to diet types and gut compartments among populations. Our results demonstrated that the host plants tested had a considerable impact on gut bacterial composition of C. suppressalis populations. Additionly, the unique gut morphology and physiological conditions (viz., oxygen content, enzymes) also contributed to variation in microbiomes. In conclusion, our study provided an important insight into investigation of insect-bacteria symbioses, and biocontrol of this species and other related lepidopterans.},
}
@article {pmid34294041,
year = {2021},
author = {Andrade, BGN and Goris, T and Afli, H and Coutinho, FH and Dávila, AMR and Cuadrat, RRC},
title = {Putative mobilized colistin resistance genes in the human gut microbiome.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {220},
pmid = {34294041},
issn = {1471-2180},
abstract = {BACKGROUND: The high incidence of bacterial genes that confer resistance to last-resort antibiotics, such as colistin, caused by mobilized colistin resistance (mcr) genes, poses an unprecedented threat to human health. Understanding the spread, evolution, and distribution of such genes among human populations will help in the development of strategies to diminish their occurrence. To tackle this problem, we investigated the distribution and prevalence of potential mcr genes in the human gut microbiome using a set of bioinformatics tools to screen the Unified Human Gastrointestinal Genome (UHGG) collection for the presence, synteny and phylogeny of putative mcr genes, and co-located antibiotic resistance genes.<br><br>RESULTS: A total of 2079 antibiotic resistance genes (ARGs) were classified as mcr genes in 2046 metagenome assembled genomes (MAGs), distributed across 1596 individuals from 41 countries, of which 215 were identified in plasmidial contigs. The genera that presented the largest number of mcr-like genes were Suterella and Parasuterella. Other potential pathogens carrying mcr genes belonged to the genus Vibrio, Escherichia and Campylobacter. Finally, we identified a total of 22,746 ARGs belonging to 21 different classes in the same 2046 MAGs, suggesting multi-resistance potential in the corresponding bacterial strains, increasing the concern of ARGs impact in the clinical settings.<br><br>CONCLUSION: This study uncovers the diversity of mcr-like genes in the human gut microbiome. We demonstrated the cosmopolitan distribution of these genes in individuals worldwide and the co-presence of other antibiotic resistance genes, including Extended-spectrum Beta-Lactamases (ESBL). Also, we described mcr-like genes fused to a PAP2-like domain in S. wadsworthensis. These novel sequences increase our knowledge about the diversity and evolution of mcr-like genes. Future research should focus on activity, genetic mobility and a potential colistin resistance in the corresponding strains to experimentally validate those findings.},
}
@article {pmid34294039,
year = {2021},
author = {Zhang, Z and Zhang, L},
title = {METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs.},
journal = {BMC bioinformatics},
volume = {22},
number = {Suppl 10},
pages = {378},
pmid = {34294039},
issn = {1471-2105},
support = {HKBU 22201419//Early Career Scheme/ ; IRCMS/19-20/D02//Hong Kong Baptist University/ ; 2019A1515011046//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Algorithms ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Software ; },
abstract = {BACKGROUND: Due to the complexity of microbial communities, de novo assembly on next generation sequencing data is commonly unable to produce complete microbial genomes. Metagenome assembly binning becomes an essential step that could group the fragmented contigs into clusters to represent microbial genomes based on contigs' nucleotide compositions and read depths. These features work well on the long contigs, but are not stable for the short ones. Contigs can be linked by sequence overlap (assembly graph) or by the paired-end reads aligned to them (PE graph), where the linked contigs have high chance to be derived from the same clusters.<br><br>RESULTS: We developed METAMVGL, a multi-view graph-based metagenomic contig binning algorithm by integrating both assembly and PE graphs. It could strikingly rescue the short contigs and correct the binning errors from dead ends. METAMVGL learns the two graphs' weights automatically and predicts the contig labels in a uniform multi-view label propagation framework. In experiments, we observed METAMVGL made use of significantly more high-confidence edges from the combined graph and linked dead ends to the main graph. It also outperformed many state-of-the-art contig binning algorithms, including MaxBin2, MetaBAT2, MyCC, CONCOCT, SolidBin and GraphBin on the metagenomic sequencing data from simulation, two mock communities and Sharon infant fecal samples.<br><br>CONCLUSIONS: Our findings demonstrate METAMVGL outstandingly improves the short contig binning and outperforms the other existing contig binning tools on the metagenomic sequencing data from simulation, mock communities and infant fecal samples.},
}
@article {pmid34290346,
year = {2021},
author = {de la Cruz Peña, MJ and Gonzalez-Granado, LI and Garcia-Heredia, I and Carballa, LM and Martinez-Garcia, M},
title = {Minimal-moderate variation of human oral virome and microbiome in IgA deficiency.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14913},
pmid = {34290346},
issn = {2045-2322},
mesh = {Adolescent ; Adult ; Aged ; Child ; Female ; Humans ; IgA Deficiency/*microbiology/*virology ; Immunoglobulin A/physiology ; Immunoglobulin M/deficiency ; Male ; Metagenomics ; *Microbiota/genetics ; Middle Aged ; Mouth/*microbiology/*virology ; Saliva/microbiology/virology ; *Virome/genetics ; Young Adult ; },
abstract = {Immunoglobulin A (IgA) is the dominant antibody found in our mucosal secretions and has long been recognized to play an important role in protecting our epithelium from pathogens. Recently, IgA has been shown to be involved in gut homeostatic regulation by 'recognizing' and shaping our commensal microbes. Paradoxically, yet selective IgA-deficiency is often described as asymptomatic and there is a paucity of studies only focused on the mice and human gut microbiome context fully ignoring other niches of our body and our commensal viruses. Here, we used as a model the human oral cavity and employed a holistic view and studied the impact of IgA deficiency and also common variable IgA and IgM immunodeficiencies (CVID), on both the human virome and microbiome. Unexpectedly, metagenomic and experimental data in human IgA deficiency and CVID indicate minimal-moderate changes in microbiome and virome composition compared to healthy control group and point out to a rather functional, resilient oral commensal viruses and microbes. However, a significant depletion (two fold) of bacterial cells (p-value < 0.01) and viruses was observed in IgA-deficiency. Our results demonstrate that, within the limits of our cohort, IgA role is not critical for maintaining a rather functional salivary microbiome and suggest that IgA is not a major influence on the composition of abundant commensal microbes.},
}
@article {pmid34290321,
year = {2021},
author = {Sun, S and Zhu, X and Huang, X and Murff, HJ and Ness, RM and Seidner, DL and Sorgen, AA and Blakley, IC and Yu, C and Dai, Q and Azcarate-Peril, MA and Shrubsole, MJ and Fodor, AA},
title = {On the robustness of inference of association with the gut microbiota in stool, rectal swab and mucosal tissue samples.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14828},
pmid = {34290321},
issn = {2045-2322},
support = {R01CA149633/NH/NIH HHS/United States ; R03CA183019/NH/NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; UL1 TR000445/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents ; Anti-Inflammatory Agents, Non-Steroidal ; Bacteria/*classification/*isolation &amp; purification ; Body Mass Index ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/*microbiology ; Male ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Rectum/*microbiology ; Sex Factors ; },
abstract = {The gut microbiota plays an important role in human health and disease. Stool, rectal swab and rectal mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. In this study, we report differences in stool, rectal swab and rectal mucosal tissue microbial communities with shotgun metagenome sequencing of 1397 stool, swab and mucosal tissue samples from 240 participants. The taxonomic composition of stool and swab samples was distinct, but less different to each other than mucosal tissue samples. Functional profile differences between stool and swab samples are smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or rectal swab gave broadly significantly correlated results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for determination of how inference can change for taxa and pathways depending on the choice of where to sample within the human gut.},
}
@article {pmid34287529,
year = {2021},
author = {Baima, DC and Carvalho, NS and Barbuti, RC and Navarro-Rodriguez, T},
title = {ASSESSMENT OF THE INTESTINAL MICROBIOTA IN ADULTS WITH EROSIVE ESOPHAGITIS.},
journal = {Arquivos de gastroenterologia},
volume = {58},
number = {2},
pages = {168-174},
doi = {10.1590/S0004-2803.202100000-29},
pmid = {34287529},
issn = {1678-4219},
mesh = {Adolescent ; Adult ; Dysbiosis ; *Esophagitis ; Feces ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {BACKGROUND: The intestinal microbiota influences the appropriate function of the gastrointestinal tract. Intestinal dysbiosis may be associated with a higher risk of esophageal lesions, mainly due to changes in gastroesophageal motility patterns, elevation of intra-abdominal pressure, and increased frequency of transient relaxation of the lower esophageal sphincter.<br><br>OBJECTIVE: The aim of this study was to evaluate the intestinal microbiota in individuals with erosive esophagitis and in healthy individuals using metagenomics.<br><br>METHODS: A total of 22 fecal samples from adults aged between 18 and 60 years were included. Eleven individuals had esophagitis (eight men and three women) and 11 were healthy controls (10 men and one woman). The individuals were instructed to collect and store fecal material into a tube containing guanidine solution. The DNA of the microbiota was extracted from each fecal samples and PCR amplification was performed using primers for the V4 region of the 16S rRNA gene. The amplicons were sequenced using the Ion Torrent PGM platform and the data were analyzed using the QIIME™ software version 1.8. Statistical analyses were performed using the Mann-Whitney non-parametric test and the ANOSIM non-parametric method based on distance matrix.<br><br>RESULTS: The alpha-diversity and beta-diversity indices were similar between the two groups, without statistically significant differences. There was no statistically significant difference in the phylum level. However, a statistically significant difference was observed in the abundance of the family Clostridiaceae (0.3% vs 2.0%, P=0.032) and in the genus Faecaliumbacterium (10.5% vs 4.5%, P=0.045) between healthy controls and esophagitis patients.<br><br>CONCLUSION: The findings suggest that reduced abundance of the genus Faecaliumbacterium and greater abundance of the family Clostridiaceae may be risk factors for the development of erosive esophagitis. Intervention in the composition of the intestinal microbiota should be considered as an adjunct to current therapeutic strategies for this clinical condition.},
}
@article {pmid34287254,
year = {2021},
author = {Agrawal, R and Ajami, NJ and Malhotra, S and Chen, L and White, DL and Sharafkhaneh, A and Hoffman, KL and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L},
title = {Habitual Sleep Duration and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Pilot Study.},
journal = {Clocks &amp; sleep},
volume = {3},
number = {3},
pages = {387-397},
pmid = {34287254},
issn = {2624-5175},
support = {CX001430.//U.S. Department of Veterans Affairs/ ; I01 CX001430/CX/CSRD VA/United States ; R01CA172880/CA/NCI NIH HHS/United States ; RP#140767//Cancer Prevention and Research Institute of Texas/ ; CIN13-413//the Houston Veterans Affairs Health Services Research Center of Innovations/ ; 0000//Golfers Against Cancer Organization/ ; 0000//Gillson Longenbaugh Foundation/ ; },
abstract = {We examined the association between the colonic adherent microbiota and nocturnal sleep duration in humans. In a cross-sectional study, 63 polyp-free adults underwent a colonoscopy and donated 206 mucosal biopsies. The gut microbiota was profiled using the 16S rRNA gene sequencing targeting the V4 region. The sequence reads were processed using UPARSE and DADA2, respectively. Lifestyle factors, including sleep habits, were obtained using an interviewer-administered questionnaire. We categorized the participants into short sleepers (<6 h per night; n = 16) and normal sleepers (6-8 h per night; n = 47) based on self-reported data. Differences in bacterial biodiversity and the taxonomic relative abundance were compared between short vs. normal sleepers, followed by multivariable analysis. A false discovery rate-adjusted p value (q value) < 0.05 indicated statistical significance. The bacterial community composition differed in short and normal sleepers. The relative abundance of Sutterella was significantly lower (0.38% vs. 1.25%) and that of Pseudomonas was significantly higher (0.14% vs. 0.08%) in short sleepers than in normal sleepers (q values < 0.01). The difference was confirmed in the multivariable analysis. Nocturnal sleep duration was associated with the bacterial community composition and structure in the colonic gut microbiota in adults.},
}
@article {pmid34287009,
year = {2021},
author = {Aljabr, W and Alruwaili, M and Penrice-Randal, R and Alrezaihi, A and Harrison, AJ and Ryan, Y and Bentley, E and Jones, B and Alhatlani, BY and AlShahrani, D and Mahmood, Z and Rickett, NY and Alosaimi, B and Naeem, A and Alamri, S and Alsran, H and Hamed, ME and Dong, X and Assiri, AM and Alrasheed, AR and Hamza, M and Carroll, MW and Gemmell, M and Darby, A and Donovan-Banfield, I and Stewart, JP and Matthews, DA and Davidson, AD and Hiscox, JA},
title = {Amplicon and Metagenomic Analysis of Middle East Respiratory Syndrome (MERS) Coronavirus and the Microbiome in Patients with Severe MERS.},
journal = {mSphere},
volume = {6},
number = {4},
pages = {e0021921},
pmid = {34287009},
issn = {2379-5042},
support = {5F40120C00085//HHS | U.S. Food and Drug Administration (FDA)/ ; 019-003//King Fahad Medical City (KFMC)/ ; },
mesh = {Aged ; Animals ; COVID-19/virology ; Coronavirus Infections/*virology ; Female ; Humans ; Male ; Microbiota/*genetics ; Middle Aged ; Middle East Respiratory Syndrome Coronavirus/*genetics ; SARS-CoV-2/genetics ; },
abstract = {Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastrointestinal illnesses. The virus is mainly present in camel populations with occasional zoonotic spill over into humans. The severity of infection in humans is influenced by numerous factors, and similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), underlying health complications can play a major role. Currently, MERS-CoV and SARS-CoV-2 are coincident in the Middle East and thus a rapid way of sequencing MERS-CoV to derive genotype information for molecular epidemiology is needed. Additionally, complicating factors in MERS-CoV infections are coinfections that require clinical management. The ability to rapidly characterize these infections would be advantageous. To rapidly sequence MERS-CoV, an amplicon-based approach was developed and coupled to Oxford Nanopore long read length sequencing. This and a metagenomic approach were evaluated with clinical samples from patients with MERS. The data illustrated that whole-genome or near-whole-genome information on MERS-CoV could be rapidly obtained. This approach provided data on both consensus genomes and the presence of minor variants, including deletion mutants. The metagenomic analysis provided information of the background microbiome. The advantage of this approach is that insertions and deletions can be identified, which are the major drivers of genotype change in coronaviruses. IMPORTANCE Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in late 2012 in Saudi Arabia. The virus is a serious threat to people not only in the Middle East but also in the world and has been detected in over 27 countries. MERS-CoV is spreading in the Middle East and neighboring countries, and approximately 35% of reported patients with this virus have died. This is the most severe coronavirus infection so far described. Saudi Arabia is a destination for many millions of people in the world who visit for religious purposes (Umrah and Hajj), and so it is a very vulnerable area, which imposes unique challenges for effective control of this epidemic. The significance of our study is that clinical samples from patients with MERS were used for rapid in-depth sequencing and metagenomic analysis using long read length sequencing.},
}
@article {pmid34282606,
year = {2021},
author = {Choi, SJ and Kim, Y and Jeon, J and Gwak, HJ and Kim, M and Kang, K and Kim, Y and Jeong, J and Jung, YK and Lee, KG and Choi, HS and Jung, DH and Lee, SG and Lee, Y and Shin, SJ and Jang, K and Rho, M and Choi, D},
title = {Association of Microbial Dysbiosis with Gallbladder Diseases Identified by Bile Microbiome Profiling.},
journal = {Journal of Korean medical science},
volume = {36},
number = {28},
pages = {e189},
pmid = {34282606},
issn = {1598-6357},
support = {NRF-2014R1A1A1005144/NRF/National Research Foundation of Korea/Korea ; NRF-2021M3E5D1A01015177/NRF/National Research Foundation of Korea/Korea ; },
mesh = {Adult ; Bacteria/classification/*isolation &amp; purification ; Bile/*metabolism/*microbiology ; Case-Control Studies ; Cholecystitis/microbiology/pathology ; Dysbiosis/*microbiology ; Gallbladder/*microbiology ; Gallbladder Diseases/*microbiology ; Gallbladder Neoplasms/*microbiology ; Humans ; Metagenomics ; Microbiota ; Middle Aged ; Phylogeny ; },
abstract = {BACKGROUND: Cholecystitis is an important risk factor for gallbladder cancer, but the bile microbiome and its association with gallbladder disease has not been investigated fully. We aimed to analyze the bile microbiome in normal conditions, chronic cholecystitis, and gallbladder cancer, and to identify candidate bacteria that play an important role in gallbladder carcinogenesis.<br><br>METHODS: We performed metagenome sequencing on bile samples of 10 healthy individuals, 10 patients with chronic cholecystitis, and 5 patients with gallbladder cancer, and compared the clinical, radiological, and pathological characteristics of the participants.<br><br>RESULTS: No significant bacterial signal was identified in the normal bile. The predominant dysbiotic bacteria in both chronic cholecystitis and gallbladder cancer were those belonging to the Enterobacteriaceae family. Klebsiella increased significantly in the order of normal, chronic cholecystitis, and gallbladder cancer. Patients with chronic cholecystitis and dysbiotic microbiome patterns had larger gallstones and showed marked epithelial atypia, which are considered as precancerous conditions.<br><br>CONCLUSION: We investigated the bile microbiome in normal, chronic cholecystitis, and gallbladder cancer. We suggest possible roles of Enterobacteriaceae, including Klebsiella, in gallbladder carcinogenesis. Our findings reveal a possible link between a dysbiotic bile microbiome and the development of chronic calculous cholecystitis and gallbladder cancer.},
}
@article {pmid34282338,
year = {2021},
author = {Vogl, T and Klompus, S and Leviatan, S and Kalka, IN and Weinberger, A and Wijmenga, C and Fu, J and Zhernakova, A and Weersma, RK and Segal, E},
title = {Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota.},
journal = {Nature medicine},
volume = {27},
number = {8},
pages = {1442-1450},
pmid = {34282338},
issn = {1546-170X},
mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; Child ; Child, Preschool ; Epitopes/*immunology ; Female ; Humans ; Immunoglobulins/*immunology ; Infant ; Infant, Newborn ; Machine Learning ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; Peptide Library ; Young Adult ; },
abstract = {Serum antibodies can recognize both pathogens and commensal gut microbiota. However, our current understanding of antibody repertoires is largely based on DNA sequencing of the corresponding B-cell receptor genes, and actual bacterial antigen targets remain incompletely characterized. Here we have profiled the serum antibody responses of 997 healthy individuals against 244,000 rationally selected peptide antigens derived from gut microbiota and pathogenic and probiotic bacteria. Leveraging phage immunoprecipitation sequencing (PhIP-Seq) based on phage-displayed synthetic oligo libraries, we detect a wide breadth of individual-specific as well as shared antibody responses against microbiota that associate with age and gender. We also demonstrate that these antibody epitope repertoires are more longitudinally stable than gut microbiome species abundances. Serum samples of more than 200 individuals collected five years apart could be accurately matched and could serve as an immunologic fingerprint. Overall, our results suggest that systemic antibody responses provide a non-redundant layer of information about microbiota beyond gut microbial species composition.},
}
@article {pmid34281625,
year = {2021},
author = {Zhong, ZP and Tian, F and Roux, S and Gazitúa, MC and Solonenko, NE and Li, YF and Davis, ME and Van Etten, JL and Mosley-Thompson, E and Rich, VI and Sullivan, MB and Thompson, LG},
title = {Glacier ice archives nearly 15,000-year-old microbes and phages.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {160},
pmid = {34281625},
issn = {2049-2618},
mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Ice Cover ; Metagenomics ; *Microbiota ; },
abstract = {BACKGROUND: Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination.<br><br>RESULTS: We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants.<br><br>CONCLUSIONS: Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally. Video Abstract.},
}
@article {pmid34280721,
year = {2021},
author = {Fan, H and Wu, S and Dong, W and Li, X and Dong, Y and Wang, S and Zhu, YG and Zhuang, X},
title = {Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H218O-based DNA-Stable isotope probing and metagenomics.},
journal = {Journal of hazardous materials},
volume = {420},
number = {},
pages = {126440},
doi = {10.1016/j.jhazmat.2021.126440},
pmid = {34280721},
issn = {1873-3336},
mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents ; DNA ; Genes, Bacterial ; Isotopes ; Manure/analysis ; Metagenomics ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; Tetracycline ; },
abstract = {The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H218O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.},
}
@article {pmid34273006,
year = {2021},
author = {Dalal, N and Jalandra, R and Bayal, N and Yadav, AK and Harshulika, and Sharma, M and Makharia, GK and Kumar, P and Singh, R and Solanki, PR and Kumar, A},
title = {Gut microbiota-derived metabolites in CRC progression and causation.},
journal = {Journal of cancer research and clinical oncology},
volume = {147},
number = {11},
pages = {3141-3155},
pmid = {34273006},
issn = {1432-1335},
mesh = {Animals ; Colorectal Neoplasms/*microbiology/pathology ; Disease Progression ; Gastrointestinal Microbiome/*physiology ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; Humans ; Metagenomics ; },
abstract = {BACKGROUND: Based on recent research reports, dysbiosis and improper concentrations of microbial metabolites in the gut may result into the carcinogenesis of colorectal cancer. Recent advancement also highlights the involvement of bacteria and their secreted metabolites in the cancer causation. Gut microbial metabolites are functional output of the host-microbiota interactions and produced by anaerobic fermentation of food components in the diet. They contribute to influence variety of biological mechanisms including inflammation, cell signaling, cell-cycle disruption which are majorly disrupted in carcinogenic activities.<br><br>PURPOSE: In this review, we intend to discuss recent updates and possible molecular mechanisms to provide the role of bacterial metabolites, gut bacteria and diet in the colorectal carcinogenesis. Recent evidences have proposed the role of bacteria, such as Fusobacterium nucleaturm, Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis and Clostridium septicum, in the carcinogenesis of CRC. Metagenomic study confirmed that these bacteria are in increased abundance in CRC patient as compared to healthy individuals and can cause inflammation and DNA damage which can lead to development of cancer. These bacteria produce metabolites, such as secondary bile salts from primary bile salts, hydrogen sulfide, trimethylamine-N-oxide (TMAO), which are likely to promote inflammation and subsequently cancer development.<br><br>CONCLUSION: Recent studies suggest that gut microbiota-derived metabolites have a role in CRC progression and causation and hence, could be implicated in CRC diagnosis, prognosis and therapy.},
}
@article {pmid34272286,
year = {2021},
author = {Osvatic, JT and Wilkins, LGE and Leibrecht, L and Leray, M and Zauner, S and Polzin, J and Camacho, Y and Gros, O and van Gils, JA and Eisen, JA and Petersen, JM and Yuen, B},
title = {Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed symbiont groups.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {29},
pages = {},
pmid = {34272286},
issn = {1091-6490},
support = {S10 OD010786/OD/NIH HHS/United States ; },
abstract = {In the ocean, most hosts acquire their symbionts from the environment. Due to the immense spatial scales involved, our understanding of the biogeography of hosts and symbionts in marine systems is patchy, although this knowledge is essential for understanding fundamental aspects of symbiosis such as host-symbiont specificity and evolution. Lucinidae is the most species-rich and widely distributed family of marine bivalves hosting autotrophic bacterial endosymbionts. Previous molecular surveys identified location-specific symbiont types that "promiscuously" form associations with multiple divergent cooccurring host species. This flexibility of host-microbe pairings is thought to underpin their global success, as it allows hosts to form associations with locally adapted symbionts. We used metagenomics to investigate the biodiversity, functional variability, and genetic exchange among the endosymbionts of 12 lucinid host species from across the globe. We report a cosmopolitan symbiont species, Candidatus Thiodiazotropha taylori, associated with multiple lucinid host species. Ca. T. taylori has achieved more success at dispersal and establishing symbioses with lucinids than any other symbiont described thus far. This discovery challenges our understanding of symbiont dispersal and location-specific colonization and suggests both symbiont and host flexibility underpin the ecological and evolutionary success of the lucinid symbiosis.},
}
@article {pmid34271900,
year = {2021},
author = {Oliveira, SG and Nishiyama, RR and Trigo, CAC and Mattos-Guaraldi, AL and Dávila, AMR and Jardim, R and Aguiar, FHB},
title = {Core of the saliva microbiome: an analysis of the MG-RAST data.},
journal = {BMC oral health},
volume = {21},
number = {1},
pages = {351},
pmid = {34271900},
issn = {1472-6831},
mesh = {Bacteria/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Saliva ; },
abstract = {BACKGROUND: Oral microbiota is considered as the second most complex in the human body and its dysbiosis can be responsible for oral diseases. Interactions between the microorganism communities and the host allow establishing the microbiological proles. Identifying the core microbiome is essential to predicting diseases and changes in environmental behavior from microorganisms.<br><br>METHODS: Projects containing the term "SALIVA", deposited between 2014 and 2019 were recovered on the MG-RAST portal. Quality (Failed), taxonomic prediction (Unknown and Predicted), species richness (Rarefaction), and species diversity (Alpha) were analyzed according to sequencing approaches (Amplicon sequencing and Shotgun metagenomics). All data were checked for normality and homoscedasticity. Metagenomic projects were compared using the Mann-Whitney U test and Spearman's correlation. Microbiome cores were inferred by Principal Component Analysis. For all statistical tests, p < 0.05 was used.<br><br>RESULTS: The study was performed with 3 projects, involving 245 Amplicon and 164 Shotgun metagenome datasets. All comparisons of variables, according to the type of sequencing, showed significant differences, except for the Predicted. In Shotgun metagenomics datasets the highest correlation was between Rarefaction and Failed (r = - 0.78) and the lowest between Alpha and Unknown (r = - 0.12). In Amplicon sequencing datasets, the variables Rarefaction and Unknown (r = 0.63) had the highest correlation and the lowest was between Alpha and Predicted (r = - 0.03). Shotgun metagenomics datasets showed a greater number of genera than Amplicon. Propionibacterium, Lactobacillus, and Prevotella were the most representative genera in Amplicon sequencing. In Shotgun metagenomics, the most representative genera were Escherichia, Chitinophaga, and Acinetobacter.<br><br>CONCLUSIONS: Core of the salivary microbiome and genera diversity are dependent on the sequencing approaches. Available data suggest that Shotgun metagenomics and Amplicon sequencing have similar sensitivities to detect the taxonomic level investigated, although Shotgun metagenomics allows a deeper analysis of the microorganism diversity. Microbiome studies must consider characteristics and limitations of the sequencing approaches. Were identified 20 genera in the core of saliva microbiome, regardless of the health condition of the host. Some bacteria of the core need further study to better understand their role in the oral cavity.},
}
@article {pmid34266351,
year = {2021},
author = {Khattab, AR and Farag, MA},
title = {Marine and terrestrial endophytic fungi: a mine of bioactive xanthone compounds, recent progress, limitations, and novel applications.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/07388551.2021.1940087},
pmid = {34266351},
issn = {1549-7801},
abstract = {Endophytic fungi are a kind of fungi that colonizes living plant tissues presenting a myriad of microbial adaptations that have been developed in such a hidden environment. Owing to its large diversity and particular habituation, they present a golden mine for research in the field of drug discovery. Endophytic fungal communities possess unique biocatalytic machinery that furnishes a myriad of complex natural product scaffolds. Xanthone compounds are examples of endophytic secondary metabolic products with pronounced biological activity to include: antioxidant, antimicrobial, anti-inflammatory, antithrombotic, antiulcer, choleretic, diuretic, and monoamine oxidase inhibiting activity.The current review compiles the recent progress made on the microbiological production of xanthones using fungal endophytes obtained from both marine and terrestrial origins, with comparisons being made among both natural resources. The biosynthesis of xanthones in endophytic fungi is outlined along with its decoding enzymes. Biotransformation reactions reported to be carried out using different endophytic microbial models are also outlined for xanthones structural modification purposes and the production of novel molecules.A promising application of novel computational tools is presented as a future direction for the goal of optimizing microbial xanthones production to include establishing metabolic pathway databases and the in silico analysis of microbial interactions. Metagenomics methods and related bioinformatics platforms are highlighted as unexplored tools for the biodiversity analysis of endophytic microbial communities that are difficult to be cultured.},
}
@article {pmid34265247,
year = {2021},
author = {Brito, IL},
title = {The comings and goings of the healthy human gut microbiota.},
journal = {Cell host &amp; microbe},
volume = {29},
number = {7},
pages = {1163-1164},
doi = {10.1016/j.chom.2021.06.011},
pmid = {34265247},
issn = {1934-6069},
mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; },
