@article {pmid32623494,
year = {2020},
author = {Wang, TY and Zhang, XQ and Chen, AL and Zhang, J and Lv, BH and Ma, MH and Lian, J and Wu, YX and Zhou, YT and Ma, CC and Dong, RJ and Ge, DY and Gao, SH and Jiang, GJ},
title = {A comparative study of microbial community and functions of type 2 diabetes mellitus patients with obesity and healthy people.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {16},
pages = {7143-7153},
doi = {10.1007/s00253-020-10689-7},
pmid = {32623494},
issn = {1432-0614},
support = {81774171//National Natural Science Foundation of China/ ; 18130219A//Tangshan Science and Technology Innovation TeamTraining Program/ ; CYXC1719//collaborative innovation project of Chaoyang District in Beijing/ ; },
mesh = {Adult ; Bacteria/*classification/metabolism ; Computational Biology ; Diabetes Mellitus, Type 2/*microbiology/physiopathology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Humans ; Male ; *Metagenome ; Metagenomics ; Middle Aged ; Obesity/*microbiology ; },
abstract = {The gut microbiota is crucial in the pathogenesis of type 2 diabetes mellitus (T2DM). However, the metabolism of T2DM patients is not well-understood. We aimed to identify the differences on composition and function of gut microbiota between T2DM patients with obesity and healthy people. In this study, 6 T2DM patients with obesity and 6 healthy volunteers were recruited, and metagenomic approach and bioinformatics analysis methods were used to understand the composition of the gut microbiota and the metabolic network. We found a decrease in the abundance of Firmicutes, Oribacterium, and Paenibacillus; this may be attributed to a possible mechanism and biological basis of T2DM; moreover, we identified three critical bacterial taxa, Bacteroides plebeius, Phascolarctobacterium sp. CAG207, and the order Acidaminococcales that can potentially be used for T2DM treatment. We also revealed the composition of the microbiota through functional annotation based on multiple databases and found that carbohydrate metabolism contributed greatly to the pathogenesis of T2DM. This study helps in elucidating the different metabolic roles of microbes in T2DM patients with obesity.},
}

Adult
Bacteria/*classification/metabolism
Computational Biology
Diabetes Mellitus, Type 2/*microbiology/physiopathology
Feces/microbiology
Female
*Gastrointestinal Microbiome
Healthy Volunteers
Humans
Male
*Metagenome
Metagenomics
Middle Aged
Obesity/*microbiology

@article {pmid32607646,
year = {2020},
author = {Stultiens, K and van Kessel, MAHJ and Frank, J and Fischer, P and Pelzer, C and van Alen, TA and Kartal, B and Op den Camp, HJM and Jetten, MSM},
title = {Diversity, enrichment, and genomic potential of anaerobic methane- and ammonium-oxidizing microorganisms from a brewery wastewater treatment plant.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {16},
pages = {7201-7212},
pmid = {32607646},
issn = {1432-0614},
support = {669371//H2020 European Research Council/ ; 6400422//H2020 European Research Council/ ; 339880//H2020 European Research Council/ ; 13146//Stichting voor de Technische Wetenschappen/ ; 016.veni.192.062//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 024002002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Ammonium Compounds/*metabolism ; Anaerobiosis ; Bacteria/*classification/metabolism ; *Biodiversity ; Bioreactors/*microbiology ; Metagenomics ; Methane/*metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; Water Purification ; },
abstract = {Anaerobic wastewater treatment offers several advantages; however, the effluent of anaerobic digesters still contains high levels of ammonium and dissolved methane that need to be removed before these effluents can be discharged to surface waters. The simultaneous anaerobic removal of methane and ammonium by denitrifying (N-damo) methanotrophs in combination with anaerobic ammonium-oxidizing (anammox) bacteria could be a potential solution to this challenge. After a molecular survey of a wastewater plant treating brewery effluent, indicating the presence of both N-damo and anammox bacteria, we started an anaerobic bioreactor with a continuous supply of methane, ammonium, and nitrite to enrich these anaerobic microorganisms. After 14 months of operation, a stable enrichment culture containing two types of 'Candidatus Methylomirabilis oxyfera' bacteria and two strains of 'Ca. Brocadia'-like anammox bacteria was achieved. In this community, anammox bacteria converted 80% of the nitrite with ammonium, while 'Ca. Methylomirabilis' contributed to 20% of the nitrite consumption. The analysis of metagenomic 16S rRNA reads and fluorescence in situ hybridization (FISH) correlated well and showed that, after 14 months, 'Ca. Methylomirabilis' and anammox bacteria constituted approximately 30 and 20% of the total microbial community. In addition, a substantial part (10%) of the community consisted of Phycisphaera-related planctomycetes. Assembly and binning of the metagenomic sequences resulted in high-quality draft genome of two 'Ca. Methylomirabilis' species containing the marker genes pmoCAB, xoxF, and nirS and putative NO dismutase genes. The anammox draft genomes most closely related to 'Ca. Brocadia fulgida' included the marker genes hzsABC, hao, and hdh. Whole-reactor and batch anaerobic activity measurements with methane, ammonium, nitrite, and nitrate revealed an average anaerobic methane oxidation rate of 0.12 mmol h-1 L-1 and ammonium oxidation rate of 0.5 mmol h-1 L-1. Together, this study describes the enrichment and draft genomes of anaerobic methanotrophs from a brewery wastewater treatment plant, where these organisms together with anammox bacteria can contribute significantly to the removal of methane and ammonium in a more sustainable way. KEY POINTS: • An enrichment culture containing both N-damo and anammox bacteria was obtained. • Simultaneous consumption of ammonia, nitrite, and methane under anoxic conditions. • In-depth metagenomic biodiversity analysis of inoculum and enrichment culture.},
}

Ammonium Compounds/*metabolism
Anaerobiosis
Bacteria/*classification/metabolism
*Biodiversity
Bioreactors/*microbiology
Metagenomics
Methane/*metabolism
Oxidation-Reduction
RNA, Ribosomal, 16S/genetics
Water Purification

@article {pmid32572576,
year = {2020},
author = {Park, H and Choi, IG},
title = {Genomic and transcriptomic perspectives on mycoremediation of polycyclic aromatic hydrocarbons.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {16},
pages = {6919-6928},
doi = {10.1007/s00253-020-10746-1},
pmid = {32572576},
issn = {1432-0614},
support = {PJ01337602//Rural Development Administration/ ; 20173010092460//Korea Institute of Energy Technology Evaluation and Planning/ ; },
mesh = {Basidiomycota/*genetics/*metabolism ; *Biodegradation, Environmental ; *Gene Expression Profiling ; *Metagenomics ; Microbial Consortia ; Polycyclic Aromatic Hydrocarbons/*metabolism ; Soil Microbiology ; Soil Pollutants/metabolism ; Transcriptome ; },
abstract = {Mycoremediation holds great potential in remedying toxic environments contaminated with polyaromatic organic pollutants. To harness the natural process for practical applications, understanding the genetic and molecular basis of the remediation process is prerequisite. Compared to known bacterial degradation pathways of aromatic pollutants, however, the fungal degradation system is less studied and understanding of the genetic basis for biochemical activity is still incomplete. In this review, we surveyed recent findings from genomic and transcriptomic approaches to mycoremediation of aromatic pollutants, in company with the genomic basis of polycyclic aromatic hydrocarbon (PAH) degradation by basidiomycete fungi, Dentipellis sp. KUC8613. Unique features in the fungal degradation of PAHs were outlined by multiple cellular processes: (i) the initial oxidation of recalcitrant contaminants by various oxidoreductases including mono- and dioxygenases, (ii) the following detoxification, and (iii) the mineralization of activated pollutants that are common metabolism in many fungi. Along with the genomic data, the transcriptomic analysis not only posits a full repertoire of inducible genes that are common or specific to metabolize different PAHs but also leads to the discovery of uncharacterized genes with potential functions for bioremediation processes. In addition, the metagenomic study accesses community level of mycoremediation process to seek for the potential species or a microbial consortium in the natural environments. The comprehensive understanding of fungal degradation in multiple levels will accelerate practical application of mycoremediation. Key points • Mycoremediation of polyaromatic pollutants exploits a potent fungal degrader. • Fungal genomics provides a full repository of potential genes and enzymes. • Mycoremediation is a concerted cellular process involved with many novel genes. • Multi-omics approach enables the genome-scale reconstruction of remedying pathways.},
}

Basidiomycota/*genetics/*metabolism
*Biodegradation, Environmental
*Gene Expression Profiling
*Metagenomics
Microbial Consortia
Polycyclic Aromatic Hydrocarbons/*metabolism
Soil Microbiology
Soil Pollutants/metabolism
Transcriptome

@article {pmid33503844,
year = {2021},
author = {Raja, G and Gupta, H and Gebru, YA and Youn, GS and Choi, YR and Kim, HS and Yoon, SJ and Kim, DJ and Kim, TJ and Suk, KT},
title = {Recent Advances of Microbiome-Associated Metabolomics Profiling in Liver Disease: Principles, Mechanisms, and Applications.},
journal = {International journal of molecular sciences},
volume = {22},
number = {3},
pages = {},
pmid = {33503844},
issn = {1422-0067},
support = {Hallym University Research Fund//Hallym University Research Fund/ ; NRF-2018M3A9F3020956, NRF-2019R1I1A3A01060447, NRF-2020R1I1A3073530 and NRF-2020R1A6A1A03043026//Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology/ ; },
mesh = {Animals ; Biomarkers ; Computational Biology/methods ; *Disease Susceptibility ; Energy Metabolism ; Gene Expression Profiling ; Genomics/methods ; Humans ; Liver Diseases/diagnosis/*etiology/*metabolism/therapy ; *Metabolome ; *Metabolomics/methods ; *Microbiota ; Phenomics ; },
abstract = {Advances in high-throughput screening of metabolic stability in liver and gut microbiota are able to identify and quantify small-molecule metabolites (metabolome) in different cellular microenvironments that are closest to their phenotypes. Metagenomics and metabolomics are largely recognized to be the "-omics" disciplines for clinical therapeutic screening. Here, metabolomics activity screening in liver disease (LD) and gut microbiomes has significantly delivered the integration of metabolomics data (i.e., a set of endogenous metabolites) with metabolic pathways in cellular environments that can be tested for biological functions (i.e., phenotypes). A growing literature in LD and gut microbiomes reports the use of metabolites as therapeutic targets or biomarkers. Although growing evidence connects liver fibrosis, cirrhosis, and hepatocellular carcinoma, the genetic and metabolic factors are still mainly unknown. Herein, we reviewed proof-of-concept mechanisms for metabolomics-based LD and gut microbiotas' role from several studies (nuclear magnetic resonance, gas/lipid chromatography, spectroscopy coupled with mass spectrometry, and capillary electrophoresis). A deeper understanding of these axes is a prerequisite for optimizing therapeutic strategies to improve liver health.},
}

Animals
Biomarkers
Computational Biology/methods
*Disease Susceptibility
Energy Metabolism
Gene Expression Profiling
Genomics/methods
Humans
Liver Diseases/diagnosis/*etiology/*metabolism/therapy
*Metabolome
*Metabolomics/methods
*Microbiota
Phenomics

@article {pmid33181127,
year = {2020},
author = {Miyoshi, J and Rao, MC and Chang, EB},
title = {Navigating the Human Gut Microbiome: Pathway to Success from Lessons Learned.},
journal = {Gastroenterology},
volume = {159},
number = {6},
pages = {2019-2024},
doi = {10.1053/j.gastro.2020.09.002},
pmid = {33181127},
issn = {1528-0012},
mesh = {Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/genetics/isolation & purification ; Feces/microbiology ; Gastrointestinal Microbiome/*physiology ; Genetic Markers ; Host Microbial Interactions/*physiology ; Humans ; Intestinal Mucosa/microbiology ; Metadata ; Metagenomics/methods ; Molecular Typing/*methods ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Specimen Handling/methods ; },
}

Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/genetics/isolation & purification
Feces/microbiology
Gastrointestinal Microbiome/*physiology
Genetic Markers
Host Microbial Interactions/*physiology
Humans
Intestinal Mucosa/microbiology
Metadata
Metagenomics/methods
Molecular Typing/*methods
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Specimen Handling/methods

@article {pmid32860788,
year = {2020},
author = {Kong, L and Lloyd-Price, J and Vatanen, T and Seksik, P and Beaugerie, L and Simon, T and Vlamakis, H and Sokol, H and Xavier, RJ},
title = {Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn's Disease.},
journal = {Gastroenterology},
volume = {159},
number = {6},
pages = {2193-2202.e5},
pmid = {32860788},
issn = {1528-0012},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; },
mesh = {Adult ; Crohn Disease/immunology/microbiology/*therapy ; Datasets as Topic ; Fecal Microbiota Transplantation/*methods ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics/immunology ; Haplotypes ; Humans ; Male ; Metagenomics ; Middle Aged ; Molecular Typing ; Phylogeny ; Remission Induction/methods ; Treatment Outcome ; Young Adult ; },
abstract = {BACKGROUND & AIMS: Crohn's disease (CD) is a chronic gastrointestinal disease resulting from the dysfunctional interplay between genetic susceptibility, the immune system, and commensal intestinal microbiota. Emerging evidence suggests that treatment by suppression of the immune response and replacement of the microbiota through fecal microbiota transplantation (FMT) is a promising approach for the treatment of CD.

METHODS: We obtained stool metagenomes from CD patients in remission and assessed gut microbiome composition before and after FMT at the species and strain levels. Longitudinal follow-up evaluation allowed us to identify the gain, loss, and strain replacement of specific species and link these events to the maintenance of remission in CD.

RESULTS: We found that FMT had a significant long-term effect on patient microbial compositions, although this was primarily driven by the engraftment of donor species, which remained at low abundance. Thirty-eight percent of FMT-driven changes were strain replacements, emphasizing the importance of detailed profiling methods, such as metagenomics. Several instances of long-term coexistence between donor and patient strains were also observed. Engraftment of some Actinobacteria, and engraftment or loss of Proteobacteria, were related to better disease outcomes in CD patients who received FMT, and transmission of Bacteroidetes was deleterious.

CONCLUSIONS: Our results suggest clades that may be beneficial to transmit/eliminate through FMT, and provide criteria that may help identify personalized FMT donors to more effectively maintain remission in CD patients. The framework established here creates a foundation for future studies centered around the application of FMT and defined microbial communities as a therapeutic approach for treating CD.},
}

Adult
Crohn Disease/immunology/microbiology/*therapy
Datasets as Topic
Fecal Microbiota Transplantation/*methods
Feces/microbiology
Female
Gastrointestinal Microbiome/*genetics/immunology
Haplotypes
Humans
Male
Metagenomics
Middle Aged
Molecular Typing
Phylogeny
Remission Induction/methods
Treatment Outcome
Young Adult

@article {pmid32723385,
year = {2020},
author = {Yuan, X and Chen, R and Zhang, Y and Lin, X and Yang, X},
title = {Sexual dimorphism of gut microbiota at different pubertal status.},
journal = {Microbial cell factories},
volume = {19},
number = {1},
pages = {152},
pmid = {32723385},
issn = {1475-2859},
support = {2016-S-wp1//Technology Innovation Team Train Project of Fuzhou Health Committee in China/ ; 201610191//key Clinical Specialty Discipline Construction Program of Fuzhou, Fujian, P.R.C/ ; },
mesh = {Adolescent ; Bacteria/*classification ; Child ; Child, Preschool ; China ; Cross-Sectional Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metagenomics ; *Puberty ; RNA, Ribosomal, 16S/genetics ; *Sex Characteristics ; },
abstract = {BACKGROUND: Accumulating evidence infer that gut microbiome-host relations are key mediators or modulators driving the observed sexual dimorphism in some disease onset and progression. To date, the sex-differences of gut microbiota at different pubertal status have not been reported.

OBJECTIVE: To determine the characteristics of gut microbiota of both genders at different pubertal status.

METHODS: Gut microbiota was analyzed in 89 Chinese participants aged 5-15 years. Participants were divided into pre-puberty and puberty groups for both male and female. The composition of gut microbiota was investigated by 16S rRNA-based metagenomics. Ecological representations of microbial communities were computed. The prediction of metagenomic functional content from 16S rRNA gene surveys was conducted.

RESULTS: There were 49 males (9.76 ± 2.15 years) and 40 females (9.74 ± 1.63 years); 21 males and 26 females were at puberty. At genus level, Alistipes, Megamonas, Oscillospira and Parabacteroides were more prevalent in girls than in boys (p < 0.05). There were no significantly differences of alpha-diversity between genders, which was independent of pubertal status. The beta-diversity was significantly different in pubertal subjects between genders. Using statistical analyses, we assigned genera Dorea, Megamonas, Bilophila, Parabacteroides and Phascolarctobacterium as microbial markers for pubertal subjects. The predicted metabolic profiles differ in both pubertal and pre-pubertal groups between genders.