abstract = {SNP-level analysis of 5,000+ metagenomic samples enabled Hildebrand and colleagues (2021) to identify human gut microbiota by their dispersal strategies in this issue of Cell Host &amp; Microbe. This brings us a step closer in understanding how microbial communities are formed and maintained and also hints at ways in which microbiomes can be manipulated to improve human health.},
}
@article {pmid34264153,
year = {2021},
author = {Gilroy, R},
title = {Spotlight on the avian gut microbiome: fresh opportunities in discovery.},
journal = {Avian pathology : journal of the W.V.P.A},
volume = {50},
number = {4},
pages = {291-294},
doi = {10.1080/03079457.2021.1955826},
pmid = {34264153},
issn = {1465-3338},
abstract = {Chickens represent a globally ubiquitous food animal underpinning many aspects of human nutrition and health. Consumption of chicken meat continues to surge, representing a cheaper, healthier, low-carbon alternative to other livestock meats. Despite this importance, we are still unable to define what lives within the chicken gut microbiome. This complex community bridges poultry diet, health and productivity as well as providing a reservoir for zoonotic pathogens. Even with decades of intensive study, we are still discovering novel microbial species within this environment, each of which has the potential to provide an avenue for commercial microbiome modulation. The chicken gut truly represents an exhilarating challenge in turning new-found knowledge into new-won power to improve the health and wealth of poultry and people.},
}
@article {pmid34256809,
year = {2021},
author = {Chen, P and Zhou, H and Huang, Y and Xie, Z and Zhang, M and Wei, Y and Li, J and Ma, Y and Luo, M and Ding, W and Cao, J and Jiang, T and Nan, P and Fang, J and Li, X},
title = {Revealing the full biosphere structure and versatile metabolic functions in the deepest ocean sediment of the Challenger Deep.},
journal = {Genome biology},
volume = {22},
number = {1},
pages = {207},
pmid = {34256809},
issn = {1474-760X},
abstract = {BACKGROUND: The full biosphere structure and functional exploration of the microbial communities of the Challenger Deep of the Mariana Trench, the deepest known hadal zone on Earth, lag far behind that of other marine realms.<br><br>RESULTS: We adopt a deep metagenomics approach to investigate the microbiome in the sediment of Challenger Deep, Mariana Trench. We construct 178 metagenome-assembled genomes (MAGs) representing 26 phyla, 16 of which are reported from hadal sediment for the first time. Based on the MAGs, we find the microbial community functions are marked by enrichment and prevalence of mixotrophy and facultative anaerobic metabolism. The microeukaryotic community is found to be dominated by six fungal groups that are characterized for the first time in hadal sediment to possess the assimilatory and dissimilatory nitrate/sulfate reduction, and hydrogen sulfide oxidation pathways. By metaviromic analysis, we reveal novel hadal Caudovirales clades, distinctive virus-host interactions, and specialized auxiliary metabolic genes for modulating hosts' nitrogen/sulfur metabolism. The hadal microbiome is further investigated by large-scale cultivation that cataloged 1070 bacterial and 19 fungal isolates from the Challenger Deep sediment, many of which are found to be new species specialized in the hadal habitat.<br><br>CONCLUSION: Our hadal MAGs and isolates increase the diversity of the Challenger Deep sediment microbial genomes and isolates present in the public. The deep metagenomics approach fills the knowledge gaps in structure and diversity of the hadal microbiome, and provides novel insight into the ecology and metabolism of eukaryotic and viral components in the deepest biosphere on earth.},
}
@article {pmid34251746,
year = {2021},
author = {Garrido-Sanz, L and Senar, MÀ and Piñol, J},
title = {Relative species abundance estimation in artificial mixtures of insects using mito-metagenomics and a correction factor for the mitochondrial DNA copy number.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {},
doi = {10.1111/1755-0998.13464},
pmid = {34251746},
issn = {1755-0998},
support = {TIN2017-84553-C2-1-R//Spanish Government grant/ ; 2017-SGR-1001//Agència de Gestió d'Ajuts Universitaris i de Recerca (AGAUR)/ ; },
abstract = {Mito-metagenomics (MMG) is becoming an alternative to amplicon metabarcoding for the assessment of biodiversity in complex biological samples using high-throughput sequencing. Whereas MMG overcomes the biases introduced by the PCR step in the generation of amplicons, it is not yet a technique free of shortcomings. First, as the reads are obtained from shotgun sequencing, a very low proportion of reads map into the mitogenomes, so a high sequencing effort is needed. Second, as the number of mitogenomes per cell can vary among species, the relative species abundance (RSA) in a mixture could be wrongly estimated. Here, we challenge the MMG method to estimate the RSA using artificial libraries of 17 insect species whose complete genomes are available on public repositories. With fresh specimens of these species, we created single-species libraries to calibrate the bioinformatic pipeline and mixed-species libraries to estimate the RSA. Our results showed that the MMG approach confidently recovers the species list of the mixtures, even when they contain congeneric species. The method was also able to estimate the abundance of a species across different samples (within-species estimation) but failed to estimate the RSA within a single sample (across-species estimation) unless a correction factor accounting for the variable number of mitogenomes per cell was used. To estimate this correction factor, we used the proportion of reads mapping into mitogenomes in the single-species libraries and the lengths of the whole genomes and mitogenomes.},
}
@article {pmid34246242,
year = {2021},
author = {Kameoka, S and Motooka, D and Watanabe, S and Kubo, R and Jung, N and Midorikawa, Y and Shinozaki, NO and Sawai, Y and Takeda, AK and Nakamura, S},
title = {Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1-V2 and V3-V4 primer sets.},
journal = {BMC genomics},
volume = {22},
number = {1},
pages = {527},
pmid = {34246242},
issn = {1471-2164},
support = {18K08431//Ministry of Education, Culture, Sports, Science and Technology/ ; 172107106//Ministry of Internal Affairs and Communications/ ; JP18gm1010005//Japan Agency for Medical Research and Development/ ; },
mesh = {Benchmarking ; *Gastrointestinal Microbiome/genetics ; Genes, rRNA ; High-Throughput Nucleotide Sequencing ; Humans ; Japan ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: 16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here, we compared fecal 16S analysis data from 192 Japanese volunteers using the modified V1-V2 (V12) and the standard V3-V4 primer (V34) sets to optimize the gut microbiota analysis protocol.<br><br>RESULTS: QIIME1 and QIIME2 analysis revealed a higher number of unclassified representative sequences in the V34 data than in the V12 data. The comparison of bacterial composition demonstrated that at the phylum level, Actinobacteria and Verrucomicrobia were detected at higher levels with V34 than with V12. Among these phyla, we observed higher relative compositions of Bifidobacterium and Akkermansia with V34. To estimate the actual abundance, we performed quantitative real-time polymerase chain reaction (qPCR) assays for Akkermansia and Bifidobacterium. We found that the abundance of Akkermansia as detected by qPCR was close to that in V12 data, but was markedly lower than that in V34 data. The abundance of Bifidobacterium detected by qPCR was higher than that in V12 and V34 data.<br><br>CONCLUSIONS: These results indicate that the bacterial composition derived from the V34 region might differ from the actual abundance for specific gut bacteria. We conclude that the use of the modified V12 primer set is more desirable in the 16S analysis of the Japanese gut microbiota.},
}
@article {pmid34245102,
year = {2021},
author = {Bendia, AG and Lemos, LN and Mendes, LW and Signori, CN and Bohannan, BJM and Pellizari, VH},
title = {Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica.},
journal = {Environmental microbiology},
volume = {23},
number = {7},
pages = {4054-4073},
doi = {10.1111/1462-2920.15649},
pmid = {34245102},
issn = {1462-2920},
mesh = {Antarctic Regions ; Archaea/genetics ; *Bacteria/genetics ; *Microbiota/genetics ; Temperature ; },
abstract = {Active volcanoes in Antarctica have remarkable temperature and geochemical gradients that could select for a wide variety of microbial adaptive mechanisms and metabolic pathways. Deception Island is a stratovolcano flooded by the sea, resulting in contrasting ecosystems such as permanent glaciers and active fumaroles, which creates steep gradients that have been shown to affect microbial diversity. In this study, we used shotgun metagenomics and metagenome-assembled genomes to explore the metabolic potentials and survival strategies of microbial communities along an extreme temperature gradient in fumarole and glacier sediments on Deception Island. We observed that communities from a 98 °C fumarole were significantly enriched in genes related to hyperthermophilic (e.g. reverse gyrase, GroEL/GroES and thermosome) and oxidative stress responses, as well as genes related to sulfate reduction, ammonification and carbon fixation. Communities from <80 °C fumaroles possessed more genes related osmotic, cold- and heat-shock responses, and diverse metabolic potentials, such as those related to sulfur oxidation and denitrification, while glacier communities showed abundant metabolic potentials mainly related to heterotrophy. Through the reconstruction of genomes, we were able to reveal the metabolic potentials and different survival strategies of underrepresented taxonomic groups, especially those related to Nanoarchaeota, Pyrodictiaceae and thermophilic ammonia-oxidizing archaeal lineages.},
}
@article {pmid34239006,
year = {2021},
author = {Olsen, M and Nassar, R and Senok, A and Albastaki, A and Leggett, J and Lohning, A and Campos, M and Jones, P and McKirdy, S and Tajouri, L and Alghafri, R},
title = {A pilot metagenomic study reveals that community derived mobile phones are reservoirs of viable pathogenic microbes.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {14102},
pmid = {34239006},
issn = {2045-2322},
mesh = {Bacteria/*genetics ; Bacteriophages/genetics ; Biodiversity ; *Cell Phone ; Fungi/*genetics ; Metagenome ; *Metagenomics ; Virulence Factors/metabolism ; },
abstract = {There is increasing attention focussed on the risks associated with mobile phones possibly serving as 'Trojan Horse' fomites for microbial transmission in healthcare settings. However, little is reported on the presence of microbes on community derived mobile phones which in 2021, numbered in the billions in circulation with majority being used on a daily basis. Identify viable microbial organisms swabbed from smartphones on a university campus. Entire surfaces of 5 mobile phones were swabbed and examined for their microbial content using pre-agar-based growths followed by downstream DNA metagenomic next-generation sequencing analysis. All phones were contaminated with viable microbes. 173 bacteria, 8 fungi, 8 protists, 53 bacteriophages, 317 virulence factor genes and 41 distinct antibiotic resistant genes were identified. While this research represents a pilot study, the snapshot metagenomic analysis of samples collected from the surface of mobile phones has revealed the presence of a large population of viable microbes and an array of antimicrobial resistant factors. With billions of phones in circulation, these devices might be responsible for the rise of community acquired infections. These pilot results highlight the importance of public health authorities considering mobile phones as 'Trojan Horse' devices for microbial transmission and ensure appropriate decontamination campaigns are implemented.},
}
@article {pmid34234185,
year = {2021},
author = {Jones, J and Reinke, SN and Ali, A and Palmer, DJ and Christophersen, CT},
title = {Fecal sample collection methods and time of day impact microbiome composition and short chain fatty acid concentrations.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {13964},
pmid = {34234185},
issn = {2045-2322},
mesh = {Biodiversity ; Cluster Analysis ; Fatty Acids, Volatile/analysis/*metabolism ; Feces/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Microbial Viability ; Specimen Handling/*methods ; },
abstract = {Associations between the human gut microbiome and health outcomes continues to be of great interest, although fecal sample collection methods which impact microbiome studies are sometimes neglected. Here, we expand on previous work in sample optimization, to promote high quality microbiome data. To compare fecal sample collection methods, amplicons from the bacterial 16S rRNA gene (V4) and fungal (ITS2) region, as well as short chain fatty acid (SCFA) concentrations were determined in fecal material over three timepoints. We demonstrated that spot sampling of stool results in variable detection of some microbial members, and inconsistent levels of SCFA; therefore, sample homogenization prior to subsequent analysis or subsampling is recommended. We also identify a trend in microbial and metabolite composition that shifts over two consecutive stool collections less than 25 h apart. Lastly, we show significant differences in bacterial composition that result from collecting stool samples in OMNIgene·Gut tube (DNA Genotec) or Stool Nucleic Acid Collection and Preservation Tube (NORGEN) compared to immediate freezing. To assist with planning fecal sample collection and storage procedures for microbiome investigations with multiple analyses, we recommend participants to collect the first full bowel movement of the day and freeze the sample immediately after collection.},
}
@article {pmid34233671,
year = {2021},
author = {Liu, P and Jiang, Y and Gu, S and Xue, Y and Yang, H and Li, Y and Wang, Y and Yan, C and Jia, P and Lin, X and Qi, G},
title = {Metagenome-wide association study of gut microbiome revealed potential microbial marker set for diagnosis of pediatric myasthenia gravis.},
journal = {BMC medicine},
volume = {19},
number = {1},
pages = {159},
pmid = {34233671},
issn = {1741-7015},
mesh = {Adult ; Bacteroides ; Child ; Clostridiales ; Feces ; Firmicutes ; Fusobacterium ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; *Myasthenia Gravis/diagnosis ; Prevotella ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Myasthenia gravis (MG) is an acquired immune-mediated disorder of the neuromuscular junction that causes fluctuating skeletal muscle weakness and fatigue. Pediatric MG and adult MG have many different characteristics, and current MG diagnostic methods for children are not quite fit. Previous studies indicate that alterations in the gut microbiota may be associated with adult MG. However, it has not been determined whether the gut microbiota are altered in pediatric MG patients.<br><br>METHODS: Our study recruited 53 pediatric MG patients and 46 age- and gender-matched healthy controls (HC). We sequenced the fecal samples of recruited individuals using whole-genome shotgun sequencing and analyzed the data with in-house bioinformatics pipeline.<br><br>RESULTS: We built an MG disease classifier based on the abundance of five species, Fusobacterium mortiferum, Prevotella stercorea, Prevotella copri, Megamonas funiformis, and Megamonas hypermegale. The classifier obtained 94% area under the curve (AUC) in cross-validation and 84% AUC in the independent validation cohort. Gut microbiome analysis revealed the presence of human adenovirus F/D in 10 MG patients. Significantly different pathways and gene families between MG patients and HC belonged to P. copri, Clostridium bartlettii, and Bacteroides massiliensis. Based on functional annotation, we found that the gut microbiome affects the production of short-chain fatty acids (SCFAs), and we confirmed the decrease in SCFA levels in pediatric MG patients via serum tests.<br><br>CONCLUSIONS: The study indicated that altered fecal microbiota might play vital roles in pediatric MG's pathogenesis by reducing SCFAs. The microbial markers might serve as novel diagnostic methods for pediatric MG.},
}
@article {pmid34226711,
year = {2021},
author = {Montassier, E and Valdés-Mas, R and Batard, E and Zmora, N and Dori-Bachash, M and Suez, J and Elinav, E},
title = {Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner.},
journal = {Nature microbiology},
volume = {6},
number = {8},
pages = {1043-1054},
pmid = {34226711},
issn = {2058-5276},
support = {/WT_/Wellcome Trust/United Kingdom ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Adult ; Anti-Bacterial Agents/*administration &amp; dosage ; Bacteria/classification/*drug effects/*genetics/isolation &amp; purification ; Bacterial Proteins/*genetics/metabolism ; Cohort Studies ; *Drug Resistance, Bacterial ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/microbiology ; Humans ; Male ; Metagenome/drug effects ; Middle Aged ; Probiotics/*administration &amp; dosage ; Young Adult ; },
abstract = {Antimicrobial resistance poses a substantial threat to human health. The gut microbiome is considered a reservoir for potential spread of resistance genes from commensals to pathogens, termed the gut resistome. The impact of probiotics, commonly consumed by many in health or in conjunction with the administration of antibiotics, on the gut resistome is elusive. Reanalysis of gut metagenomes from healthy antibiotics-naïve humans supplemented with an 11-probiotic-strain preparation, allowing direct assessment of the gut resistome in situ along the gastrointestinal (GI) tract, demonstrated that probiotics reduce the number of antibiotic resistance genes exclusively in the gut of colonization-permissive individuals. In mice and in a separate cohort of humans, a course of antibiotics resulted in expansion of the lower GI tract resistome, which was mitigated by autologous faecal microbiome transplantation or during spontaneous recovery. In contrast, probiotics further exacerbated resistome expansion in the GI mucosa by supporting the bloom of strains carrying vancomycin resistance genes but not resistance genes encoded by the probiotic strains. Importantly, the aforementioned effects were not reflected in stool samples, highlighting the importance of direct sampling to analyse the effect of probiotics and antibiotics on the gut resistome. Analysing antibiotic resistance gene content in additional published clinical trials with probiotics further highlighted the importance of person-specific metagenomics-based profiling of the gut resistome using direct sampling. Collectively, these findings suggest opposing person-specific and antibiotic-dependent effects of probiotics on the resistome, whose contribution to the spread of antimicrobial resistance genes along the human GI tract merit further studies.},
}
@article {pmid34226572,
year = {2021},
author = {Shimada, Y and Terasawa, M and Okazaki, F and Nakayama, H and Zang, L and Nishiura, K and Matsuda, K and Nishimura, N},
title = {Rhamnan sulphate from green algae Monostroma nitidum improves constipation with gut microbiome alteration in double-blind placebo-controlled trial.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {13384},
pmid = {34226572},
issn = {2045-2322},
mesh = {Adult ; Aged ; Animals ; Bacteria/*isolation &amp; purification ; Chlorophyta/*chemistry ; Constipation/*drug therapy/microbiology ; DNA Barcoding, Taxonomic ; Double-Blind Method ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Metagenomics ; Mice ; Middle Aged ; Young Adult ; },
abstract = {Rhamnan sulphate (RS), a sulphated polysaccharide from Monostroma nitidum, possesses several biological properties that help in treating diseases such as viral infection, thrombosis, and obesity. In the present study, we first administered RS (0.25 mg/g food volume) orally to high-fat diet-treated mice for 4 weeks. RS increased the faecal volume and calorie excretion with decreased plasma lipids, which was in accordance with the results of our previous zebrafish study. Notably, as the excretion amount by RS increased in the mice, we hypothesised that RS could decrease the chance of constipation in mice and also in human subjects because RS is considered as a dietary fibre. We administrated RS (100 mg/day) to subjects with low defaecation frequencies (3-5 times/week) for 2 weeks in double-blind placebo-controlled manner. As a result, RS administration significantly increased the frequency of dejection without any side effects, although no effect was observed on the body weight and blood lipids. Moreover, we performed 16s rRNA-seq analysis of the gut microbiota in these subjects. Metagenomics profiling using PICRUSt revealed functional alternation of the KEGG pathways, which could be involved in the therapeutic effect of RS for constipation.},
}
@article {pmid34225233,
year = {2021},
author = {Borsetto, C and Raguideau, S and Travis, E and Kim, DW and Lee, DH and Bottrill, A and Stark, R and Song, L and Cha, CJ and Pearson, J and Quince, C and Singer, AC and Wellington, EMH},
title = {Impact of sulfamethoxazole on a riverine microbiome.},
journal = {Water research},
volume = {201},
number = {},
pages = {117382},
doi = {10.1016/j.watres.2021.117382},
pmid = {34225233},
issn = {1879-2448},
mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Genes, Bacterial ; *Microbiota ; Rivers ; *Sulfamethoxazole ; Waste Water ; },
abstract = {The continued emergence of bacterial pathogens presenting antimicrobial resistance is widely recognised as a global health threat and recent attention focused on potential environmental reservoirs of antibiotic resistance genes (ARGs). Freshwater environments such as rivers represent a potential hotspot for ARGs and antibiotic resistant bacteria as they are receiving systems for effluent discharges from wastewater treatment plants (WWTPs). Effluent also contains low levels of different antimicrobials including antibiotics and biocides. Sulfonamides are antibacterial chemicals widely used in clinical, veterinary and agricultural settings and are frequently detected in sewage sludge and manure in addition to riverine ecosystems. The impact of such exposure on ARG prevalence and diversity is unknown, so the aim of this study was to investigate the release of a sub-lethal concentration of the sulfonamide compound sulfamethoxazole (SMX) on the river bacterial microbiome using a flume system. This system was a semi-natural in vitro flume using river water (30 L) and sediment (6 kg) with circulation to mimic river flow. A combination of 'omics' approaches were conducted to study the impact of SMX exposure on the microbiomes within the flumes. Metagenomic analysis showed that the addition of low concentrations of SMX (<4 μg L-1) had a limited effect on the bacterial resistome in the water fraction only, with no impact observed in the sediment. Metaproteomics did not show differences in ARGs expression with SMX exposure in water. Overall, the river bacterial community was resilient to short term exposure to sub-lethal concentrations of SMX which mimics the exposure such communities experience downstream of WWTPs throughout the year.},
}
@article {pmid34223947,
year = {2021},
author = {Jiao, L and Kourkoumpetis, T and Hutchinson, D and Ajami, NJ and Hoffman, K and White, DL and Graham, DY and Hair, C and Shah, R and Kanwal, F and Jarbrink-Sehgal, M and Husain, N and Hernaez, R and Hou, J and Cole, R and Velez, M and Ketwaroo, G and Kramer, J and El-Serag, HB and Petrosino, JF},
title = {Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {34223947},
issn = {1432-184X},
support = {CIN13-413//Office of Academic Affiliations, Department of Veterans Affairs/ ; P30 DK56338/DK/NIDDK NIH HHS/United States ; R01CA172880//Division of Cancer Prevention, National Cancer Institute/ ; 000//Golfers Against Cancer/ ; I01 CX001430/CX/CSRD VA/United States ; RP#140767//Cancer Prevention and Research Institute of Texas/ ; 000//Gillson Longenbaugh Foundation/ ; CX001430//Office of Academic Affiliations, Department of Veterans Affairs/ ; },
abstract = {Limited data exist on the spatial distribution of the colonic bacteria in humans. We collected the colonic biopsies from five segments of 27 polyp-free adults and collected feces from 13 of them. We sequenced the V4 region of the bacterial 16S rRNA gene using the MiSeq platform. The sequencing data were assigned to the amplicon sequence variant (ASV) using SILVA. Biodiversity and the relative abundance of the ASV were compared across the colonic segments and between the rectal and fecal samples. Bacterial functional capacity was assessed using Tax4fun. Each individual had a unique bacterial community composition (Weighted Bray-Curtis P value = 0.001). There were no significant differences in richness, evenness, community composition, and the taxonomic structure across the colon segments in all the samples. Firmicutes (47%), Bacteroidetes (39%), and Proteobacteria (6%) were the major phyla in all segments, followed by Verrucomicrobia, Fusobacteria, Desulfobacterota, and Actinobacteria. There were 15 genera with relative abundance > 1%, including Bacteroides, Faecalibacterium, Escherichia/Shigella, Sutterella, Akkermansia, Parabacteroides, Prevotella, Lachnoclostridium, Alistipes, Fusobacterium, Erysipelatoclostridium, and four Lachnospiraceae family members. Intra-individually, the community compositional dissimilarity was the greatest between the cecum and the rectum. There were significant differences in biodiversity and the taxonomic structure between the rectal and fecal bacteria. The bacterial community composition and structure were homogeneous across the large intestine in adults. The inter-individual variability of the bacteria was greater than inter-segment variability. The rectal and fecal bacteria differed in the community composition and structure.},
}
@article {pmid34217274,
year = {2021},
author = {Kakuk, B and Wirth, R and Maróti, G and Szuhaj, M and Rakhely, G and Laczi, K and Kovács, KL and Bagi, Z},
title = {Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics.},
journal = {Microbial cell factories},
volume = {20},
number = {1},
pages = {127},
pmid = {34217274},
issn = {1475-2859},
support = {FK123902//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; PD132145//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; FK123899//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; GINOP- 2.2.1-15-2017-00081//Nemzeti Kutatási és Technológiai Hivatal/ ; EFOP- 3.6.2-16-2017-00010//Nemzeti Kutatási és Technológiai Hivatal/ ; 2020-1.1.2-PIACI-KFI-2020-00117//Nemzeti Kutatási és Technológiai Hivatal/ ; LP2020-5/2020//Magyar Tudományos Akadémia/ ; 2020-3.1.2.-ZFR-KVG-2020-00009//nemzeti kutatási és technológiai hivatal/ ; },
mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Carbon Dioxide/metabolism ; Fermentation ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Hydrogen/*metabolism ; Metagenome ; Metagenomics ; Methane/*biosynthesis ; Methanomicrobiaceae/genetics/*metabolism ; Methanosarcina/genetics/*metabolism ; Microbiota ; *Transcriptome ; },
abstract = {BACKGROUND: The molecular machinery of the complex microbiological cell factory of biomethane production is not fully understood. One of the process control elements is the regulatory role of hydrogen (H2). Reduction of carbon dioxide (CO2) by H2 is rate limiting factor in methanogenesis, but the community intends to keep H2 concentration low in order to maintain the redox balance of the overall system. H2 metabolism in methanogens becomes increasingly important in the Power-to-Gas renewable energy conversion and storage technologies.<br><br>RESULTS: The early response of the mixed mesophilic microbial community to H2 gas injection was investigated with the goal of uncovering the first responses of the microbial community in the CH4 formation and CO2 mitigation Power-to-Gas process. The overall microbial composition changes, following a 10 min excessive bubbling of H2 through the reactor, was investigated via metagenome and metatranscriptome sequencing. The overall composition and taxonomic abundance of the biogas producing anaerobic community did not change appreciably 2 hours after the H2 treatment, indicating that this time period was too short to display differences in the proliferation of the members of the microbial community. There was, however, a substantial increase in the expression of genes related to hydrogenotrophic methanogenesis of certain groups of Archaea. As an early response to H2 exposure the activity of the hydrogenotrophic methanogenesis in the genus Methanoculleus was upregulated but the hydrogenotrophic pathway in genus Methanosarcina was downregulated. The RT-qPCR data corroborated the metatranscriptomic RESULTS: H2 injection also altered the metabolism of a number of microbes belonging in the kingdom Bacteria. Many Bacteria possess the enzyme sets for the Wood-Ljungdahl pathway. These and the homoacetogens are partners for syntrophic community interactions between the distinct kingdoms of Archaea and Bacteria.<br><br>CONCLUSIONS: External H2 regulates the functional activity of certain Bacteria and Archaea. The syntrophic cross-kingdom interactions in H2 metabolism are important for the efficient operation of the Power-to-Gas process. Therefore, mixed communities are recommended for the large scale Power-to-Gas process rather than single hydrogenotrophic methanogen strains. Fast and reproducible response from the microbial community can be exploited in turn-off and turn-on of the Power-to-Gas microbial cell factories.},
}
@article {pmid34216067,
year = {2021},
author = {Kwon, MJ and Tripathi, BM and Göckede, M and Shin, SC and Myeong, NR and Lee, YK and Kim, M},
title = {Disproportionate microbial responses to decadal drainage on a Siberian floodplain.},
journal = {Global change biology},
volume = {27},
number = {20},
pages = {5124-5140},
doi = {10.1111/gcb.15785},
pmid = {34216067},
issn = {1365-2486},
mesh = {Carbon Cycle ; Carbon Dioxide/analysis ; Methane ; *Microbiota ; *Permafrost ; Soil ; },
abstract = {Permafrost thaw induces soil hydrological changes which in turn affects carbon cycle processes in the Arctic terrestrial ecosystems. However, hydrological impacts of thawing permafrost on microbial processes and greenhouse gas (GHG) dynamics are poorly understood. This study examined changes in microbial communities using gene and genome-centric metagenomics on an Arctic floodplain subject to decadal drainage, and linked them to CO2 and CH4 flux and soil chemistry. Decadal drainage led to significant changes in the abundance, taxonomy, and functional potential of microbial communities, and these modifications well explained the changes in CO2 and CH4 fluxes between ecosystem and atmosphere-increased fungal abundances potentially increased net CO2 emission rates and highly reduced CH4 emissions in drained sites corroborated the marked decrease in the abundance of methanogens and methanotrophs. Interestingly, various microbial taxa disproportionately responded to drainage: Methanoregula, one of the key players in methanogenesis under saturated conditions, almost disappeared, and also Methylococcales methanotrophs were markedly reduced in response to drainage. Seven novel methanogen population genomes were recovered, and the metabolic reconstruction of highly correlated population genomes revealed novel syntrophic relationships between methanogenic archaea and syntrophic partners. These results provide a mechanistic view of microbial processes regulating GHG dynamics in the terrestrial carbon cycle, and disproportionate microbial responses to long-term drainage provide key information for understanding the effects of warming-induced soil drying on microbial processes in Arctic wetland ecosystems.},
}
@article {pmid34215422,
year = {2021},
author = {Kothe, CI and Bolotin, A and Kraïem, BF and Dridi, B and , and Renault, P},
title = {Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches.},
journal = {International journal of food microbiology},
volume = {358},
number = {},
pages = {109312},
doi = {10.1016/j.ijfoodmicro.2021.109312},
pmid = {34215422},
issn = {1879-3460},
mesh = {Animals ; Bacteria/genetics ; Brevibacterium ; Cattle ; *Cheese/analysis ; Metagenome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Staphylococcus ; },
abstract = {Halophilic/halotolerant bacteria are generally assumed to live in natural environments, although they may also be found in foods such as cheese and seafood. These salt-loving bacteria have been occasionally characterized in cheese, and studies on their ecological and technological functions are still scarce. We therefore selected 13 traditional cheeses to systematically characterize these microorganisms in their rinds via cultural, genomic and metagenomic methods. Using different salt-based media, we identified 35 strains with unique 16S rRNA and rpoB gene sequences, whose whole genome was sequenced. Twenty are Gram-positive species including notably Brevibacterium aurantiacum (6) and Staphylococcus equorum (3), which are also frequently added as starters. ANI and pan-genomic analyses confirm the high genetic diversity of B. aurantiacum and reveal the presence of two subspecies in S. equorum, as well as the genetic proximity of several cheese strains to bovine isolates. Additionally, we isolated 15 Gram-negative strains, potentially defining ten new species of halophilic/halotolerant cheese bacteria, in particular for the genera Halomonas and Psychrobacter. The use of all the genomes sequenced in this study as a reference to complement those existing in the databases allowed us to study the representativeness of 66 species of halophilic/halotolerant bacteria in 74 cheese rind metagenomes. While Gram-positive strains may flourish in the different types of technologies, Gram-negative species are particularly abundant in cheeses with high moisture, such as washed-rind cheeses. Finally, analyses of co-occurrences reveal assemblies, including the frequent coexistence of several species of the same genus, forming moderately complex ecosystems with functional redundancies that probably ensure stable cheese development.},
}
@article {pmid34210980,
year = {2021},
author = {Wang, J and Zhang, J and Liu, W and Zhang, H and Sun, Z},
title = {Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {55},
pmid = {34210980},
issn = {2055-5008},
mesh = {Computational Biology/methods ; *Gastrointestinal Microbiome ; *Gene Expression Profiling/methods ; Gene Expression Regulation, Bacterial ; Humans ; Lactobacillus casei/*genetics ; *Metagenome ; *Metagenomics/methods ; *Transcriptome ; },
abstract = {Little is known about the replication and dynamic transcription of probiotics during their "passenger" journey in the human GI tract, which has therefore limited the understanding of their probiotic mechanisms. Here, metagenomic and metatranscriptomic sequencing was used to expose the in vivo expression patterns of the probiotic Lactobacillus casei Zhang (LcZ), which was compared with its in vitro growth transcriptomes, as well as the dynamics of the indigenous microbiome response to probiotic consumption. Extraction of the strain-specific reads revealed that replication and transcripts from the ingested LcZ were increased, while those from the resident L. casei strains remained unchanged. Mapping of all sequencing reads to LcZ genome showed that gene expression in vitro and in vivo differed dramatically. Approximately 39% of mRNAs and 45% of sRNAs of LcZ well-expressed were repressed after ingestion into human gut. The expression of ABC transporter genes and amino acid metabolism genes was induced at day 14 of ingestion, and genes for sugar and SCFA metabolism were activated at day 28 of ingestion. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in the human gut; this sRNA repressed LcZ growth and lactic acid production in vitro. However, the response of the human gut microbiome to LcZ was limited and heterogeneous. These findings implicate the ingested probiotic has to change its transcription patterns to survive and adapt in the human gut, and the time-dependent activation patterns indicate highly dynamic cross-talk between the probiotic and human gut microbes.},
}
@article {pmid34210038,
year = {2021},
author = {Olshan, KL and Zomorrodi, AR and Pujolassos, M and Troisi, J and Khan, N and Fanelli, B and Kenyon, V and Fasano, A and Leonard, MM},
title = {Microbiota and Metabolomic Patterns in the Breast Milk of Subjects with Celiac Disease on a Gluten-Free Diet.},
journal = {Nutrients},
volume = {13},
number = {7},
pages = {},
pmid = {34210038},
issn = {2072-6643},
support = {K23 DK122127/DK/NIDDK NIH HHS/United States ; R01 DK104344/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Case-Control Studies ; Celiac Disease/diet therapy/*microbiology ; Cross-Sectional Studies ; *Diet, Gluten-Free ; Female ; Glutens/metabolism ; Humans ; Infant, Newborn ; *Metabolome ; Metabolomics ; Metagenomics ; *Microbiota ; Milk, Human/*microbiology ; Prospective Studies ; },
abstract = {The intestinal microbiome may trigger celiac disease (CD) in individuals with a genetic disposition when exposed to dietary gluten. Research demonstrates that nutrition during infancy is crucial to the intestinal microbiome engraftment. Very few studies to date have focused on the breast milk composition of subjects with a history of CD on a gluten-free diet. Here, we utilize a multi-omics approach with shotgun metagenomics to analyze the breast milk microbiome integrated with metabolome profiling of 36 subjects, 20 with CD on a gluten-free diet and 16 healthy controls. These analyses identified significant differences in bacterial and viral species/strains and functional pathways but no difference in metabolite abundance. Specifically, three bacterial strains with increased abundance were identified in subjects with CD on a gluten-free diet of which one (Rothia mucilaginosa) has been previously linked to autoimmune conditions. We also identified five pathways with increased abundance in subjects with CD on a gluten-free diet. We additionally found four bacterial and two viral species/strains with increased abundance in healthy controls. Overall, the differences observed in bacterial and viral species/strains and in functional pathways observed in our analysis may influence microbiome engraftment in neonates, which may impact their future clinical outcomes.},
}
@article {pmid34204939,
year = {2021},
author = {Zampieri, A and Babbucci, M and Carraro, L and Milan, M and Fasolato, L and Cardazzo, B},
title = {Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum.},
journal = {Foods (Basel, Switzerland)},
volume = {10},
number = {6},
pages = {},
pmid = {34204939},
issn = {2304-8158},
support = {C26C18000030004//Dipartimenti di Eccellenza/ ; CARD_SID18_01//Department of Comparative Biomedicine and Food Science/ ; ID 10062983//PORFESR/ ; },
abstract = {Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam Vibrio community composition. Here, 16S and recA-pyrH metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and Vibrio species (recA-pyrH). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several Vibrio species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic Vibrio species and a higher number of vibrios with respect to the recA-pyrH metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of Vibrio biodiversity.},
}
@article {pmid34202675,
year = {2021},
author = {Jo, Y and Back, CG and Kim, KH and Chu, H and Lee, JH and Moh, SH and Cho, WK},
title = {Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes.},
journal = {International journal of molecular sciences},
volume = {22},
number = {13},
pages = {},
pmid = {34202675},
issn = {1422-0067},
support = {120085-3//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; NRF-2018R1D1A1B07043597//National Research Foundation of Korea/ ; },
mesh = {Bacteria/classification/genetics ; Computational Biology/methods ; Garlic/*microbiology ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; Organ Specificity ; Phylogeny ; Sequence Analysis, RNA ; },
abstract = {Garlic (Allium sativum) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.},
}
@article {pmid34202141,
year = {2021},
author = {Yuan, X and Zhang, X and Liu, X and Dong, Y and Yan, Z and Lv, D and Wang, P and Li, Y},
title = {Comparison of Gut Bacterial Communities of Grapholita molesta (Lepidoptera: Tortricidae) Reared on Different Host Plants.},
journal = {International journal of molecular sciences},
volume = {22},
number = {13},
pages = {},
pmid = {34202141},
issn = {1422-0067},
support = {31871971//National Natural Science Foundation of China/ ; 31772503//National Natural Science Foundation of China/ ; },
mesh = {Analysis of Variance ; Animals ; Computational Biology/methods ; *Gastrointestinal Microbiome ; Host-Parasite Interactions ; Lepidoptera/*microbiology ; Metagenomics/methods ; Plants/parasitology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Intestinal symbiotic bacteria have played an important role in the digestion, immunity detoxification, mating, and reproduction of insects during long-term coevolution. The oriental fruit moth, Grapholita molesta, is an important fruit tree pest worldwide. However, the composition of the G. molesta microbial community, especially of the gut microbiome, remains unclear. To explore the differences of gut microbiota of G. molesta when reared on different host plants, we determined the gut bacterial structure when G. molesta was transferred from an artificial diet to different host plants (apples, peaches, nectarines, crisp pears, plums, peach shoots) by amplicon sequencing technology. The results showed that Proteobacteria and Firmicutes are dominant in the gut microbiota of G. molesta. Plum-feeding G. molesta had the highest richness and diversity of gut microbiota, while apple-feeding G. molesta had the lowest. PCoA and PERMANOVA analysis revealed that there were significant differences in the gut microbiota structure of G. molesta on different diets. PICRUSt2 analysis indicated that most of the functional prediction pathways were concentrated in metabolic and cellular processes. Our results confirmed that gut bacterial communities of G. molesta can be influenced by host diets and may play an important role in host adaptation.},
}
@article {pmid34198177,
year = {2021},
author = {Uke, A and Nakazono-Nagaoka, E and Chuah, JA and Zain, NA and Amir, HG and Sudesh, K and Abidin, NZHAZ and Hashim, Z and Kosugi, A},
title = {Effect of decomposing oil palm trunk fibers on plant growth and soil microbial community composition.},
journal = {Journal of environmental management},
volume = {295},
number = {},
pages = {113050},
doi = {10.1016/j.jenvman.2021.113050},
pmid = {34198177},
issn = {1095-8630},
mesh = {Biomass ; Humans ; *Microbiota ; *Saccharum ; Soil ; Soil Microbiology ; *Trichoderma ; },
abstract = {Oil palm trunks (OPT) are logged for replantation and the fiber residues are disposed of into the palm plantation area. The fiber residues are expected to increase soil fertility through recycling of carbon and minerals via fiber decomposition. This study investigated the effects of OPT fiber disposal and other lignocellulosic biomass on plant growth and microbial diversity in the soil environment. Four treatment plots were tested: (A) soil+OPT fiber (1:20), (B) soil+sugarcane bagasse (1:20), (C) soil+cellulose powder (1:20), and (D) unamended soil as a negative control. Low plant height, decreased chlorophyll content, and low biomass was observed in corn grown on soil mixed with OPT fiber, cellulose, and sugarcane bagasse, when compared with those of the control. The plants grown with OPT fiber were deficient in total nitrogen and magnesium when compared with those without fiber amendment, which suggested that nitrogen and minerals in soil might be taken up by changing microflora because of the OPT fibers presence. To confirm differences in the soil microflora, metagenomics analysis was performed on untreated soil and soil from each lignocellulose treatment. The microflora of soils mixed with OPT fiber, cellulose and sugarcane bagasse revealed substantial increases in bacteria such as families Cytophagaceae and Oscillospiraceae, and two major fungal genera, Trichoderma and Trichocladium, that are involved in lignocellulose degradation. OPT fiber resulted in a drastic increase in the ratios and amounts of Trichocladium in the soil when compared with those of cellulose and sugarcane bagasse. These results indicate that unregulated disposal of OPT fiber into plantation areas could result in nutrient loss from soil by increasing the abundance of microorganisms involved in lignocellulose decomposition.},
}
@article {pmid34193290,
year = {2021},
author = {Huang, S and Jiang, S and Huo, D and Allaband, C and Estaki, M and Cantu, V and Belda-Ferre, P and Vázquez-Baeza, Y and Zhu, Q and Ma, C and Li, C and Zarrinpar, A and Liu, YY and Knight, R and Zhang, J},
title = {Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {151},
pmid = {34193290},
issn = {2049-2618},
support = {R01 HL148801/HL/NHLBI NIH HHS/United States ; K08 DK102902/NH/NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R21 MH117780/MH/NIMH NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; T32 OD017863/OD/NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; DP1-AT010885/AT/NCCIH NIH HHS/United States ; R03 DK114536/DK/NIDDK NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; K08 DK102902/DK/NIDDK NIH HHS/United States ; R01AI141529, R01HD093761, R01AG067744/NH/NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; 31701577//National Natural Science Foundation of China/ ; T32 GM127235/GM/NIGMS NIH HHS/United States ; P30 DK120515, P30 DK063491, and UL1 TR001442/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bifidobacterium ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Microbiota ; *Probiotics ; Zebrafish ; },
abstract = {BACKGROUND: Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods.<br><br>RESULTS: We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10-70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice.<br><br>CONCLUSIONS: Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans. Video abstract.},
}
@article {pmid34192637,
year = {2021},
author = {Li, P and Li, K and Xu, P and Liu, X and Pu, Y},
title = {Treatment of wastewater with high carbon-to-nitrogen ratio using a waterfall aeration biofilm reactor combined with sequencing batch reactor: Microbial community structure and metabolism analysis.},
journal = {Bioresource technology},
volume = {337},
number = {},
pages = {125450},
doi = {10.1016/j.biortech.2021.125450},
pmid = {34192637},
issn = {1873-2976},
mesh = {Biofilms ; Bioreactors ; Carbon ; Denitrification ; *Microbiota ; Nitrification ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; *Waste Water ; },
abstract = {A low-cost and high-efficiency waterfall aeration biofilm reactor (WABR) combined with a sequencing batch reactor (SBR) was established to treat wastewater with a C/N ratio of 50. Three WABR-SBR systems with different fillers were used. In the stable operation phase, the removal efficiency of chemical oxygen demand was R1 (approximately 99%), R2 (97-99%), and R3 (96-99%); the effluent concentration of NH4+-N was 0.5 mg/L without nitrite or nitrate accumulation. High-throughput 16S rRNA sequencing revealed that the dominant phyla in the microbial community structure were Proteobacteria, Bacteroidetes, and Planctomycetes. Quantitative PCR was used to quantify the nitrification and denitrification gene expressions (Nitrobacter, nirS, and nirK) to evaluate the simultaneous nitrification and denitrification processes. Both anammox and denitrifying bacteria were abundant. Metagenomic annotation of genes that revealed the metabolic pathways of carbohydrates, amino acids, and the two dominant enzymes (GH and GT) provide valuable information for microbial ecology analysis.},
}
@article {pmid34191855,
year = {2021},
author = {Jung, TH and Han, KS},
title = {Imbalanced dietary intake alters the colonic microbial profile in growing rats.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0253959},
pmid = {34191855},
issn = {1932-6203},
mesh = {Animals ; Bacteria/genetics/*growth &amp; development ; Colon/*microbiology ; DNA, Bacterial/genetics ; Diet ; *Eating ; Fatty Acids/metabolism ; Immunoglobulins/blood ; Male ; Metagenomics ; Microbiota/genetics ; Rats, Sprague-Dawley ; Sequence Analysis, DNA ; },
abstract = {An imbalanced dietary intake is associated with alteration of intestinal ecosystem. We investigated the impact of imbalanced diets on colonic microbiota, concentrations of short chain fatty acid in colonic digesta and serum immunoglobulins (Igs) of growing rats. Compared to the control diet, consuming diets high in fat, sucrose, or processed meat, or low in iron, increased the abundance of the pathogenic bacteria such as Clostridium, Escherichia coli, and Salmonella species, and decreased the beneficial bacteria, like Bifidobacteria, Lactobacillus, Akkermansia, Phascolarctobacterium, Alistipes, and butyrate producing species of bacteria in the colon of growing rats. The heatmap of metagenomics indicated that each group was separated into distinct clusters, and the ID group in particular, showed significantly (P < 0.01) reduced alpha diversity of colonic microbiota in comparison to the control group. All experimental groups showed significantly (P < 0.05 or P < 0.01) decreased concentration of acetate and butyrate in the colonic digesta and lower levels of serum IgG or IgA, compared to the control. These results indicated that the imbalanced dietary intake negatively altered intestinal ecosystem and immunity.},
}
@article {pmid34187542,
year = {2021},
author = {Kim, JY and Yi, MH and Mahdi, AAS and Yong, TS},
title = {iSeq 100 for metagenomic pathogen screening in ticks.},
journal = {Parasites &amp; vectors},
volume = {14},
number = {1},
pages = {346},
pmid = {34187542},
issn = {1756-3305},
support = {NRF-2019R1A2B5B01069843//National Research Foundation of Korea/ ; 2020R1I1A2074562//National Research Foundation of Korea/ ; 2020R1I1A1A0105358211//National Research Foundation of Korea/ ; },
mesh = {Animals ; Bacteria/classification/*genetics/isolation &amp; purification/*pathogenicity ; High-Throughput Nucleotide Sequencing/*instrumentation/*methods ; Metagenomics ; Microbiota/genetics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Ticks/*microbiology ; },
abstract = {BACKGROUND: Ticks are blood-sucking ectoparasites that play a pivotal role in the transmission of various pathogens to humans and animals. In Korea, Haemaphysalis longicornis is the predominant tick species and is recognized as the vector of pathogens causing various diseases such as babesiosis, borreliosis, rickettsiosis, and severe fever with thrombocytopenia syndrome.<br><br>METHODS: In this study, the targeted high-throughput sequencing of the 16S rRNA V4 region was performed using the state-of-the-art sequencing instrument, iSeq 100, to screen bacterial pathogens in H. longicornis, and the findings were compared with those using conventional PCR with specific primers. Microbiome analyses were performed with EzBioCloud, a commercially available ChunLab bioinformatics cloud platform. ANOVA-Like Differential Expression tool (ALDEx2) was used for differential abundance analysis.<br><br>RESULTS: Rickettsia spp. were detected in 16 out of 37 samples using iSeq 100, and this was confirmed using a PCR assay. In the phylogenetic analysis using gltA and ompA sequences of the detected Rickettsia, the highest sequence similarity was found with 'Candidatus Rickettsia jingxinensis' isolate Xian-Hl-79, 'Ca. R. jingxinensis' isolate F18, and 'Ca. R. longicornii' isolate ROK-HL727. In the microbiome study, Coxiella AB001519, a known tick symbiont, was detected in all 37 tick samples. Actinomycetospora chiangmaiensis was more abundant in Rickettsia-positive samples than in Rickettsia-negative samples.<br><br>CONCLUSIONS: In this study, iSeq 100 was used to investigate the microbiome of H. longicornis, and the potentially pathogenic Rickettsia strain was detected in 16 out of 37 ticks. We believe that this approach will aid in large-scale pathogen screening of arthropods to be used in vector-borne disease control programs.},
}
@article {pmid34186487,
year = {2021},
author = {Wilson, BC and Butler, ÉM and Grigg, CP and Derraik, JGB and Chiavaroli, V and Walker, N and Thampi, S and Creagh, C and Reynolds, AJ and Vatanen, T and O'Sullivan, JM and Cutfield, WS},
title = {Oral administration of maternal vaginal microbes at birth to restore gut microbiome development in infants born by caesarean section: A pilot randomised placebo-controlled trial.},
journal = {EBioMedicine},
volume = {69},
number = {},
pages = {103443},
doi = {10.1016/j.ebiom.2021.103443},
pmid = {34186487},
issn = {2352-3964},
mesh = {Administration, Oral ; Adult ; Bacteroides/pathogenicity ; Cesarean Section/*adverse effects ; Fecal Microbiota Transplantation/adverse effects/*methods ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; Infant, Newborn, Diseases/etiology/*microbiology/prevention &amp; control ; Male ; Vagina/*microbiology ; },
abstract = {BACKGROUND: Birth by caesarean section (CS) is associated with aberrant gut microbiome development and greater disease susceptibility later in life. We investigated whether oral administration of maternal vaginal microbiota to infants born by CS could restore their gut microbiome development in a pilot single-blinded, randomised placebo-controlled trial (Australian New Zealand Clinical Trials Registry, ACTRN12618000339257).<br><br>METHODS: Pregnant women scheduled for a CS underwent comprehensive antenatal pathogen screening. At birth, healthy neonates were randomised to receive a 3 ml solution of either maternal vaginal microbes (CS-seeded, n = 12) or sterile water (CS-placebo, n = 13). Vaginally-born neonates were used as the reference control (VB, n = 22). Clinical assessments occurred within the first 2 h of birth, and at 1 month and 3 months of age. Infant stool samples and maternal vaginal extracts from CS women underwent shotgun metagenomic sequencing. The primary outcome was gut microbiome composition at 1 month of age. Secondary outcomes included maternal strain engraftment, functional potential of the gut microbiome, anthropometry, body composition, and adverse events.<br><br>FINDINGS: Despite the presence of viable microbial cells within transplant solutions, there were no observed differences in gut microbiome composition or functional potential between CS-seeded and CS-placebo infants at 1 month or 3 months of age. Both CS groups displayed the characteristic signature of low Bacteroides abundance, which contributed to a number of biosynthesis pathways being underrepresented when compared with VB microbiomes. Maternal vaginal strain engraftment was rare. Vaginal seeding had no observed effects on anthropometry or body composition. There were no serious adverse events associated with treatment.<br><br>INTERPRETATION: Our pilot findings question the value of vaginal seeding given that oral administration of maternal vaginal microbiota did not alter early gut microbiome development in CS-born infants. The limited colonisation of maternal vaginal strains suggest that other maternal sources, such as the perianal area, may play a larger role in seeding the neonatal gut microbiome.<br><br>FUNDING: Health Research Council of New Zealand, A Better Start - National Science Challenge.},
}
@article {pmid34177841,
year = {2021},
author = {Selari, PJRG and Olchanheski, LR and Ferreira, AJ and Paim, TDP and Calgaro Junior, G and Claudio, FL and Alves, EM and Santos, DC and Araújo, WL and Silva, FG},
title = {Short-Term Effect in Soil Microbial Community of Two Strategies of Recovering Degraded Area in Brazilian Savanna: A Pilot Case Study.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {661410},
pmid = {34177841},
issn = {1664-302X},
abstract = {The Brazilian Cerrado is a highland tropical savanna considered a biodiversity hotspot with many endemic species of plants and animals. Over the years, most of the native areas of this biome became arable areas, and with inadequate management, some are nowadays at varying levels of degradation stage. Crop-livestock integrated systems (CLIS) are one option for the recovery of areas in degradation, improving the physicochemical and biological characteristics of the soil while increasing income and mitigating risks due to product diversification. Little is known about the effect of CLIS on the soil microbial community. Therefore, we perform this pilot case study to support further research on recovering degraded areas. The bacterial and fungal soil communities in the area with CLIS were compared to an area under moderate recovery (low-input recovering - LI) and native savanna (NS) area. Bacterial and fungal communities were investigated by 16S and ITS rRNA gene sequencing (deep rRNA sequencing). Ktedonobacteraceae and AD3 families were found predominantly in LI, confirming the relationship of the members of the Chloroflexi phylum in challenging environmental conditions, which can be evidenced in LI. The CLIS soil presented 63 exclusive bacterial families that were not found in LI or NS and presented a higher bacterial richness, which can be related to good land management. The NS area shared 21 and 6 families with CLIS and LI, respectively, suggesting that the intervention method used in the analyzed period brings microbial diversity closer to the conditions of the native area, demonstrating a trend of approximation between NS and CLIS even in the short term. The most abundant fungal phylum in NS treatment was Basidiomycota and Mucoromycota, whereas Ascomycota predominated in CLIS and LI. The fungal community needs more time to recover and to approximate from the native area than the bacterial community. However, according to the analysis of bacteria, the CLIS area behaved differently from the LI area, showing that this treatment induces a faster response to the increase in species richness, tending to more accelerated recovery. Results obtained herein encourage CLIS as a sustainable alternative for recovery and production in degraded areas.},
}
@article {pmid34176489,
year = {2021},
author = {Berry, ASF and Pierdon, MK and Misic, AM and Sullivan, MC and O'Brien, K and Chen, Y and Murray, SJ and Ramharack, LA and Baldassano, RN and Parsons, TD and Beiting, DP},
title = {Remodeling of the maternal gut microbiome during pregnancy is shaped by parity.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {146},
pmid = {34176489},
issn = {2049-2618},
support = {4100068710//Commonwealth Universal Research Enhancement (CURE) program/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Parity ; Pregnancy ; *Premature Birth ; Prevotella ; Swine ; Treponema ; },
abstract = {BACKGROUND: The maternal microbiome has emerged as an important factor in gestational health and outcome and is associated with risk of preterm birth and offspring morbidity. Epidemiological evidence also points to successive pregnancies-referred to as maternal parity-as a risk factor for preterm birth, infant mortality, and impaired neonatal growth. Despite the fact that both the maternal microbiome and parity are linked to maternal-infant health, the impact of parity on the microbiome remains largely unexplored, in part due to the challenges of studying parity in humans.<br><br>RESULTS: Using synchronized pregnancies and dense longitudinal monitoring of the microbiome in pigs, we describe a microbiome trajectory during pregnancy and determine the extent to which parity modulates this trajectory. We show that the microbiome changes reproducibly during gestation and that this remodeling occurs more rapidly as parity increases. At the time of parturition, parity was linked to the relative abundance of several bacterial species, including Treponema bryantii, Lactobacillus amylovorus, and Lactobacillus reuteri. Strain tracking carried out in 18 maternal-offspring "quadrads"-each consisting of one mother sow and three piglets-linked maternal parity to altered levels of Akkermansia muciniphila, Prevotella stercorea, and Campylobacter coli in the infant gut 10 days after birth.<br><br>CONCLUSIONS: Collectively, these results identify parity as an important environmental factor that modulates the gut microbiome during pregnancy and highlight the utility of a swine model for investigating the microbiome in maternal-infant health. In addition, our data show that the impact of parity extends beyond the mother and is associated with alterations in the community of bacteria that colonize the offspring gut early in life. The bacterial species we identified as parity-associated in the mother and offspring have been shown to influence host metabolism in other systems, raising the possibility that such changes may influence host nutrient acquisition or utilization. These findings, taken together with our observation that even subtle differences in parity are associated with microbiome changes, underscore the importance of considering parity in the design and analysis of human microbiome studies during pregnancy and in infants. Video abstract.},
}
@article {pmid34168315,
year = {2021},
author = {Nayfach, S and Páez-Espino, D and Call, L and Low, SJ and Sberro, H and Ivanova, NN and Proal, AD and Fischbach, MA and Bhatt, AS and Hugenholtz, P and Kyrpides, NC},
title = {Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome.},
journal = {Nature microbiology},
volume = {6},
number = {7},
pages = {960-970},
pmid = {34168315},
issn = {2058-5276},
support = {P30 CA124435/CA/NCI NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/virology ; Bacteria/virology ; Bacteriophages/genetics ; Catalogs as Topic ; DNA Viruses/classification/*genetics ; DNA, Viral/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genetic Variation ; Genome, Viral/*genetics ; Humans ; Metagenomics ; Phylogeny ; Viral Proteins/genetics ; },
abstract = {Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.},
}
@article {pmid34168163,
year = {2021},
author = {Petersen, AØ and Julienne, H and Hyötyläinen, T and Sen, P and Fan, Y and Pedersen, HK and Jäntti, S and Hansen, TH and Nielsen, T and Jørgensen, T and Hansen, T and Myers, PN and Nielsen, HB and Ehrlich, SD and Orešič, M and Pedersen, O},
title = {Conjugated C-6 hydroxylated bile acids in serum relate to human metabolic health and gut Clostridia species.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {13252},
pmid = {34168163},
issn = {2045-2322},
mesh = {Adiposity ; Bile Acids and Salts/*blood ; Body Mass Index ; Cholic Acids/blood ; Chromatography, High Pressure Liquid ; Clostridium/genetics/*metabolism ; Deoxycholic Acid/blood ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Logistic Models ; Male ; Metagenomics ; Middle Aged ; Obesity/blood/microbiology ; Tandem Mass Spectrometry ; Taurocholic Acid/blood ; Waist Circumference ; },
abstract = {Knowledge about in vivo effects of human circulating C-6 hydroxylated bile acids (BAs), also called muricholic acids, is sparse. It is unsettled if the gut microbiome might contribute to their biosynthesis. Here, we measured a range of serum BAs and related them to markers of human metabolic health and the gut microbiome. We examined 283 non-obese and obese Danish adults from the MetaHit study. Fasting concentrations of serum BAs were quantified using ultra-performance liquid chromatography-tandem mass-spectrometry. The gut microbiome was characterized with shotgun metagenomic sequencing and genome-scale metabolic modeling. We find that tauro- and glycohyocholic acid correlated inversely with body mass index (P = 4.1e-03, P = 1.9e-05, respectively), waist circumference (P = 0.017, P = 1.1e-04, respectively), body fat percentage (P = 2.5e-03, P = 2.3e-06, respectively), insulin resistance (P = 0.051, P = 4.6e-4, respectively), fasting concentrations of triglycerides (P = 0.06, P = 9.2e-4, respectively) and leptin (P = 0.067, P = 9.2e-4). Tauro- and glycohyocholic acids, and tauro-a-muricholic acid were directly linked with a distinct gut microbial community primarily composed of Clostridia species (P = 0.037, P = 0.013, P = 0.027, respectively). We conclude that serum conjugated C-6-hydroxylated BAs associate with measures of human metabolic health and gut communities of Clostridia species. The findings merit preclinical interventions and human feasibility studies to explore the therapeutic potential of these BAs in obesity and type 2 diabetes.},
}
@article {pmid34162081,
year = {2021},
author = {Kaur, I and Gaur, VK and Regar, RK and Roy, A and Srivastava, PK and Gaur, R and Manickam, N and Barik, SK},
title = {Plants exert beneficial influence on soil microbiome in a HCH contaminated soil revealing advantage of microbe-assisted plant-based HCH remediation of a dumpsite.},
journal = {Chemosphere},
volume = {280},
number = {},
pages = {130690},
doi = {10.1016/j.chemosphere.2021.130690},
pmid = {34162081},
issn = {1879-1298},