CONCLUSION: This cross-sectional study revealed that sex differences in the gut microbiota composition and predicted metabolic profiles exist before puberty, which become more significant at puberty. The identification of novel puberty bacterial markers may disclose a potential effects of gender-related microbiota profiles on puberty onset.},
}

Adolescent
Bacteria/*classification
Child
Child, Preschool
China
Cross-Sectional Studies
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Male
*Metagenomics
*Puberty
RNA, Ribosomal, 16S/genetics
*Sex Characteristics

@article {pmid32467975,
year = {2020},
author = {Brealey, JC and Leitão, HG and van der Valk, T and Xu, W and Bougiouri, K and Dalén, L and Guschanski, K},
title = {Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome.},
journal = {Molecular biology and evolution},
volume = {37},
number = {10},
pages = {3003-3022},
pmid = {32467975},
issn = {1537-1719},
mesh = {Animals ; Biological Evolution ; Dental Calculus/*microbiology ; Diet ; Drug Resistance, Microbial/genetics ; Gorilla gorilla ; Mammals/*microbiology ; Metagenome ; *Microbiota ; Mouth/*microbiology ; Reindeer ; Ursidae ; },
abstract = {Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.},
}

Animals
Biological Evolution
Dental Calculus/*microbiology
Diet
Drug Resistance, Microbial/genetics
Gorilla gorilla
Mammals/*microbiology
Metagenome
*Microbiota
Mouth/*microbiology
Reindeer
Ursidae

@article {pmid32998695,
year = {2020},
author = {Soverini, M and Rampelli, S and Turroni, S and Brigidi, P and Biagi, E and Candela, M},
title = {Do the human gut metagenomic species possess the minimal set of core functionalities necessary for life?.},
journal = {BMC genomics},
volume = {21},
number = {1},
pages = {678},
pmid = {32998695},
issn = {1471-2164},
mesh = {*Gastrointestinal Microbiome ; *Genes, Bacterial ; Genes, Essential ; Humans ; Intestinal Mucosa/metabolism/microbiology ; *Metagenome ; Metagenomics/methods/standards ; },
abstract = {BACKGROUND: Advances in bioinformatics recently allowed for the recovery of 'metagenomes assembled genomes' from human microbiome studies carried on with shotgun sequencing techniques. Such approach is used as a mean to discover new unclassified metagenomic species, putative biological entities having distinct metabolic traits.

RESULTS: In the present analysis we compare 400 genomes from isolates available on NCBI database and 10,000 human gut metagenomic species, screening all of them for the presence of a minimal set of core functionalities necessary, but not sufficient, for life. As a result, the metagenome-assembled genomes resulted systematically depleted in genes encoding for essential functions apparently needed to support autonomous bacterial life.

CONCLUSIONS: The relevant degree of lacking core functionalities that we observed in metagenome-assembled genomes raises some concerns about the effective completeness of metagenome-assembled genomes, suggesting caution in extrapolating biological information about their metabolic propensity and ecology in a complex environment like the human gastrointestinal tract.},
}

*Gastrointestinal Microbiome
*Genes, Bacterial
Genes, Essential
Humans
Intestinal Mucosa/metabolism/microbiology
*Metagenome
Metagenomics/methods/standards

@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 ; Data Visualization ; Humans ; Internet ; Metagenome ; *Microbiota ; *Software ; },
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.},
}

*Data Analysis
Data Interpretation, Statistical
Data Visualization
Humans
Internet
Metagenome
*Microbiota
*Software

@article {pmid32568184,
year = {2020},
author = {Pi, H and Huang, L and Liu, H and Liang, S and Mei, J},
title = {Effects of PD-1/PD-L1 signaling pathway on intestinal flora in patients with colorectal cancer.},
journal = {Cancer biomarkers : section A of Disease markers},
volume = {28},
number = {4},
pages = {529-535},
doi = {10.3233/CBM-201606},
pmid = {32568184},
issn = {1875-8592},
mesh = {Aged ; Animals ; Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; B7-H1 Antigen/immunology/metabolism ; Cell Line, Tumor ; Colorectal Neoplasms/*drug therapy/immunology/microbiology/mortality ; DNA, Bacterial/isolation & purification ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/drug effects/genetics/*immunology ; Humans ; Immune Checkpoint Inhibitors/*pharmacology/therapeutic use ; Immunologic Surveillance/drug effects ; Intestinal Mucosa/immunology/microbiology ; Male ; Metagenomics ; Mice ; Middle Aged ; Programmed Cell Death 1 Receptor/*antagonists & inhibitors/immunology/metabolism ; Progression-Free Survival ; RNA, Ribosomal, 16S/genetics ; Signal Transduction/drug effects/immunology ; },
abstract = {OBJECTIVE: To explore the effects of the programmed death-1/programmed death-ligand 1 (PD-1/PD-L1) signaling pathway on the intestinal flora in patients with colorectal cancer (CRC).

METHODS: A total of 30 CRC patients treated with PD-1 monoclonal antibody therapy in the Oncology Department of our hospital from January 2018 to January 2019, and another 30 patients treated with routine non-immune therapy were enrolled. The feces specimens were collected for sequencing, the CRC model was established, and the 16S rRNA gene sequences in intestinal flora in feces specimens of mice were analyzed.

RESULTS: The 3-month progression-free survival could not be predicted through the gene count or abundance of metagenomic species (MGS) in intestinal microflora of patients. The gene count or MGS abundance was related to the clinical progression-free response. There were abundant unclassified Escherichia coli, s_lactobacillus and s_unclassified parasutterella in patients treated with PD-1. The reflection curve of microbiota had an obvious difference in richness (Chao1), but had no apparent difference in diversity (Shannon).

CONCLUSION: The PD-1/PD-L1 signaling pathway can regulate the metabolic activity of intestinal flora, thereby promoting immune surveillance of tumors.},
}

Aged
Animals
Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
B7-H1 Antigen/immunology/metabolism
Cell Line, Tumor
Colorectal Neoplasms/*drug therapy/immunology/microbiology/mortality
DNA, Bacterial/isolation & purification
Disease Models, Animal
Feces/microbiology
Female
Gastrointestinal Microbiome/drug effects/genetics/*immunology
Humans
Immune Checkpoint Inhibitors/*pharmacology/therapeutic use
Immunologic Surveillance/drug effects
Intestinal Mucosa/immunology/microbiology
Male
Metagenomics
Mice
Middle Aged
Programmed Cell Death 1 Receptor/*antagonists & inhibitors/immunology/metabolism
Progression-Free Survival
RNA, Ribosomal, 16S/genetics
Signal Transduction/drug effects/immunology

@article {pmid33669932,
year = {2021},
author = {Pane, S and Sacco, A and Iorio, A and Romani, L and Putignani, L},
title = {Strongyloides stercoralis Infestation in a Child: How a Nematode Can Affect Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {22},
number = {4},
pages = {},
pmid = {33669932},
issn = {1422-0067},
support = {Ricerca Corrente 201905_ Genetica_Putignani and 202005_ Genetica_Putignani//Italian Ministry of Health/ ; },
mesh = {Animals ; Biodiversity ; Child ; Cluster Analysis ; Female ; *Gastrointestinal Microbiome ; Humans ; Phylogeny ; Principal Component Analysis ; Strongyloides stercoralis/genetics/isolation & purification/*physiology ; Strongyloidiasis/metabolism/*microbiology/*parasitology ; },
abstract = {Background: Strongyloidiasis is a neglected tropical disease caused by the intestinal nematode Strongyloides stercoralis and characterized by gastrointestinal and pulmonary involvement. We report a pediatric case of strongyloidiasis to underline the response of the host microbiota to the perturbation induced by the nematode. Methods: We performed a 16S rRNA-metagenomic analysis of the gut microbiota of a 7-year-old female during and after S. stercolaris infection, investigating three time-point of stool samples' ecology: T0- during parasite infection, T1- a month after parasite infection, and T2- two months after parasite infection. Targeted-metagenomics were used to investigate ecology and to predict the functional pathways of the gut microbiota. Results: an increase in the alpha-diversity indices in T0-T1 samples was observed compared to T2 and healthy controls (CTRLs). Beta-diversity analysis showed a shift in the relative abundance of specific gut bacterial species from T0 to T2 samples. Moreover, the functional prediction of the targeted-metagenomics profiles suggested an enrichment of microbial glycan and carbohydrate metabolisms in the T0 sample compared with CTRLs. Conclusions: The herein report reinforces the literature suggestion of a putative direct or immune-mediated ability of S. stercolaris to promote the increase in bacterial diversity.},
}

Animals
Biodiversity
Child
Cluster Analysis
Female
*Gastrointestinal Microbiome
Humans
Phylogeny
Principal Component Analysis
Strongyloides stercoralis/genetics/isolation & purification/*physiology
Strongyloidiasis/metabolism/*microbiology/*parasitology

@article {pmid32450738,
year = {2020},
author = {Chakraborty, S and Mandal, J and Cheng, X and Galla, S and Hindupur, A and Saha, P and Yeoh, BS and Mell, B and Yeo, JY and Vijay-Kumar, M and Yang, T and Joe, B},
title = {Diurnal Timing Dependent Alterations in Gut Microbial Composition Are Synchronously Linked to Salt-Sensitive Hypertension and Renal Damage.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {76},
number = {1},
pages = {59-72},
pmid = {32450738},
issn = {1524-4563},
support = {R01 CA219144/CA/NCI NIH HHS/United States ; R01 HL143082/HL/NHLBI NIH HHS/United States ; },
mesh = {3-Hydroxybutyric Acid/blood ; Animals ; Base Sequence ; Blood Pressure/drug effects/*physiology ; Circadian Rhythm/*physiology ; Diet, Sodium-Restricted ; Energy Metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*physiology ; Genes, Bacterial ; Hypertension/etiology/*microbiology/physiopathology ; Kidney/*drug effects ; Male ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Inbred Dahl ; Sodium Chloride, Dietary/*administration & dosage/adverse effects ; },
abstract = {Alterations of diurnal rhythms of blood pressure (BP) and reshaping of gut microbiota are both independently associated with hypertension. However, the relationships between biorhythms of BP and gut microbial composition are unknown. We hypothesized that diurnal timing-associated alterations of microbial compositions are synchronous with diurnal rhythmicity, dip in BP, and renal function. To test this hypothesis, Dahl salt-sensitive (S) rats on low- and high-salt diets were examined for time of day effects on gut microbiota, BP, and indicators of renal damage. Major shifts in night and day patterns of specific groups of microbiota were observed between the dark (active) and light (rest) phases, which correlated with diurnal rhythmicity of BP. The diurnal abundance of Firmicutes, Bacteroidetes, and Actinobacteria were independently associated with BP. Discrete bacterial taxa were observed to correlate independently or interactively with one or more of the following 3 factors: (1) BP rhythm, (2) dietary salt, and (3) dip in BP. Phylogenetic Investigation of Communities revealed diurnal timing effects on microbial pathways, characterized by upregulated biosynthetic processes during the active phase of host, and upregulated degradation pathways of metabolites in the resting phase. Additional metagenomics functional pathways with rhythm variations were noted for aromatic amino acid metabolism and taurine metabolism. These diurnal timing dependent changes in microbiota, their functional pathways, and BP dip were associated with concerted effects of the levels of renal lipocalin 2 and kidney injury molecule-1 expression. These data provide evidence for a firm and concerted diurnal timing effects of BP, renal damage, and select microbial communities.},
}

3-Hydroxybutyric Acid/blood
Animals
Base Sequence
Blood Pressure/drug effects/*physiology
Circadian Rhythm/*physiology
Diet, Sodium-Restricted
Energy Metabolism
Feces/microbiology
Gastrointestinal Microbiome/drug effects/*physiology
Genes, Bacterial
Hypertension/etiology/*microbiology/physiopathology
Kidney/*drug effects
Male
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Rats
Rats, Inbred Dahl
Sodium Chloride, Dietary/*administration & dosage/adverse effects

@article {pmid32233019,
year = {2020},
author = {Mai, BHA and Drancourt, M and Aboudharam, G},
title = {Ancient dental pulp: Masterpiece tissue for paleomicrobiology.},
journal = {Molecular genetics & genomic medicine},
volume = {8},
number = {6},
pages = {e1202},
pmid = {32233019},
issn = {2324-9269},
mesh = {Bacterial Infections/epidemiology/*microbiology ; *DNA, Ancient ; Dental Pulp/*microbiology ; Fossils/*microbiology ; Humans ; Metagenome ; Microbiota ; },
abstract = {INTRODUCTION: Dental pulp with special structure has become a good reference sample in paleomicrobiology-related blood-borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins.

OBJECTIVES: This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe.

METHODS: The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: "ancient," "dental pulp," "teeth," "anatomy," "structure," "collection," "preservation," "selection," "photography," "radiography," "contamination," "decontamination," "DNA," "protein," "extraction," "bone," "paleomicrobiology," "bacteria," "virus," "pathogen," "molecular biology," "proteomics," "PCR," "MALDI-TOF," "LC/MS," "ELISA," "immunology," "immunochromatography," "genome," "microbiome," "metagenomics."

RESULTS: The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty-seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species.

CONCLUSIONS: Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.},
}

Bacterial Infections/epidemiology/*microbiology
*DNA, Ancient
Dental Pulp/*microbiology
Fossils/*microbiology
Humans
Metagenome
Microbiota

@article {pmid32470263,
year = {2020},
author = {Uberos, J},
title = {Perinatal microbiota: review of its importance in newborn health.},
journal = {Archivos argentinos de pediatria},
volume = {118},
number = {3},
pages = {e265-e270},
doi = {10.5546/aap.2020.eng.e265},
pmid = {32470263},
issn = {1668-3501},
mesh = {Breast Feeding ; Delivery, Obstetric/adverse effects/methods ; Female ; *Gastrointestinal Microbiome ; Humans ; *Infant Health ; Infant, Newborn ; Pregnancy ; },
abstract = {The use of metagenomics in the study of gut bacterial ecosystems has helped to define a standard, functional genetic profile in newborn infants, so that a bacterial ecosystem will be deemed more "normal" the more similar its functional genetic profile is to a standard. The development of a specific functional enterotype in the first days of life after birth is critical for the priming of the immune system with certain bacterial antigens. Regardless of whether the first gut bacteria are acquired before or just after birth, the newborn microbiota will result from the symbiosis with the environmental microbial flora, especially with the bacterial flora of the mother. The type of delivery, the administration of perinatal antibiotics, the environment, and nutritional exposure, especially breastfeeding, have demonstrated an important relationship with the prevalent gut microbiome.},
}

Breast Feeding
Delivery, Obstetric/adverse effects/methods
Female
*Gastrointestinal Microbiome
Humans
*Infant Health
Infant, Newborn
Pregnancy

@article {pmid33649957,
year = {2021},
author = {Milani, C},
title = {Metagenomic Analyses of Bifidobacterial Communities.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2278},
number = {},
pages = {183-193},
pmid = {33649957},
issn = {1940-6029},
mesh = {Animals ; Bifidobacterium/classification/*genetics ; Gastrointestinal Microbiome ; Gene Expression Profiling/methods ; *Genome, Bacterial ; Humans ; Metagenome ; Metagenomics/*methods ; RNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Software ; },
abstract = {Bifidobacteria represent highly prevalent and abundant members of the gut microbiota during mammalian infancy. In this context, bifidobacterial species have been shown to be correlated with many aspects of host health by means of direct interactions with the host and cohabiting microbes. Metagenomic sequencing of fecal DNA represents a valuable approach for taxonomic and functional profiling of bacterial populations, and has allowed us to appreciate the relevance of bifidobacterial taxa in such complex bacterial communities, especially during the first stages of life.},
}

Animals
Bifidobacterium/classification/*genetics
Gastrointestinal Microbiome
Gene Expression Profiling/methods
*Genome, Bacterial
Humans
Metagenome
Metagenomics/*methods
RNA, Bacterial/genetics
RNA, Ribosomal, 16S/genetics
Software