mesh = {Biodegradation, Environmental ; Hexachlorocyclohexane/analysis ; *Microbiota ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Persistence of hexachlorocyclohexane (HCH) pesticide is a major problem for its disposal. Soil microflora plays an important role in remediating contaminated sites. Keeping concepts of microbial- and phyto-remediation together, the difference between soil microflora with and without association of HCH accumulating plant species was studied. Metagenomic analysis among the non-plant soil (BS) (∑HCH 434.19 mg/g), rhizospheric soil of shrubs (RSS) (∑HCH 157.31 mg/g), and rhizospheric soil of trees (RSD) (∑HCH 105.39 mg/g) revealed significant differences in microbial communities. Shrubs and trees occurred at a long-term dumpsite accumulated α- and β- HCH residues. Plant rhizospheric soils exhibited high richness and evenness with higher diversity indices compared to the non-plant soil. Order Rhizobiales was most abundant in all soils and Streptomycetales was absent in the BS soil. Proteobacteria and Ascomycota were highest in BS soil, while Actinobacteria was enriched in both the plant rhizospheric soil samples. In BS soil, Pseudomonas, Sordaria, Caulobacter, Magnetospirillum, Rhodospirillum were abundant. While, genera Actinoplanes, Streptomyces, Bradyrhizobium, Rhizobium, Azospirillum, Agrobacterium are abundant in RSD soil. Selected plants have accumulated HCH residues from soil and exerted positive impacts on soil microbial communities in HCH contaminated site. This study advocates microbe-assisted plant-based bioremediation strategy to remediate HCH contamination.},
}
@article {pmid34160629,
year = {2021},
author = {Aguirre-von-Wobeser, E and Alonso-Sánchez, A and Méndez-Bravo, A and Villanueva Espino, LA and Reverchon, F},
title = {Barks from avocado trees of different geographic locations have consistent microbial communities.},
journal = {Archives of microbiology},
volume = {203},
number = {7},
pages = {4593-4607},
pmid = {34160629},
issn = {1432-072X},
support = {CB-2014-01-242956//SEP/CONACyT/ ; },
mesh = {Archaea/genetics ; Bacteria/genetics ; *Biodiversity ; Fungi/genetics/physiology ; Metagenomics ; *Microbiota/genetics/physiology ; *Persea/microbiology ; *Plant Bark/microbiology ; Soil Microbiology ; },
abstract = {Bark is a permanent surface for microbial colonization at the interface of trees and the surrounding air, but little is known about its microbial communities. We used shotgun metagenomic sequencing to analyze the bark microbiomes of avocado trees from two orchards, and compared one of them to rhizospheric soil. It was shown that the microbial communities of avocado bark have a well-defined taxonomic structure, with consistent patterns of abundance of bacteria, fungi, and archaea, even in trees from two different locations. Bark microbial communities were distinct from rhizospheric soil, although they showed overlap in some taxa. Thus, avocado bark is a well-defined environment, providing niches for specific taxonomic groups, many of which are also found in other aerial plant tissues. The present in-depth characterization of bark microbial communities can form a basis for their future manipulation for agronomical purposes.},
}
@article {pmid34158518,
year = {2021},
author = {Shin, CM and Choi, YJ and Lee, DH and Moon, JS and Kim, TY and Kim, YK and Lee, WH and Yoon, H and Park, YS and Kim, N},
title = {Validity and safety of ID-JPL934 in lower gastrointestinal symptom improvement.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {13046},
pmid = {34158518},
issn = {2045-2322},
mesh = {Adult ; Cytokines/blood ; Extracellular Vesicles/drug effects/metabolism ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Tract/drug effects/*pathology ; Humans ; Inflammation Mediators/blood ; Male ; Metagenomics ; Probiotics/*adverse effects/*pharmacology ; },
abstract = {The study evaluated the efficacy of ID-JPL934, a probiotic preparation containing Lactobacillus johnsonii IDCC 9203, Lactobacillus plantarum IDCC 3501 and Bifidobacterium lactis IDCC 4301, in relieving lower gastrointestinal symptoms. A total of 112 subjects with lower gastrointestinal symptoms were consecutively enrolled. They were randomized into either ID-JPL934 administration group or placebo group. Bristol stool form, stool frequency, and abnormal bowel movement symptoms were recorded at baseline and week 2, 6, and 8. Primary endpoint was improvement in overall symptoms at week 8. Fecal samples were collected to measure the probiotic levels in feces using quantitative polymerase chain reaction (qPCR), and to perform metagenomic analysis of microbiome originating from bacteria-derived extracellular vesicles and bacterial cells via 16S rDNA sequencing. Of the 112 subjects, 104 (54 in ID-JPL934 group and 50 in placebo group) completed the entire study protocol. A higher relief of overall symptoms was found in ID-JPL934 group than in placebo group (p = 0.016). Among lower gastrointestinal symptoms, abdominal pain and bloating scores were more decreased in ID-JPL934 group than in placebo group (p < 0.05). The fecal microbiome profiles of the two groups did not differ. However, the qPCR analysis showed significant increase in the levels of Lactobacillus johnsonii and Bifidobacterium lactis in feces post-treatment in ID-JPL934 group than in placebo group (p < 0.05 by repeated measure ANOVA). In conclusion, ID-JPL934 is effective in relieving lower gastrointestinal symptoms. Exposure to ID-JPL934 may increase the abundance of Lactobacillus johnsonii and Bifidobacterium lactis in the gut.Trial registration: ClinicalTrials.gov number, NCT03395626.},
}
@article {pmid32742640,
year = {2020},
author = {Wagner, J and Kancherla, J and Braccia, D and Matsumara, J and Felix, V and Crabtree, J and Mahurkar, A and Corrada Bravo, H},
title = {Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz.},
journal = {F1000Research},
volume = {9},
number = {},
pages = {601},
pmid = {32742640},
issn = {2046-1402},
support = {R01 GM114267/GM/NIGMS NIH HHS/United States ; U54 DK102556/DK/NIDDK NIH HHS/United States ; },
mesh = {*Data Analysis ; Data Interpretation, Statistical ; Humans ; *Microbiota ; Research Design ; },
abstract = {The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual's health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analysis and visualization tool, with the iHMP Data Coordination Center web portal and the HMP2Data R/Bioconductor package. We describe integrative statistical and visual analyses of two datasets from iHMP using Metaviz along with the metagenomeSeq R/Bioconductor package for statistical analysis of differential abundance analysis. These use cases demonstrate the utility of a combined approach to access and analyze data from this resource.},
}
@article {pmid34154658,
year = {2021},
author = {West, PT and Peters, SL and Olm, MR and Yu, FB and Gause, H and Lou, YC and Firek, BA and Baker, R and Johnson, AD and Morowitz, MJ and Hettich, RL and Banfield, JF},
title = {Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {142},
pmid = {34154658},
issn = {2049-2618},
support = {S10 OD018174/OD/NIH HHS/United States ; },
mesh = {Candida parapsilosis/genetics ; *Candidiasis ; Humans ; Infant ; Infant, Newborn ; Microbial Sensitivity Tests ; *Microbiota ; Proteomics ; Transcriptome ; },
abstract = {BACKGROUND: Candida parapsilosis is a common cause of invasive candidiasis, especially in newborn infants, and infections have been increasing over the past two decades. C. parapsilosis has been primarily studied in pure culture, leaving gaps in understanding of its function in a microbiome context.<br><br>RESULTS: Here, we compare five unique C. parapsilosis genomes assembled from premature infant fecal samples, three of which are newly reconstructed, and analyze their genome structure, population diversity, and in situ activity relative to reference strains in pure culture. All five genomes contain hotspots of single nucleotide variants, some of which are shared by strains from multiple hospitals. A subset of environmental and hospital-derived genomes share variants within these hotspots suggesting derivation of that region from a common ancestor. Four of the newly reconstructed C. parapsilosis genomes have 4 to 16 copies of the gene RTA3, which encodes a lipid translocase and is implicated in antifungal resistance, potentially indicating adaptation to hospital antifungal use. Time course metatranscriptomics and metaproteomics on fecal samples from a premature infant with a C. parapsilosis blood infection revealed highly variable in situ expression patterns that are distinct from those of similar strains in pure cultures. For example, biofilm formation genes were relatively less expressed in situ, whereas genes linked to oxygen utilization were more highly expressed, indicative of growth in a relatively aerobic environment. In gut microbiome samples, C. parapsilosis co-existed with Enterococcus faecalis that shifted in relative abundance over time, accompanied by changes in bacterial and fungal gene expression and proteome composition.<br><br>CONCLUSIONS: The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes. Video abstract.},
}
@article {pmid34152440,
year = {2021},
author = {Schmidt, BM and Erb-Downward, J and Ranjan, P and Dickson, R},
title = {Metagenomics to Identify Pathogens in Diabetic Foot Ulcers and the Potential Impact for Clinical Care.},
journal = {Current diabetes reports},
volume = {21},
number = {8},
pages = {26},
pmid = {34152440},
issn = {1539-0829},
mesh = {Adult ; *Diabetes Mellitus ; *Diabetic Foot ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Wound Healing ; },
abstract = {PURPOSE OF REVIEW: Diabetes mellitus may affect every third adult American by 2050, and about one-third will develop a diabetic foot ulcer (DFU) during their lifetime. The current standard of care results in healing of less than 50% of all DFUs. Many individuals with DFU develop limb-threatening infection which place them at risk for additional morbidity and mortality. We review research associated with culture-independent next-generation sequencing techniques pertaining to diabetic foot ulcers and their potential for clinical application.<br><br>RECENT FINDINGS: Diabetic foot ulcers are a growing problem and clinicians are limited by their reliance on conventional culture. Metagenomic sequencing technology provides an unparalleled viewpoint of the polymicrobial constituency of DFU. The microbiome techniques used to study the microbial constituency of DFU may offer insight to improve care for these patients, but without standardized approaches in research based on real-world clinical practices, a significant knowledge gap will remain.},
}
@article {pmid34150671,
year = {2021},
author = {Townsend, EM and Kelly, L and Muscatt, G and Box, JD and Hargraves, N and Lilley, D and Jameson, E},
title = {The Human Gut Phageome: Origins and Roles in the Human Gut Microbiome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {643214},
pmid = {34150671},
issn = {2235-2988},
support = {BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Bacteria ; *Bacteriophages ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Virome ; },
abstract = {The investigation of the microbial populations of the human body, known as the microbiome, has led to a revolutionary field of science, and understanding of its impacts on human development and health. The majority of microbiome research to date has focussed on bacteria and other kingdoms of life, such as fungi. Trailing behind these is the interrogation of the gut viruses, specifically the phageome. Bacteriophages, viruses that infect bacterial hosts, are known to dictate the dynamics and diversity of bacterial populations in a number of ecosystems. However, the phageome of the human gut, while of apparent importance, remains an area of many unknowns. In this paper we discuss the role of bacteriophages within the human gut microbiome. We examine the methods used to study bacteriophage populations, how this evolved over time and what we now understand about the phageome. We review the phageome development in infancy, and factors that may influence phage populations in adult life. The role and action of the phageome is then discussed at both a biological-level, and in the broader context of human health and disease.},
}
@article {pmid34149688,
year = {2021},
author = {Pérez-Sáez, MJ and Uffing, A and Leon, J and Murakami, N and Watanabe, A and Borges, TJ and Sabbisetti, VS and Cureton, P and Kenyon, V and Keating, L and Yee, K and Fernandes Satiro, CA and Serena, G and Hildebrandt, F and Riella, CV and Libermann, TA and Wang, M and Pascual, J and Bonventre, JV and Cravedil, P and Fasano, A and Riella, LV},
title = {Immunological Impact of a Gluten-Free Dairy-Free Diet in Children With Kidney Disease: A Feasibility Study.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {624821},
pmid = {34149688},
issn = {1664-3224},
support = {K08 DK120868/DK/NIDDK NIH HHS/United States ; R01 DK076683/DK/NIDDK NIH HHS/United States ; },
mesh = {Adolescent ; Biomarkers/blood/urine ; Child ; Child, Preschool ; Cytokines/blood ; Dairy Products/*adverse effects ; *Diet, Gluten-Free/adverse effects ; Feasibility Studies ; Female ; Gastrointestinal Microbiome ; Humans ; Infant ; Inflammation Mediators/blood ; Intestines/microbiology ; Male ; Nephrotic Syndrome/*congenital/diagnosis/diet therapy/immunology/microbiology ; Pilot Projects ; Proof of Concept Study ; Prospective Studies ; T-Lymphocytes, Regulatory/immunology/metabolism ; Th17 Cells/immunology/metabolism ; Time Factors ; Treatment Outcome ; Young Adult ; },
abstract = {Kidney disease affects 10% of the world population and is associated with increased mortality. Steroid-resistant nephrotic syndrome (SRNS) is a leading cause of end-stage kidney disease in children, often failing standard immunosuppression. Here, we report the results of a prospective study to investigate the immunological impact and safety of a gluten-free and dairy-free (GF/DF) diet in children with SRNS. The study was organized as a four-week summer camp implementing a strict GF/DF diet with prospective collection of blood, urine and stool in addition to whole exome sequencing WES of DNA of participants. Using flow cytometry, proteomic assays and microbiome metagenomics, we show that GF/DF diet had a major anti-inflammatory effect in all participants both at the protein and cellular level with 4-fold increase in T regulatory/T helper 17 cells ratio and the promotion of a favorable regulatory gut microbiota. Overall, GF/DF can have a significant anti-inflammatory effect in children with SRNS and further trials are warranted to investigate this potential dietary intervention in children with SRNS.},
}
@article {pmid34149685,
year = {2021},
author = {Das, Q and Shay, J and Gauthier, M and Yin, X and Hasted, TL and Ross, K and Julien, C and Yacini, H and Kennes, YM and Warriner, K and Marcone, MF and Diarra, MS},
title = {Effects of Vaccination Against Coccidiosis on Gut Microbiota and Immunity in Broiler Fed Bacitracin and Berry Pomace.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {621803},
pmid = {34149685},
issn = {1664-3224},
mesh = {Animal Feed ; Animal Nutritional Physiological Phenomena ; Animals ; Bacitracin ; Bacterial Infections/*immunology ; Bird Diseases/*immunology ; Blueberry Plants ; Cecum/*microbiology ; Chickens/*immunology ; Coccidia/*physiology ; Coccidiosis/*immunology ; Eimeria/*physiology ; Gastrointestinal Microbiome/*immunology ; Immunity, Humoral ; Lipid Metabolism ; Protozoan Vaccines/*immunology ; Vaccination ; Vaccinium macrocarpon ; },
abstract = {Feeding practices have been found to influence gut microbiota which play a major role in immunity of poultry. In the present study, changes in cecal microbiota and humoral responses resulting in the 55 ppm bacitracin (BACI), 1% each of cranberry (CP1) and wild blueberry (BP1) pomace alone or in combination (CP+BP) feeding in broiler Cobb 500 vaccinated or not against coccidiosis were investigated. In the non-vaccinated group, no significant treatment effects were observed on performance parameters. Vaccination significantly affected bird's performance parameters particularly during the growing phase from 10 to 20 days of age. In general, the prevalence of coccidiosis and necrotic enteritis (NE) was reduced by vaccination (P < 0.05). BACI-treated birds showed low intestinal lesion scores, and both CP1 and BP1 feed supplementations reduced Eimeria acervulina and Clostridium perfringens incidences similar to BACI. Vaccination induced change in serum enzymes, minerals, and lipid levels in 21-day old birds while, levels of triglyceride (TRIG) and non-esterified fatty acids (NEFA) were higher (P < 0.05) in CP1 treated non-vaccinated group than in the control. The levels of NEFA were lower in BACI- and CP1-fed birds than in the control in non-vaccinated day 28 old birds. The highest levels of all estimated three immunoglobulins (IgY, IgM, and IgA) were found in the vaccinated birds. Metagenomics analysis of the cecal bacterial community in 21-day old birds showed the presence of Firmicutes (90%), Proteobacteria (5%), Actinobacteria (2%), and Bacteroidetes (2%). In the vaccinated group, an effect of BACI was noted on Proteobacteria (P = 0.03). Vaccination and/or dietary treatments influenced the population of Lactobacillaceae, Enterobacteriaceae, Clostridiaceae, and Streptococcaceae which were among the most abundant families. Overall, this study revealed that besides their beneficial effects on performance, alike bacitracin, berry pomaces in poultry feed have profound impacts on the chicken cecal microbiota and blood metabolites that could be influenced by vaccination against coccidiosis.},
}
@article {pmid34149649,
year = {2021},
author = {Morrison, MD and Thissen, JB and Karouia, F and Mehta, S and Urbaniak, C and Venkateswaran, K and Smith, DJ and Jaing, C},
title = {Investigation of Spaceflight Induced Changes to Astronaut Microbiomes.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {659179},
pmid = {34149649},
issn = {1664-302X},
abstract = {The International Space Station (ISS) is a uniquely enclosed environment that has been continuously occupied for the last two decades. Throughout its operation, protecting the health of the astronauts on-board has been a high priority. The human microbiome plays a significant role in maintaining human health, and disruptions in the microbiome have been linked to various diseases. To evaluate the effects of spaceflight on the human microbiome, body swabs and saliva samples were collected from four ISS astronauts on consecutive expeditions. Astronaut samples were analyzed using shotgun metagenomic sequencing and microarrays to characterize the microbial biodiversity before, during, and after the astronauts' time onboard the ISS. Samples were evaluated at an individual and population level to identify changes in microbial diversity and abundance. No significant changes in the number or relative abundance of taxa were observed between collection time points when samples from all four astronauts were analyzed together. When the astronauts' saliva samples were analyzed individually, the saliva samples of some astronauts showed significant changes in the relative abundance of taxa during and after spaceflight. The relative abundance of Prevotella in saliva samples increased during two astronauts' time onboard the ISS while the relative abundance of other commensal taxa such as Neisseria, Rothia, and Haemophilus decreased. The abundance of some antimicrobial resistance genes within the saliva samples also showed significant changes. Most notably, elfamycin resistance gene significantly increased in all four astronauts post-flight and a CfxA6 beta-lactam marker significantly increased during spaceflight but returned to normal levels post-flight. The combination of both shotgun metagenomic sequencing and microarrays showed the benefit of both technologies in monitoring microbes on board the ISS. There were some changes in each astronaut's microbiome during spaceflight, but these changes were not universal for all four astronauts. Two antimicrobial resistance gene markers did show a significant change in abundance in the saliva samples of all four astronauts across their collection times. These results provide insight for future ISS microbial monitoring studies and targets for antimicrobial resistance screenings.},
}
@article {pmid34143768,
year = {2021},
author = {Prost, V and Gazut, S and Brüls, T},
title = {A zero inflated log-normal model for inference of sparse microbial association networks.},
journal = {PLoS computational biology},
volume = {17},
number = {6},
pages = {e1009089},
pmid = {34143768},
issn = {1553-7358},
mesh = {Algorithms ; Computational Biology ; Computer Simulation ; Metagenome ; Metagenomics/statistics &amp; numerical data ; Microbial Consortia/genetics/physiology ; *Microbiota/genetics/physiology ; *Models, Biological ; Multivariate Analysis ; Normal Distribution ; Synthetic Biology ; },
abstract = {The advent of high-throughput metagenomic sequencing has prompted the development of efficient taxonomic profiling methods allowing to measure the presence, abundance and phylogeny of organisms in a wide range of environmental samples. Multivariate sequence-derived abundance data further has the potential to enable inference of ecological associations between microbial populations, but several technical issues need to be accounted for, like the compositional nature of the data, its extreme sparsity and overdispersion, as well as the frequent need to operate in under-determined regimes. The ecological network reconstruction problem is frequently cast into the paradigm of Gaussian Graphical Models (GGMs) for which efficient structure inference algorithms are available, like the graphical lasso and neighborhood selection. Unfortunately, GGMs or variants thereof can not properly account for the extremely sparse patterns occurring in real-world metagenomic taxonomic profiles. In particular, structural zeros (as opposed to sampling zeros) corresponding to true absences of biological signals fail to be properly handled by most statistical methods. We present here a zero-inflated log-normal graphical model (available at https://github.com/vincentprost/Zi-LN) specifically aimed at handling such "biological" zeros, and demonstrate significant performance gains over state-of-the-art statistical methods for the inference of microbial association networks, with most notable gains obtained when analyzing taxonomic profiles displaying sparsity levels on par with real-world metagenomic datasets.},
}
@article {pmid34140187,
year = {2021},
author = {Cruz-O'Byrne, R and Piraneque-Gambasica, N and Aguirre-Forero, S},
title = {Microbial diversity associated with spontaneous coffee bean fermentation process and specialty coffee production in northern Colombia.},
journal = {International journal of food microbiology},
volume = {354},
number = {},
pages = {109282},
doi = {10.1016/j.ijfoodmicro.2021.109282},
pmid = {34140187},
issn = {1879-3460},
mesh = {Bacteria/classification/metabolism ; *Biodiversity ; *Coffea/microbiology ; Colombia ; *Fermentation ; Fungi/classification/metabolism ; *Microbiota/physiology ; *Seeds/metabolism/microbiology ; },
abstract = {Coffee fermentation involves the action of microorganisms, whose metabolism has a significant influence on the composition of the beans and, consequently, on the beverage's sensory characteristics. In this study, the microbial diversity during the wet fermentation of Coffea arabica L. in the Sierra Nevada of Santa Marta (SNSM) in Colombia was explored by high-throughput sequencing and the resulting cup quality through the standards of the Specialty Coffee Association. The taxonomic assignment of sequence reads showed a high microbial diversity comprised of 695 bacterial and 156 fungal genera. The microbial community was dominated by the Lactic Acid Bacteria (LAB) Leuconostoc, the yeast Kazachstania, and the Acetic Acid Bacteria (AAB) Acetobacter. Co-occurrence relationships suggested synergistic patterns between populations of LAB-AAB, yeasts-AAB, Leuconostoc-Prevotella, LAB-ABB-Selenomonas, and yeasts-fungi-nonLAB-nonAAB, which may result in the production of metabolites that positively impact the sensory attributes of coffee. The beverages produced were classified as specialty coffees, and their score was positively influenced by the fungal richness and the abundance of unclassified Lactobacillales, Pichia, and Pseudomonas. The findings show the richness and microbial diversity of the SNSM and serve as input for future research such as the analysis of microbial-derived metabolites and the establishment of starter cultures in coffee processing that guarantee the generation of high-quality beverages, the standardization of processes, the reduction of economic losses, and the production of value-added products that allow taking advantage of specialty coffee market.},
}
@article {pmid34133435,
year = {2021},
author = {Hardmeier, I and Aeberhard, N and Qi, W and Schoenbaechler, K and Kraettli, H and Hatt, JM and Fraefel, C and Kubacki, J},
title = {Metagenomic analysis of fecal and tissue samples from 18 endemic bat species in Switzerland revealed a diverse virus composition including potentially zoonotic viruses.},
journal = {PloS one},
volume = {16},
number = {6},
pages = {e0252534},
pmid = {34133435},
issn = {1932-6203},
mesh = {Adenoviridae/classification/genetics ; Animals ; Chiroptera/classification/*virology ; Disease Reservoirs/virology ; Feces/*virology ; Genetic Variation ; Genome, Viral/genetics ; Hepevirus/classification/genetics ; Humans ; Metagenomics/*methods ; Middle East Respiratory Syndrome Coronavirus/classification/genetics ; Phylogeny ; Rotavirus/classification/genetics ; Sequence Analysis, DNA/methods ; Switzerland ; Virome/*genetics ; Viruses/classification/*genetics ; Zoonoses/*virology ; },
abstract = {Many recent disease outbreaks in humans had a zoonotic virus etiology. Bats in particular have been recognized as reservoirs to a large variety of viruses with the potential to cross-species transmission. In order to assess the risk of bats in Switzerland for such transmissions, we determined the virome of tissue and fecal samples of 14 native and 4 migrating bat species. In total, sequences belonging to 39 different virus families, 16 of which are known to infect vertebrates, were detected. Contigs of coronaviruses, adenoviruses, hepeviruses, rotaviruses A and H, and parvoviruses with potential zoonotic risk were characterized in more detail. Most interestingly, in a ground stool sample of a Vespertilio murinus colony an almost complete genome of a Middle East respiratory syndrome-related coronavirus (MERS-CoV) was detected by Next generation sequencing and confirmed by PCR. In conclusion, bats in Switzerland naturally harbour many different viruses. Metagenomic analyses of non-invasive samples like ground stool may support effective surveillance and early detection of viral zoonoses.},
}
@article {pmid34130621,
year = {2021},
author = {Glickman, C and Hendrix, J and Strong, M},
title = {Simulation study and comparative evaluation of viral contiguous sequence identification tools.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {329},
pmid = {34130621},
issn = {1471-2105},
mesh = {*Bacteriophages/genetics ; Genome, Viral/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbiota ; *Viruses/genetics ; },
abstract = {BACKGROUND: Viruses, including bacteriophages, are important components of environmental and human associated microbial communities. Viruses can act as extracellular reservoirs of bacterial genes, can mediate microbiome dynamics, and can influence the virulence of clinical pathogens. Various targeted metagenomic analysis techniques detect viral sequences, but these methods often exclude large and genome integrated viruses. In this study, we evaluate and compare the ability of nine state-of-the-art bioinformatic tools, including Vibrant, VirSorter, VirSorter2, VirFinder, DeepVirFinder, MetaPhinder, Kraken 2, Phybrid, and a BLAST search using identified proteins from the Earth Virome Pipeline to identify viral contiguous sequences (contigs) across simulated metagenomes with different read distributions, taxonomic compositions, and complexities.<br><br>RESULTS: Of the tools tested in this study, VirSorter achieved the best F1 score while Vibrant had the highest average F1 score at predicting integrated prophages. Though less balanced in its precision and recall, Kraken2 had the highest average precision by a substantial margin. We introduced the machine learning tool, Phybrid, which demonstrated an improvement in average F1 score over tools such as MetaPhinder. The tool utilizes machine learning with both gene content and nucleotide features. The addition of nucleotide features improves the precision and recall compared to the gene content features alone.Viral identification by all tools was not impacted by underlying read distribution but did improve with contig length. Tool performance was inversely related to taxonomic complexity and varied by the phage host. For instance, Rhizobium and Enterococcus phages were identified consistently by the tools; whereas, Neisseria prophage sequences were commonly missed in this study.<br><br>CONCLUSION: This study benchmarked the performance of nine state-of-the-art bioinformatic tools to identify viral contigs across different simulation conditions. This study explored the ability of the tools to identify integrated prophage elements traditionally excluded from targeted sequencing approaches. Our comprehensive analysis of viral identification tools to assess their performance in a variety of situations provides valuable insights to viral researchers looking to mine viral elements from publicly available metagenomic data.},
}
@article {pmid34125646,
year = {2021},
author = {Hong, Y and Sheng, L and Zhong, J and Tao, X and Zhu, W and Ma, J and Yan, J and Zhao, A and Zheng, X and Wu, G and Li, B and Han, B and Ding, K and Zheng, N and Jia, W and Li, H},
title = {Desulfovibrio vulgaris, a potent acetic acid-producing bacterium, attenuates nonalcoholic fatty liver disease in mice.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-20},
pmid = {34125646},
issn = {1949-0984},
mesh = {Acetic Acid/*metabolism ; Animals ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; CD36 Antigens/genetics/metabolism ; Desulfovibrio vulgaris/growth &amp; development/*metabolism ; Diet, High-Fat/adverse effects ; Fatty Acid Synthases/genetics/metabolism ; Fatty Acids, Volatile/metabolism ; Gastrointestinal Microbiome ; Humans ; Liver/enzymology/metabolism ; Male ; Mice ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/*drug therapy/etiology/genetics/microbiology ; Probiotics/*administration &amp; dosage ; },
abstract = {The emerging evidence supports the use of prebiotics like herb-derived polysaccharides for treating nonalcoholic fatty liver disease (NAFLD) by modulating gut microbiome. The present study was initiated on the microbiota-dependent anti-NAFLD effect of Astragalus polysaccharides (APS) extracted from Astragalus mongholicus Bunge in high-fat diet (HFD)-fed mice. However, the exact mechanisms underlying the beneficial effects of APS on NAFLD formation remain poorly understood.Co-housing experiment was used to assess the microbiota dependent anti-NAFLD effect of APS. Then, targeted metabolomics and metagenomics were adopted for determining short-chain fatty acids (SCFAs) and bacteria that were specifically enriched by APS. Further in vitro experiment was carried out to test the capacity of SCFAs-producing of identified bacterium. Finally, the anti-NAFLD efficacy of identified bacterium was tested in HFD-fed mice.Our results first demonstrated the anti-NAFLD effect of APS in HFD-fed mice and the contribution of gut microbiota. Moreover, our results indicated that SCFAs, predominantly acetic acid were elevated in APS-supplemented mice and ex vivo experiment. Metagenomics revealed that D. vulgaris from Desulfovibrio genus was not only enriched by APS, but also a potent generator of acetic acid, which showed significant anti-NAFLD effects in HFD-fed mice. In addition, D. vulgaris modulated the hepatic gene expression pattern of lipids metabolism, particularly suppressed hepatic fatty acid synthase (FASN) and CD36 protein expression.Our results demonstrate that APS enriched D. vulgaris is effective on attenuating hepatic steatosis possibly through producing acetic acid, and modulation on hepatic lipids metabolism in mice. Further studies are warranted to explore the long-term impacts of D. vulgaris on host metabolism and the underlying mechanism.},
}
@article {pmid34119873,
year = {2021},
author = {Batool, M and Blazier, JC and Rogovska, YV and Wang, J and Liu, S and Nebogatkin, IV and Rogovskyy, AS},
title = {Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus.},
journal = {Ticks and tick-borne diseases},
volume = {12},
number = {5},
pages = {101768},
doi = {10.1016/j.ttbdis.2021.101768},