@article {pmid33371686,
year = {2021},
author = {Jiang, L and Luo, C and Zhang, D and Song, M and Mei, W and Sun, Y and Zhang, G},
title = {Shifts in a Phenanthrene-Degrading Microbial Community are Driven by Carbohydrate Metabolism Selection in a Ryegrass Rhizosphere.},
journal = {Environmental science & technology},
volume = {55},
number = {2},
pages = {962-973},
doi = {10.1021/acs.est.0c04951},
pmid = {33371686},
issn = {1520-5851},
mesh = {Biodegradation, Environmental ; Carbohydrate Metabolism ; *Lolium ; *Microbiota ; *Phenanthrenes/analysis ; Phylogeny ; Plant Roots/chemistry ; Rhizosphere ; Soil Microbiology ; *Soil Pollutants/analysis ; },
abstract = {Plants usually promote pollutant bioremediation by several mechanisms including modifying the diversity of functional microbial species. However, conflicting results are reported that root exudates have no effects or negative effects on organic pollutant degradation. In this study, we investigated the roles of ryegrass in phenanthrene degradation in soils using DNA stable isotope probing (SIP) and metagenomics to reveal a potential explanation for conflicting results among phytoremediation studies. Phenanthrene biodegradation efficiency was improved by 8% after 14 days of cultivation. Twelve and ten operational taxonomic units (OTUs) were identified as active phenanthrene degraders in non-rhizosphere and rhizosphere soils, respectively. The active phenanthrene degraders exhibited higher average phylogenetic distances in rhizosphere soils (0.33) than non-rhizosphere soils (0.26). The Ka/Ks values (the ratio of nonsynonymous to synonymous substitutions) were about 10.37% higher in the rhizosphere treatment among >90% of all key carbohydrate metabolism-related genes, implying that ryegrass may be an important driver of microbial community variation in the rhizosphere by relieving the carbohydrate metabolism pressure and improving the survival ability of r-strategy microbes. Most Ka/Ks values of root-exudate-related metabolism genes exhibited little change, except for fumarate hydratase that increased 13-fold in the rhizosphere compared to that in the non-rhizosphere treatment. The Ka/Ks values of less than 50% phenanthrene-degradation-related genes were affected, 30% of which increased and 70% behaved oppositely. Genes with altered Ka/Ks values had a low percentage and followed an inconsistent changing tendency, indicating that phenanthrene and its metabolites are not major factors influencing the active degraders. These results suggested the importance of carbohydrate metabolism, especially fumaric acid, in rhizosphere community shift, and hinted at a new hypothesis that the rhizosphere effect on phenanthrene degradation efficiency depends on the existence of active degraders that have competitive advantages in carbohydrate and fumaric acid metabolism.},
}

Biodegradation, Environmental
Carbohydrate Metabolism
*Lolium
*Microbiota
*Phenanthrenes/analysis
Phylogeny
Plant Roots/chemistry
Rhizosphere
Soil Microbiology
*Soil Pollutants/analysis

@article {pmid32859198,
year = {2020},
author = {Neukamm, J and Pfrengle, S and Molak, M and Seitz, A and Francken, M and Eppenberger, P and Avanzi, C and Reiter, E and Urban, C and Welte, B and Stockhammer, PW and Teßmann, B and Herbig, A and Harvati, K and Nieselt, K and Krause, J and Schuenemann, VJ},
title = {2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals.},
journal = {BMC biology},
volume = {18},
number = {1},
pages = {108},
pmid = {32859198},
issn = {1741-7007},
support = {845479//the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie/International ; ALTF 1086-2018//European Molecular Biology Organization (EMBO) long-term fellowship/International ; },
mesh = {DNA, Ancient/analysis ; Egypt ; *Genome, Bacterial ; *Genome, Viral ; Hepatitis B virus/*genetics ; Humans ; Metagenomics ; Microbiota ; Mummies/*microbiology/virology ; Mycobacterium leprae/*genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging.

RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus' microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed.

CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.},
}

DNA, Ancient/analysis
Egypt
*Genome, Bacterial
*Genome, Viral
Hepatitis B virus/*genetics
Humans
Metagenomics
Microbiota
Mummies/*microbiology/virology
Mycobacterium leprae/*genetics
Sequence Analysis, DNA

@article {pmid32830371,
year = {2020},
author = {Mukherjee, I and Salcher, MM and Andrei, AŞ and Kavagutti, VS and Shabarova, T and Grujčić, V and Haber, M and Layoun, P and Hodoki, Y and Nakano, SI and Šimek, K and Ghai, R},
title = {A freshwater radiation of diplonemids.},
journal = {Environmental microbiology},
volume = {22},
number = {11},
pages = {4658-4668},
doi = {10.1111/1462-2920.15209},
pmid = {32830371},
issn = {1462-2920},
support = {MSM200961801//Akademie Věd České Republiky/ ; 17-04828S//Grant Agency of the Czech Republic/ ; 19-23469S//Grant Agency of the Czech Republic/ ; 20-12496X//Grant Agency of the Czech Republic/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 116/2019/P//Grant Agency of the University of South Bohemia/ ; JSPS-17-17//JSPS Bilateral Japanese-Czech Joint Research Project/ ; 310030_185108/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Biodiversity ; Ecosystem ; Euglenozoa/*classification/cytology/genetics/*isolation & purification ; In Situ Hybridization, Fluorescence ; Japan ; Lakes/*microbiology ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Species Specificity ; },
abstract = {Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Japanese deep freshwater lakes. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and catalysed reporter deposition-fluorescent in situ hybridization (CARD-FISH). We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to a marine clade, which are mainly isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single-cell genomes of marine diplonemids show they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.},
}

Biodiversity
Ecosystem
Euglenozoa/*classification/cytology/genetics/*isolation & purification
In Situ Hybridization, Fluorescence
Japan
Lakes/*microbiology
Metagenomics
Phylogeny
RNA, Ribosomal, 18S/genetics
Species Specificity

@article {pmid32605986,
year = {2020},
author = {Cao, H and Shimura, Y and Steffen, MM and Yang, Z and Lu, J and Joel, A and Jenkins, L and Kawachi, M and Yin, Y and Garcia-Pichel, F},
title = {The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics.},
journal = {mBio},
volume = {11},
number = {3},
pages = {},
pmid = {32605986},
issn = {2150-7511},
mesh = {Cyanobacteria/*genetics/physiology ; Ecosystem ; *Eutrophication ; *Gene Expression Profiling ; *Genome, Bacterial ; Genomics ; Lakes/*microbiology ; Metabolic Networks and Pathways ; Metagenomics ; Phenotype ; },
abstract = {Water bloom development due to eutrophication constitutes a case of niche specialization among planktonic cyanobacteria, but the genomic repertoire allowing bloom formation in only some species has not been fully characterized. We posited that the habitat relevance of a trait begets its underlying genomic complexity, so that traits within the repertoire would be differentially more complex in species successfully thriving in that habitat than in close species that cannot. To test this for the case of bloom-forming cyanobacteria, we curated 17 potentially relevant query metabolic pathways and five core pathways selected according to existing ecophysiological literature. The available 113 genomes were split into those of blooming (45) or nonblooming (68) strains, and an index of genomic complexity for each strain's version of each pathway was derived. We show that strain versions of all query pathways were significantly more complex in bloomers, with complexity in fact correlating positively with strain blooming incidence in 14 of those pathways. Five core pathways, relevant everywhere, showed no differential complexity or correlations. Gas vesicle, toxin and fatty acid synthesis, amino acid uptake, and C, N, and S acquisition systems were most strikingly relevant in the blooming repertoire. Further, we validated our findings using metagenomic gene expression analyses of blooming and nonblooming cyanobacteria in natural settings, where pathways in the repertoire were differentially overexpressed according to their relative complexity in bloomers, but not in nonbloomers. We expect that this approach may find applications to other habitats and organismal groups.IMPORTANCE We pragmatically delineate the trait repertoire that enables organismal niche specialization. We based our approach on the tenet, derived from evolutionary and complex-system considerations, that genomic units that can significantly contribute to fitness in a certain habitat will be comparatively more complex in organisms specialized to that habitat than their genomic homologs found in organisms from other habitats. We tested this in cyanobacteria forming harmful water blooms, for which decades-long efforts in ecological physiology and genomics exist. Our results essentially confirm that genomics and ecology can be linked through comparative complexity analyses, providing a tool that should be of general applicability for any group of organisms and any habitat, and enabling the posing of grounded hypotheses regarding the ecogenomic basis for diversification.},
}

Cyanobacteria/*genetics/physiology
Ecosystem
*Eutrophication
*Gene Expression Profiling
*Genome, Bacterial
Genomics
Lakes/*microbiology
Metabolic Networks and Pathways
Metagenomics
Phenotype

@article {pmid32546614,
year = {2020},
author = {Sharrar, AM and Crits-Christoph, A and Méheust, R and Diamond, S and Starr, EP and Banfield, JF},
title = {Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type.},
journal = {mBio},
volume = {11},
number = {3},
pages = {},
pmid = {32546614},
issn = {2150-7511},
mesh = {Bacteria/classification/*metabolism ; Biosynthetic Pathways ; California ; Metagenome ; *Microbiota ; Multigene Family ; Phylogeny ; *Secondary Metabolism ; *Soil ; *Soil Microbiology ; Trees ; },
abstract = {Bacteria isolated from soils are major sources of specialized metabolites, including antibiotics and other compounds with clinical value that likely shape interactions among microbial community members and impact biogeochemical cycles. Yet, isolated lineages represent a small fraction of all soil bacterial diversity. It remains unclear how the production of specialized metabolites varies across the phylogenetic diversity of bacterial species in soils and whether the genetic potential for production of these metabolites differs with soil depth and vegetation type within a geographic region. We sampled soils and saprolite from three sites in a northern California Critical Zone Observatory with various vegetation and bedrock characteristics and reconstructed 1,334 metagenome-assembled genomes containing diverse biosynthetic gene clusters (BGCs) for secondary metabolite production. We obtained genomes for prolific producers of secondary metabolites, including novel groups within the Actinobacteria, Chloroflexi, and candidate phylum "Candidatus Dormibacteraeota." Surprisingly, one genome of a candidate phyla radiation (CPR) bacterium coded for a ribosomally synthesized linear azole/azoline-containing peptide, a capacity we found in other publicly available CPR bacterial genomes. Overall, bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with patterns of abundance of BGC type varying by taxonomy.IMPORTANCE Microbes produce specialized compounds to compete or communicate with one another and their environment. Some of these compounds, such as antibiotics, are also useful in medicine and biotechnology. Historically, most antibiotics have come from soil bacteria which can be isolated and grown in the lab. Though the vast majority of soil bacteria cannot be isolated, we can extract their genetic information and search it for genes which produce these specialized compounds. These understudied soil bacteria offer a wealth of potential for the discovery of new and important microbial products. Here, we identified the ability to produce these specialized compounds in diverse and novel bacteria in a range of soil environments. This information will be useful to other researchers who wish to isolate certain products. Beyond their use to humans, understanding the distribution and function of microbial products is key to understanding microbial communities and their effects on biogeochemical cycles.},
}

Bacteria/classification/*metabolism
Biosynthetic Pathways
California
Metagenome
*Microbiota
Multigene Family
Phylogeny
*Secondary Metabolism
*Soil
*Soil Microbiology
Trees

@article {pmid31809634,
year = {2020},
author = {Mack, A and Bobardt, JS and Haß, A and Nichols, KB and Schmid, RM and Stein-Thoeringer, CK},
title = {Changes in gut microbial metagenomic pathways associated with clinical outcomes after the elimination of malabsorbed sugars in an IBS cohort.},
journal = {Gut microbes},
volume = {11},
number = {3},
pages = {620-631},
pmid = {31809634},
issn = {1949-0984},
mesh = {Adult ; Aged ; Cohort Studies ; DNA, Bacterial ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/*diet therapy/metabolism/*microbiology ; Malabsorption Syndromes/*diet therapy/metabolism/*microbiology ; Male ; Metabolic Networks and Pathways/*genetics ; Metagenome ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S ; Sugars/metabolism/*therapeutic use ; },
abstract = {Specific diets to manage sugar malabsorption are reported to reduce clinical symptoms of irritable bowel syndrome (IBS). However, the effects of diets for malabsorbed sugars on gut microbiota signatures have not been studied, and associations with clinical outcomes in IBS have not been characterized. 22 IBS patients positively tested for either lactose-, fructose-, sorbitol- or combined malabsorptions were subjected to 2-weeks sugar elimination and subsequent 4-weeks re-introduction. 7 IBS patients tested negative for sugar malabsorption were used as controls. Nutrition and clinical symptoms were recorded throughout the study. Fecal samples were serially collected for 16S rRNA amplicon and shotgun-metagenome sequencing. Dietary intervention supervised by nutrition counseling reduced IBS symptoms during the elimination and tolerance phases. Varying clinical response rates were observed between subjects, and used to dichotomize our cohort into visual analogue scale (VAS) responders and non-responders. Alpha -and beta-diversity analyzes revealed only minor differences regarding 16S rRNA-based fecal microbiota compositions between responder and non-responder patients during baseline or tolerance phase. In shotgun-metagenome analyzes, however, we analyzed microbial metabolic pathways and found significant differences in pathways encoding starch degradation and complex amino acid biosynthesis at baseline between IBS controls and malabsorbers, and notably, between diet responder and non-responders. Faecalibacterium prausnitzii, Ruminococcus spp. and Bifidobacterium longum largely informed these metabolic pathways. Our study demonstrates that diet interventions for specific, malabsorbed carbohydrates reshaped the metagenomic composition of the gut microbiota, with a small community of bacterial taxa contributing to these changes rather than a single species.},
}

Adult
Aged
Cohort Studies
DNA, Bacterial
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Irritable Bowel Syndrome/*diet therapy/metabolism/*microbiology
Malabsorption Syndromes/*diet therapy/metabolism/*microbiology
Male
Metabolic Networks and Pathways/*genetics
Metagenome
Metagenomics
Middle Aged
RNA, Ribosomal, 16S
Sugars/metabolism/*therapeutic use

@article {pmid31629058,
year = {2020},
author = {Tilocca, B and Costanzo, N and Morittu, VM and Spina, AA and Soggiu, A and Britti, D and Roncada, P and Piras, C},
title = {Milk microbiota: Characterization methods and role in cheese production.},
journal = {Journal of proteomics},
volume = {210},
number = {},
pages = {103534},
doi = {10.1016/j.jprot.2019.103534},
pmid = {31629058},
issn = {1876-7737},
mesh = {Animals ; Cheese/*microbiology ; Dairying/standards ; Food Microbiology/*standards ; *Genome ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota ; Milk/metabolism/*microbiology ; Proteome/*metabolism ; *Transcriptome ; },
abstract = {Milk is a complex body fluid aimed at addressing the nutritional and defensive needs of the mammal's newborns. Harbored microbiota plays a pivotal role throughout the cheesemaking process and contributes to the development of flavor and texture typical of different type of cheeses. Understanding the dairy microbiota dynamics is of paramount importance for controlling the qualitative, sensorial and biosafety features of the dairy products. Although many studies investigated the contribution of single or few microorganisms, still there is some information lacking about microbial communities. The widespread of the omics platforms and bioinformatic tools enable the investigation of the cheese-associated microbial community in both phylogenetical and functional terms, highlighting the effects of the diverse cheesemaking variables. In this review, the most relevant literature is revised to provide an introduction of the milk- and cheese-associated microbiota, along with their structural and functional dynamics in relation to the diverse cheesemaking technologies and influencing variables. Also, we focus our attention on the latest omics technologies adopted in dairy microbiota investigation. Discussion on the key-steps and major drawbacks of each omics discipline is provided along with a collection of results from the latest research studies performed to unravel the fascinating world of the dairy-associated microbiota. SIGNIFICANCE: Understanding the milk- and cheese- associated microbial community is nowadays considered a key factor in the dairy industry, since it allows a comprehensive knowledge on how all phases of the cheesemaking process impact the harbored microflora; thus, predict the consequences in the finished products in terms of texture, organoleptic characteristics, palatability and biosafety. This review, collect the pioneering and milestones works so far performed in the field of dairy microbiota, and provide the basic guidance to whom approaching the cheese microbiota investigation by means of the latest omics technologies. Also, the review emphasizes the benefits and drawbacks of the omics disciplines, and underline how the integration of diverse omics sciences enhance a comprehensive depiction of the cheese microbiota. In turn, a better consciousness of the dairy microbiota might results in the application of improved starter cultures, cheesemaking practices and technologies; supporting a bio-safe and standardized production of cheese, with a strong economic benefit for both large-scale industries and local traditional dairy farms.},
}

Animals
Cheese/*microbiology
Dairying/standards
Food Microbiology/*standards
*Genome
High-Throughput Nucleotide Sequencing
Humans
*Microbiota
Milk/metabolism/*microbiology
Proteome/*metabolism
*Transcriptome

@article {pmid31411526,
year = {2020},
author = {Peng, M and Tabashsum, Z and Patel, P and Bernhardt, C and Biswas, C and Meng, J and Biswas, D},
title = {Prevention of enteric bacterial infections and modulation of gut microbiota with conjugated linoleic acids producing Lactobacillus in mice.},
journal = {Gut microbes},
volume = {11},
number = {3},
pages = {433-452},
pmid = {31411526},
issn = {1949-0984},
mesh = {Animals ; Cecum/microbiology ; Cytokines/genetics/metabolism ; DNA, Bacterial/genetics ; Enterohemorrhagic Escherichia coli/growth & development ; Escherichia coli Infections/pathology/*prevention & control ; Female ; *Gastrointestinal Microbiome ; Ileum/microbiology ; Inflammation/genetics/microbiology ; Jejunum/microbiology ; Lactobacillus casei/*physiology ; Linoleic Acids, Conjugated/metabolism/*pharmacology ; Male ; Mice ; Mice, Inbred BALB C ; Probiotics/pharmacology ; RNA, Ribosomal, 16S/genetics ; Salmonella Infections/pathology/*prevention & control ; Salmonella typhimurium/growth & development ; },
abstract = {Probiotics are recognized for outcompeting pathogenic bacteria by competitive receptor-mediated colonization and secretion of functional metabolites which are antimicrobial against certain microbes as well as improving host's gut health and immunity. Recently, we have constructed a bioactive Lactobacillus casei (LC) strain, LC+mcra , by inserting mcra (myosin cross-reactive antigen) gene, which stimulates the conversion of conjugated linoleic acids. In this study, we evaluated the modulation of gut microbiome and protective roles of LC+mcra against pathogenic Salmonella enterica serovar Typhimurium (ST) and enterohemorrhagic E. coli (EHEC) infections in BALB/cJ mice. We observed that LC+mcra colonized efficiently in mice gut intestine and competitively reduced the infection with ST and EHEC in various locations of small and large intestine, specifically cecum, jejunum, and ileum (p < 0.05). Positive modulation of the cecal microbiota, for example, higher relative abundances of Firmicutes, lower relative abundances of Proteobacteria, and increased bacterial species diversity/richness, was detected in ST-challenged mice pretreated with LC+mcra based on 16S metagenomic sequencing. Cytokine gene expression analysis indicated that mice pretreated with LC+mcra associated with attenuated bacterial pathogen-induced gut inflammation. Furthermore, mice fed daily with LC+mcra for one week could protect themselves from the impairments caused by enteric infections with ST or EHEC. These impairments include weight loss, negative hematological changes, intestinal histological alterations, and potential death. This in vivo study suggests that daily consumption of novel conjugated linoleic acids over-producing probiotic effectively improves intestinal microbiota composition and prevents/combats foodborne enteric bacterial infections with pathogenic Salmonella and diarrheagenic E. coli.},
}

Animals
Cecum/microbiology
Cytokines/genetics/metabolism
DNA, Bacterial/genetics
Enterohemorrhagic Escherichia coli/growth & development
Escherichia coli Infections/pathology/*prevention & control
Female
*Gastrointestinal Microbiome
Ileum/microbiology
Inflammation/genetics/microbiology
Jejunum/microbiology
Lactobacillus casei/*physiology
Linoleic Acids, Conjugated/metabolism/*pharmacology
Male
Mice
Mice, Inbred BALB C
Probiotics/pharmacology
RNA, Ribosomal, 16S/genetics
Salmonella Infections/pathology/*prevention & control
Salmonella typhimurium/growth & development

@article {pmid33618119,
year = {2021},
author = {Pu, Y and Pan, J and Yao, Y and Ngan, WY and Yang, Y and Li, M and Habimana, O},
title = {Ecotoxicological effects of erythromycin on a multispecies biofilm model, revealed by metagenomic and metabolomic approaches.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {276},
number = {},
pages = {116737},
doi = {10.1016/j.envpol.2021.116737},
pmid = {33618119},
issn = {1873-6424},
mesh = {Biofilms ; *Erythromycin/toxicity ; Metabolomics ; Metagenome ; *Microbiota ; },
abstract = {The presence of antibiotics such as erythromycin, even in trace amounts, has long been acknowledged for negatively impacting ecosystems in freshwater environments. Although many studies have focused on the impact of antibiotic pollution at a macroecological level, the impact of erythromycin on microecosystems, such as freshwater biofilms, is still not fully understood. This knowledge gap may be attributed to the lack of robust multispecies biofilm models for fundamental investigations. Here, we used a lab-cultured multispecies biofilm model to elucidate the holistic response of a microbial community to erythromycin exposure using metagenomic and metabolomic approaches. Metagenomic analyses revealed that biofilm microbial diversity did not alter following erythromycin exposure. Notably, certain predicted metabolic pathways such as cell-cell communication pathways, amino acid metabolism, and peptidoglycan biosynthesis, mainly by the phyla Actinobacteria, Alpha/Beta-proteobacteria, Bacteroidetes, and Verrucomicrobia, were found to be involved in the maintenance of homeostasis-like balance in the freshwater biofilm. Further untargeted metabolomics data highlighted changes in lipid metabolism and linoleic acid metabolism and their related molecules as a direct consequence of erythromycin exposure. Overall, the study presented a unique picture of how multispecies biofilms respond to single environmental stress exposures. Moreover, the study demonstrated the feasibility of using lab simulated multispecies biofilms for investigating their interaction and reactivity of specific bioactive compounds or pollutants at a fundamental level.},
}

Biofilms
*Erythromycin/toxicity
Metabolomics
Metagenome
*Microbiota

@article {pmid33606255,
year = {2021},
author = {Joseph, TA and Pe'er, I},
title = {An Introduction to Whole-Metagenome Shotgun Sequencing Studies.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2243},
number = {},
pages = {107-122},
pmid = {33606255},
issn = {1940-6029},
mesh = {Archaea/genetics ; Bacteria/genetics ; Humans ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Viruses/genetics ; },
abstract = {Microbial communities are found across diverse environments, including within and across the human body. As many microbes are unculturable in the lab, much of what is known about a microbiome-a collection of bacteria, fungi, archaea, and viruses inhabiting an environment--is from the sequencing of DNA from within the constituent community. Here, we provide an introduction to whole-metagenome shotgun sequencing studies, a ubiquitous approach for characterizing microbial communities, by reviewing three major research areas in metagenomics: assembly, community profiling, and functional profiling. Though not exhaustive, these areas encompass a large component of the metagenomics literature. We discuss each area in depth, the challenges posed by whole-metagenome shotgun sequencing, and approaches fundamental to the solutions of each. We conclude by discussing promising areas for future research. Though our emphasis is on the human microbiome, the methods discussed are broadly applicable across study systems.},
}

Archaea/genetics
Bacteria/genetics
Humans
Metagenome/*genetics
Metagenomics/methods
Microbiota/*genetics
Sequence Analysis, DNA/methods
Viruses/genetics

@article {pmid33522965,
year = {2021},
author = {Dada, N and Jupatanakul, N and Minard, G and Short, SM and Akorli, J and Villegas, LM},
title = {Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {36},
pmid = {33522965},
issn = {2049-2618},
mesh = {Animals ; Culicidae/*microbiology ; *Metagenomics ; *Microbiota ; Reproducibility of Results ; Research/*organization & administration/*trends ; },
abstract = {In the past decade, there has been increasing interest in mosquito microbiome research, leading to large amounts of data on different mosquito species, with various underlying physiological characteristics, and from diverse geographical locations. However, guidelines and standardized methods for conducting mosquito microbiome research are lacking. To streamline methods in mosquito microbiome research and optimize data quality, reproducibility, and comparability, as well as facilitate data curation in a centralized location, we are establishing the Mosquito Microbiome Consortium, a collaborative initiative for the advancement of mosquito microbiome research. Our overall goal is to collectively work on unraveling the role of the mosquito microbiome in mosquito biology, while critically evaluating its potential for mosquito-borne disease control. This perspective serves to introduce the consortium and invite broader participation. It highlights the issues we view as most pressing to the community and proposes guidelines for conducting mosquito microbiome research. We focus on four broad areas in this piece: (1) sampling/experimental design for field, semi-field, or laboratory studies; (2) metadata collection; (3) sample processing, sequencing, and use of appropriate controls; and (4) data handling and analysis. We finally summarize current challenges and highlight future directions in mosquito microbiome research. We hope that this piece will spark discussions around this area of disease vector biology, as well as encourage careful considerations in the design and implementation of mosquito microbiome research. Video Abstract.},
}

Animals
Culicidae/*microbiology
*Metagenomics
*Microbiota
Reproducibility of Results
Research/*organization & administration/*trends

@article {pmid33517907,
year = {2021},
author = {Blaustein, RA and Michelitsch, LM and Glawe, AJ and Lee, H and Huttelmaier, S and Hellgeth, N and Ben Maamar, S and Hartmann, EM},
title = {Toothbrush microbiomes feature a meeting ground for human oral and environmental microbiota.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {32},
pmid = {33517907},
issn = {2049-2618},
support = {TL1 TR001423/TR/NCATS NIH HHS/United States ; },
mesh = {Adolescent ; Adult ; Aged ; *Built Environment ; Drug Resistance, Microbial/drug effects/genetics ; Humans ; Metagenome/drug effects/genetics ; *Microbiota/drug effects/genetics ; Middle Aged ; Mouth/drug effects/*microbiology ; *Toothbrushing ; Triclosan/pharmacology ; Young Adult ; },
abstract = {BACKGROUND: While indoor microbiomes impact our health and well-being, much remains unknown about taxonomic and functional transitions that occur in human-derived microbial communities once they are transferred away from human hosts. Toothbrushes are a model to investigate the potential response of oral-derived microbiota to conditions of the built environment. Here, we characterize metagenomes of toothbrushes from 34 subjects to define the toothbrush microbiome and resistome and possible influential factors.

RESULTS: Toothbrush microbiomes often comprised a dominant subset of human oral taxa and less abundant or site-specific environmental strains. Although toothbrushes contained lower taxonomic diversity than oral-associated counterparts (determined by comparison with the Human Microbiome Project), they had relatively broader antimicrobial resistance gene (ARG) profiles. Toothbrush resistomes were enriched with a variety of ARGs, notably those conferring multidrug efflux and putative resistance to triclosan, which were primarily attributable to versatile environmental taxa. Toothbrush microbial communities and resistomes correlated with a variety of factors linked to personal health, dental hygiene, and bathroom features.

CONCLUSIONS: Selective pressures in the built environment may shape the dynamic mixture of human (primarily oral-associated) and environmental microbiota that encounter each other on toothbrushes. Harboring a microbial diversity and resistome distinct from human-associated counterparts suggests toothbrushes could potentially serve as a reservoir that may enable the transfer of ARGs. Video abstract.},
}

Adolescent
Adult
Aged
*Built Environment
Drug Resistance, Microbial/drug effects/genetics
Humans
Metagenome/drug effects/genetics
*Microbiota/drug effects/genetics
Middle Aged
Mouth/drug effects/*microbiology
*Toothbrushing
Triclosan/pharmacology
Young Adult

@article {pmid33509277,
year = {2021},
author = {Arnold, JW and Roach, J and Fabela, S and Moorfield, E and Ding, S and Blue, E and Dagher, S and Magness, S and Tamayo, R and Bruno-Barcena, JM and Azcarate-Peril, MA},
title = {The pleiotropic effects of prebiotic galacto-oligosaccharides on the aging gut.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {31},
pmid = {33509277},
issn = {2049-2618},
support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; },
mesh = {Aging/drug effects/genetics/*physiology ; Animals ; Female ; Gastrointestinal Microbiome/*drug effects ; Intestines/drug effects/microbiology/physiology ; Mice ; Mice, Inbred C57BL ; Oligosaccharides/*pharmacology ; Phosphatidylinositol 3-Kinases/metabolism ; *Prebiotics ; Proto-Oncogene Proteins c-akt/metabolism ; },
abstract = {BACKGROUND: Prebiotic galacto-oligosaccharides (GOS) have an extensively demonstrated beneficial impact on intestinal health. In this study, we determined the impact of GOS diets on hallmarks of gut aging: microbiome dysbiosis, inflammation, and intestinal barrier defects ("leaky gut"). We also evaluated if short-term GOS feeding influenced how the aging gut responded to antibiotic challenges in a mouse model of Clostridioides difficile infection. Finally, we assessed if colonic organoids could reproduce the GOS responder-non-responder phenotypes observed in vivo.

RESULTS: Old animals had a distinct microbiome characterized by increased ratios of non-saccharolytic versus saccharolytic bacteria and, correspondingly, a lower abundance of β-galactosidases compared to young animals. GOS reduced the overall diversity, increased the abundance of specific saccharolytic bacteria (species of Bacteroides and Lactobacillus), increased the abundance of β-galactosidases in young and old animals, and increased the non-saccharolytic organisms; however, a robust, homogeneous bifidogenic effect was not observed. GOS reduced age-associated increased intestinal permeability and increased MUC2 expression and mucus thickness in old mice. Clyndamicin reduced the abundance Bifidobacterium while increasing Akkermansia, Clostridium, Coprococcus, Bacillus, Bacteroides, and Ruminococcus in old mice. The antibiotics were more impactful than GOS on modulating serum markers of inflammation. Higher serum levels of IL-17 and IL-6 were observed in control and GOS diets in the antibiotic groups, and within those groups, levels of IL-6 were higher in the GOS groups, regardless of age, and higher in the old compared to young animals in the control diet groups. RTqPCR revealed significantly increased gene expression of TNFα in distal colon tissue of old mice, which was decreased by the GOS diet. Colon transcriptomics analysis of mice fed GOS showed increased expression of genes involved in small-molecule metabolic processes and specifically the respirasome in old animals, which could indicate an increased oxidative metabolism and energetic efficiency. In young mice, GOS induced the expression of binding-related genes. The galectin gene Lgals1, a β-galactosyl-binding lectin that bridges molecules by their sugar moieties and is an important modulator of the immune response, and the PI3K-Akt and ECM-receptor interaction pathways were also induced in young mice. Stools from mice exhibiting variable bifidogenic response to GOS injected into colon organoids in the presence of prebiotics reproduced the response and non-response phenotypes observed in vivo suggesting that the composition and functionality of the microbiota are the main contributors to the phenotype.

CONCLUSIONS: Dietary GOS modulated homeostasis of the aging gut by promoting changes in microbiome composition and host gene expression, which was translated into decreased intestinal permeability and increased mucus production. Age was a determining factor on how prebiotics impacted the microbiome and expression of intestinal epithelial cells, especially apparent from the induction of galectin-1 in young but not old mice. Video abstract.},
}

Aging/drug effects/genetics/*physiology
Animals
Female
Gastrointestinal Microbiome/*drug effects
Intestines/drug effects/microbiology/physiology
Mice
Mice, Inbred C57BL
Oligosaccharides/*pharmacology
Phosphatidylinositol 3-Kinases/metabolism
*Prebiotics
Proto-Oncogene Proteins c-akt/metabolism

@article {pmid33452024,
year = {2021},
author = {Zhu, HZ and Zhang, ZF and Zhou, N and Jiang, CY and Wang, BJ and Cai, L and Wang, HM and Liu, SJ},
title = {Bacteria and Metabolic Potential in Karst Caves Revealed by Intensive Bacterial Cultivation and Genome Assembly.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {6},
pages = {},
pmid = {33452024},
issn = {1098-5336},
mesh = {Bacteria/genetics/isolation & purification/metabolism ; Bacterial Proteins/genetics/metabolism ; Biodiversity ; Caves/*microbiology ; Coenzyme A-Transferases/genetics/metabolism ; *Genome, Bacterial ; Metagenome ; Metagenomics ; Microbiota ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfur/metabolism ; },
abstract = {Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived hypothesis and to disclose the microbial functions in cave ecosystems. In this study, the microbiomes of two karst caves in Guizhou Province in southwest China were examined. A total of 3,562 bacterial strains were cultivated from rock, water, and sediment samples, and 329 species (including 14 newly described species) of 102 genera were found. We created a cave bacterial genome collection of 218 bacterial genomes from a karst cave microbiome through the extraction of 204 database-derived genomes and de novo sequencing of 14 new bacterial genomes. The cultivated genome collection obtained in this study and the metagenome data from previous studies were used to investigate the bacterial metabolism and potential involvement in the carbon, nitrogen, and sulfur biogeochemical cycles in the cave ecosystem. New N2-fixing Azospirillum and alkane-oxidizing Oleomonas species were documented in the karst cave microbiome. Two pcaIJ clusters of the β-ketoadipate pathway that were abundant in both the cultivated microbiomes and the metagenomic data were identified, and their representatives from the cultivated bacterial genomes were functionally demonstrated. This large-scale cultivation of a cave microbiome represents the most intensive collection of cave bacterial resources to date and provides valuable information and diverse microbial resources for future cave biogeochemical research.IMPORTANCE Karst caves are oligotrophic environments that are dark and humid and have a relatively stable annual temperature. The diversity of bacteria and their metabolisms are crucial for understanding the biogeochemical cycling in cave ecosystems. We integrated large-scale bacterial cultivation with metagenomic data mining to explore the compositions and metabolisms of the microbiomes in two karst cave systems. Our results reveal the presence of a highly diversified cave bacterial community, and 14 new bacterial species were described and their genomes sequenced. In this study, we obtained the most intensive collection of cultivated microbial resources from karst caves to date and predicted the various important routes for the biogeochemical cycling of elements in cave ecosystems.},
}

Bacteria/genetics/isolation & purification/metabolism
Bacterial Proteins/genetics/metabolism
Biodiversity
Caves/*microbiology
Coenzyme A-Transferases/genetics/metabolism
*Genome, Bacterial
Metagenome
Metagenomics
Microbiota
Nitrogen/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
Sulfur/metabolism

@article {pmid32888329,
year = {2021},
author = {Yang, J and Li, F and Zhang, Y and He, Z},
title = {Metagenomic analysis of microbial community succession during the pickling process of Zhacai (preserved mustard tuber) and its correlation with Zhacai biochemical indices.},
journal = {Journal of the science of food and agriculture},
volume = {101},
number = {4},
pages = {1646-1658},
doi = {10.1002/jsfa.10785},
pmid = {32888329},
issn = {1097-0010},
support = {cstc2017jcyjAX0249//Chongqing Research Program of Basic Research and Frontier Technology/ ; XDJK2018C070 XDJK2015C135 SWU113035//Fundamental Research Funds for the Central Universities/ ; 31801529//National Natural Science Foundation of China/ ; CC18Z20//Scientific research project of Sichuan Cuisine Development Research Center, Sichuan Tourism University/ ; },
mesh = {Bacteria/classification/genetics/*isolation & purification ; Fermentation ; Fermented Foods and Beverages/*microbiology ; Fungi/classification/genetics/*isolation & purification ; Metagenomics ; *Microbiota ; Mustard Plant/*microbiology ; },
abstract = {BACKGROUND: Industrial Fuling Zhacai is pickled by a method summarized as 'three times pickled and pressed', in which raw mustard tubers are subjected to three stages of pickling in different salt concentrations, with a pressing operation at the end of each stage to remove brine. This study used Illumina MiSeq technology and multivariate statistical analyses to investigate microbial community succession during the pickling process and its correlation with Zhacai biochemical indices.