pmid = {34119873},
issn = {1877-9603},
mesh = {Animals ; Bacteria/genetics/*isolation &amp; purification ; Female ; Geography ; Ixodes/*microbiology ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Sex Factors ; Ukraine ; },
abstract = {Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.},
}
@article {pmid34118976,
year = {2021},
author = {Xie, F and Jin, W and Si, H and Yuan, Y and Tao, Y and Liu, J and Wang, X and Yang, C and Li, Q and Yan, X and Lin, L and Jiang, Q and Zhang, L and Guo, C and Greening, C and Heller, R and Guan, LL and Pope, PB and Tan, Z and Zhu, W and Wang, M and Qiu, Q and Li, Z and Mao, S},
title = {An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {137},
pmid = {34118976},
issn = {2049-2618},
mesh = {Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Phylogeny ; Ruminants ; },
abstract = {BACKGROUND: Gastrointestinal tract (GIT) microbiomes in ruminants play major roles in host health and thus animal production. However, we lack an integrated understanding of microbial community structure and function as prior studies. are predominantly biased towards the rumen. Therefore, to acquire a microbiota inventory of the discrete GIT compartments, In this study, we used shotgun metagenomics to profile the microbiota of 370 samples that represent 10 GIT regions of seven ruminant species.<br><br>RESULTS: Our analyses reconstructed a GIT microbial reference catalog with > 154 million nonredundant genes and identified 8745 uncultured candidate species from over 10,000 metagenome-assembled genomes. The integrated gene catalog across the GIT regions demonstrates spatial associations between the microbiome and physiological adaptations, and 8745 newly characterized genomes substantially expand the genomic landscape of ruminant microbiota, particularly those from the lower gut. This substantially expands the previously known set of endogenous microbial diversity and the taxonomic classification rate of the GIT microbiome. These candidate species encode hundreds of enzymes and novel biosynthetic gene clusters that improve our understanding concerning methane production and feed efficiency in ruminants. Overall, this study expands the characterization of the ruminant GIT microbiota at unprecedented spatial resolution and offers clues for improving ruminant livestock production in the future.<br><br>CONCLUSIONS: Having access to a comprehensive gene catalog and collections of microbial genomes provides the ability to perform efficiently genome-based analysis to achieve a detailed classification of GIT microbial ecosystem composition. Our study will bring unprecedented power in future association studies to investigate the impact of the GIT microbiota in ruminant health and production. Video abstract.},
}
@article {pmid34118665,
year = {2021},
author = {Zhang, L and Gong, X and Wang, L and Guo, K and Cao, S and Zhou, Y},
title = {Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system.},
journal = {The Science of the total environment},
volume = {791},
number = {},
pages = {148096},
doi = {10.1016/j.scitotenv.2021.148096},
pmid = {34118665},
issn = {1879-1026},
mesh = {Anaerobiosis ; Bioreactors ; Hydrolysis ; *Metagenomics ; Methane ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sewage ; },
abstract = {Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.},
}
@article {pmid34117246,
year = {2021},
author = {Lloréns-Rico, V and Vieira-Silva, S and Gonçalves, PJ and Falony, G and Raes, J},
title = {Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3562},
pmid = {34117246},
issn = {2041-1723},
mesh = {Benchmarking/*methods ; Classification ; Computational Biology/*methods ; Dysbiosis/microbiology ; Electronic Data Processing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Selection Bias ; },
abstract = {While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.},
}
@article {pmid34114607,
year = {2021},
author = {Aevarsson, A and Kaczorowska, AK and Adalsteinsson, BT and Ahlqvist, J and Al-Karadaghi, S and Altenbuchner, J and Arsin, H and Átlasson, ÚÁ and Brandt, D and Cichowicz-Cieślak, M and Cornish, KAS and Courtin, J and Dabrowski, S and Dahle, H and Djeffane, S and Dorawa, S and Dusaucy, J and Enault, F and Fedøy, AE and Freitag-Pohl, S and Fridjonsson, OH and Galiez, C and Glomsaker, E and Guérin, M and Gundesø, SE and Gudmundsdóttir, EE and Gudmundsson, H and Håkansson, M and Henke, C and Helleux, A and Henriksen, JR and Hjörleifdóttir, S and Hreggvidsson, GO and Jasilionis, A and Jochheim, A and Jónsdóttir, I and Jónsdóttir, LB and Jurczak-Kurek, A and Kaczorowski, T and Kalinowski, J and Kozlowski, LP and Krupovic, M and Kwiatkowska-Semrau, K and Lanes, O and Lange, J and Lebrat, J and Linares-Pastén, J and Liu, Y and Lorentsen, SA and Lutterman, T and Mas, T and Merré, W and Mirdita, M and Morzywołek, A and Ndela, EO and Karlsson, EN and Olgudóttir, E and Pedersen, C and Perler, F and Pétursdóttir, SK and Plotka, M and Pohl, E and Prangishvili, D and Ray, JL and Reynisson, B and Róbertsdóttir, T and Sandaa, RA and Sczyrba, A and Skírnisdóttir, S and Söding, J and Solstad, T and Steen, IH and Stefánsson, SK and Steinegger, M and Overå, KS and Striberny, B and Svensson, A and Szadkowska, M and Tarrant, EJ and Terzian, P and Tourigny, M and Bergh, TVD and Vanhalst, J and Vincent, J and Vroling, B and Walse, B and Wang, L and Watzlawick, H and Welin, M and Werbowy, O and Wons, E and Zhang, R},
title = {Going to extremes - a metagenomic journey into the dark matter of life.},
journal = {FEMS microbiology letters},
volume = {368},
number = {12},
pages = {},
doi = {10.1093/femsle/fnab067},
pmid = {34114607},
issn = {1574-6968},
mesh = {Bioprospecting/organization &amp; administration ; Computational Biology ; Databases, Genetic ; Europe ; Genome, Viral/*genetics ; Hydrothermal Vents/virology ; *Metagenomics ; Viral Proteins/chemistry/genetics/metabolism ; Virome/genetics ; Viruses/classification/genetics ; },
abstract = {The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.},
}
@article {pmid34112927,
year = {2021},
author = {Ericsson, AC and Hart, ML and Kwan, J and Lanoue, L and Bower, LR and Araiza, R and Kent Lloyd, KC and Franklin, CL},
title = {Supplier-origin mouse microbiomes significantly influence locomotor and anxiety-related behavior, body morphology, and metabolism.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {716},
pmid = {34112927},
issn = {2399-3642},
mesh = {Animals ; Anxiety/metabolism/microbiology/physiopathology ; Behavior, Animal ; Disease Models, Animal ; Exploratory Behavior ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Locomotion ; Lymphopoiesis ; Male ; Mice/anatomy &amp; histology/*microbiology/physiology ; Mice, Inbred ICR ; },
abstract = {The mouse is the most commonly used model species in biomedical research. Just as human physical and mental health are influenced by the commensal gut bacteria, mouse models of disease are influenced by the fecal microbiome (FM). The source of mice represents one of the strongest influences on the FM and can influence the phenotype of disease models. The FM influences behavior in mice leading to the hypothesis that mice of the same genetic background from different vendors, will have different behavioral phenotypes. To test this hypothesis, colonies of CD-1 mice, rederived via embryo transfer into surrogate dams from four different suppliers, were subjected to phenotyping assays assessing behavior and physiological parameters. Significant differences in behavior, growth rate, metabolism, and hematological parameters were observed. Collectively, these findings show the profound influence of supplier-origin FMs on host behavior and physiology in healthy, genetically similar, wild-type mice maintained in identical environments.},
}
@article {pmid34111423,
year = {2021},
author = {Hildebrand, F and Gossmann, TI and Frioux, C and Özkurt, E and Myers, PN and Ferretti, P and Kuhn, M and Bahram, M and Nielsen, HB and Bork, P},
title = {Dispersal strategies shape persistence and evolution of human gut bacteria.},
journal = {Cell host &amp; microbe},
volume = {29},
number = {7},
pages = {1167-1176.e9},
pmid = {34111423},
issn = {1934-6069},
support = {/ERC_/European Research Council/International ; },
mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/classification/drug effects/genetics/*isolation &amp; purification ; Child, Preschool ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Male ; Metagenome ; Middle Aged ; Phylogeny ; Young Adult ; },
abstract = {Human gut bacterial strains can co-exist with their hosts for decades, but little is known about how these microbes persist and disperse, and evolve thereby. Here, we examined these processes in 5,278 adult and infant fecal metagenomes, longitudinally sampled in individuals and families. Our analyses revealed that a subset of gut species is extremely persistent in individuals, families, and geographic regions, represented often by locally successful strains of the phylum Bacteroidota. These "tenacious" bacteria show high levels of genetic adaptation to the human host but a high probability of loss upon antibiotic interventions. By contrast, heredipersistent bacteria, notably Firmicutes, often rely on dispersal strategies with weak phylogeographic patterns but strong family transmissions, likely related to sporulation. These analyses describe how different dispersal strategies can lead to the long-term persistence of human gut microbes with implications for gut flora modulations.},
}
@article {pmid34110473,
year = {2021},
author = {Rivera, AJ and Tyx, RE},
title = {Microbiology of the American Smokeless Tobacco.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {12},
pages = {4843-4853},
pmid = {34110473},
issn = {1432-0614},
mesh = {Carcinogens ; Humans ; Metagenomics ; *Microbiota ; Tobacco ; *Tobacco, Smokeless ; United States ; },
abstract = {Smokeless tobacco products (STP) contain diverse microbial communities that contribute to the formation of harmful chemical byproducts. This is concerning since 300 million individuals around the globe are users of smokeless tobacco. Significant evidence has shown that microbial metabolic activities mediate the formation of carcinogens during manufacturing. In recent years, studies have revealed a series of additional health impacts that include lesions and inflammation of the oral mucosa and the gastrointestinal tract, as well as alterations of the endogenous microbiota. These findings are due to recent developments in molecular technologies that allowed researchers to better examine the microbial component of these products. This new information illustrates the scale of the STP microbiota and its diversity in the finished product that is sold for consumption. Additionally, the application of metagenomics and metatranscriptomics has provided the tools to look at phylogenies across bacterial, viral, and eukaryotic groups, their functional capacities, and viability. Here we present key examples of tobacco microbiology research that utilizes newer approaches and strategies to define the microbial component of smokeless tobacco products. We also highlight challenges in these approaches, the knowledge gaps being filled, and those gaps that warrant further study. A better understanding of the microbiology of STP brings vast public health benefits. It will provide important information for the product consumer, impact manufacturing practices, and provide support for the development of attainable and more meaningful regulatory goals. KEY POINTS: Newer technologies allowed quicker and more comprehensive identification of microbes in tobacco samples, encapsulating microorganisms difficult or impossible to culture. Current research in smokeless tobacco microbiology is filling knowledge gaps previously unfilled due to the lack of suitable approaches. The microbial ecology of smokeless tobacco presents a clearer picture of diversity and variability not considered before.},
}
@article {pmid34108585,
year = {2021},
author = {Yoshitake, K and Kimura, G and Sakami, T and Watanabe, T and Taniuchi, Y and Kakehi, S and Kuwata, A and Yamaguchi, H and Kataoka, T and Kawachi, M and Ikeo, K and Tan, E and Igarashi, Y and Ohtsubo, M and Watabe, S and Suzuki, Y and Asakawa, S and Ishino, S and Tashiro, K and Ishino, Y and Kobayashi, T and Mineta, K and Gojobori, T},
title = {Development of a time-series shotgun metagenomics database for monitoring microbial communities at the Pacific coast of Japan.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {12222},
pmid = {34108585},
issn = {2045-2322},
mesh = {*Databases, Factual ; Japan ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; RNA, Ribosomal, 16S/*genetics ; Seawater/*microbiology ; Sequence Analysis, DNA ; Time Factors ; },
abstract = {Although numerous metagenome, amplicon sequencing-based studies have been conducted to date to characterize marine microbial communities, relatively few have employed full metagenome shotgun sequencing to obtain a broader picture of the functional features of these marine microbial communities. Moreover, most of these studies only performed sporadic sampling, which is insufficient to understand an ecosystem comprehensively. In this study, we regularly conducted seawater sampling along the northeastern Pacific coast of Japan between March 2012 and May 2016. We collected 213 seawater samples and prepared size-based fractions to generate 454 subsets of samples for shotgun metagenome sequencing and analysis. We also determined the sequences of 16S rRNA (n = 111) and 18S rRNA (n = 47) gene amplicons from smaller sample subsets. We thereafter developed the Ocean Monitoring Database for time-series metagenomic data (http://marine-meta.healthscience.sci.waseda.ac.jp/omd/), which provides a three-dimensional bird's-eye view of the data. This database includes results of digital DNA chip analysis, a novel method for estimating ocean characteristics such as water temperature from metagenomic data. Furthermore, we developed a novel classification method that includes more information about viruses than that acquired using BLAST. We further report the discovery of a large number of previously overlooked (TAG)n repeat sequences in the genomes of marine microbes. We predict that the availability of this time-series database will lead to major discoveries in marine microbiome research.},
}
@article {pmid34107988,
year = {2021},
author = {Flachs, A and Orkin, JD},
title = {On pickles: biological and sociocultural links between fermented foods and the human gut microbiome.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {17},
number = {1},
pages = {39},
pmid = {34107988},
issn = {1746-4269},
support = {Global Synergy Grant//College of Liberal Arts, Purdue University/ ; },
mesh = {Fermentation ; *Fermented Foods/microbiology ; *Food Microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; },
abstract = {BACKGROUND: The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa.<br><br>METHODS: In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods.<br><br>RESULTS: We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes.<br><br>CONCLUSIONS: By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.},
}
@article {pmid34105982,
year = {2021},
author = {Almeida, OGG and De Martinis, ECP},
title = {Metagenome-Assembled Genomes Contribute to Unraveling of the Microbiome of Cocoa Fermentation.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {16},
pages = {e0058421},
pmid = {34105982},
issn = {1098-5336},
mesh = {Bacteria/classification/genetics/*isolation &amp; purification/metabolism ; Cacao/metabolism/*microbiology ; Chocolate/analysis/*microbiology ; Fermentation ; Fungi/classification/genetics/*isolation &amp; purification/metabolism ; Metagenome ; *Microbiota ; Phylogeny ; Seeds/metabolism/microbiology ; },
abstract = {Metagenomic studies about cocoa fermentation have mainly reported on the analysis of short reads for determination of operational taxonomic units. However, it is also important to determine metagenome-assembled genomes (MAGs), which are genomes deriving from the assembly of metagenomics. For this research, all the cocoa metagenomes from public databases were downloaded, resulting in five data sets: one from Ghana and four from Brazil. In addition, in silico approaches were used to describe putative phenotypes and the metabolic potential of MAGs. A total of 17 high-quality MAGs were recovered from these microbiomes, as follows: (i) for fungi, Yamadazyma tenuis (n = 1); (ii) lactic acid bacteria, Limosilactobacillus fermentum (n = 5), Liquorilactobacillus cacaonum (n = 1), Liquorilactobacillus nagelli (n = 1), Leuconostoc pseudomesenteroides (n = 1), and Lactiplantibacillus plantarum subsp. plantarum (n = 1); (iii) acetic acid bacteria, Acetobacter senegalensis (n = 2) and Kozakia baliensis (n = 1); and (iv) Bacillus subtilis (n = 1), Brevundimonas sp. (n = 2), and Pseudomonas sp. (n = 1). Medium-quality MAGs were also recovered from cocoa microbiomes, including some that, to our knowledge, were not previously detected in this environment (Liquorilactobacillus vini, Komagataeibacter saccharivorans, and Komagataeibacter maltaceti) and others previously described (Fructobacillus pseudoficulneus and Acetobacter pasteurianus). Taken together, the MAGs were useful for providing an additional description of the microbiome of cocoa fermentation, revealing previously overlooked microorganisms, with prediction of key phenotypes and biochemical pathways. IMPORTANCE The production of chocolate starts with the harvesting of cocoa fruits and the spontaneous fermentation of the seeds in a microbial succession that depends on yeasts, lactic acid bacteria, and acetic acid bacteria in order to eliminate bitter and astringent compounds present in the raw material, which will be further roasted and grinded to originate the cocoa powder that will enter the food processing industry. The microbiota of cocoa fermentation is not completely known, and yet it advanced from culture-based studies to the advent of next-generation DNA sequencing, with the generation of a myriad of data that need bioinformatic approaches to be properly analyzed. Although the majority of metagenomic studies have been based on short reads (operational taxonomic units), it is also important to analyze entire genomes to determine more precisely possible ecological roles of different species. Metagenome-assembled genomes (MAGs) are very useful for this purpose; here, MAGs from cocoa fermentation microbiomes are described, and the possible implications of their phenotypic and metabolic potentials are discussed.},
}
@article {pmid34103703,
year = {2021},
author = {Wang, W and Wei, X and Wu, L and Shang, X and Cheng, F and Li, B and Zhou, X and Zhang, J},
title = {The occurrence of antibiotic resistance genes in the microbiota of yak, beef and dairy cattle characterized by a metagenomic approach.},
journal = {The Journal of antibiotics},
volume = {74},
number = {8},
pages = {508-518},
pmid = {34103703},
issn = {1881-1469},
mesh = {Animal Feed ; Animals ; Cattle/*microbiology ; Dairy Products ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Humans ; Integrons/genetics ; Interspersed Repetitive Sequences/genetics ; Meat ; Metagenomics/*methods ; Microbiota/*genetics ; Soil Microbiology ; Species Specificity ; },
abstract = {Drug resistance has been partly driven by the overuse of antimicrobials in agricultural animal feed. Better understanding of antibiotic resistance in bovine gut is needed to assess its potential effects based on metagenomic approach and analysis. In this study, we collected 40 fecal samples to explore drug resistance derived from antibiotic use in the bacterial community by an analysis of the diversities and differences of antibiotic-resistant genes (ARGs) in the gut microbiota from yak, beef, and dairy cattle. Overall, 1688 genes were annotated, including 734 ARG subtypes. The ARGs were related to tetracyclines, quinolones, β-lactam, and aminoglycosides, in accordance with the antibiotics widely used in the clinic for humans or animals. The emergence, prevalence, and differences in resistance genes in the intestines of yaks, beef, and dairy cattle may be caused by the selective pressure of different feeding patterns, where yaks were raised without antibiotics for growth promotion. In addition, the abundance of ARGs in yak was lower than in beef and dairy cattle, whereas the abundance of integron, a kind of mobile genetic elements (MGEs) was higher in yaks than those in beef and dairy cattle. Furthermore, the results of this study could provide the basis for a comprehensive profile of various ARGs among yak, beef, and dairy cattle in future.},
}
@article {pmid34103263,
year = {2021},
author = {Miao, Q and Ma, Y and Ling, Y and Jin, W and Su, Y and Wang, Q and Pan, J and Zhang, Y and Chen, H and Yuan, J and Wu, H and Hu, B},
title = {Evaluation of superinfection, antimicrobial usage, and airway microbiome with metagenomic sequencing in COVID-19 patients: A cohort study in Shanghai.},
journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi},
volume = {54},
number = {5},
pages = {808-815},
doi = {10.1016/j.jmii.2021.03.015},
pmid = {34103263},
issn = {1995-9133},
mesh = {Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/*therapeutic use ; Antimicrobial Stewardship ; *COVID-19 ; China ; Cohort Studies ; Coinfection/drug therapy ; Critical Illness ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Metagenomics ; Microbiota/genetics/*physiology ; Middle Aged ; Mycoses/drug therapy ; Respiratory System/*microbiology ; Retrospective Studies ; SARS-CoV-2 ; Superinfection/*drug therapy ; },
abstract = {BACKGROUND: In COVID-19 patients, information regarding superinfection, antimicrobial assessment, and the value of metagenomic sequencing (MS) could help develop antimicrobial stewardship.<br><br>METHOD: This retrospective study analyzed 323 laboratory-confirmed COVID-19 patients for co-infection rate and antimicrobial usage in the Shanghai Public Health Clinical Center (SPHCC) from January 23rd to March 14th 2020. The microbiota composition was also investigated in patients with critically severe COVID-19.<br><br>RESULTS: The total population co-infection rate was 17/323 (5.3%) and 0/229 (0), 4/78 (5.1%), and 13/16 (81.3%) for the mild, severe, and critically severe subgroups, respectively. Proven fungal infection was significantly associated with a higher mortality rate (p = 0.029). In critically severe patients, the rate of antimicrobials and carbapenem usage were 16/16 (100%) and 13/16 (81.3%), respectively, in which the preemptive and empiric antimicrobial days accounted for 51.6% and 30.1%, respectively. Targeted therapy only accounted for 18.3%. MS was implemented to detect non-COVID-19 virus co-existence and the semi-quantitative surveillance of bacteremia, with clear clinical benefit seen in cases with MS-based precision antimicrobial management. Airway microbiome analysis suggested that the microbiota compositions in critically severe COVID-19 patients were likely due to intubation and mechanical ventilation.<br><br>CONCLUSIONS: In the SPHCC cohort, we observed a non-negligible rate of super-infection, especially for the critically ill COVID-19 patients. Fungal co-infection requires intensive attention due to the high risk of mortality, and the clinical benefit of MS in guiding antimicrobial management warrants further investigation.},
}
@article {pmid34100638,
year = {2021},
author = {Wei, ST and Chen, YL and Wu, YW and Wu, TY and Lai, YL and Wang, PH and Ismail, W and Lee, TH and Chiang, YR},
title = {Integrated Multi-omics Investigations Reveal the Key Role of Synergistic Microbial Networks in Removing Plasticizer Di-(2-Ethylhexyl) Phthalate from Estuarine Sediments.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {e0035821},
pmid = {34100638},
issn = {2379-5077},
support = {AS-CDA-110-L13//Academia Sinica/ ; MOST 109-2221-E-001-002//Ministry of Science and Technology, Taiwan (MOST)/ ; MOST 110-2222-E-008-002//Ministry of Science and Technology, Taiwan (MOST)/ ; },
abstract = {Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide, with an annual global production of more than 8 million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at submillimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O2-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl coenzyme A (benzoyl-CoA) pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side chains of DEHP. Interestingly, genes encoding DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase and phthaloyl-CoA decarboxylase-key enzymes for side chain hydrolysis and o-phthalic acid degradation, respectively-are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities. IMPORTANCE Xenobiotic phthalate esters (PAEs) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O2-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggested that the side chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O2-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O2-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/mono-(2-ethylhexyl) phthalate (MEHP) hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.},
}
@article {pmid34097462,
year = {2021},
author = {Breen, P and Winters, AD and Theis, KR and Withey, JH},
title = {The Vibrio cholerae Type Six Secretion System Is Dispensable for Colonization but Affects Pathogenesis and the Structure of Zebrafish Intestinal Microbiome.},
journal = {Infection and immunity},
volume = {89},
number = {9},
pages = {e0015121},
pmid = {34097462},
issn = {1098-5522},
support = {R01 AI127390/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cholera/*microbiology ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; *Host-Pathogen Interactions ; Metagenomics/methods ; RNA, Ribosomal, 16S ; Type VI Secretion Systems/*physiology ; Vibrio cholerae/*physiology ; Zebrafish ; },
abstract = {Zebrafish (Danio rerio) are an attractive model organism for a variety of scientific studies, including host-microbe interactions. The organism is particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae, an intestinal pathogen. V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. While numerous studies have explored various aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms, few, if any, have examined how a V. cholerae infection alters the resident intestinal microbiome and the role of the type six secretion system (T6SS) in that process. In this study, 16S rRNA gene sequencing was utilized to investigate how strains of V. cholerae both with and without the T6SS alter the aforementioned microbial profiles following an infection. V. cholerae infection induced significant changes in the zebrafish intestinal microbiome, and while not necessary for colonization, the T6SS was important for inducing mucin secretion, a marker for diarrhea. Additional salient differences to the microbiome were observed based on the presence or absence of the T6SS in the V. cholerae utilized for challenging the zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiome to enable colonization and that the T6SS is important for pathogenesis induced by the examined V. cholerae strains. Furthermore, the presence or absence of T6SS differentially and significantly affected the composition and structure of the intestinal microbiome, with an increased abundance of other Vibrio bacteria observed in the absence of V. cholerae T6SS.},
}
@article {pmid34091278,
year = {2021},
author = {Dall'Agnol, B and McCulloch, JA and Mayer, FQ and Souza, U and Webster, A and Antunes, P and Doyle, RL and Reck, J and Ferreira, CAS},
title = {Molecular characterization of bacterial communities of two neotropical tick species (Amblyomma aureolatum and Ornithodoros brasiliensis) using rDNA 16S sequencing.},
journal = {Ticks and tick-borne diseases},
volume = {12},
number = {5},
pages = {101746},
doi = {10.1016/j.ttbdis.2021.101746},
pmid = {34091278},
issn = {1877-9603},
mesh = {Amblyomma/*microbiology ; Animals ; Bacteria/genetics/isolation &amp; purification ; Coxiella/genetics/isolation &amp; purification ; DNA, Bacterial/isolation &amp; purification ; Francisella/genetics/isolation &amp; purification ; Ixodidae/microbiology ; Metagenomics ; *Microbiota ; Ornithodoros/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rickettsia/genetics/isolation &amp; purification ; },
abstract = {Ticks are one of the main vectors of pathogens for humans and animals worldwide. However, they harbor non-pathogenic microorganisms that are important for their survival, facilitating both their nutrition and immunity. We investigated the bacterial communities associated with two neotropical tick species of human and veterinary potential health importance from Brazil: Amblyomma aureolatum and Ornithodoros brasiliensis. In A. aureolatum (adult ticks collected from wild canids from Southern Brazil), the predominant bacterial phyla were Proteobacteria (98.68%), Tenericutes (0.70%), Bacteroidetes (0.14%), Actinobacteria (0.13%), and Acidobacteria (0.05%). The predominant genera were Francisella (97.01%), Spiroplasma (0.70%), Wolbachia (0.51%), Candidatus Midichloria (0.25%), and Alkanindiges (0.13%). The predominant phyla in O. brasiliensis (adults, fed and unfed nymphs collected at the environment from Southern Brazil) were Proteobacteria (90.27%), Actinobacteria (7.38%), Firmicutes (0.77%), Bacteroidetes (0.44%), and Planctomycetes (0.22%). The predominant bacterial genera were Coxiella (87.71%), Nocardioides (1.73%), Saccharopolyspora (0.54%), Marmoricola (0.42%), and Staphylococcus (0.40%). Considering the genera with potential importance for human and animal health which can be transmitted by ticks, Coxiella sp. was found in all stages of O. brasiliensis, Francisella sp. in all stages of A. aureolatum and in unfed nymphs of O. brasiliensis, and Rickettsia sp. in females of A. aureolatum from Banhado dos Pachecos (BP) in Viamão municipality, Brazil, and in females and unfed nymphs of O. brasiliensis. These results deepen our understanding of the tick-microbiota relationship in Ixodidae and Argasidae, driving new studies with the focus on the manipulation of tick microbiota to prevent outbreaks of tick-borne diseases in South America.},
}
@article {pmid34090540,
year = {2021},
author = {Callahan, BJ and Grinevich, D and Thakur, S and Balamotis, MA and Yehezkel, TB},
title = {Ultra-accurate microbial amplicon sequencing with synthetic long reads.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {130},
pmid = {34090540},
issn = {2049-2618},
support = {R35 GM133745/GM/NIGMS NIH HHS/United States ; },
mesh = {*High-Throughput Nucleotide Sequencing ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge.<br><br>METHODS: Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads.<br><br>RESULTS: LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens.<br><br>CONCLUSIONS: The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics. Video abstract.},
}
@article {pmid34090519,
year = {2021},
author = {Wilkins, D and Tong, X and Leung, MHY and Mason, CE and Lee, PKH},
title = {Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {129},
pmid = {34090519},
issn = {2049-2618},
support = {R01 AI151059/AI/NIAID NIH HHS/United States ; },
mesh = {Bayes Theorem ; Hong Kong ; Humans ; Metagenomics ; *Microbiota/genetics ; },
abstract = {BACKGROUND: The human skin microbiome has been recently investigated as a potential forensic tool, as people leave traces of their potentially unique microbiomes on objects and surfaces with which they interact. In this metagenomic study of four people in Hong Kong, their homes, and public surfaces in their neighbourhoods, we investigated the stability and identifiability of these microbiota traces on a timescale of hours to days.<br><br>RESULTS: Using a Canberra distance-based method of comparing skin and surface microbiomes, we found that a person could be accurately matched to their household in 84% of tests and to their neighbourhood in 50% of tests, and that matching accuracy did not decay for household surfaces over the 10-day study period, although it did for public surfaces. The time of day at which a skin or surface sample was taken affected matching accuracy, and 160 species across all sites were found to have a significant variation in abundance between morning and evening samples. We hypothesised that daily routines drive a rhythm of daytime dispersal from the pooled public surface microbiome followed by normalisation of a person's microbiome by contact with their household microbial reservoir, and Dynamic Bayesian Networks (DBNs) supported dispersal from public surfaces to skin as the major dispersal route among all sites studied.<br><br>CONCLUSIONS: These results suggest that in addition to considering the decay of microbiota traces with time, diurnal patterns in microbiome exposure that contribute to the human skin microbiome assemblage must also be considered in developing this as a potential forensic method. Video Abstract.},