RESULTS: A total of 19 phyla, 208 genera, and 295 species of bacteria were identified. Lactobacillus was the dominant genus of bacteria in all three stages and Lactobacillus sakei was the dominant species in the first and second stages. A total of six phyla, 200 genera and 301 species of fungi were also identified. According to a PICRUSt2 prediction, the main functions of the bacterial and fungal communities were carbohydrate and protein metabolism, while alcohol metabolism was also a function of fungi. Nine bacterial genera closely correlated with Zhacai biochemical indices: Acinetobacter, Pseudomonas, Pedobacter, Erwinia, Lactobacillus, Chryseobacterium, Flavobacterium, Duganella, and Paenarthrobacter. Six genera of fungi correlated closely: Penicillium, Cystobasidium, Cladosporium, Plenodomus, Aspergillus, and Simplicillium. All these genera probably originated from the surface microorganisms of raw mustard tuber.

CONCLUSION: This study reveals the succession patterns of microbial community structures during the pickling process of industrial Zhacai and infers the core functional flora, providing reference data for Zhacai pickling process control. © 2020 Society of Chemical Industry.},
}

Bacteria/classification/genetics/*isolation & purification
Fermentation
Fermented Foods and Beverages/*microbiology
Fungi/classification/genetics/*isolation & purification
Metagenomics
*Microbiota
Mustard Plant/*microbiology

@article {pmid32761733,
year = {2020},
author = {Overholt, WA and Hölzer, M and Geesink, P and Diezel, C and Marz, M and Küsel, K},
title = {Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome-assembled genomes from a complex aquifer system.},
journal = {Environmental microbiology},
volume = {22},
number = {9},
pages = {4000-4013},
doi = {10.1111/1462-2920.15186},
pmid = {32761733},
issn = {1462-2920},
support = {CRC 1076 AquaDiva//Deutsche Forschungsgemeinschaft/International ; //Joachim Herz Stiftung/International ; },
mesh = {Genome, Microbial/*genetics ; Groundwater/*microbiology/virology ; High-Throughput Nucleotide Sequencing ; Metagenome/*genetics ; Metagenomics ; *Nanopore Sequencing ; Water Microbiology ; Whole Genome Sequencing ; },
abstract = {Assembling microbial and viral genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments. To compare the recovery of genomes from microorganisms and their viruses from groundwater, we generated shotgun metagenomes with Illumina sequencing accompanied by long reads derived from the Oxford Nanopore Technologies (ONT) sequencing platform. Assembly and metagenome-assembled genome (MAG) metrics for both microbes and viruses were determined from an Illumina-only assembly, ONT-only assembly, and a hybrid assembly approach. The hybrid approach recovered 2× more mid to high-quality MAGs compared to the Illumina-only approach and 4× more than the ONT-only approach. A similar number of viral genomes were reconstructed using the hybrid and ONT methods, and both recovered nearly fourfold more viral genomes than the Illumina-only approach. While yielding fewer MAGs, the ONT-only approach generated MAGs with a high probability of containing rRNA genes, 3× higher than either of the other methods. Of the shared MAGs recovered from each method, the ONT-only approach generated the longest and least fragmented MAGs, while the hybrid approach yielded the most complete. This work provides quantitative data to inform a cost-benefit analysis of the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups.},
}

Genome, Microbial/*genetics
Groundwater/*microbiology/virology
High-Throughput Nucleotide Sequencing
Metagenome/*genetics
Metagenomics
*Nanopore Sequencing
Water Microbiology
Whole Genome Sequencing

@article {pmid32655541,
year = {2020},
author = {Hu, Q and Liu, C and Zhang, D and Wang, R and Qin, L and Xu, Q and Che, L and Gao, F},
title = {Effects of Low-Dose Antibiotics on Gut Immunity and Antibiotic Resistomes in Weaned Piglets.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {903},
pmid = {32655541},
issn = {1664-3224},
mesh = {Animals ; Anti-Bacterial Agents/*administration & dosage ; Bacteria/*drug effects/genetics/immunology ; Bacterial Proteins/genetics ; Colon/*drug effects/immunology/microbiology ; *Drug Resistance, Bacterial/genetics ; Female ; Gastrointestinal Microbiome/*drug effects ; Gene Expression Profiling ; Host-Pathogen Interactions ; Ileum/*drug effects/immunology/microbiology ; Immunity, Innate/*drug effects/genetics ; Interspersed Repetitive Sequences ; Metagenomics ; Methyltransferases/genetics ; Sus scrofa ; Transcriptome ; Weaning ; },
abstract = {Widespread antibiotic use increases the risk of livestock acting as potential reservoirs of antimicrobial resistance genes (ARGs) that may be transferred to human and animal pathogens. Particularly, maternal-infant transmission of antibiotics via breastmilk represents a great concern regarding infant health. In this study, we investigated the effects of 4-week low-dose antibiotic (LDA) treatment on the host immunity and antibiotic resistomes in weaned piglets. Transcriptomic analyses of ileum tissues revealed that the affected genes were largely enriched in innate immunity-related pathways. Significantly reduced protein expression of inflammatory factors, i.e., IFN-γ, IL-6 were observed. In addition, analyses of antibiotic resistomes identified a total of 1,021 ARGs related to 39 classes of antibiotics. The samples exhibited highly individual-specific diversity and no significant difference in the structure and diversity of ARGs and mobile gene elements (MGE) after LDA exposure for both colon and ileum samples. Despite of that, there were significant changes in the abundance of two transferrable ARGs [Erm(T) and tcr3] related to the antibiotics administered, implying an increased risk of transferrable antibiotic resistance. There was a significant change in the abundance of one pathogenic species after LDA exposure in the colon samples and one in the ileum samples, but there were no significant differences in the matched ARGs. Collectively, our findings reveal considerable changes in intestinal immunity-related genes, but minimal effects on gut antibiotic resistomes (ARGs and MGEs) in weaned piglets after 4 weeks LDA exposure. Our study provides a foundation for evaluating the longer-term cumulative effects of LDA use, especially the effects of maternal-infant LDA transmission, on antibiotic resistance and risks to infant health.},
}

Animals
Anti-Bacterial Agents/*administration & dosage
Bacteria/*drug effects/genetics/immunology
Bacterial Proteins/genetics
Colon/*drug effects/immunology/microbiology
*Drug Resistance, Bacterial/genetics
Female
Gastrointestinal Microbiome/*drug effects
Gene Expression Profiling
Host-Pathogen Interactions
Ileum/*drug effects/immunology/microbiology
Immunity, Innate/*drug effects/genetics
Interspersed Repetitive Sequences
Metagenomics
Methyltransferases/genetics
Sus scrofa
Transcriptome
Weaning

@article {pmid32531290,
year = {2020},
author = {Khoruts, A and Hoffmann, DE and Britton, RA},
title = {Probiotics: Promise, Evidence, and Hope.},
journal = {Gastroenterology},
volume = {159},
number = {2},
pages = {409-413},
doi = {10.1053/j.gastro.2020.05.058},
pmid = {32531290},
issn = {1528-0012},
mesh = {Digestive System Diseases/*diet therapy/microbiology/prevention & control ; Gastrointestinal Microbiome/*physiology ; Humans ; Probiotics/*administration & dosage/adverse effects ; },
}

Digestive System Diseases/*diet therapy/microbiology/prevention & control
Gastrointestinal Microbiome/*physiology
Humans
Probiotics/*administration & dosage/adverse effects

@article {pmid33482026,
year = {2021},
author = {Canivet, CM and David, N and Pailhoriès, H and Briand, M and Guy, CD and Bouchez, O and Hunault, G and Fizanne, L and Lannes, A and Oberti, F and Fouchard, I and Calès, P and Diehl, AM and Barret, M and Boursier, J},
title = {Cross-linkage between bacterial taxonomy and gene functions: a study of metagenome-assembled genomes of gut microbiota in adult non-alcoholic fatty liver disease.},
journal = {Alimentary pharmacology & therapeutics},
volume = {53},
number = {6},
pages = {722-732},
doi = {10.1111/apt.16262},
pmid = {33482026},
issn = {1365-2036},
mesh = {Adult ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; *Non-alcoholic Fatty Liver Disease/genetics ; },
abstract = {BACKGROUND: The reconstruction of metagenome-assembled genomes (MAGs) has emerged as a powerful approach for combining the taxonomic and functional content of microbial populations.

AIM: To use this new approach to highlight mechanisms linking gut microbiota to NAFLD severity METHODS: Stool samples were collected from 96 NAFLD patients on the day of liver biopsy. Shotgun DNA sequencing of the gut microbiota was performed on an Illumina HiSeq3000 system. Contigs were binned into MAGs according to their co-abundances and tetranucleotide frequencies using Metabat v.0.32.4. Predicted protein-coding genes were clustered in orthologous groups (OGs) with DIAMOND against the EggNOG v4.5 database. Liver biopsies were read in accordance with the NASH CRN classification.

RESULTS: Fifty-four patients had NASH and 44 had significant fibrosis (F ≥ 2). Sequencing of DNA extracted from stools resulted in 13.8 + 3.2 million paired-end reads per sample. Of the 4,000 reconstructed MAGs, 220 in NASH patients, 192 in non-NASH patients, 203 in F ≥ 2 patients and 230 in F0-1 patients had > 70% completeness and < 5% contamination. Within these MAGs, 28 OGs were associated with NASH, 33 with significant fibrosis, and seven with both NASH and significant fibrosis. The study of MAGs showed associations between NAFLD severity and some gut bacteria with microbiota functions related to hydrogen sulfide production, citrate transport, hemicellulose degradation, aldehyde production and vitamin B12 synthesis.

CONCLUSION: Using new metagenomics methods, our study unveils potential mechanisms by which certain bacteria from the gut microbiota could protect or contribute to the development of NASH and liver fibrosis in NAFLD.},
}

Adult
*Gastrointestinal Microbiome/genetics
Humans
Metagenome
Metagenomics
*Microbiota
*Non-alcoholic Fatty Liver Disease/genetics

@article {pmid33176883,
year = {2020},
author = {Zhang, L and Fang, X and Liao, H and Zhang, Z and Zhou, X and Han, L and Chen, Y and Qiu, Q and Li, SC},
title = {A comprehensive investigation of metagenome assembly by linked-read sequencing.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {156},
pmid = {33176883},
issn = {2049-2618},
mesh = {High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {BACKGROUND: The human microbiota are complex systems with important roles in our physiological activities and diseases. Sequencing the microbial genomes in the microbiota can help in our interpretation of their activities. The vast majority of the microbes in the microbiota cannot be isolated for individual sequencing. Current metagenomics practices use short-read sequencing to simultaneously sequence a mixture of microbial genomes. However, these results are in ambiguity during genome assembly, leading to unsatisfactory microbial genome completeness and contig continuity. Linked-read sequencing is able to remove some of these ambiguities by attaching the same barcode to the reads from a long DNA fragment (10-100 kb), thus improving metagenome assembly. However, it is not clear how the choices for several parameters in the use of linked-read sequencing affect the assembly quality.

RESULTS: We first examined the effects of read depth (C) on metagenome assembly from linked-reads in simulated data and a mock community. The results showed that C positively correlated with the length of assembled sequences but had little effect on their qualities. The latter observation was corroborated by tests using real data from the human gut microbiome, where C demonstrated minor impact on the sequence quality as well as on the proportion of bins annotated as draft genomes. On the other hand, metagenome assembly quality was susceptible to read depth per fragment (CR) and DNA fragment physical depth (CF). For the same C, deeper CR resulted in more draft genomes while deeper CF improved the quality of the draft genomes. We also found that average fragment length (μFL) had marginal effect on assemblies, while fragments per partition (NF/P) impacted the off-target reads involved in local assembly, namely, lower NF/P values would lead to better assemblies by reducing the ambiguities of the off-target reads. In general, the use of linked-reads improved the assembly for contig N50 when compared to Illumina short-reads, but not when compared to PacBio CCS (circular consensus sequencing) long-reads.

CONCLUSIONS: We investigated the influence of linked-read sequencing parameters on metagenome assembly comprehensively. While the quality of genome assembly from linked-reads cannot rival that from PacBio CCS long-reads, the case for using linked-read sequencing remains persuasive due to its low cost and high base-quality. Our study revealed that the probable best practice in using linked-reads for metagenome assembly was to merge the linked-reads from multiple libraries, where each had sufficient CR but a smaller amount of input DNA. Video Abstract.},
}

High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenome/*genetics
Metagenomics/*methods
Microbiota/*genetics
Sequence Analysis, DNA/*methods

@article {pmid32408110,
year = {2020},
author = {Wei, M and Huang, F and Zhao, L and Zhang, Y and Yang, W and Wang, S and Li, M and Han, X and Ge, K and Qu, C and Rajani, C and Xie, G and Zheng, X and Zhao, A and Bian, Z and Jia, W},
title = {A dysregulated bile acid-gut microbiota axis contributes to obesity susceptibility.},
journal = {EBioMedicine},
volume = {55},
number = {},
pages = {102766},
pmid = {32408110},
issn = {2352-3964},
support = {U01 CA188387/CA/NCI NIH HHS/United States ; },
mesh = {Adipose Tissue, Brown/metabolism ; Animals ; Body Mass Index ; Chenodeoxycholic Acid/*metabolism ; Cholestenones/metabolism ; Clostridiales/metabolism/pathogenicity ; Cohort Studies ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Disease Susceptibility ; *Gastrointestinal Microbiome ; Gene Expression Regulation ; Glucagon-Like Peptide 1/genetics/metabolism ; Humans ; Ileum/metabolism/*microbiology ; Lithocholic Acid/*metabolism ; Male ; Metagenomics/methods ; Mice ; Mice, Inbred C57BL ; Obesity/etiology/genetics/metabolism/*microbiology ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics/metabolism ; Uncoupling Protein 1/genetics/metabolism ; Ursodeoxycholic Acid/*metabolism ; },
abstract = {BACKGROUND: The composition of the bile acid (BA) pool is closely associated with obesity and is modified by gut microbiota. Perturbations of gut microbiota shape the BA composition, which, in turn, may alter important BA signaling and affect host metabolism.

METHODS: We investigated BA composition of high BMI subjects from a human cohort study and a high fat diet (HFD) obesity prone (HF-OP) / HFD obesity resistant (HF-OR) mice model. Gut microbiota was analysed by metagenomics sequencing. GLP-1 secretion and gene regulation studies involved ELISA, qPCR, Western blot, Immunohistochemistry, and Immunofluorescence staining.

FINDINGS: We found that the proportion of non-12-OH BAs was significantly decreased in the unhealthy high BMI subjects. The HF-OR mice had an enhanced level of non-12-OH BAs. Non-12-OH BAs including ursodeoxycholate (UDCA), chenodeoxycholate (CDCA), and lithocholate (LCA) were decreased in the HF-OP mice and associated with altered gut microbiota. Clostridium scindens was decreased in HF-OP mice and had a positive correlation with UDCA and LCA. Gavage of Clostridium scindens in mice increased the levels of hepatic non-12-OH BAs, accompanied by elevated serum 7α-hydroxy-4-cholesten-3-one (C4) levels. In HF-OP mice, altered BA composition was associated with significantly downregulated expression of GLP-1 in ileum and PGC1α, UCP1 in brown adipose tissue. In addition, we identified that UDCA attenuated the high fat diet-induced obesity via enhancing levels of non-12-OH BAs.

INTERPRETATION: Our study highlights that dysregulated BA signaling mediated by gut microbiota contributes to obesity susceptibility, suggesting modulation of BAs could be a promising strategy for obesity therapy.},
}

Adipose Tissue, Brown/metabolism
Animals
Body Mass Index
Chenodeoxycholic Acid/*metabolism
Cholestenones/metabolism
Clostridiales/metabolism/pathogenicity
Cohort Studies
Diet, High-Fat/adverse effects
Disease Models, Animal
Disease Susceptibility
*Gastrointestinal Microbiome
Gene Expression Regulation
Glucagon-Like Peptide 1/genetics/metabolism
Humans
Ileum/metabolism/*microbiology
Lithocholic Acid/*metabolism
Male
Metagenomics/methods
Mice
Mice, Inbred C57BL
Obesity/etiology/genetics/metabolism/*microbiology
Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/genetics/metabolism
Uncoupling Protein 1/genetics/metabolism
Ursodeoxycholic Acid/*metabolism

@article {pmid33786001,
year = {2021},
author = {Sehli, S and Allali, I and Chahboune, R and Bakri, Y and Al Idrissi, N and Hamdi, S and Nejjari, C and Amzazi, S and Ghazal, H},
title = {Metagenomics Approaches to Investigate the Gut Microbiome of COVID-19 Patients.},
journal = {Bioinformatics and biology insights},
volume = {15},
number = {},
pages = {1177932221999428},
doi = {10.1177/1177932221999428},
pmid = {33786001},
issn = {1177-9322},
abstract = {Over the last decade, it has become increasingly apparent that the microbiome is a central component in human well-being and illness. However, to establish innovative therapeutic methods, it is crucial to learn more about the microbiota. Thereby, the area of metagenomics and associated bioinformatics methods and tools has become considerable in the study of the human microbiome biodiversity. The application of these metagenomics approaches to studying the gut microbiome in COVID-19 patients could be one of the promising areas of research in the fight against the SARS-CoV-2 infection and disparity. Therefore, understanding how the gut microbiome is affected by or could affect the SARS-CoV-2 is very important. Herein, we present an overview of approaches and methods used in the current published studies on COVID-19 patients and the gut microbiome. The accuracy of these researches depends on the appropriate choice and the optimal use of the metagenomics bioinformatics platforms and tools. Interestingly, most studies reported that COVID-19 patients' microbiota are enriched with opportunistic microorganisms. The choice and use of appropriate computational tools and techniques to accurately investigate the gut microbiota is therefore critical in determining the appropriate microbiome profile for diagnosis and the most reliable antiviral or preventive microbial composition.},
}

@article {pmid33600956,
year = {2021},
author = {Zhang, S and Zeng, B and Chen, Y and Yang, M and Kong, F and Wei, L and Li, F and Zhao, J and Li, Y},
title = {Gut microbiota in healthy and unhealthy long-living people.},
journal = {Gene},
volume = {779},
number = {},
pages = {145510},
doi = {10.1016/j.gene.2021.145510},
pmid = {33600956},
issn = {1879-0038},
mesh = {Aged, 80 and over ; Amino Acids/metabolism ; Asian Continental Ancestry Group ; Carbohydrate Metabolism ; Drug Resistance, Microbial/genetics ; Dysbiosis/*microbiology ; Enzymes/genetics ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Metagenome ; Streptococcus/pathogenicity ; Virulence Factors/genetics ; },
abstract = {The human gut microbiota in long-living people has been characterized, however, its metabolic potential is still largely unknown in this group. In this study, the gut microbiota was assessed in 37 Chinese long-living participants (aged 90 + years) by metagenomic sequencing of stool samples. Participants were categorized into two groups, healthy long-living (n = 28) and unhealthy long-living (n = 9). Gut microbiota composition and function were compared among these two groups. We found that the gut microbiota in the healthy long-living group was significantly separated from the unhealthy group. The healthy long-living group contained a higher abundance of Bacteroidetes and more functional pathways in energy metabolism, glycan biosynthesis and metabolism, metabolism of cofactors and vitamins, and biosynthesis of other secondary metabolites. The unhealthy group contained a higher abundance of Streptococcus and other pathogenic bacteria, and also contained more functional pathways for xenobiotics biodegradation and metabolism than the healthy group. Additionally, the unhealthy group had decreased levels of carbohydrate-active enzymes, including host-glycan and fiber degrading enzymes, and an increase in starch-degrading enzymes. In conclusion, the gut microbiota of unhealthy long-living people contains more pathogenic bacteria, and the overall gut microbiota may be in an unhealthy state, "dysbiosis", which leads to a decrease in carbohydrate digestion, glycan and thiamine (B1) metabolites, and fatty acid biosynthesis.},
}

Aged, 80 and over
Amino Acids/metabolism
Asian Continental Ancestry Group
Carbohydrate Metabolism
Drug Resistance, Microbial/genetics
Dysbiosis/*microbiology
Enzymes/genetics
Feces/microbiology
Gastrointestinal Microbiome/genetics/*physiology
Humans
Metagenome
Streptococcus/pathogenicity
Virulence Factors/genetics

@article {pmid33003412,
year = {2020},
author = {Reilly, AM and Tsai, AP and Lin, PB and Ericsson, AC and Oblak, AL and Ren, H},
title = {Metabolic Defects Caused by High-Fat Diet Modify Disease Risk through Inflammatory and Amyloidogenic Pathways in a Mouse Model of Alzheimer's Disease.},
journal = {Nutrients},
volume = {12},
number = {10},
pages = {},
pmid = {33003412},
issn = {2072-6643},
support = {UL1TR002529/TR/NCATS NIH HHS/United States ; R01DK120772/DK/NIDDK NIH HHS/United States ; P30DK097512/DK/NIDDK NIH HHS/United States ; T32 DK064466/DK/NIDDK NIH HHS/United States ; R01 DK120772/DK/NIDDK NIH HHS/United States ; T32DK064466/DK/NIDDK NIH HHS/United States ; R00 DK098294/DK/NIDDK NIH HHS/United States ; R00DK098294/DK/NIDDK NIH HHS/United States ; },
mesh = {Alzheimer Disease/etiology/*metabolism ; Amyloidogenic Proteins/*metabolism ; Animals ; Apoptosis Regulatory Proteins/metabolism ; Cytokines/metabolism ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Eating/physiology ; Energy Metabolism/physiology ; Gastrointestinal Microbiome/genetics ; Gene Expression ; Genotype ; Glucose Intolerance/blood/etiology ; Hippocampus/metabolism ; Inflammation ; Insulin/metabolism ; Lipids/blood ; Locomotion/physiology ; Male ; Mice ; Microglia/metabolism ; Neurogenic Inflammation/etiology/*metabolism ; RNA, Messenger/metabolism ; Risk Factors ; Signal Transduction/*physiology ; Synaptic Transmission/genetics ; },
abstract = {High-fat diet (HFD) has been shown to accelerate Alzheimer's disease (AD) pathology, but the exact molecular and cellular mechanisms remain incompletely understood. Moreover, it is unknown whether AD mice are more susceptible to HFD-induced metabolic dysfunctions. To address these questions, we used 5xFAD mice as an Alzheimer's disease model to study the physiological and molecular underpinning between HFD-induced metabolic defects and AD pathology. We systematically profiled the metabolic parameters, the gut microbiome composition, and hippocampal gene expression in 5xFAD and wild type (WT) mice fed normal chow diet and HFD. HFD feeding impaired energy metabolism in male 5xFAD mice, leading to increased locomotor activity, energy expenditure, and food intake. 5xFAD mice on HFD had elevated circulating lipids and worsened glucose intolerance. HFD caused profound changes in gut microbiome compositions, though no difference between genotype was detected. We measured hippocampal mRNAs related to AD neuropathology and neuroinflammation and showed that HFD elevated the expression of apoptotic, microglial, and amyloidogenic genes in 5xFAD mice. Pathway analysis revealed that differentially regulated genes were involved in insulin signaling, cytokine signaling, cellular stress, and neurotransmission. Collectively, our results showed that 5xFAD mice were more susceptible to HFD-induced metabolic dysregulation and suggest that targeting metabolic dysfunctions can ameliorate AD symptoms via effects on insulin signaling and neuroinflammation in the hippocampus.},
}

Alzheimer Disease/etiology/*metabolism
Amyloidogenic Proteins/*metabolism
Animals
Apoptosis Regulatory Proteins/metabolism
Cytokines/metabolism
Diet, High-Fat/*adverse effects
Disease Models, Animal
Eating/physiology
Energy Metabolism/physiology
Gastrointestinal Microbiome/genetics
Gene Expression
Genotype
Glucose Intolerance/blood/etiology
Hippocampus/metabolism
Inflammation
Insulin/metabolism
Lipids/blood
Locomotion/physiology
Male
Mice
Microglia/metabolism
Neurogenic Inflammation/etiology/*metabolism
RNA, Messenger/metabolism
Risk Factors
Signal Transduction/*physiology
Synaptic Transmission/genetics

@article {pmid32111636,
year = {2020},
author = {Seyed Tabib, NS and Madgwick, M and Sudhakar, P and Verstockt, B and Korcsmaros, T and Vermeire, S},
title = {Big data in IBD: big progress for clinical practice.},
journal = {Gut},
volume = {69},
number = {8},
pages = {1520-1532},
pmid = {32111636},
issn = {1468-3288},
support = {BB/S50743X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/J004529/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016774/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Big Data ; Gastrointestinal Microbiome ; Gene Expression Profiling ; *Genomics ; Humans ; Image Interpretation, Computer-Assisted ; Inflammatory Bowel Diseases/diagnosis/drug therapy/*genetics/*metabolism ; *Machine Learning ; Metagenomics ; Precision Medicine ; Prognosis ; Proteomics ; Risk Assessment ; Translational Medical Research ; },
abstract = {IBD is a complex multifactorial inflammatory disease of the gut driven by extrinsic and intrinsic factors, including host genetics, the immune system, environmental factors and the gut microbiome. Technological advancements such as next-generation sequencing, high-throughput omics data generation and molecular networks have catalysed IBD research. The advent of artificial intelligence, in particular, machine learning, and systems biology has opened the avenue for the efficient integration and interpretation of big datasets for discovering clinically translatable knowledge. In this narrative review, we discuss how big data integration and machine learning have been applied to translational IBD research. Approaches such as machine learning may enable patient stratification, prediction of disease progression and therapy responses for fine-tuning treatment options with positive impacts on cost, health and safety. We also outline the challenges and opportunities presented by machine learning and big data in clinical IBD research.},
}

*Big Data
Gastrointestinal Microbiome
Gene Expression Profiling
*Genomics
Humans
Image Interpretation, Computer-Assisted
Inflammatory Bowel Diseases/diagnosis/drug therapy/*genetics/*metabolism
*Machine Learning
Metagenomics
Precision Medicine
Prognosis
Proteomics
Risk Assessment
Translational Medical Research

@article {pmid32088998,
year = {2020},
author = {Kim, S and Rigatto, K and Gazzana, MB and Knorst, MM and Richards, EM and Pepine, CJ and Raizada, MK},
title = {Altered Gut Microbiome Profile in Patients With Pulmonary Arterial Hypertension.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {75},
number = {4},
pages = {1063-1071},
pmid = {32088998},
issn = {1524-4563},
support = {R01 HL102033/HL/NHLBI NIH HHS/United States ; R01 HL146158/HL/NHLBI NIH HHS/United States ; R01 HL132448/HL/NHLBI NIH HHS/United States ; R01 HL091005/HL/NHLBI NIH HHS/United States ; U01 HL064924/HL/NHLBI NIH HHS/United States ; U01 HL087366/HL/NHLBI NIH HHS/United States ; UM1 HL087366/HL/NHLBI NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; },
mesh = {Adult ; Feces/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenomics ; Middle Aged ; Pulmonary Arterial Hypertension/*microbiology ; },
abstract = {Pulmonary arterial hypertension (PAH) is considered a disease of the pulmonary vasculature. Limited progress has been made in preventing or arresting progression of PAH despite extensive efforts. Our previous studies indicated that PAH could be considered a systemic disease since its pathology involves interplay of multiple organs. This, coupled with increasing implication of the gut and its microbiome in chronic diseases, led us to hypothesize that patients with PAH exhibit a distinct gut microbiome that contributes to, and predicts, the disease. Fecal microbiome of 18 type 1 PAH patients (mean pulmonary arterial pressure, 57.4, SD 16.7 mm Hg) and 13 reference subjects were compared by shotgun metagenomics to evaluate this hypothesis. Significant taxonomic and functional changes in microbial communities in the PAH cohort were observed. Pathways for the synthesis of arginine, proline, and ornithine were increased in PAH cohort compared with reference cohort. Additionally, groups of bacterial communities associated with trimethylamine/ trimethylamine N-oxide and purine metabolism were increased in PAH cohort. In contrast, butyrate-and propionate-producing bacteria such as Coprococcus, Butyrivibrio, Lachnospiraceae, Eubacterium, Akkermansia, and Bacteroides were increased in reference cohort. A random forest model predicted PAH from the composition of the gut microbiome with 83% accuracy. Finally, virome analysis showed enrichment of Enterococcal and relative depletion of Lactococcal phages in the PAH cohort. In conclusion, patients with PAH exhibit a unique microbiome profile that has the high predictive potential for PAH. This highlights previously unknown roles of gut bacteria in this disease and could lead to new therapeutic, diagnostic, or management paradigms for PAH.},
}

Adult
Feces/*microbiology
Female
Gastrointestinal Microbiome/*physiology
Humans
Male
Metagenomics
Middle Aged
Pulmonary Arterial Hypertension/*microbiology

@article {pmid31953253,
year = {2020},
author = {Erawijantari, PP and Mizutani, S and Shiroma, H and Shiba, S and Nakajima, T and Sakamoto, T and Saito, Y and Fukuda, S and Yachida, S and Yamada, T},
title = {Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles.},
journal = {Gut},
volume = {69},
number = {8},
pages = {1404-1415},
pmid = {31953253},
issn = {1468-3288},
mesh = {Actinobacteria/isolation & purification/metabolism ; Aged ; Amino Acids, Branched-Chain/metabolism ; Bacillus/isolation & purification/metabolism ; Bacteroidetes/isolation & purification/*metabolism ; Bifidobacterium/isolation & purification/metabolism ; Bile Acids and Salts/*metabolism ; Case-Control Studies ; Clostridiales/isolation & purification/metabolism ; Deoxycholic Acid/metabolism ; Feces/*chemistry/*microbiology ; Female ; Firmicutes/isolation & purification/*metabolism ; *Gastrectomy ; Gastrointestinal Microbiome ; Humans ; Lactobacillus/isolation & purification/metabolism ; Male ; Metabolome ; Metagenomics ; Middle Aged ; Prevotella/isolation & purification/metabolism ; Sequence Analysis, DNA ; Stomach Neoplasms/*surgery ; Streptococcus/isolation & purification/metabolism ; Veillonella/isolation & purification/metabolism ; },
abstract = {OBJECTIVE: Recent evidence points to the gut microbiome's involvement in postoperative outcomes, including after gastrectomy. Here, we investigated the influence of gastrectomy for gastric cancer on the gut microbiome and metabolome, and how it related to postgastrectomy conditions.

DESIGN: We performed shotgun metagenomics sequencing and capillary electrophoresis time-of-flight mass spectrometry-based metabolomics analyses on faecal samples collected from participants with a history of gastrectomy for gastric cancer (n=50) and compared them with control participants (n=56).