}
@article {pmid34085924,
year = {2021},
author = {Hughes, ER and Winter, MG and Alves da Silva, L and Muramatsu, MK and Jimenez, AG and Gillis, CC and Spiga, L and Chanin, RB and Santos, RL and Zhu, W and Winter, SE},
title = {Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34085924},
issn = {2050-084X},
support = {R01 AI118807/AI/NIAID NIH HHS/United States ; R21 AI128151/AI/NIAID NIH HHS/United States ; T32 AI007520/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cecum/metabolism/*microbiology/pathology ; Colitis/*chemically induced/metabolism/*microbiology/pathology ; Colon/metabolism/*microbiology/pathology ; Databases, Genetic ; Dextran Sulfate ; Disease Models, Animal ; Dysbiosis ; Escherichia coli/genetics/growth &amp; development/*metabolism ; Escherichia coli Infections/metabolism/*microbiology/pathology ; Escherichia coli Proteins/genetics/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Hydrogen/*metabolism ; Hydrogenase/genetics/metabolism ; Interleukin-10/genetics/metabolism ; Male ; Metagenome ; Metagenomics ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mice, Knockout ; Piroxicam ; },
abstract = {The composition of gut-associated microbial communities changes during intestinal inflammation, including an expansion of Enterobacteriaceae populations. The mechanisms underlying microbiota changes during inflammation are incompletely understood. Here, we analyzed previously published metagenomic datasets with a focus on microbial hydrogen metabolism. The bacterial genomes in the inflamed murine gut and in patients with inflammatory bowel disease contained more genes encoding predicted hydrogen-utilizing hydrogenases compared to communities found under non-inflamed conditions. To validate these findings, we investigated hydrogen metabolism of Escherichia coli, a representative Enterobacteriaceae, in mouse models of colitis. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed cecum and colon. Utilization of molecular hydrogen was in part dependent on respiration of inflammation-derived electron acceptors. This work highlights the contribution of hydrogenases to alterations of the gut microbiota in the context of non-infectious colitis.},
}
@article {pmid34083731,
year = {2021},
author = {Kullapanich, C and Jandang, S and Palasuk, M and Viyakarn, V and Chavanich, S and Somboonna, N},
title = {First dynamics of bacterial community during development of Acropora humilis larvae in aquaculture.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11762},
pmid = {34083731},
issn = {2045-2322},
mesh = {Animals ; Anthozoa/growth &amp; development/*microbiology ; *Bacteria/classification/genetics ; High-Throughput Nucleotide Sequencing ; Larva/growth &amp; development/*microbiology ; Life Cycle Stages ; Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S ; Symbiosis ; },
abstract = {A symbiosis of bacterial community (sometimes called microbiota) play essential roles in developmental life cycle and health of coral, starting since a larva. For examples, coral bacterial holobionts function nitrogen fixation, carbon supply, sulfur cycling and antibiotic production. Yet, a study of the dynamic of bacteria associated coral larvae development is complicated owning to a vast diversity and culturable difficulty of bacteria; hence this type of study remains unexplored for Acropora humilis larvae in Thai sea. This study represented the first to utilize 16S rRNA gene sequencing to describe the timely bacterial compositions during successfully cultured and reared A. humilis larval transformation in aquaculture (gametes were collected from Sattahip Bay, Chonburi province, Thailand), from gamete spawning (0 h) and fertilization stage (1 h), to embryonic cleavage (8 h), round cell development (28, 39 and 41 h), and planula formation (48 h). The sequencing results as estimated by Good's coverage at genus level covered 99.65 ± 0.24% of total bacteria. While core phyla of bacteria were observed (Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes), changes in bacterial population structures and differential predominant core bacterial orders were denoted for each larval developmental stage, from fertilization to embryonic cleavage and subsequently from the embryonic cleavage to round cell development (P = 0.007). For instances, Pseudoalteromonas and Oceanospirillales were found prevalent at 8 h, and Rhizobiales were at 48 h. The bacterial population structures from the round cell stage, particularly at 41 h, showed gradual drift towards those of the planula formation stage, suggesting microbial selection. Overall, this study provides preliminary insights into the dynamics of bacterial community and their potentially functional association (estimated from the bacterial compositions) during the developmental embryonic A. humilis in a cultivation system in Southeast Asia region.},
}
@article {pmid34083661,
year = {2021},
author = {Zheng, L and Sun, R and Zhu, Y and Li, Z and She, X and Jian, X and Yu, F and Deng, X and Sai, B and Wang, L and Zhou, W and Wu, M and Li, G and Tang, J and Jia, W and Xiang, J},
title = {Lung microbiome alterations in NSCLC patients.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11736},
pmid = {34083661},
issn = {2045-2322},
mesh = {Adult ; Aged ; Biomarkers ; Carcinoma, Non-Small-Cell Lung/*complications/diagnosis ; *Dysbiosis ; Female ; Humans ; Lung/*microbiology ; Lung Neoplasms/*complications/diagnosis ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Pneumonia/*etiology ; Risk Assessment ; Risk Factors ; },
abstract = {Lung is colonized by a diverse array of microbes and the lung microbiota is profoundly involved in the development of respiratory diseases. There is little knowledge about the role of lung microbiota dysbiosis in lung cancer. In this study, we performed metagenomic sequencing on bronchoalveolar lavage (BAL) from two different sampling methods in non-small cell lung cancer (NSCLC) patients and non-cancer controls. We found the obvious variation between bronchoscopy samples and lobectomy samples. Oral taxa can be found in both bronchoscopy and lobectomy samples and higher abundance of oral taxa can be found in bronchoscopy samples. Although the NSCLC patients had similar microbial communities with non-cancer controls, rare species such as Lactobacillus rossiae, Bacteroides pyogenes, Paenibacillus odorifer, Pseudomonas entomophila, Magnetospirillum gryphiswaldense, fungus Chaetomium globosum et al. showed obvious difference between NSCLC patients and non-cancer controls. Age-, gender-, and smoking-specific species and EGFR expression-related species in NSCLC patients were detected. There results implicated that different lung segments have differential lung microbiome composition. The oral taxa are found in the lobectomy samples suggesting that oral microbiota are the true members of lung microbiota, rather than contamination during bronchoscopy. Lung cancer does not obviously alter the global microbial composition, while rare species are altered more than common species. Certain microbes may be associated with lung cancer progression.},
}
@article {pmid34083632,
year = {2021},
author = {Grisnik, M and Grinath, JB and Walker, DM},
title = {The presence of Pseudogymnoascus destructans, a fungal pathogen of bats, correlates with changes in microbial metacommunity structure.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11685},
pmid = {34083632},
issn = {2045-2322},
mesh = {Animal Diseases/*microbiology ; Animals ; *Ascomycota ; Biodiversity ; Chiroptera/*microbiology ; Computational Biology/methods ; Metagenome ; Metagenomics/methods ; *Microbiota ; Mycoses/*veterinary ; },
abstract = {Metacommunity theory provides a framework for how community patterns arise from processes across scales, which is relevant for understanding patterns in host-associated microbial assemblages. Microbial metacommunities may have important roles in host health through interactions with pathogens; however, it is unclear how pathogens affect host microbial metacommunities. Here, we studied relationships between a fungal pathogen and a host-associated microbial metacommunity. We hypothesized that a fungal pathogen of bats, Pseudogymnoascus destructans, correlates with a shift in metacommunity structure and changes in relationships between community composition, and factors shaping these assemblages, such as ecoregion. We sampled bat cutaneous microbial assemblages in the presence/absence of P. destructans and analyzed microbial metacommunity composition and relationships with structuring variables. Absence of P. destructans correlated with a metacommunity characterized by a common core microbial group that was lacking in disease positive bats. Additionally, P. destructans presence correlated with a change in the relationship between community structure and ecoregion. Our results suggest that the fungal pathogen intensifies local processes influencing a microbial metacommunity and highlights the importance of cutaneous microbial assemblages in host-pathogen interactions.},
}
@article {pmid34081399,
year = {2021},
author = {Kumar, N and Hitch, TCA and Haller, D and Lagkouvardos, I and Clavel, T},
title = {MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes.},
journal = {Microbial biotechnology},
volume = {14},
number = {4},
pages = {1757-1770},
pmid = {34081399},
issn = {1751-7915},
support = {395357507//Deutsche Forschungsgemeinschaft/ ; 403224013//Deutsche Forschungsgemeinschaft/ ; SFB 1371//Deutsche Forschungsgemeinschaft/ ; SFB 1382//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Bacteria/genetics ; Computational Biology ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {Environmental and host-associated microbial communities are complex ecosystems, of which many members are still unknown. Hence, it is challenging to study community dynamics and important to create model systems of reduced complexity that mimic major community functions. Therefore, we developed MiMiC, a computational approach for data-driven design of simplified communities from shotgun metagenomes. We first built a comprehensive database of species-level bacterial and archaeal genomes (n = 22 627) consisting of binary (presence/absence) vectors of protein families (Pfam = 17 929). MiMiC predicts the composition of minimal consortia using an iterative scoring system based on maximal match-to-mismatch ratios between this database and the Pfam binary vector of any input metagenome. Pfam vectorization retained enough resolution to distinguish metagenomic profiles between six environmental and host-derived microbial communities (n = 937). The calculated number of species per minimal community ranged between 5 and 11, with MiMiC selected communities better recapitulating the functional repertoire of the original samples than randomly selected species. The inferred minimal communities retained habitat-specific features and were substantially different from communities consisting of most abundant members. The use of a mixture of known microbes revealed the ability to select 23 of 25 target species from the entire genome database. MiMiC is open source and available at https://github.com/ClavelLab/MiMiC.},
}
@article {pmid34079525,
year = {2021},
author = {Sisk-Hackworth, L and Ortiz-Velez, A and Reed, MB and Kelley, ST},
title = {Compositional Data Analysis of Periodontal Disease Microbial Communities.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {617949},
pmid = {34079525},
issn = {1664-302X},
abstract = {Periodontal disease (PD) is a chronic, progressive polymicrobial disease that induces a strong host immune response. Culture-independent methods, such as next-generation sequencing (NGS) of bacteria 16S amplicon and shotgun metagenomic libraries, have greatly expanded our understanding of PD biodiversity, identified novel PD microbial associations, and shown that PD biodiversity increases with pocket depth. NGS studies have also found PD communities to be highly host-specific in terms of both biodiversity and the response of microbial communities to periodontal treatment. As with most microbiome work, the majority of PD microbiome studies use standard data normalization procedures that do not account for the compositional nature of NGS microbiome data. Here, we apply recently developed compositional data analysis (CoDA) approaches and software tools to reanalyze multiomics (16S, metagenomics, and metabolomics) data generated from previously published periodontal disease studies. CoDA methods, such as centered log-ratio (clr) transformation, compensate for the compositional nature of these data, which can not only remove spurious correlations but also allows for the identification of novel associations between microbial features and disease conditions. We validated many of the studies' original findings, but also identified new features associated with periodontal disease, including the genera Schwartzia and Aerococcus and the cytokine C-reactive protein (CRP). Furthermore, our network analysis revealed a lower connectivity among taxa in deeper periodontal pockets, potentially indicative of a more "random" microbiome. Our findings illustrate the utility of CoDA techniques in multiomics compositional data analysis of the oral microbiome.},
}
@article {pmid34071172,
year = {2021},
author = {Chukwuma, OB and Rafatullah, M and Tajarudin, HA and Ismail, N},
title = {Bacterial Diversity and Community Structure of a Municipal Solid Waste Landfill: A Source of Lignocellulolytic Potential.},
journal = {Life (Basel, Switzerland)},
volume = {11},
number = {6},
pages = {},
pmid = {34071172},
issn = {2075-1729},
support = {1001/PTEKIND/8011044//Universiti Sains Malaysia/ ; },
abstract = {Omics have given rise to research on sparsely studied microbial communities such as the landfill, lignocellulolytic microorganisms and enzymes. The bacterial diversity of Municipal Solid Waste sediments was determined using the illumina MiSeq system after DNA extraction and Polymerase chain reactions. Data analysis was used to determine the community's richness, diversity, and correlation with environmental factors. Physicochemical studies revealed sites with mesophilic and thermophilic temperature ranges and a mixture of acidic and alkaline pH values. Temperature and moisture content showed the highest correlation with the bacteria community. The bacterial analysis of the community DNA revealed 357,030 effective sequences and 1891 operational taxonomic units (OTUs) assigned. Forty phyla were found, with the dominant phyla Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidota, while Aerococcus, Stenotrophomonas, and Sporosarcina were the dominant species. PICRUSt provided insight on community's metabolic function, which was narrowed down to search for lignocellulolytic enzymes' function. Cellulase, xylanase, esterase, and peroxidase were gene functions inferred from the data. This article reports on the first phylogenetic analysis of the Pulau Burung landfill bacterial community. These results will help to improve the understanding of organisms dominant in the landfill and the corresponding enzymes that contribute to lignocellulose breakdown.},
}
@article {pmid34069990,
year = {2021},
author = {Ansorge, R and Birolo, G and James, SA and Telatin, A},
title = {Dadaist2: A Toolkit to Automate and Simplify Statistical Analysis and Plotting of Metabarcoding Experiments.},
journal = {International journal of molecular sciences},
volume = {22},
number = {10},
pages = {},
pmid = {34069990},
issn = {1422-0067},
support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R506552/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1//UK Research and Innovation/ ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; DNA Barcoding, Taxonomic/*statistics &amp; numerical data ; Data Interpretation, Statistical ; High-Throughput Nucleotide Sequencing ; Metadata ; Metagenomics/*statistics &amp; numerical data ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Software ; },
abstract = {The taxonomic composition of microbial communities can be assessed using universal marker amplicon sequencing. The most common taxonomic markers are the 16S rDNA for bacterial communities and the internal transcribed spacer (ITS) region for fungal communities, but various other markers are used for barcoding eukaryotes. A crucial step in the bioinformatic analysis of amplicon sequences is the identification of representative sequences. This can be achieved using a clustering approach or by denoising raw sequencing reads. DADA2 is a widely adopted algorithm, released as an R library, that denoises marker-specific amplicons from next-generation sequencing and produces a set of representative sequences referred to as 'Amplicon Sequence Variants' (ASV). Here, we present Dadaist2, a modular pipeline, providing a complete suite for the analysis that ranges from raw sequencing reads to the statistics of numerical ecology. Dadaist2 implements a new approach that is specifically optimised for amplicons with variable lengths, such as the fungal ITS. The pipeline focuses on streamlining the data flow from the command line to R, with multiple options for statistical analysis and plotting, both interactive and automatic.},
}
@article {pmid34069916,
year = {2021},
author = {Izawa, K and Okamoto-Shibayama, K and Kita, D and Tomita, S and Saito, A and Ishida, T and Ohue, M and Akiyama, Y and Ishihara, K},
title = {Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis.},
journal = {International journal of molecular sciences},
volume = {22},
number = {10},
pages = {},
pmid = {34069916},
issn = {1422-0067},
support = {18K09559//Japan Society for Promotion of Science/ ; 45//MEXT Private University Research Branding Project/ ; },
mesh = {Adult ; Aged ; Bacteria/genetics ; Dental Plaque/genetics/*microbiology ; Dysbiosis/genetics ; Female ; Gingiva/*microbiology ; High-Throughput Nucleotide Sequencing ; Humans ; Japan/epidemiology ; Male ; Metagenome ; Microbiota/genetics ; Middle Aged ; Periodontal Pocket/genetics/microbiology ; Periodontitis/genetics/*microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Periodontitis is an inflammation of tooth-supporting tissues, which is caused by bacteria in the subgingival plaque (biofilm) and the host immune response. Traditionally, subgingival pathogens have been investigated using methods such as culturing, DNA probes, or PCR. The development of next-generation sequencing made it possible to investigate the whole microbiome in the subgingival plaque. Previous studies have implicated dysbiosis of the subgingival microbiome in the etiology of periodontitis. However, details are still lacking. In this study, we conducted a metagenomic analysis of subgingival plaque samples from a group of Japanese individuals with and without periodontitis. In the taxonomic composition analysis, genus Bacteroides and Mycobacterium demonstrated significantly different compositions between healthy sites and sites with periodontal pockets. The results from the relative abundance of functional gene categories, carbohydrate metabolism, glycan biosynthesis and metabolism, amino acid metabolism, replication and repair showed significant differences between healthy sites and sites with periodontal pockets. These results provide important insights into the shift in the taxonomic and functional gene category abundance caused by dysbiosis, which occurs during the progression of periodontal disease.},
}
@article {pmid34065683,
year = {2021},
author = {Daugrois, JH and Filloux, D and Julian, C and Claude, L and Ferdinand, R and Fernandez, E and Fontes, H and Rott, PC and Roumagnac, P},
title = {Comparison of the Virome of Quarantined Sugarcane Varieties and the Virome of Grasses Growing near the Quarantine Station.},
journal = {Viruses},
volume = {13},
number = {5},
pages = {},
pmid = {34065683},
issn = {1999-4915},
mesh = {*Metagenome ; *Metagenomics/methods ; Phylogeny ; Plant Diseases/virology ; Poaceae/*virology ; Quarantine ; Saccharum/*virology ; Virion ; *Virome ; },
abstract = {Visacane is a sugarcane quarantine station located in the South of France, far away from sugarcane growing areas. Visacane imports up to 100 sugarcane varieties per year, using safe control and confinement measures of plants and their wastes to prevent any risk of pathogen spread outside of the facilities. Viruses hosted by the imported material are either known or unknown to cause disease in cultivated sugarcane. Poaceae viruses occurring in plants surrounding the quarantine glasshouse are currently unknown. These viruses could be considered as a source of new sugarcane infections and potentially cause new sugarcane diseases in cases of confinement barrier failure. The aim of this study was to compare the plant virome inside and outside of the quarantine station to identify potential confinement failures and risks of cross infections. Leaves from quarantined sugarcane varieties and from wild Poaceae growing near the quarantine were collected and processed by a metagenomics approach based on virion-associated nucleic acids extraction and library preparation for Illumina sequencing. While viruses belonging to the same virus genus or family were identified in the sugarcane quarantine and its surroundings, no virus species was detected in both environments. Based on the data obtained in this study, no virus movement between quarantined sugarcane and nearby grassland has occurred so far, and the confinement procedures of Visacane appear to be properly implemented.},
}
@article {pmid34064231,
year = {2021},
author = {Alanin, KWS and Junco, LMF and Jørgensen, JB and Nielsen, TK and Rasmussen, MA and Kot, W and Hansen, LH},
title = {Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay.},
journal = {Viruses},
volume = {13},
number = {6},
pages = {},
pmid = {34064231},
issn = {1999-4915},
mesh = {Computational Biology ; Host Specificity ; *Metagenome ; *Metagenomics/methods ; Pseudomonas/*virology ; Pseudomonas Phages/classification/*physiology ; *Viral Plaque Assay/methods ; *Virome ; },
abstract = {Isolating single phages using plaque assays is a laborious and time-consuming process. Whether single isolated phages are the most lyse-effective, the most abundant in viromes, or those with the highest ability to make plaques in solid media is not well known. With the increasing accessibility of high-throughput sequencing, metaviromics is often used to describe viruses in environmental samples. By extracting and sequencing metaviromes from organic waste with and without exposure to a host-of-interest, we show a host-related phage community's shift, as well as identify the most enriched phages. Moreover, we isolated plaque-forming single phages using the same virome-host matrix to observe how enrichments in liquid media correspond to the metaviromic data. In this study, we observed a significant shift (p = 0.015) of the 47 identified putative Pseudomonas phages with a minimum twofold change above zero in read abundance when adding a Pseudomonas&amp;nbsp;syringae DC3000 host. Surprisingly, it appears that only two out of five plaque-forming phages from the same organic waste sample, targeting the Pseudomonas strain, were highly abundant in the metavirome, while the other three were almost absent despite host exposure. Lastly, our sequencing results highlight how long reads from Oxford Nanopore elevates the assembly quality of metaviromes, compared to short reads alone.},
}
@article {pmid34061623,
year = {2021},
author = {Breen, P and Winters, AD and Theis, KR and Withey, JH},
title = {Vibrio cholerae Infection Induces Strain-Specific Modulation of the Zebrafish Intestinal Microbiome.},
journal = {Infection and immunity},
volume = {89},
number = {9},
pages = {e0015721},
pmid = {34061623},
issn = {1098-5522},
support = {R01 AI127390/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cholera/*microbiology ; Disease Models, Animal ; *Disease Susceptibility ; *Gastrointestinal Microbiome ; *Host-Pathogen Interactions ; Metagenomics/methods ; *Microbial Interactions ; RNA, Ribosomal, 16S ; Vibrio cholerae/*physiology ; Zebrafish ; },
abstract = {Zebrafish (Danio rerio) is an attractive model organism to use for an array of scientific studies, including host-microbe interactions. Zebrafish contain a core (i.e., consistently detected) intestinal microbiome consisting primarily of Proteobacteria. Furthermore, this core intestinal microbiome is plastic and can be significantly altered due to external factors. Zebrafish are particularly useful for the study of aquatic microbes that can colonize vertebrate hosts, including Vibrio cholerae. As an intestinal pathogen, V. cholerae must colonize the intestine of an exposed host for pathogenicity to occur. Members of the resident intestinal microbial community likely must be reduced or eliminated by V. cholerae for colonization, and subsequent disease, to occur. Many studies have explored a variety of aspects of the pathogenic effects of V. cholerae on zebrafish and other model organisms but few have researched how a V. cholerae infection changes the resident intestinal microbiome. In this study, 16S rRNA gene sequencing was used to examine how five genetically diverse V. cholerae strains alter the intestinal microbiome following an infection. We found that V. cholerae colonization induced significant changes in the zebrafish intestinal microbiome. Notably, changes in the microbial profile were significantly different from each other, based on the particular strain of V. cholerae used to infect zebrafish hosts. We conclude that V. cholerae significantly modulates the zebrafish intestinal microbiota to enable colonization and that specific microbes that are targeted depend on the V. cholerae genotype.},
}
@article {pmid34061597,
year = {2021},
author = {Lindstad, LJ and Lo, G and Leivers, S and Lu, Z and Michalak, L and Pereira, GV and Røhr, ÅK and Martens, EC and McKee, LS and Louis, P and Duncan, SH and Westereng, B and Pope, PB and La Rosa, SL},
title = {Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides.},
journal = {mBio},
volume = {12},
number = {3},
pages = {e0362820},
pmid = {34061597},
issn = {2150-7511},
mesh = {Bacteroides/genetics/metabolism ; Clostridiales/genetics/metabolism ; Colon/microbiology ; Diet ; Faecalibacterium prausnitzii/*genetics/growth &amp; development/*metabolism ; Gastrointestinal Microbiome/*genetics/physiology ; Humans ; Mannans/classification/*metabolism ; Metagenomics ; Oligosaccharides/*metabolism ; },
abstract = {β-Mannans are hemicelluloses that are abundant in modern diets as components in seed endosperms and common additives in processed food. Currently, the collective understanding of β-mannan saccharification in the human colon is limited to a few keystone species, which presumably liberate low-molecular-weight mannooligosaccharide fragments that become directly available to the surrounding microbial community. Here, we show that a dominant butyrate producer in the human gut, Faecalibacterium prausnitzii, is able to acquire and degrade various β-mannooligosaccharides (β-MOS), which are derived by the primary mannanolytic activity of neighboring gut microbiota. Detailed biochemical analyses of selected protein components from their two β-MOS utilization loci (F. prausnitzii β-MOS utilization loci [FpMULs]) supported a concerted model whereby the imported β-MOS are stepwise disassembled intracellularly by highly adapted enzymes. Coculturing experiments of F. prausnitzii with the primary degraders Bacteroides ovatus and Roseburia intestinalis on polymeric β-mannan resulted in syntrophic growth, thus confirming the high efficiency of the FpMULs' uptake system. Genomic comparison with human F. prausnitzii strains and analyses of 2,441 public human metagenomes revealed that FpMULs are highly conserved and distributed worldwide. Together, our results provide a significant advance in the knowledge of β-mannan metabolism and the degree to which its degradation is mediated by cross-feeding interactions between prominent beneficial microbes in the human gut. IMPORTANCE Commensal butyrate-producing bacteria belonging to the Firmicutes phylum are abundant in the human gut and are crucial for maintaining health. Currently, insight is lacking into how they target otherwise indigestible dietary fibers and into the trophic interactions they establish with other glycan degraders in the competitive gut environment. By combining cultivation, genomic, and detailed biochemical analyses, this work reveals the mechanism enabling F. prausnitzii, as a model Ruminococcaceae within Firmicutes, to cross-feed and access β-mannan-derived oligosaccharides released in the gut ecosystem by the action of primary degraders. A comprehensive survey of human gut metagenomes shows that FpMULs are ubiquitous in human populations globally, highlighting the importance of microbial metabolism of β-mannans/β-MOS as a common dietary component. Our findings provide a mechanistic understanding of the β-MOS utilization capability by F. prausnitzii that may be exploited to select dietary formulations specifically boosting this beneficial symbiont, and thus butyrate production, in the gut.},
}
@article {pmid34059794,
year = {2021},
author = {Sun, P and Yang, J and Wang, B and Ma, H and Zhang, Y and Guo, J and Chen, X and Zhao, J and Sun, H and Yang, J and Yang, H and Cui, Y},
title = {The effects of combined environmental factors on the intestinal flora of mice based on ground simulation experiments.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {11373},
pmid = {34059794},
issn = {2045-2322},
mesh = {Animals ; *Astronauts ; Biomarkers/metabolism ; Cluster Analysis ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Mice ; Mice, Inbred C57BL ; *Weightlessness Simulation ; },
abstract = {The composition and function of intestinal microbial communities are important for human health. However, these intestinal floras are sensitive to changes in the environment. Adverse changes to intestinal flora can affect the health of astronauts, resulting in difficulties in implementing space missions. We randomly divided mice into three groups and placed each group in either a normal environment, simulated microgravity environment or a combined effects environment, which included simulated microgravity, low pressure and noise. Fecal samples of the mice were collected for follow-up analysis based on metagenomics technology. With the influence of different space environmental factors, the species composition at the phylum and genus levels were significantly affected by the combined effects environment, especially the abundance of the Firmicutes and Bacteroidetes. Furthermore, screening was conducted to identify biomarkers that could be regarded as environmental markers. And there have also been some noticeable changes in the function of intestinal floras. Moreover, the abundance of antibiotic resistance genes (ARGs) was also found to be changed under different environmental conditions, such as bacitracin and vancomycin. The combined effects environment could significantly affect the species composition, function, and the expression of ARGs of intestinal flora of mice which may provide a theoretical basis for space medical supervision and healthcare.},
}
@article {pmid34053518,
year = {2021},
author = {Franciosa, I and Ferrocino, I and Giordano, M and Mounier, J and Rantsiou, K and Cocolin, L},
title = {Specific metagenomic asset drives the spontaneous fermentation of Italian sausages.},
journal = {Food research international (Ottawa, Ont.)},
volume = {144},
number = {},
pages = {110379},
doi = {10.1016/j.foodres.2021.110379},
pmid = {34053518},
issn = {1873-7145},
mesh = {Fermentation ; Food Microbiology ; Italy ; *Lactobacillus ; *Metagenomics ; },