RESULTS: The gut microbiota in the gastrectomy group showed higher species diversity and richness (p<0.05), together with greater abundance of aerobes, facultative anaerobes and oral microbes. Moreover, bile acids such as genotoxic deoxycholic acid and branched-chain amino acids were differentially abundant between the two groups (linear discriminant analysis (LDA) effect size (LEfSe): p<0.05, q<0.1, LDA>2.0), as were also Kyoto Encyclopedia of Genes and Genomes modules involved in nutrient transport and organic compounds biosynthesis (LEfSe: p<0.05, q<0.1, LDA>2.0).

CONCLUSION: Our results reveal alterations of gut microbiota after gastrectomy, suggesting its association with postoperative comorbidities. The multi-omic approach applied in this study could complement the follow-up of patients after gastrectomy.},
}

Actinobacteria/isolation & purification/metabolism
Aged
Amino Acids, Branched-Chain/metabolism
Bacillus/isolation & purification/metabolism
Bacteroidetes/isolation & purification/*metabolism
Bifidobacterium/isolation & purification/metabolism
Bile Acids and Salts/*metabolism
Case-Control Studies
Clostridiales/isolation & purification/metabolism
Deoxycholic Acid/metabolism
Feces/*chemistry/*microbiology
Female
Firmicutes/isolation & purification/*metabolism
*Gastrectomy
Gastrointestinal Microbiome
Humans
Lactobacillus/isolation & purification/metabolism
Male
Metabolome
Metagenomics
Middle Aged
Prevotella/isolation & purification/metabolism
Sequence Analysis, DNA
Stomach Neoplasms/*surgery
Streptococcus/isolation & purification/metabolism
Veillonella/isolation & purification/metabolism

@article {pmid33219314,
year = {2020},
author = {Antonson, AM and Evans, MV and Galley, JD and Chen, HJ and Rajasekera, TA and Lammers, SM and Hale, VL and Bailey, MT and Gur, TL},
title = {Unique maternal immune and functional microbial profiles during prenatal stress.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {20288},
pmid = {33219314},
issn = {2045-2322},
support = {5T32DE014320/NH/NIH HHS/United States ; },
mesh = {Animals ; Brain/*embryology/immunology ; Burkholderiales/genetics/immunology ; Disease Models, Animal ; Female ; Fetal Development/*immunology ; Gastrointestinal Microbiome/genetics/*immunology ; Glucocorticoids/metabolism ; Humans ; Leukocytes, Mononuclear/immunology ; Maternal-Fetal Exchange/immunology ; Mental Health ; Metagenomics ; Mice ; Neuroimmunomodulation/immunology ; Placenta/cytology/immunology ; Pregnancy ; Pregnancy Complications/*immunology/metabolism/psychology ; Prenatal Exposure Delayed Effects/immunology ; Stress, Psychological/*immunology/metabolism/psychology ; },
abstract = {Maternal stress during pregnancy is widespread and is associated with poor offspring outcomes, including long-term mental health issues. Prenatal stress-induced fetal neuroinflammation is thought to underlie aberrant neurodevelopment and to derive from a disruption in intrauterine immune homeostasis, though the exact origins are incompletely defined. We aimed to identify divergent immune and microbial metagenome profiles of stressed gestating mice that may trigger detrimental inflammatory signaling at the maternal-fetal interface. In response to stress, maternal glucocorticoid circuit activation corresponded with indicators of systemic immunosuppression. At the maternal-fetal interface, density of placental mononuclear leukocytes decreased with stress, yet maternal whole blood leukocyte analysis indicated monocytosis and classical M1 phenotypic shifts. Genome-resolved microbial metagenomic analyses revealed reductions in genes, microbial strains, and metabolic pathways in stressed dams that are primarily associated with pro-inflammatory function. In particular, disrupted Parasutterella excrementihominis appears to be integral to inflammatory and metabolic dysregulation during prenatal stress. Overall, these perturbations in maternal immunological and microbial regulation during pregnancy may displace immune equilibrium at the maternal-fetal interface. Notably, the absence of and reduction in overt maternal inflammation during stress indicates that the signaling patterns driving fetal outcomes in this context are more nuanced and complex than originally anticipated.},
}

Animals
Brain/*embryology/immunology
Burkholderiales/genetics/immunology
Disease Models, Animal
Female
Fetal Development/*immunology
Gastrointestinal Microbiome/genetics/*immunology
Glucocorticoids/metabolism
Humans
Leukocytes, Mononuclear/immunology
Maternal-Fetal Exchange/immunology
Mental Health
Metagenomics
Mice
Neuroimmunomodulation/immunology
Placenta/cytology/immunology
Pregnancy
Pregnancy Complications/*immunology/metabolism/psychology
Prenatal Exposure Delayed Effects/immunology
Stress, Psychological/*immunology/metabolism/psychology

@article {pmid33004077,
year = {2020},
author = {Tauzin, AS and Pereira, MR and Van Vliet, LD and Colin, PY and Laville, E and Esque, J and Laguerre, S and Henrissat, B and Terrapon, N and Lombard, V and Leclerc, M and Doré, J and Hollfelder, F and Potocki-Veronese, G},
title = {Investigating host-microbiome interactions by droplet based microfluidics.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {141},
pmid = {33004077},
issn = {2049-2618},
mesh = {Bacteria/genetics ; *Host Microbial Interactions ; Humans ; Male ; Metagenomics ; Microbiota/genetics/*physiology ; *Microfluidics ; Middle Aged ; },
abstract = {BACKGROUND: Despite the importance of the mucosal interface between microbiota and the host in gut homeostasis, little is known about the mechanisms of bacterial gut colonization, involving foraging for glycans produced by epithelial cells. The slow pace of progress toward understanding the underlying molecular mechanisms is largely due to the lack of efficient discovery tools, especially those targeting the uncultured fraction of the microbiota.

RESULTS: Here, we introduce an ultra-high-throughput metagenomic approach based on droplet microfluidics, to screen fosmid libraries. Thousands of bacterial genomes can be covered in 1 h of work, with less than ten micrograms of substrate. Applied to the screening of the mucosal microbiota for β-N-acetylgalactosaminidase activity, this approach allowed the identification of pathways involved in the degradation of human gangliosides and milk oligosaccharides, the structural homologs of intestinal mucin glycans. These pathways, whose prevalence is associated with inflammatory bowel diseases, could be the result of horizontal gene transfers with Bacteroides species. Such pathways represent novel targets to study the microbiota-host interactions in the context of inflammatory bowel diseases, in which the integrity of the mucosal barrier is impaired.

CONCLUSION: By compartmentalizing experiments inside microfluidic droplets, this method speeds up and miniaturizes by several orders of magnitude the screening process compared to conventional approaches, to capture entire metabolic pathways from metagenomic libraries. The method is compatible with all types of (meta)genomic libraries, and employs a commercially available flow cytometer instead of a custom-made sorting system to detect intracellular or extracellular enzyme activities. This versatile and generic workflow will accelerate experimental exploration campaigns in functional metagenomics and holobiomics studies, to further decipher host-microbiota relationships. Video Abstract.},
}

Bacteria/genetics
*Host Microbial Interactions
Humans
Male
Metagenomics
Microbiota/genetics/*physiology
*Microfluidics
Middle Aged

@article {pmid32919472,
year = {2020},
author = {Seelbinder, B and Chen, J and Brunke, S and Vazquez-Uribe, R and Santhaman, R and Meyer, AC and de Oliveira Lino, FS and Chan, KF and Loos, D and Imamovic, L and Tsang, CC and Lam, RP and Sridhar, S and Kang, K and Hube, B and Woo, PC and Sommer, MOA and Panagiotou, G},
title = {Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {133},
pmid = {32919472},
issn = {2049-2618},
mesh = {Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/*pharmacology ; Bacteria/*drug effects/genetics ; Fungi/*drug effects/genetics ; Gastrointestinal Microbiome/*drug effects/genetics ; Humans ; Middle Aged ; Symbiosis/*drug effects ; Time Factors ; Young Adult ; },
abstract = {BACKGROUND: Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over 3 months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing.

RESULTS: While the bacterial community recovered mostly over 3 months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared 3 months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrated in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate.

CONCLUSIONS: We demonstrated that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition. Video abstract.},
}

Adolescent
Adult
Aged
Anti-Bacterial Agents/*pharmacology
Bacteria/*drug effects/genetics
Fungi/*drug effects/genetics
Gastrointestinal Microbiome/*drug effects/genetics
Humans
Middle Aged
Symbiosis/*drug effects
Time Factors
Young Adult

@article {pmid32917289,
year = {2020},
author = {Leonard, MM and Karathia, H and Pujolassos, M and Troisi, J and Valitutti, F and Subramanian, P and Camhi, S and Kenyon, V and Colucci, A and Serena, G and Cucchiara, S and Montuori, M and Malamisura, B and Francavilla, R and Elli, L and Fanelli, B and Colwell, R and Hasan, N and Zomorrodi, AR and Fasano, A and , },
title = {Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {130},
pmid = {32917289},
issn = {2049-2618},
support = {R01 DK104344/DK/NIDDK NIH HHS/United States ; K23 DK122127/DK/NIDDK NIH HHS/United States ; F32 DK109620/DK/NIDDK NIH HHS/United States ; P30 DK040561/DK/NIDDK NIH HHS/United States ; },
mesh = {Bacteroides/genetics/isolation & purification ; Celiac Disease/*genetics/*microbiology ; Cesarean Section ; Cross-Sectional Studies ; *Environment ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Longitudinal Studies ; Male ; *Metabolomics ; *Metagenomics ; Methane/metabolism ; Pregnancy ; Prospective Studies ; Risk Factors ; Thioctic Acid/metabolism ; },
abstract = {BACKGROUND: Celiac disease (CD) is an autoimmune digestive disorder that occurs in genetically susceptible individuals in response to ingesting gluten, a protein found in wheat, rye, and barley. Research shows that genetic predisposition and exposure to gluten are necessary but not sufficient to trigger the development of CD. This suggests that exposure to other environmental stimuli early in life, e.g., cesarean section delivery and exposure to antibiotics or formula feeding, may also play a key role in CD pathogenesis through yet unknown mechanisms. Here, we use multi-omics analysis to investigate how genetic and early environmental risk factors alter the development of the gut microbiota in infants at risk of CD.

RESULTS: Toward this end, we selected 31 infants from a large-scale prospective birth cohort study of infants with a first-degree relative with CD. We then performed rigorous multivariate association, cross-sectional, and longitudinal analyses using metagenomic and metabolomic data collected at birth, 3 months and 6 months of age to explore the impact of genetic predisposition and environmental risk factors on the gut microbiota composition, function, and metabolome prior to the introduction of trigger (gluten). These analyses revealed several microbial species, functional pathways, and metabolites that are associated with each genetic and environmental risk factor or that are differentially abundant between environmentally exposed and non-exposed infants or between time points. Among our significant findings, we found that cesarean section delivery is associated with a decreased abundance of Bacteroides vulgatus and Bacteroides dorei and of folate biosynthesis pathway and with an increased abundance of hydroxyphenylacetic acid, alterations that are implicated in immune system dysfunction and inflammatory conditions. Additionally, longitudinal analysis revealed that, in infants not exposed to any environmental risk factor, the abundances of Bacteroides uniformis and of metabolite 3-3-hydroxyphenylproprionic acid increase over time, while those for lipoic acid and methane metabolism pathways decrease, patterns that are linked to beneficial immunomodulatory and anti-inflammatory effects.

CONCLUSIONS: Overall, our study provides unprecedented insights into major taxonomic and functional shifts in the developing gut microbiota of infants at risk of CD linking genetic and environmental risk factors to detrimental immunomodulatory and inflammatory effects. Video Abstract.},
}

Bacteroides/genetics/isolation & purification
Celiac Disease/*genetics/*microbiology
Cesarean Section
Cross-Sectional Studies
*Environment
Female
*Gastrointestinal Microbiome/genetics
Humans
Infant
Infant, Newborn
Longitudinal Studies
Male
*Metabolomics
*Metagenomics
Methane/metabolism
Pregnancy
Prospective Studies
Risk Factors
Thioctic Acid/metabolism

@article {pmid32859275,
year = {2020},
author = {Lu, J and Salzberg, SL},
title = {Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {124},
pmid = {32859275},
issn = {2049-2618},
support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; },
mesh = {Bacteria/*genetics/*isolation & purification ; Humans ; Metagenome/*genetics ; *Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; *Software ; Time Factors ; },
abstract = {BACKGROUND: For decades, 16S ribosomal RNA sequencing has been the primary means for identifying the bacterial species present in a sample with unknown composition. One of the most widely used tools for this purpose today is the QIIME (Quantitative Insights Into Microbial Ecology) package. Recent results have shown that the newest release, QIIME 2, has higher accuracy than QIIME, MAPseq, and mothur when classifying bacterial genera from simulated human gut, ocean, and soil metagenomes, although QIIME 2 also proved to be the most computationally expensive. Kraken, first released in 2014, has been shown to provide exceptionally fast and accurate classification for shotgun metagenomics sequencing projects. Bracken, released in 2016, then provided users with the ability to accurately estimate species or genus relative abundances using Kraken classification results. Kraken 2, which matches the accuracy and speed of Kraken 1, now supports 16S rRNA databases, allowing for direct comparisons to QIIME and similar systems.

METHODS: For a comprehensive assessment of each tool, we compare the computational resources and speed of QIIME 2's q2-feature-classifier, Kraken 2, and Bracken in generating the three main 16S rRNA databases: Greengenes, SILVA, and RDP. For an evaluation of accuracy, we evaluated each tool using the same simulated 16S rRNA reads from human gut, ocean, and soil metagenomes that were previously used to compare QIIME, MAPseq, mothur, and QIIME 2. We evaluated accuracy based on the accuracy of the final genera read counts assigned by each tool. Finally, as Kraken 2 is the only tool providing per-read taxonomic assignments, we evaluate the sensitivity and precision of Kraken 2's per-read classifications.

RESULTS: For both the Greengenes and SILVA database, Kraken 2 and Bracken are up to 100 times faster at database generation. For classification, using the same data as previous studies, Kraken 2 and Bracken are up to 300 times faster, use 100x less RAM, and generate results that more accurate at 16S rRNA profiling than QIIME 2's q2-feature-classifier.

CONCLUSION: Kraken 2 and Bracken provide a very fast, efficient, and accurate solution for 16S rRNA metataxonomic data analysis. Video Abstract.},
}

Bacteria/*genetics/*isolation & purification
Humans
Metagenome/*genetics
*Metagenomics
Microbiota/*genetics
RNA, Ribosomal, 16S/*genetics
*Software
Time Factors

@article {pmid32247457,
year = {2020},
author = {Zhao, CC and Eun, JB},
title = {Shotgun metagenomics approach reveals the bacterial community and metabolic pathways in commercial hongeo product, a traditional Korean fermented skate product.},
journal = {Food research international (Ottawa, Ont.)},
volume = {131},
number = {},
pages = {109030},
doi = {10.1016/j.foodres.2020.109030},
pmid = {32247457},
issn = {1873-7145},
mesh = {Ammonia/metabolism ; Animals ; Bacteria/*classification/genetics/*metabolism ; Fermentation ; Fermented Foods and Beverages/*microbiology ; Lactobacillales/metabolism ; *Metabolic Networks and Pathways ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; Republic of Korea ; Seafood/*microbiology ; *Skates, Fish ; },
abstract = {The aim of this study was to investigate the microbial diversity and microbial metabolic pathways using a metagenomic approach in commercial hongeo samples collected from five different fish processing plants. Community comparison analysis indicated that hongeo samples from different fish processing plants have a similar microbial structure at genus level, but the relative abundance of these genera showed a significant difference among different hongeo samples. Four bacterial genera including Psychrobacter, Pseudomonas, Clostridium, and Oblitimonas were detected in all hongeo samples with a high relative abundance, which associated with the nitrogen compound accumulation and ammonia flavor formation in hongeo samples. In addition, some alkaliphilic marine lactic acid bacteria (LAB) belonging to the genera Marinilactibacillus and Jeotgalibaca were detected in hongeo samples, indicating that this product might be a useful source for finding novel bacteria and possibly marine LAB. Through functional profiling analysis, it was found that hongeo samples had higher bacterial gene content related to amino acid metabolism, followed by carbohydrate metabolism and inorganic ion metabolism. The results of this study provide an important information for understanding the mechanism of quality characteristics and ammonia flavor formation in hongeo products.},
}

Ammonia/metabolism
Animals
Bacteria/*classification/genetics/*metabolism
Fermentation
Fermented Foods and Beverages/*microbiology
Lactobacillales/metabolism
*Metabolic Networks and Pathways
Metagenomics/*methods
Microbiota/genetics
Phylogeny
Republic of Korea
Seafood/*microbiology
*Skates, Fish