abstract = {Metagenomics is a powerful tool to study and understand the microbial dynamics that occur during food fermentation and allows to close the link between microbial diversity and final sensory characteristics. Each food matrix can be colonized by different microbes, but also by different strains of the same species. In this study, using an innovative integrated approach combining culture-dependent method with a shotgun sequencing, we were able to show how strain-level biodiversity could influence the quality characteristics of the final product. The attention was placed on a model food fermentation process: Salame Piemonte, a Protected Geographical Indication (PGI) Italian fermented sausage. Three independent batches produced in February, March and May 2018 were analysed. The sausages were manufactured, following the production specification, in a local meat factory in the area of Turin (Italy) without the use of starter cultures. A pangenomic approach was applied in order to identify and evaluate the lactic acid bacteria (LAB) population driving the fermentation process. It was observed that all batches were characterized by the presence of few LAB species, namely Pediococcus pentosaceus, Latilactobacillus curvatus and Latilactobacillus sakei. Sausages from the different batches were different when the volatilome was taken into consideration, and a strong association between quality attributes and strains present was determined. In particular, different strains of L. sakei, showing heterogeneity at genomic level, colonized the meat at the beginning of each production and deeply influenced the fermentation process by distinctive metabolic pathways that affected the fermentation process and the final sensory aspects.},
}
@article {pmid34051218,
year = {2021},
author = {Wang, H and Banerjee, N and Liang, Y and Wang, G and Hoffman, KL and Khan, MF},
title = {Gut microbiome-host interactions in driving environmental pollutant trichloroethene-mediated autoimmunity.},
journal = {Toxicology and applied pharmacology},
volume = {424},
number = {},
pages = {115597},
pmid = {34051218},
issn = {1096-0333},
support = {R01 ES016302/ES/NIEHS NIH HHS/United States ; R01 ES026887/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; Autoimmunity/*drug effects ; Bacteria/*drug effects ; Drug Administration Schedule ; Environmental Pollutants/*toxicity ; Female ; Gastrointestinal Microbiome/*drug effects/physiology ; Inflammation ; Liver/drug effects ; Mice ; Mice, Inbred Strains ; Oxidative Stress ; Spleen/drug effects ; Trichloroethylene/*toxicity ; },
abstract = {Trichloroethene (TCE), a widely used industrial solvent, is associated with the development of autoimmune diseases (ADs), including systemic lupus erythematosus and autoimmune hepatitis. Increasing evidence support a linkage between altered gut microbiome composition and the onset of ADs. However, it is not clear how gut microbiome contributes to TCE-mediated autoimmunity, and initial triggers for microbiome-host interactions leading to systemic autoimmune responses remain unknown. To achieve this, female MRL+/+ mice were treated with 0.5 mg/ml TCE for 52 weeks and fecal samples were subjected to 16S rRNA sequencing to determine the microbiome composition. TCE exposure resulted in distinct bacterial community revealed by β-diversity analysis. Notably, we observed reduction in Lactobacillaceae, Rikenellaceae and Bifidobacteriaceae families, and enrichment of Akkermansiaceae and Lachnospiraceae families after TCE exposure. We also observed significantly increased colonic oxidative stress and inflammatory markers (CD14 and IL-1β), and decreased tight junction proteins (ZO-2, occludin and claudin-3). These changes were associated with increases in serum antinuclear and anti-smooth muscle antibodies and cytokines (IL-6 and IL-12), together with increased PD1 + CD4+ T cells in TCE-exposed spleen and liver tissues. Importantly, fecal microbiota transplantation (FMT) using feces from TCE-treated mice to antibiotics-treated mice induced increased anti-dsDNA antibodies and hepatic CD4+ T cell infiltration in the recipient mice. Our studies thus delineate how imbalance in gut microbiome and mucosal redox status together with gut inflammatory response and permeability changes could be the key factors in contributing to TCE-mediated ADs. Furthermore, FMT studies provide a solid support to a causal role of microbiome in TCE-mediated autoimmunity.},
}
@article {pmid34051009,
year = {2021},
author = {Matsushita, M and Fujita, K and Motooka, D and Hatano, K and Fukae, S and Kawamura, N and Tomiyama, E and Hayashi, Y and Banno, E and Takao, T and Takada, S and Yachida, S and Uemura, H and Nakamura, S and Nonomura, N},
title = {The gut microbiota associated with high-Gleason prostate cancer.},
journal = {Cancer science},
volume = {112},
number = {8},
pages = {3125-3135},
pmid = {34051009},
issn = {1349-7006},
support = {//Yakult Bio-Science Foundation/ ; //Japanese Urological Association/ ; },
mesh = {Aged ; Bacteria/*classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; Gastrointestinal Microbiome ; Humans ; Japan ; Male ; Middle Aged ; Neoplasm Grading ; Phylogeny ; Prostatic Neoplasms/microbiology/*pathology ; RNA, Ribosomal, 16S/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {We have found that intestinal bacteria and their metabolites, short-chain fatty acids (SCFAs), promote cancer growth in prostate cancer (PCa) mouse models. To clarify the association between gut microbiota and PCa in humans, we analyzed the gut microbiota profiles of men with suspected PCa. One hundred and fifty-two Japanese men undergoing prostate biopsies (96 with cancer and 56 without cancer) were included in the study and randomly divided into two cohorts: a discovery cohort (114 samples) and a test cohort (38 samples). The gut microbiota was compared between two groups, a high-risk group (men with Grade group 2 or higher PCa) and a negative + low-risk group (men with negative biopsy or Grade group 1 PCa), using 16S rRNA gene sequencing. The relative abundances of Rikenellaceae, Alistipes, and Lachnospira, all SCFA-producing bacteria, were significantly increased in high-risk group. In receiver operating characteristic curve analysis, the index calculated from the abundance of 18 bacterial genera which were selected by least absolute shrinkage and selection operator regression detected high-risk PCa in the discovery cohort with higher accuracy than the prostate specific antigen test (area under the curve [AUC] = 0.85 vs 0.74). Validation of the index in the test cohort showed similar results (AUC = 0.81 vs 0.67). The specific bacterial taxa were associated with high-risk PCa. The gut microbiota profile could be a novel useful marker for the detection of high-risk PCa and could contribute to the carcinogenesis of PCa.},
}
@article {pmid34050180,
year = {2021},
author = {Xu, L and Dong, Z and Chiniquy, D and Pierroz, G and Deng, S and Gao, C and Diamond, S and Simmons, T and Wipf, HM and Caddell, D and Varoquaux, N and Madera, MA and Hutmacher, R and Deutschbauer, A and Dahlberg, JA and Guerinot, ML and Purdom, E and Banfield, JF and Taylor, JW and Lemaux, PG and Coleman-Derr, D},
title = {Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3209},
pmid = {34050180},
issn = {2041-1723},
support = {P42 ES007373/ES/NIEHS NIH HHS/United States ; },
mesh = {Acclimatization ; Actinobacteria/genetics/*metabolism ; Crop Production ; *Droughts ; Food Security ; Iron/*metabolism ; Metagenomics/methods ; Microbiota/*physiology ; Plant Roots/microbiology ; RNA-Seq ; Rhizosphere ; Soil Microbiology ; Sorghum/microbiology/*physiology ; Stress, Physiological ; },
abstract = {Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal that bacterial iron transport and metabolism functionality is highly correlated with drought enrichment. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress, and that loss of a plant phytosiderophore iron transporter impacts microbial community composition, leading to significant increases in the drought-enriched lineage, Actinobacteria. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria, as well as their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome's response to drought and may inform efforts to improve plant drought tolerance to increase food security.},
}
@article {pmid34050176,
year = {2021},
author = {Behsaz, B and Bode, E and Gurevich, A and Shi, YN and Grundmann, F and Acharya, D and Caraballo-Rodríguez, AM and Bouslimani, A and Panitchpakdi, M and Linck, A and Guan, C and Oh, J and Dorrestein, PC and Bode, HB and Pevzner, PA and Mohimani, H},
title = {Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {3225},
pmid = {34050176},
issn = {2041-1723},
support = {DP2 GM126893/GM/NIGMS NIH HHS/United States ; DP2 GM137413/GM/NIGMS NIH HHS/United States ; },
mesh = {Algorithms ; Amino Acid Sequence/genetics ; Anti-Bacterial Agents/biosynthesis/*isolation &amp; purification ; Biological Products/*isolation &amp; purification/metabolism ; Computational Biology/*methods ; Datasets as Topic ; Drug Discovery/*methods ; Humans ; Mass Spectrometry ; Metabolic Networks and Pathways/genetics ; Metabolomics/methods ; Metagenomics/methods ; Microbiota/genetics ; Multigene Family ; Peptide Biosynthesis ; Peptide Synthases/genetics/metabolism ; Peptides/genetics/*isolation &amp; purification/metabolism ; Soil Microbiology ; },
abstract = {Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.},
}
@article {pmid34047368,
year = {2021},
author = {Leonardi, A and Modugno, RL and Cavarzeran, F and Rosani, U},
title = {Metagenomic analysis of the conjunctival bacterial and fungal microbiome in vernal keratoconjunctivitis.},
journal = {Allergy},
volume = {76},
number = {10},
pages = {3215-3217},
doi = {10.1111/all.14963},
pmid = {34047368},
issn = {1398-9995},
mesh = {Bacteria/genetics ; *Conjunctivitis, Allergic ; Humans ; Metagenome ; Metagenomics ; *Mycobiome ; RNA, Ribosomal, 16S ; },
}
@article {pmid34044757,
year = {2021},
author = {Guo, J and Pang, E and Song, H and Lin, K},
title = {A tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.},
journal = {BMC bioinformatics},
volume = {22},
number = {1},
pages = {282},
pmid = {34044757},
issn = {1471-2105},
mesh = {*Algorithms ; Genome ; *Genomics ; Metagenomics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge.<br><br>RESULTS: We developed a new method, a colored superbubble (cSupB), that can overcome the complexity of graphs and organize a set of species- or population-specific haplotype sequences of interest. Based on this model, we propose a tri-tuple coordinate system that combines an offset value, topological structure and sample information. Additionally, cSupB provides a novel method that utilizes complete topological information and efficiently detects small indels (< 50 bp) for highly similar samples, which can be validated by simulated datasets. Moreover, we demonstrated that cSupB can adapt to the complex cycle structure.<br><br>CONCLUSIONS: Although the solution is made suitable for increasingly complex genome graphs by relaxing the constraint, the directed acyclic graph, the motif cSupB and the cSupB method can be extended to any colored directed acyclic graph. We anticipate that our method will facilitate the analysis of individual haplotype variants and population genomic diversity. We have developed a C + + program for implementing our method that is available at https://github.com/eggleader/cSupB .},
}
@article {pmid34040607,
year = {2021},
author = {Gonçalves, E and Guillén, Y and Lama, JR and Sanchez, J and Brander, C and Paredes, R and Combadière, B},
title = {Host Transcriptome and Microbiota Signatures Prior to Immunization Profile Vaccine Humoral Responsiveness.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {657162},
pmid = {34040607},
issn = {1664-3224},
mesh = {Adolescent ; Adult ; Antibodies, Neutralizing/immunology ; Biodiversity ; Biomarkers ; Female ; Host Microbial Interactions/*genetics/*immunology ; Humans ; *Immunity, Humoral ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; *Transcriptome ; Vaccination ; Vaccines/*immunology ; Young Adult ; },
abstract = {The identification of new biomarkers is essential to predict responsiveness to vaccines. We investigated the whole-blood transcriptome and microbiome prior to immunization, in order to assess their involvement in induction of humoral responses two months later. We based our analyses on stool and skin microbiota, and blood transcriptome prior to immunization, in a randomized clinical study in which participants were vaccinated with the MVA-HIV clade B vaccine (MVA-B). We found that the levels of neutralizing antibody responses were correlated with abundance of Eubacterium in stool and Prevotella in skin. In addition, genus diversity and bacterial species abundance were also correlated with the expression of genes involved in B cell development prior to immunization and forecast strong responders to MVA-B. To our knowledge, this is the first study integrating host blood gene expression and microbiota that might open an avenue of research in this field and to optimize vaccination strategies and predict responsiveness to vaccines.},
}
@article {pmid34039428,
year = {2021},
author = {Amar, Y and Lagkouvardos, I and Silva, RL and Ishola, OA and Foesel, BU and Kublik, S and Schöler, A and Niedermeier, S and Bleuel, R and Zink, A and Neuhaus, K and Schloter, M and Biedermann, T and Köberle, M},
title = {Pre-digest of unprotected DNA by Benzonase improves the representation of living skin bacteria and efficiently depletes host DNA.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {123},
pmid = {34039428},
issn = {2049-2618},
mesh = {*Bacteria/genetics ; DNA/genetics ; DNA, Bacterial/genetics ; Endodeoxyribonucleases ; Endoribonucleases ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Skin/*microbiology ; },
abstract = {BACKGROUND: The identification of microbiota based on next-generation sequencing (NGS) of extracted DNA has drastically improved our understanding of the role of microbial communities in health and disease. However, DNA-based microbiome analysis cannot per se differentiate between living and dead microorganisms. In environments such as the skin, host defense mechanisms including antimicrobial peptides and low cutaneous pH result in a high microbial turnover, likely resulting in high numbers of dead cells present and releasing substantial amounts of microbial DNA. NGS analyses may thus lead to inaccurate estimations of microbiome structures and consequently functional capacities.<br><br>RESULTS: We investigated in this study the feasibility of a Benzonase-based approach (BDA) to pre-digest unprotected DNA, i.e., of dead microbial cells, as a method to overcome these limitations, thus offering a more accurate assessment of the living microbiome. A skin mock community as well as skin microbiome samples were analyzed using 16S rRNA gene sequencing and metagenomics sequencing after DNA extraction with and without a Benzonase digest to assess bacterial diversity patterns. The BDA method resulted in less reads from dead bacteria both in the skin mock community and skin swabs spiked with either heat-inactivated bacteria or bacterial-free DNA. This approach also efficiently depleted host DNA reads in samples with high human-to-microbial DNA ratios, with no obvious impact on the microbiome profile. We further observed that low biomass samples generate an α-diversity bias when the bacterial load is lower than 105 CFU and that Benzonase digest is not sufficient to overcome this bias.<br><br>CONCLUSIONS: The BDA approach enables both a better assessment of the living microbiota and depletion of host DNA reads. Video abstract.},
}
@article {pmid34039416,
year = {2021},
author = {Leung, MHY and Tong, X and Bøifot, KO and Bezdan, D and Butler, DJ and Danko, DC and Gohli, J and Green, DC and Hernandez, MT and Kelly, FJ and Levy, S and Mason-Buck, G and Nieto-Caballero, M and Syndercombe-Court, D and Udekwu, K and Young, BG and Mason, CE and Dybwad, M and Lee, PKH},
title = {Characterization of the public transit air microbiome and resistome reveals geographical specificity.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {112},
pmid = {34039416},
issn = {2049-2618},
support = {R25 EB020393/EB/NIBIB NIH HHS/United States ; R01 NS076465/NS/NINDS NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; U01 DA053941/DA/NIDA NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; },
mesh = {Bacteria/genetics ; Geography ; Hong Kong ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; },
abstract = {BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.<br><br>RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.<br><br>CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.},
}
@article {pmid34037469,
year = {2021},
author = {Fulci, V and Carissimi, C and Laudadio, I},
title = {COVID-19 and Preparing for Future Ecological Crises: Hopes from Metagenomics in Facing Current and Future Viral Pandemic Challenges.},
journal = {Omics : a journal of integrative biology},
volume = {25},
number = {6},
pages = {336-341},
doi = {10.1089/omi.2021.0058},
pmid = {34037469},
issn = {1557-8100},
mesh = {Animals ; COVID-19/*diagnosis/*drug therapy ; Ecosystem ; Humans ; Metagenomics/methods ; Pandemics/*prevention &amp; control ; SARS-CoV-2/drug effects ; },
abstract = {The current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak demonstrates the potential of coronaviruses, especially bat-derived beta coronaviruses to rapidly escalate to a global pandemic that has caused deaths in the order of several millions already. The huge efforts put in place by the scientific community to address this emergency have disclosed how the implementation of new technologies is crucial in the prepandemic period to timely face future ecological crises. In this context, we argue that metagenomics and new approaches to understanding ecosystems and biodiversity offer veritable prospects to innovate therapeutics and diagnostics against novel and existing infectious agents. We discuss the opportunities and challenges associated with the science of metagenomics, specifically with an eye to inform and prevent future ecological crises and pandemics that are looming on the horizon in the 21st century.},
}
@article {pmid34037156,
year = {2021},
author = {Valença, IN and Santos, RBD and Peronni, KC and Sauvage, V and Vandenbogaert, M and Caro, V and Silva Junior, WAD and Covas, DT and Silva-Pinto, AC and Laperche, S and Kashima, S and Slavov, SN},
title = {Deep sequencing applied to the analysis of viromes in patients with beta-thalassemia.},
journal = {Revista do Instituto de Medicina Tropical de Sao Paulo},
volume = {63},
number = {},
pages = {e40},
pmid = {34037156},
issn = {1678-9946},
mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Seroepidemiologic Studies ; Virome ; *beta-Thalassemia/genetics ; },
abstract = {To date, blood banks apply routine diagnosis to a specific spectrum of transfusion-transmitted viruses. Even though this measure is considered highly efficient to control their transmission, the threat imposed by emerging viruses is increasing globally, which can impact transfusion safety, especially in the light of the accelerated viral discovery by novel sequencing technologies. One of the most important groups of patients, who may indicate the presence of emerging viruses in the field of blood transfusion, is the group of individuals who receive multiple transfusions due to hereditary hemoglobinopathies. It is possible that they harbor unknown or unsuspected parenterally-transmitted viruses. In order to elucidate this, nucleic acids from 30 patients with beta-thalassemia were analyzed by Illumina next-generation sequencing and bioinformatics analysis. Three major viral families: Anelloviridae, Flaviviridae and Hepadnaviridae were identified. Among them, anelloviruses were the most representative, being detected with high number of reads in all tested samples. Human Pegivirus 1 (HPgV-1, or GBV-C), Hepatitis B Virus (HBV) and Hepatitis C Virus (HCV) were also identified. HBV and HCV detection was expected due to the high seroprevalence in patients with beta thalassemia. Our results do not confirm the presence of emerging or unsuspected viruses threatening the transfusion safety at present, but can be used to actively search for viruses that threaten blood transfusion safety. We believe that the application of viral metagenomics in multiple-transfused patients is highly useful to monitor possible viral transfusion threats and for the annotation of their virome composition.},
}
@article {pmid34035441,
year = {2021},
author = {Teh, JJ and Berendsen, EM and Hoedt, EC and Kang, S and Zhang, J and Zhang, F and Liu, Q and Hamilton, AL and Wilson-O'Brien, A and Ching, J and Sung, JJY and Yu, J and Ng, SC and Kamm, MA and Morrison, M},
title = {Novel strain-level resolution of Crohn's disease mucosa-associated microbiota via an ex vivo combination of microbe culture and metagenomic sequencing.},
journal = {The ISME journal},
volume = {15},
number = {11},
pages = {3326-3338},
pmid = {34035441},
issn = {1751-7370},
mesh = {*Crohn Disease ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Mucous Membrane ; },
abstract = {The mucosa-associated microbiota is widely recognized as a potential trigger for Crohn's disease pathophysiology but remains largely uncharacterised beyond its taxonomic composition. Unlike stool microbiota, the functional characterisation of these communities using current DNA/RNA sequencing approaches remains constrained by the relatively small microbial density on tissue, and the overwhelming amount of human DNA recovered during sample preparation. Here, we have used a novel ex vivo approach that combines microbe culture from anaerobically preserved tissue with metagenome sequencing (MC-MGS) to reveal patient-specific and strain-level differences among these communities in post-operative Crohn's disease patients. The 16 S rRNA gene amplicon profiles showed these cultures provide a representative and holistic representation of the mucosa-associated microbiota, and MC-MGS produced both high quality metagenome-assembled genomes of recovered novel bacterial lineages. The MC-MGS approach also produced a strain-level resolution of key Enterobacteriacea and their associated virulence factors and revealed that urease activity underpins a key and diverse metabolic guild in these communities, which was confirmed by culture-based studies with axenic cultures. Collectively, these findings using MC-MGS show that the Crohn's disease mucosa-associated microbiota possesses taxonomic and functional attributes that are highly individualistic, borne at least in part by novel bacterial lineages not readily isolated or characterised from stool samples using current sequencing approaches.},
}
@article {pmid34035399,
year = {2021},
author = {Zhao, Z and Chu, C and Zhou, D and Wang, Q and Wu, S and Zheng, X and Song, K and Lv, W},
title = {Soil bacterial community composition in rice-fish integrated farming systems with different planting years.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {10855},
pmid = {34035399},
issn = {2045-2322},
mesh = {Agriculture ; Animals ; *Bacteria ; Biodiversity ; *Farms ; *Fishes ; Metagenome ; Metagenomics/methods ; *Microbiota ; *Oryza ; *Soil Microbiology ; },
abstract = {The high productivity and efficient nutrient utilization in rice-fish integrated farming system are well reported. However, the characteristics of soil bacterial communities and their relationship with soil nutrient availability in rice-fish field remain unclear. In this study, we selected three paddy fields, including a rice monoculture field and two rice-fish fields with different planting years, to investigate the soil bacterial community composition with Illumina MiSeq sequencing technology. The results indicated that the soil properties were significantly different among different rice farming systems. The soil bacterial community composition in the rice-fish field was significantly different from that in the rice monoculture field. Five of the top 15 phyla were observed with significant differences and Nitrospirae was the most significant one. However, no taxa observed with significance between the rice planting area and aquaculture area no matter in the 1st or 5th year of rice-fish field. RDA analysis showed that the soil bacterial community differentiation in the 5th year of rice-fish field was positively correlated with soil properties, such as AN and OM contents, EC and pH value. Although the rice yields in rice-fish field decreased, the net economic benefit of the rice-fish system enhanced obviously due to the high value of aquaculture animals.},
}
@article {pmid34034165,
year = {2021},
author = {Wu, X and Liu, P and Wegner, CE and Luo, Y and Xiao, KQ and Cui, Z and Zhang, F and Liesack, W and Peng, J},
title = {Deciphering microbial mechanisms underlying soil organic carbon storage in a wheat-maize rotation system.},
journal = {The Science of the total environment},
volume = {788},
number = {},
pages = {147798},
doi = {10.1016/j.scitotenv.2021.147798},
pmid = {34034165},
issn = {1879-1026},
mesh = {Agriculture ; *Carbon ; Fertilizers/analysis ; Manure ; RNA, Ribosomal, 16S ; Rotation ; *Soil ; Soil Microbiology ; Triticum ; Zea mays ; },
abstract = {A link between microbial life history strategies and soil organic carbon storage in agroecosystems is presumed, but largely unexplored at the gene level. We aimed to elucidate whether and how differential organic material amendments (manure versus peat-vermiculite) affect, relative to sole chemical fertilizer application, the link between microbial life history strategies and soil organic carbon storage in a wheat-maize rotation field experiment. To achieve this goal, we combined bacterial 16S rRNA gene and fungal ITS amplicon sequencing, metagenomics and the assembly of genomes. Fertilizer treatments had a significantly greater effect on microbial community composition than aggregate size, with soil available phosphorus and potassium being the most important community-shaping factors. Limitation in labile carbon was linked to a K-selected oligotrophic life history strategy (Gemmatimonadetes, Acidobacteria) under sole chemical fertilizer application; defined by a significant enrichment of genes involved in resource acquisition, polymer hydrolysis, and competition. By contrast, excess of labile carbon promoted an r-selected copiotrophic life history strategy (Cytophagales, Bacillales, Mortierellomycota) under manure treatment; defined by a significant enrichment of genes involved in cellular growth. A distinct life history strategy was not observed under peat-vermiculite treatment, but rather a mix of both K-selected (Acidobacteria) and r-selected (Actinobacteria, Mortierellomycota) microorganisms. Compared to sole chemical fertilizer application, soil organic carbon storage efficiency was significantly increased by 26.5% and 50.0% under manure and peat-vermiculite treatments, respectively. Taken together, our results highlight the importance of organic material amendments, but in particular a one-time peat-vermiculite application, to promote soil organic carbon storage as a potential management strategy for sustainable agriculture.},
}
@article {pmid34030239,
year = {2021},
author = {Qiao, L and Liu, X and Zhang, S and Zhang, L and Li, X and Hu, X and Zhao, Q and Wang, Q and Yu, C},
title = {Distribution of the microbial community and antibiotic resistance genes in farmland surrounding gold tailings: A metagenomics approach.},
journal = {The Science of the total environment},
volume = {779},
number = {},
pages = {146502},
doi = {10.1016/j.scitotenv.2021.146502},
pmid = {34030239},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents/pharmacology ; China ; Drug Resistance, Microbial/genetics ; Farms ; Gold ; Metagenomics ; *Metals, Heavy/analysis ; *Microbiota ; *Soil Pollutants/analysis ; },
abstract = {Metal mining has caused the accumulation of waste mine tailing dumps from abandoned mines. The pollution of farmlands surrounding metal tailings by heavy metals has been a long-recognized problem. However, the distribution of antibiotic resistance genes (ARGs) in tailings and the main factors influencing this distribution have rarely been reported. In this study, a metagenomics approach was used to investigate the microbial community and ARGs present in farmland surrounding gold tailings in northern China. The results showed that the main pollutants in the farmland were As, Pb, and Cd. Proteobacteria and Actinobacteria were the dominant phyla of microbes in farmlands surrounding gold tailings. A total of 75 ARGs with 327 ARG subtypes were detected in soil samples. Macrolide-, lincosaminide-, and streptogramin B resistant genes accounted for the majority of ARGs in this study, and Actinobacteria, Proteobacteria, and Acidobacteria were the hosts of most ARGs. Partial least squares path modeling revealed that the microbial community was the most influential driver moderating the distribution of soil ARGs near tailings, and heavy metals have direct and partially indirect effects on these ARGs. In contrast to previous analyses of ARGs, our study found that mobile gene elements had a minimal impact on ARGs. Overall, this study presents a complete ARG survey that sheds light on the distribution and fate of ARGs under heavy metal contamination in farmland around gold tailings.},
}
@article {pmid34029816,
year = {2021},
author = {Ramírez-Fernández, L and Orellana, LH and Johnston, ER and Konstantinidis, KT and Orlando, J},
title = {Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes.},
journal = {The Science of the total environment},
volume = {788},
number = {},
pages = {147693},
doi = {10.1016/j.scitotenv.2021.147693},
pmid = {34029816},
issn = {1879-1026},
mesh = {Animals ; Antarctic Regions ; *Metagenome ; Metagenomics ; *Microbiota ; Nitrous Oxide ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; },
abstract = {Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.},
}
@article {pmid34029658,
year = {2021},
author = {Nodari, R and Drancourt, M and Barbieri, R},
title = {Paleomicrobiology of the human digestive tract: A review.},
journal = {Microbial pathogenesis},
volume = {157},
number = {},
pages = {104972},
doi = {10.1016/j.micpath.2021.104972},
pmid = {34029658},
issn = {1096-1208},
mesh = {Gastrointestinal Tract ; Humans ; *Metagenomics ; *Microbiota ; },
abstract = {The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.},
}
@article {pmid34022966,
year = {2021},
author = {Matheus Carnevali, PB and Lavy, A and Thomas, AD and Crits-Christoph, A and Diamond, S and Méheust, R and Olm, MR and Sharrar, A and Lei, S and Dong, W and Falco, N and Bouskill, N and Newcomer, ME and Nico, P and Wainwright, H and Dwivedi, D and Williams, KH and Hubbard, S and Banfield, JF},
title = {Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {121},
pmid = {34022966},
issn = {2049-2618},
mesh = {Carbon ; *Microbiota/genetics ; Nitrogen ; Rivers ; *Soil ; },
abstract = {BACKGROUND: Biogeochemical exports from watersheds are modulated by the activity of microorganisms that function over micron scales. Here, we tested the hypothesis that meander-bound regions share a core microbiome and exhibit patterns of metabolic potential that broadly predict biogeochemical processes in floodplain soils along a river corridor.<br><br>RESULTS: We intensively sampled the microbiomes of floodplain soils located in the upper, middle, and lower reaches of the East River, Colorado. Despite the very high microbial diversity and complexity of the soils, we reconstructed 248 quality draft genomes representative of subspecies. Approximately one third of these bacterial subspecies was detected across all three locations at similar abundance levels, and ~ 15% of species were detected in two consecutive years. Within the meander-bound floodplains, we did not detect systematic patterns of gene abundance based on sampling position relative to the river. However, across meanders, we identified a core floodplain microbiome that is enriched in capacities for aerobic respiration, aerobic CO oxidation, and thiosulfate oxidation with the formation of elemental sulfur. Given this, we conducted a transcriptomic analysis of the middle floodplain. In contrast to predictions made based on the prominence of gene inventories, the most highly transcribed genes were relatively rare amoCAB and nxrAB (for nitrification) genes, followed by genes involved in methanol and formate oxidation, and nitrogen and CO2 fixation. Within all three meanders, low soil organic carbon correlated with high activity of genes involved in methanol, formate, sulfide, hydrogen, and ammonia oxidation, nitrite oxidoreduction, and nitrate and nitrite reduction. Overall, the results emphasize the importance of sulfur, one-carbon and nitrogen compound metabolism in soils of the riparian corridor.<br><br>CONCLUSIONS: The disparity between the scale of a microbial cell and the scale of a watershed currently limits the development of genomically informed predictive models describing watershed biogeochemical function. Meander-bound floodplains appear to serve as scaling motifs that predict aggregate capacities for biogeochemical transformations, providing a foundation for incorporating riparian soil microbiomes in watershed models. Widely represented genetic capacities did not predict in situ activity at one time point, but rather they define a reservoir of biogeochemical potential available as conditions change. Video abstract.},
}
@article {pmid34021204,
year = {2021},
author = {Lima, KM and Davis, RR and Liu, SY and Greenhalgh, DG and Tran, NK},
title = {Longitudinal profiling of the burn patient cutaneous and gastrointestinal microbiota: a pilot study.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {10667},
pmid = {34021204},
issn = {2045-2322},
support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; },
mesh = {Adult ; Aged ; Bacterial Infections ; Biodiversity ; Burns/complications/*epidemiology/therapy ; Computational Biology ; Female ; *Gastrointestinal Microbiome ; Humans ; Longitudinal Studies ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Skin/*microbiology ; },
abstract = {Sepsis is a leading cause of morbidity and mortality in patients that have sustained a severe burn injury. Early detection and treatment of infections improves outcomes and understanding changes in the host microbiome following injury and during treatment may aid in burn care. The loss of functional barriers, systemic inflammation, and commensal community perturbations all contribute to a burn patient's increased risk of infection. We sampled 10 burn patients to evaluate cutaneous microbial populations on the burn wound and corresponding spared skin on days 0, 3, 7, 14, 21, and 28 post-intensive care unit admission. In addition, skin samples were paired with perianal and rectal locations to evaluate changes in the burn patient gut microbiome following injury and treatment. We found significant (P = 0.011) reduction in alpha diversity on the burn wound compared to spared skin throughout the sampling period as well as reduction in common skin commensal bacteria such as Propionibacterium acnes and Staphylococcus epidermitis. Compared to healthy volunteers (n = 18), the burn patient spared skin also exhibited a significant reduction in alpha diversity (P = 0.001). Treatments such as systemic or topical antibiotic administration, skin grafting, and nutritional formulations also impact diversity and community composition at the sampling locations. When evaluating each subject individually, an increase in relative abundance of taxa isolated clinically by bacterial culture could be seen in 5/9 infections detected among the burn patient cohort.},
}
@article {pmid34020448,
year = {2021},
author = {Koponen, KK and Salosensaari, A and Ruuskanen, MO and Havulinna, AS and Männistö, S and Jousilahti, P and Palmu, J and Salido, R and Sanders, K and Brennan, C and Humphrey, GC and Sanders, JG and Meric, G and Cheng, S and Inouye, M and Jain, M and Niiranen, TJ and Valsta, LM and Knight, R and Salomaa, VV},
title = {Associations of healthy food choices with gut microbiota profiles.},
journal = {The American journal of clinical nutrition},
volume = {114},
number = {2},
pages = {605-616},
pmid = {34020448},
issn = {1938-3207},
support = {R01 ES027595/ES/NIEHS NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; R01ES027595/GF/NIH HHS/United States ; },
mesh = {Adult ; Aged ; Bacteria/classification ; *Choice Behavior ; Diet Surveys ; *Diet, Healthy ; Female ; *Food ; *Gastrointestinal Microbiome ; Humans ; Male ; Middle Aged ; },
abstract = {BACKGROUND: Diet has a major influence on the human gut microbiota, which has been linked to health and disease. However, epidemiological studies on associations of a healthy diet with the microbiota utilizing a whole-diet approach are still scant.<br><br>OBJECTIVES: To assess associations between healthy food choices and human gut microbiota composition, and to determine the strength of association with functional potential.<br><br>METHODS: This population-based study sample consisted of 4930 participants (ages 25-74; 53% women) in the FINRISK 2002 study. Intakes of recommended foods were assessed using a food propensity questionnaire, and responses were transformed into healthy food choices (HFC) scores. Microbial diversity (alpha diversity) and compositional differences (beta diversity) and their associations with the HFC score and its components were assessed using linear regression. Multiple permutational multivariate ANOVAs were run from whole-metagenome shallow shotgun-sequenced samples. Associations between specific taxa and HFC were analyzed using linear regression. Functional associations were derived from Kyoto Encyclopedia of Genes and Genomes orthologies with linear regression models.<br><br>RESULTS: Both microbial alpha diversity (β/SD, 0.044; SE, 6.18 × 10-5; P = 2.21 × 10-3) and beta diversity (R2, 0.12; P ≤ 1.00 × 10-3) were associated with the HFC score. For alpha diversity, the strongest associations were observed for fiber-rich breads, poultry, fruits, and low-fat cheeses (all positive). For beta diversity, the most prominent associations were observed for vegetables, followed by berries and fruits. Genera with fiber-degrading and SCFA-producing capacities were positively associated with the HFC score. The HFC score was associated positively with functions such as SCFA metabolism and synthesis, and inversely with functions such as fatty acid biosynthesis and the sulfur relay system.<br><br>CONCLUSIONS: Our results from a large, population-based survey confirm and extend findings of other, smaller-scale studies that plant- and fiber-rich dietary choices are associated with a more diverse and compositionally distinct microbiota, and with a greater potential to produce SCFAs.},
}
@article {pmid34014265,
year = {2021},
author = {Quiza, L and Tremblay, J and Greer, CW and Hemmingsen, SM and St-Arnaud, M and Pozniak, CJ and Yergeau, E},
title = {Rhizosphere shotgun metagenomic analyses fail to show differences between ancestral and modern wheat genotypes grown under low fertilizer inputs.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {6},
pages = {},
doi = {10.1093/femsec/fiab071},
pmid = {34014265},
issn = {1574-6941},
mesh = {Fertilizers ; Genotype ; Metagenome ; *Microbiota ; *Rhizosphere ; Soil ; Soil Microbiology ; Triticum ; },
abstract = {It is thought that modern wheat genotypes have lost their capacity to associate with soil microbes that would help them acquire nutrients from the soil. To test this hypothesis, ten ancestral and modern wheat genotypes were seeded in a field experiment under low fertilization conditions. The rhizosphere soil was collected, its DNA extracted and submitted to shotgun metagenomic sequencing. In contrast to our hypothesis, there was no significant difference in the global rhizosphere metagenomes of the different genotypes, and this held true when focusing the analyses on specific taxonomic or functional categories of genes. Some genes were significantly more abundant in the rhizosphere of one genotype or another, but they comprised only a small portion of the total genes identified and did not affect the global rhizosphere metagenomes. Our study shows for the first time that the rhizosphere metagenome of wheat is stable across a wide variety of genotypes when growing under nutrient poor conditions.},
}
@article {pmid34012005,
year = {2021},
author = {O'Sullivan, DM and Doyle, RM and Temisak, S and Redshaw, N and Whale, AS and Logan, G and Huang, J and Fischer, N and Amos, GCA and Preston, MD and Marchesi, JR and Wagner, J and Parkhill, J and Motro, Y and Denise, H and Finn, RD and Harris, KA and Kay, GL and O'Grady, J and Ransom-Jones, E and Wu, H and Laing, E and Studholme, DJ and Benavente, ED and Phelan, J and Clark, TG and Moran-Gilad, J and Huggett, JF},
title = {An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {10590},
pmid = {34012005},
issn = {2045-2322},
support = {MR/N013956/1//UK Antimicrobial Resistance Cross Council Initiative/ ; MR/N013956/1//UK Antimicrobial Resistance Cross Council Initiative/ ; MR/K000551/1//MRC UK/ ; MR/M01360X/1//MRC UK/ ; MR/N010469/1//MRC UK/ ; MR/R020973/1//MRC UK/ ; BB/R013063/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Computational Biology ; *Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Despite the advent of whole genome metagenomics, targeted approaches (such as 16S rRNA gene amplicon sequencing) continue to be valuable for determining the microbial composition of samples. Amplicon microbiome sequencing can be performed on clinical samples from a normally sterile site to determine the aetiology of an infection (usually single pathogen identification) or samples from more complex niches such as human mucosa or environmental samples where multiple microorganisms need to be identified. The methodologies are frequently applied to determine both presence of micro-organisms and their quantity or relative abundance. There are a number of technical steps required to perform microbial community profiling, many of which may have appreciable precision and bias that impacts final results. In order for these methods to be applied with the greatest accuracy, comparative studies across different laboratories are warranted. In this study we explored the impact of the bioinformatic approaches taken in different laboratories on microbiome assessment using 16S rRNA gene amplicon sequencing results. Data were generated from two mock microbial community samples which were amplified using primer sets spanning five different variable regions of 16S rRNA genes. The PCR-sequencing analysis included three technical repeats of the process to determine the repeatability of their methods. Thirteen laboratories participated in the study, and each analysed the same FASTQ files using their choice of pipeline. This study captured the methods used and the resulting sequence annotation and relative abundance output from bioinformatic analyses. Results were compared to digital PCR assessment of the absolute abundance of each target representing each organism in the mock microbial community samples and also to analyses of shotgun metagenome sequence data. This ring trial demonstrates that the choice of bioinformatic analysis pipeline alone can result in different estimations of the composition of the microbiome when using 16S rRNA gene amplicon sequencing data. The study observed differences in terms of both presence and abundance of organisms and provides a resource for ensuring reproducible pipeline development and application. The observed differences were especially prevalent when using custom databases and applying high stringency operational taxonomic unit (OTU) cut-off limits. In order to apply sequencing approaches with greater accuracy, the impact of different analytical steps needs to be clearly delineated and solutions devised to harmonise microbiome analysis results.},
}
@article {pmid34008889,
year = {2021},
author = {Xia, Y and Wang, J and Fang, X and Dou, T and Han, L and Yang, C},
title = {Combined analysis of metagenomic data revealed consistent changes of gut microbiome structure and function in inflammatory bowel disease.},
journal = {Journal of applied microbiology},
volume = {131},
number = {6},
pages = {3018-3031},
doi = {10.1111/jam.15154},
pmid = {34008889},
issn = {1365-2672},
support = {81603187//National Natural Science Foundation of China/ ; 2017YFC1700200//National Key Research and Development Program of China/ ; 2017YFC1702000//National Key Research and Development Program of China/ ; DUT18LK39//Fundamental Research Funds for the Central Universities/ ; DUT18RC(4)057//Fundamental Research Funds for the Central Universities/ ; DUT20RC(4)013//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Clostridiales ; Escherichia coli/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Inflammatory Bowel Diseases ; Metagenome ; },
abstract = {AIMS: To reveal the consistency and discrepancy in the gut microbial structure and function in inflammatory bowel disease (IBD) patients from different regions.<br><br>METHODS AND RESULTS: Gut microbes, antibiotic resistance genes (ARGs) and virulence factors genes (VFGs) were analysed using metagenome data from three cohorts. The abundance of Escherichia coli extensively increased in IBD patients, whereas Subdoligranulum unclassified decreased dramatically in IBD patients from three countries. Escherichia coli showed a positive correlation with multiple ARGs and VFGs in cohorts from China and the United States, including multidrug-related resistance genes and Capsule and LOS-related virulence factors genes. Escherichia coli biofilm synthesis pathways significantly enriched in IBD patients from three different regions. Notably, Subdoligranulum unclassified and Eubacterium hallii were negatively related to ARGs and VFGs.<br><br>CONCLUSIONS: Consistent changes of microbiome structure and function were observed in IBD patients from three different regions. As pathogenic bacteria, E. coli may accelerate IBD progression through encapsulation in biofilms by upregulating antibiotic resistance in Crohn's disease patients. Subdoligranulum unclassified and E. hallii may be beneficial for IBD patients and could serve as potential probiotics for IBD treatment.<br><br>This work dispels worries about the regional differences in gut microbial changes in IBD patients and provides useful guidance for more rational microbiome-based therapies.},
}
@article {pmid34006865,
year = {2021},
author = {Tierney, BT and Tan, Y and Kostic, AD and Patel, CJ},
title = {Gene-level metagenomic architectures across diseases yield high-resolution microbiome diagnostic indicators.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2907},
pmid = {34006865},
issn = {2041-1723},
support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; T32 DK110919/DK/NIDDK NIH HHS/United States ; },
mesh = {Bacteria/classification/genetics ; Cluster Analysis ; Colorectal Neoplasms/genetics/microbiology ; Computational Biology/*methods ; Diabetes Mellitus, Type 2/genetics/microbiology ; Firmicutes/genetics/physiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Inflammatory Bowel Diseases/genetics/microbiology ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Phylogeny ; Species Specificity ; },
abstract = {We propose microbiome disease "architectures": linking >1 million microbial features (species, pathways, and genes) to 7 host phenotypes from 13 cohorts using a pipeline designed to identify associations that are robust to analytical model choice. Here, we quantify conservation and heterogeneity in microbiome-disease associations, using gene-level analysis to identify strain-specific, cross-disease, positive and negative associations. We find coronary artery disease, inflammatory bowel diseases, and liver cirrhosis to share gene-level signatures ascribed to the Streptococcus genus. Type 2 diabetes, by comparison, has a distinct metagenomic signature not linked to any one specific species or genus. We additionally find that at the species-level, the prior-reported connection between Solobacterium moorei and colorectal cancer is not consistently identified across models-however, our gene-level analysis unveils a group of robust, strain-specific gene associations. Finally, we validate our findings regarding colorectal cancer and inflammatory bowel diseases in independent cohorts and identify that features inversely associated with disease tend to be less reproducible than features enriched in disease. Overall, our work is not only a step towards gene-based, cross-disease microbiome diagnostic indicators, but it also illuminates the nuances of the genetic architecture of the human microbiome, including tension between gene- and species-level associations.},
}
@article {pmid34006626,
year = {2021},
author = {Hwang, Y and Rahlff, J and Schulze-Makuch, D and Schloter, M and Probst, AJ},
title = {Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil.},
journal = {mSystems},
volume = {6},
number = {3},
pages = {},
pmid = {34006626},
issn = {2379-5077},
abstract = {Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.},
}
@article {pmid34006335,
year = {2021},
author = {Nearing, JT and Comeau, AM and Langille, MGI},
title = {Identifying biases and their potential solutions in human microbiome studies.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {113},
pmid = {34006335},
issn = {2049-2618},
support = {2016-05039//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (CA)/ ; },
mesh = {Bias ; Humans ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; Specimen Handling ; },
abstract = {Advances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for the disagreement in these results is due to the multitude of systemic biases that are introduced during sequence-based microbiome studies. These biases begin with sample collection and continue to be introduced throughout the entire experiment leading to an observed community that is significantly altered from the true underlying microbial composition. In this review, we will highlight the various steps in typical sequence-based human microbiome studies where significant bias can be introduced, and we will review the current efforts within the field that aim to reduce the impact of these biases. Video abstract.},
}
@article {pmid34006193,
year = {2021},
author = {Wang, K and Zhang, Z and Mo, ZS and Yang, XH and Lin, BL and Peng, L and Xu, Y and Lei, CY and Zhuang, XD and Lu, L and Yang, RF and Chen, T and Gao, ZL},
title = {Gut microbiota as prognosis markers for patients with HBV-related acute-on-chronic liver failure.},
journal = {Gut microbes},
volume = {13},
number = {1},
pages = {1-15},
pmid = {34006193},
issn = {1949-0984},
mesh = {Acute-On-Chronic Liver Failure/*microbiology/virology ; Adult ; Bacteria/classification/genetics/*isolation &amp; purification ; Disease Progression ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatitis B virus/physiology ; Hepatitis B, Chronic/*microbiology/virology ; Humans ; Male ; Metagenomics ; Middle Aged ; },
abstract = {The gut microbiota in the hepatitis B virus related acute-on-chronic liver failure (HBV-ACLF) is poorly defined. We aim to uncover the characteristics of the gut microbiota in HBV-ACLF and in other HBV associated pathologies. We analyzed the gut microbiome in patients with HBV-ACLF or other HBV associated pathologies and healthy individuals by 16S rRNA sequencing and metagenomic sequencing of fecal samples. 212 patients with HBV-ACLF, 252 with chronic hepatitis B (CHB), 162 with HBV-associated cirrhosis (HBV-LC) and 877 healthy individuals were recruited for the study. CHB and HBV-LC patients are grouped as HBV-Other. We discovered striking differences in the microbiome diversity between the HBV-ACLF, HBV-Other and healthy groups using 16S rRNA sequencing. The ratio of cocci to bacilli was significantly elevated in the HBV-ACLF group compared with healthy group. Further analysis within the HBV-ACLF group identified 52 genera showing distinct richness within the group where Enterococcus was enriched in the progression group whilst Faecalibacterium was enriched in the regression group. Metagenomic sequencing validated these findings and further uncovered an enrichment of Lactobacillus casei paracasei in progression group, while Alistipes senegalensis, Faecalibacterium prausnitzii and Parabacteroides merdae dominated the regression group. Importantly, our analysis revealed that there was a rapid increase of Enterococcus faecium during the progression of HBV-ACLF. The gut microbiota displayed distinct composition at different phases of HBV-ACLF. High abundance of Enterococcus is associated with progression while that of Faecalibacterium is associated with regression of HBV-ACLF. Therefore, the microbiota features hold promising potential as prognostic markers for HBV-ACLF.},
}
@article {pmid34002024,
year = {2021},
author = {Ni, Y and Lohinai, Z and Heshiki, Y and Dome, B and Moldvay, J and Dulka, E and Galffy, G and Berta, J and Weiss, GJ and Sommer, MOA and Panagiotou, G},
title = {Distinct composition and metabolic functions of human gut microbiota are associated with cachexia in lung cancer patients.},
journal = {The ISME journal},
volume = {15},
number = {11},
pages = {3207-3220},
pmid = {34002024},
issn = {1751-7370},
mesh = {Cachexia ; *Gastrointestinal Microbiome ; Humans ; *Lung Neoplasms/complications ; Prevotella ; },
abstract = {Cachexia is associated with decreased survival in cancer patients and has a prevalence of up to 80%. The etiology of cachexia is poorly understood, and limited treatment options exist. Here, we investigated the role of the human gut microbiome in cachexia by integrating shotgun metagenomics and plasma metabolomics of 31 lung cancer patients. The cachexia group showed significant differences in the gut microbial composition, functional pathways of the metagenome, and the related plasma metabolites compared to non-cachectic patients. Branched-chain amino acids (BCAAs), methylhistamine, and vitamins were significantly depleted in the plasma of cachexia patients, which was also reflected in the depletion of relevant gut microbiota functional pathways. The enrichment of BCAAs and 3-oxocholic acid in non-cachectic patients were positively correlated with gut microbial species Prevotella copri and Lactobacillus gasseri, respectively. Furthermore, the gut microbiota capacity for lipopolysaccharides biosynthesis was significantly enriched in cachectic patients. The involvement of the gut microbiome in cachexia was further observed in a high-performance machine learning model using solely gut microbial features. Our study demonstrates the links between cachectic host metabolism and specific gut microbial species and functions in a clinical setting, suggesting that the gut microbiota could have an influence on cachexia with possible therapeutic applications.},
}
@article {pmid33995413,
year = {2021},
author = {Alam, MS and Gangiredla, J and Hasan, NA and Barnaba, T and Tartera, C},
title = {Aging-Induced Dysbiosis of Gut Microbiota as a Risk Factor for Increased Listeria monocytogenes Infection.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {672353},
pmid = {33995413},
issn = {1664-3224},
mesh = {Aging/*physiology ; Animals ; Dysbiosis/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Listeria monocytogenes ; Listeriosis/*microbiology ; Mice ; Mice, Inbred C57BL ; Risk Factors ; },
abstract = {Invasive foodborne Listeria monocytogenes infection causes gastroenteritis, septicemia, meningitis, and chorioamnionitis, and is associated with high case-fatality rates in the elderly. It is unclear how aging alters gut microbiota, increases risk of listeriosis, and causes dysbiosis post-infection. We used a geriatric murine model of listeriosis as human surrogate of listeriosis for aging individuals to study the effect of aging and L. monocytogenes infection. Aging and listeriosis-induced perturbation of gut microbiota and disease severity were compared between young-adult and old mice. Young-adult and old mice were dosed intragastrically with L. monocytogenes. Fecal pellets were collected pre- and post-infection for microbiome analysis. Infected old mice had higher Listeria colonization in liver, spleen, and feces. Metagenomics analyses of fecal DNA-sequences showed increase in α-diversity as mice aged, and infection reduced its diversity. The relative abundance of major bacterial phylum like, Bacteroidetes and Firmicutes remained stable over aging or infection, while the Verrucomicrobia phylum was significantly reduced only in infected old mice. Old mice showed a marked reduction in Clostridaiceae and Lactobacillaceae bacteria even before infection when compared to uninfected young-adult mice. L. monocytogenes infection increased the abundance of Porphyromonadaceae and Prevotellaceae in young-adult mice, while members of the Ruminococcaceae and Lachnospiraceae family were significantly increased in old mice. The abundance of the genera Blautia and Alistipes were significantly reduced post-infection in young-adult and in old mice as compared to their uninfected counterparts. Butyrate producing, immune-modulating bacterial species, like Pseudoflavonifractor and Faecalibacterium were significantly increased only in old infected mice, correlating with increased intestinal inflammatory mRNA up-regulation from old mice tissue. Histologic analyses of gastric tissues showed extensive lesions in the Listeria-infected old mice, more so in the non-glandular region and fundus than in the pylorus. Commensal species like Lactobacillus, Clostridiales, and Akkermansia were only abundant in infected young-adult mice but their abundance diminished in the infected old mice. Listeriosis in old mice enhances the abundance of butyrate-producing inflammatory members of the Ruminococcaceae/Lachnospiraceae bacteria while reducing/eliminating beneficial commensals in the gut. Results of this study indicate that, aging may affect the composition of gut microbiota and increase the risk of invasive L. monocytogenes infection.},
}
@article {pmid33991864,
year = {2021},
author = {Kalcioglu, MT and Durmaz, R and Ari, O and Celik, S and Karabudak, S},
title = {Microbiological investigation of samples collected from healthy middle ears during cochlear implant surgery.},
journal = {Diagnostic microbiology and infectious disease},
volume = {100},
number = {4},
pages = {115390},
doi = {10.1016/j.diagmicrobio.2021.115390},
pmid = {33991864},
issn = {1879-0070},
mesh = {Adult ; Bacteria/*classification/*genetics/isolation &amp; purification ; Child, Preschool ; Cochlear Implants/*adverse effects ; Ear, Middle/*microbiology ; Genetic Variation ; Healthy Volunteers/statistics &amp; numerical data ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Newborn ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {This study aimed to investigate the bacteriome in microscopically healthy middle ear mucosa using Next-generation sequencing (NGS) technology. A total of 60 middle ear washing fluids of pediatric and adult were obtained from 47 patients (35 children and 12 adults). Both children and adults with normal middle ears harbored diverse bacteriome. Seventeen different genera with a mean relative abundance of more than 1% were detected in all samples. Both in adult and children, the most abundant genus was Propionibacterium followed by Streptococcus, Staphylococcus, and Ralstonia. The species Propionibacterium acnes and Corynebacterium tuberculostearicum were significantly more abundant in the adult group. Although there were differences in the prevalence and relative abundance of some bacteria observed from adult and child groups, no specific genus or species was detected only in children or adults.},
}
@article {pmid33990699,
year = {2021},
author = {Rasmussen, JA and Villumsen, KR and Duchêne, DA and Puetz, LC and Delmont, TO and Sveier, H and Jørgensen, LVG and Præbel, K and Martin, MD and Bojesen, AM and Gilbert, MTP and Kristiansen, K and Limborg, MT},
title = {Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {579},
pmid = {33990699},
issn = {2399-3642},
mesh = {Animals ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; *Metagenome ; Mycoplasma/*genetics ; Phylogeny ; Salmonidae/*microbiology ; Sequence Analysis, DNA ; *Symbiosis ; },
abstract = {Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.},
}
@article {pmid33990301,
year = {2021},
author = {Mota-Gutierrez, J and Ferrocino, I and Giordano, M and Suarez-Quiroz, ML and Gonzalez-Ríos, O and Cocolin, L},
title = {Influence of Taxonomic and Functional Content of Microbial Communities on the Quality of Fermented Cocoa Pulp-Bean Mass.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {14},
pages = {e0042521},
pmid = {33990301},
issn = {1098-5336},
mesh = {Adult ; Bacteria/genetics ; Cacao/*microbiology ; Female ; Fermentation ; Fungi/genetics ; Humans ; Male ; Metagenomics ; Microbiota/*genetics ; Odorants ; Taste ; Young Adult ; },
abstract = {Microbial metabolism drives changes in the physicochemical properties and, consequently, the sensory characteristics of fermented cocoa beans. In this context, information regarding the structure, function, and metabolic potential of microbial communities' present during cocoa pulp-bean mass fermentation is limited, especially concerning the formation of aromatic compounds. To bridge the gap, the metagenome of fermented cocoa pulp-bean mass (Criollo and Forastero) has been investigated using shotgun metagenomics coupled with physicochemical, microbiological, quality, and sensory analyses to explore the impact of microbial communities on the quality of fermented cocoa pulp-bean mass on one farm in one season and in one region under the same environmental conditions. Our findings showed that the metagenomic diversity in cocoa, the fermentation length, and the diversity and function of metagenome-assembled genomes (MAGs) greatly influence the resulting distinctive flavors. From the metabolic perspective, multiple indicators suggest that the heterolactic metabolism was more dominant in Criollo fermentations. KEGG genes were linked with the biosynthesis of acetic acid, ethanol, lactic acid, acetoin, and phenylacetaldehyde during Criollo and Forastero fermentations. MAGs belonging to Lactiplantibacillus plantarum, Limosilactobacillus reuteri, and Acetobacter pasteurianus were the most prevalent. Fermentation time and roasting are the most important determinants of cocoa quality, while the difference between the two varieties are relatively minor. The assessment of microbiological and chemical analysis is urgently needed for developing fermentation protocols according to regions, countries, and cocoa varieties to guarantee safety and desirable flavor development. IMPORTANCE Monitoring the composition, structure, functionalities, and metabolic potential encoded at the level of DNA of fermented cocoa pulp-bean mass metagenome is of great importance for food safety and quality implications.},
}
@article {pmid33986544,
year = {2021},
author = {Sun, Z and Huang, S and Zhang, M and Zhu, Q and Haiminen, N and Carrieri, AP and Vázquez-Baeza, Y and Parida, L and Kim, HC and Knight, R and Liu, YY},
title = {Challenges in benchmarking metagenomic profilers.},
journal = {Nature methods},
volume = {18},
number = {6},
pages = {618-626},
pmid = {33986544},
issn = {1548-7105},
support = {RF1 AG067744/AG/NIA NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; },
mesh = {Benchmarking/*methods ; Computational Biology/methods ; Gene Expression Profiling ; *Metagenomics ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Accurate microbial identification and abundance estimation are crucial for metagenomics analysis. Various methods for classification of metagenomic data and estimation of taxonomic profiles, broadly referred to as metagenomic profilers, have been developed. Nevertheless, benchmarking of metagenomic profilers remains challenging because some tools are designed to report relative sequence abundance while others report relative taxonomic abundance. Here we show how misleading conclusions can be drawn by neglecting this distinction between relative abundance types when benchmarking metagenomic profilers. Moreover, we show compelling evidence that interchanging sequence abundance and taxonomic abundance will influence both per-sample summary statistics and cross-sample comparisons. We suggest that the microbiome research community pay attention to potentially misleading biological conclusions arising from this issue when benchmarking metagenomic profilers, by carefully considering the type of abundance data that were analyzed and interpreted and clearly stating the strategy used for metagenomic profiling.},
}
@article {pmid33986295,
year = {2021},
author = {Huang, HJ and Ye, ZX and Wang, X and Yan, XT and Zhang, Y and He, YJ and Qi, YH and Zhang, XD and Zhuo, JC and Lu, G and Lu, JB and Mao, QZ and Sun, ZT and Yan, F and Chen, JP and Zhang, CX and Li, JM},
title = {Diversity and infectivity of the RNA virome among different cryptic species of an agriculturally important insect vector: whitefly Bemisia tabaci.},
journal = {NPJ biofilms and microbiomes},
volume = {7},
number = {1},
pages = {43},
pmid = {33986295},
issn = {2055-5008},
mesh = {Animals ; Databases, Genetic ; Hemiptera/*virology ; Host Specificity ; Insect Vectors/virology ; Metagenome ; Metagenomics/methods ; Phylogeny ; RNA Viruses/*classification/*genetics ; RNA, Viral ; *Virome ; },
abstract = {A large number of insect-specific viruses (ISVs) have recently been discovered, mostly from hematophagous insect vectors because of their medical importance, but little attention has been paid to important plant virus vectors such as the whitefly Bemisia tabaci, which exists as a complex of cryptic species. Public SRA datasets of B. tabaci and newly generated transcriptomes of three Chinese populations are here comprehensively investigated to characterize the whitefly viromes of different cryptic species. Twenty novel ISVs were confidently identified, mostly associated with a parti