@article {pmid32159510,
year = {2020},
author = {Ghosh, TS and Das, M and Jeffery, IB and O'Toole, PW},
title = {Adjusting for age improves identification of gut microbiome alterations in multiple diseases.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {32159510},
issn = {2050-084X},
support = {APC/SFI/12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; 13/SIRG/2128/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Adult ; Age Factors ; Aged ; Aged, 80 and over ; Computational Biology ; Data Interpretation, Statistical ; *Disease Susceptibility ; *Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Microbiota ; Middle Aged ; Reproducibility of Results ; Young Adult ; },
abstract = {Interaction between disease-microbiome associations and ageing has not been explored in detail. Here, using age/region-matched sub-sets, we analysed the gut microbiome differences across five major diseases in a multi-cohort dataset constituting more than 2500 individuals from 20 to 89 years old. We show that disease-microbiome associations display specific age-centric trends. Ageing-associated microbiome alterations towards a disease-like configuration occur in colorectal cancer patients, thereby masking disease signatures. We identified a microbiome disease response shared across multiple diseases in elderly subjects that is distinct from that in young/middle-aged individuals, but also a novel set of taxa consistently gained in disease across all age groups. A subset of these taxa was associated with increased frailty in subjects from the ELDERMET cohort. The relevant taxa differentially encode specific functions that are known to have disease associations.},
}

Adult
Age Factors
Aged
Aged, 80 and over
Computational Biology
Data Interpretation, Statistical
*Disease Susceptibility
*Dysbiosis
Female
*Gastrointestinal Microbiome
Humans
Male
Metagenome
Metagenomics/methods
Microbiota
Middle Aged
Reproducibility of Results
Young Adult

@article {pmid33512248,
year = {2021},
author = {Shaffer, JP and Marotz, C and Belda-Ferre, P and Martino, C and Wandro, S and Estaki, M and Salido, RA and Carpenter, CS and Zaramela, LS and Minich, JJ and Bryant, M and Sanders, K and Fraraccio, S and Ackermann, G and Humphrey, G and Swafford, AD and Miller-Montgomery, S and Knight, R},
title = {A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities.},
journal = {BioTechniques},
volume = {70},
number = {3},
pages = {149-159},
doi = {10.2144/btn-2020-0153},
pmid = {33512248},
issn = {1940-9818},
support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; W81XWH-17-1-0589//DOD/ ; U01 AI124316/AI/NIAID NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; 2019-67013-29137//USDA-NIFA/ ; GI18518//Defense Advanced Research Projects Agency/ ; R01 HL134887/HL/NHLBI NIH HHS/United States ; 5K12GM068524-17//NIH-SD-IRACDA/ ; 675191//Crohn's and Colitis Foundation of America/ ; RF1 AG058942/AG/NIA NIH HHS/United States ; R01 DK102932/DK/NIDDK NIH HHS/United States ; //NSF/CAICE/ ; 1RF1-AG058942-01,R01DK102932,R01HL134887,R01HL140976,U01AI124316,U19AG063744/GF/NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Biodiversity ; Cats ; Chemical Fractionation/methods ; DNA, Viral/*isolation & purification ; Feces/microbiology/virology ; Female ; Fermented Foods and Beverages/microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Limit of Detection ; Male ; Metagenomics/methods ; Mice ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*isolation & purification ; SARS-CoV-2/*genetics ; Saliva/microbiology/virology ; Skin/microbiology/virology ; },
abstract = {One goal of microbial ecology researchers is to capture the maximum amount of information from all organisms in a sample. The recent COVID-19 pandemic, caused by the RNA virus SARS-CoV-2, has highlighted a gap in traditional DNA-based protocols, including the high-throughput methods the authors previously established as field standards. To enable simultaneous SARS-CoV-2 and microbial community profiling, the authors compared the relative performance of two total nucleic acid extraction protocols with the authors' previously benchmarked protocol. The authors included a diverse panel of environmental and host-associated sample types, including body sites commonly swabbed for COVID-19 testing. Here the authors present results comparing the cost, processing time, DNA and RNA yield, microbial community composition, limit of detection and well-to-well contamination between these protocols.},
}

Animals
Biodiversity
Cats
Chemical Fractionation/methods
DNA, Viral/*isolation & purification
Feces/microbiology/virology
Female
Fermented Foods and Beverages/microbiology
High-Throughput Nucleotide Sequencing/*methods
Humans
Limit of Detection
Male
Metagenomics/methods
Mice
Microbiota/*genetics
RNA, Ribosomal, 16S/*isolation & purification
SARS-CoV-2/*genetics
Saliva/microbiology/virology
Skin/microbiology/virology

@article {pmid33231748,
year = {2021},
author = {Noor, SO and Al-Zahrani, DA and Hussein, RM and Baeshen, MN and Moussa, TAA and Abo-Aba, SM and Al-Hejin, AM and Baeshen, NA and Huelsenbeck, JP},
title = {Assessment of fungal diversity in soil rhizosphere associated with Rhazya stricta and some desert plants using metagenomics.},
journal = {Archives of microbiology},
volume = {203},
number = {3},
pages = {1211-1219},
pmid = {33231748},
issn = {1432-072X},
support = {HiCi 1-363-1434H//King Abdulaziz University/ ; },
mesh = {*Biodiversity ; Desert Climate ; Fungi/classification/*genetics ; *Metagenomics ; Mycobiome/*genetics ; Phylogeny ; Plant Roots/microbiology ; Plants/*microbiology ; *Rhizosphere ; *Soil Microbiology ; },
abstract = {This study aimed to compare the fungal rhizosphere communities of Rhazya stricta, Enneapogon desvauxii, Citrullus colocynthis, Senna italica, and Zygophyllum simplex, and the gut mycobiota of Poekilocerus bufonius (Orthoptera, Pyrgomorphidae, "Usherhopper"). A total of 164,485 fungal reads were observed from the five plant rhizospheres and Usherhopper gut. The highest reads were in S. italica rhizosphere (29,883 reads). Species richness in the P. bufonius gut was the highest among the six samples. Ascomycota was dominant in all samples, with the highest reads in E. desvauxii (26,734 reads) rhizosphere. Sordariomycetes and Dothideomycetes were the dominant classes detected with the highest abundance in C. colocynthis and E. desvauxii rhizospheres. Aspergillus and Ceratobasidium were the most abundant genera in the R. stricta rhizosphere, Fusarium and Penicillium in the E. desvauxii rhizosphere and P. bufonius gut, Ceratobasidium and Myrothecium in the C. colocynthis rhizosphere, Aspergillus and Fusarium in the S. italica rhizosphere, and Cochliobolus in the Z. simplex rhizosphere. Aspergillus terreus was the most abundant species in the R. stricta and S. italica rhizospheres, Fusarium sp. in E. desvauxii rhizosphere, Ceratobasidium sp. in C. colocynthis rhizosphere, Cochliobolus sp. in Z. simplex rhizosphere, and Penicillium sp. in P. bufonius gut. The phylogenetic results revealed the unclassified species were related closely to Ascomycota and the species in E. desvauxii, S. italica and Z. simplex rhizospheres were closely related, where the species in the P. bufonius gut, were closely related to the species in the R. stricta, and C. colocynthis rhizospheres.},
}

*Biodiversity
Desert Climate
Fungi/classification/*genetics
*Metagenomics
Mycobiome/*genetics
Phylogeny
Plant Roots/microbiology
Plants/*microbiology
*Rhizosphere
*Soil Microbiology

@article {pmid33127812,
year = {2021},
author = {Díaz-García, L and Huang, S and Spröer, C and Sierra-Ramírez, R and Bunk, B and Overmann, J and Jiménez, DJ},
title = {Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {2},
pages = {},
pmid = {33127812},
issn = {1098-5336},
mesh = {Bacteria/genetics/metabolism ; Forests ; Genome, Bacterial ; Lignin/*metabolism ; Metagenomics ; *Microbial Consortia ; RNA, Ribosomal, 16S ; Soil Microbiology ; },
abstract = {The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid medium with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae, and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (>99%) within the MELMC, indicating that these are the key players in degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling, and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secretes an array of endoenzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose, and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition along with an analysis of carbohydrate-active enzymes of 20 bacterial genomes support the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp.IMPORTANCE The significance of our study mainly lies in the development of a combined top-down enrichment strategy (i.e., dilution to stimulation coupled to dilution to extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive the effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e., the release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.},
}

Bacteria/genetics/metabolism
Forests
Genome, Bacterial
Lignin/*metabolism
Metagenomics
*Microbial Consortia
RNA, Ribosomal, 16S
Soil Microbiology

@article {pmid32867153,
year = {2020},
author = {Fart, F and Rajan, SK and Wall, R and Rangel, I and Ganda-Mall, JP and Tingö, L and Brummer, RJ and Repsilber, D and Schoultz, I and Lindqvist, CM},
title = {Differences in Gut Microbiome Composition between Senior Orienteering Athletes and Community-Dwelling Older Adults.},
journal = {Nutrients},
volume = {12},
number = {9},
pages = {},
pmid = {32867153},
issn = {2072-6643},
support = {F0514//Bo Rydins Stiftelse för Vetenskaplig Forskning/ ; 20110225//Stiftelsen för Kunskaps- och Kompetensutveckling/ ; },
mesh = {Aged ; Athletes/*statistics & numerical data ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Geriatric Assessment/*methods/*statistics & numerical data ; Humans ; Independent Living ; Male ; },
abstract = {BACKGROUND: Gastrointestinal (GI) health is an important aspect of general health. Gastrointestinal symptoms are of specific importance for the elderly, an increasing group globally. Hence, promoting the elderly's health and especially gastrointestinal health is important. Gut microbiota can influence gastrointestinal health by modulation of the immune system and the gut-brain axis. Diverse gut microbiota have been shown to be beneficial; however, for the elderly, the gut microbiota is often less diverse. Nutrition and physical activity, in particular, are two components that have been suggested to influence composition or diversity.

MATERIALS AND METHODS: In this study, we compared gut microbiota between two groups of elderly individuals: community-dwelling older adults and physically active senior orienteering athletes, where the latter group has less gastrointestinal symptoms and a reported better well-being. With this approach, we explored if certain gut microbiota were related to healthy ageing. The participant data and faecal samples were collected from these two groups and the microbiota was whole-genome sequenced and taxonomically classified with MetaPhlAn.

RESULTS: The physically active senior orienteers had a more homogeneous microbiota within the group and a higher abundance of Faecalibacterium prausnitzii compared to the community-dwelling older adults. Faecalibacterium prausnitzii has previously shown to have beneficial properties. Senior orienteers also had a lower abundance of Parasutterella excrementihominis and Bilophila unclassified, which have been associated with impaired GI health. We could not observe any difference between the groups in terms of Shannon diversity index. Interestingly, a subgroup of community-dwelling older adults showed an atypical microbiota profile as well as the parameters for gastrointestinal symptoms and well-being closer to senior orienteers.

CONCLUSIONS: Our results suggest specific composition characteristics of healthy microbiota in the elderly, and show that certain components of nutrition as well as psychological distress are not as tightly connected with composition or diversity variation in faecal microbiota samples.},
}

Aged
Athletes/*statistics & numerical data
Feces/microbiology
Female
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology
Geriatric Assessment/*methods/*statistics & numerical data
Humans
Independent Living
Male

@article {pmid32522544,
year = {2020},
author = {Xu, M and Mo, X and Huang, H and Chen, X and Liu, H and Peng, Z and Chen, L and Rong, S and Yang, W and Xu, S and Liu, L},
title = {Yeast β-glucan alleviates cognitive deficit by regulating gut microbiota and metabolites in Aβ1-42-induced AD-like mice.},
journal = {International journal of biological macromolecules},
volume = {161},
number = {},
pages = {258-270},
doi = {10.1016/j.ijbiomac.2020.05.180},
pmid = {32522544},
issn = {1879-0003},
mesh = {Alzheimer Disease/etiology/metabolism/pathology ; Amyloid beta-Peptides/*adverse effects ; Animals ; Biomarkers ; Cognition/*drug effects ; Disease Models, Animal ; Fungal Polysaccharides/*chemistry/pharmacology ; Gastrointestinal Microbiome/*drug effects ; Hippocampus/metabolism ; Insulin/metabolism ; Male ; Metagenome ; Metagenomics ; Mice ; Peptide Fragments/*adverse effects ; Prebiotics ; RNA, Ribosomal, 16S ; beta-Glucans/*chemistry/pharmacology ; },
abstract = {Alzheimer's disease (AD) is a neurodegenerative disease that remarkably imposes a huge global public health burden. Yeast β-glucans have been incorporated in functional foods and used in prophylactic applications owing to their biological effects. However, few studies had investigated the effects of yeast β-glucans on neurodegenerative diseases. Here, gut microbiota and metabolites SCFAs were analyzed through high-throughput 16S rRNA gene sequencing and GC-MS, respectively. Results indicated that yeast β-glucans could prominently shape the intestinal flora and produce SCFAs. Aβ1-42-induced AD mice treated with small-molecular yeast β-glucan (S-β-Glu) or macro-molecular yeast β-glucan (M-β-Glu) exhibited evident alterations of the composition of the gut microbiota, especially in some beneficial bacteria and inflammatory-related bacteria such as Lactobacillus, Bifidobacterium, Desulfovibrio, Oscillibacter, Mucispirillum, Alistipes, Anaerotruncus, and Rikenella. M-β-Glu regulated gut microbiota act as prebiotics better than S-β-Glu. Correlation analysis demonstrated the key microbiota closely associated with AD-related pathologies and cognition. Moreover, M-β-Glu and S-β-Glu ameliorated neuroinflammation and brain insulin resistance (IR), which played a central role in the process of AD pathology. This study broadened the underlying applications of yeast β-glucans as a novel dietary supplementation to prevent early-stage pathologies associated with AD by regulating gut microbiota and the potential mechanism might be ameliorating brain IR.},
}

Alzheimer Disease/etiology/metabolism/pathology
Amyloid beta-Peptides/*adverse effects
Animals
Biomarkers
Cognition/*drug effects
Disease Models, Animal
Fungal Polysaccharides/*chemistry/pharmacology
Gastrointestinal Microbiome/*drug effects
Hippocampus/metabolism
Insulin/metabolism
Male
Metagenome
Metagenomics
Mice
Peptide Fragments/*adverse effects
Prebiotics
RNA, Ribosomal, 16S
beta-Glucans/*chemistry/pharmacology

@article {pmid33218999,
year = {2021},
author = {Zheng, J and Reed, E and Ramachandran, P and Ottesen, A and Brown, EW and Wang, Y},
title = {Taxonomic and Functional Shifts in the Sprout Spent Irrigation Water Microbiome in Response to Salmonella Contamination of Alfalfa Seeds.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {3},
pages = {},
pmid = {33218999},
issn = {1098-5336},
mesh = {Agricultural Irrigation ; Genes, Bacterial ; Medicago sativa/*microbiology ; Metagenomics ; Microbial Interactions ; Microbiota ; Salmonella enterica/*genetics ; Seedlings/*microbiology ; Waste Water/microbiology ; },
abstract = {Despite recent advances in Salmonella-sprout research, little is known about the relationship between Salmonella and the sprout microbiome during sprouting. Sprout spent irrigation water (SSIW) provides an informative representation of the total microbiome of this primarily aquaponic crop. This study was designed to characterize the function and taxonomy of the most actively transcribed genes in SSIW from Salmonella enterica serovar Cubana-contaminated alfalfa seeds throughout the sprouting process. Genomic DNA and total RNA from SSIW was collected at regular intervals and sequenced using Illumina MiSeq and NextSeq platforms. Nucleic acid data were annotated using four different pipelines. Both metagenomic and metatranscriptomic analyses revealed a diverse and highly dynamic SSIW microbiome. A "core" SSIW microbiome comprised Klebsiella, Enterobacter, Pantoea, and Cronobacter The impact, however, of Salmonella contamination on alfalfa seeds influenced SSIW microbial community dynamics not only structurally but also functionally. Changes in genes associated with metabolism, genetic information processing, environmental information processing, and cellular processes were abundant and time dependent. At time points of 24 h, 48 h, and 96 h, totals of 541, 723, and 424 S Cubana genes, respectively, were transcribed at either higher or lower levels than at 0 h in SSIW during sprouting. An array of S Cubana genes (107) were induced at all three time points, including genes involved in biofilm formation and modulation, stress responses, and virulence and tolerance to antimicrobials. Taken together, these findings expand our understanding of the effect of Salmonella seed contamination on the sprout crop microbiome and metabolome.IMPORTANCE Interactions of human enteric pathogens like Salmonella with plants and plant microbiomes remain to be elucidated. The rapid development of next-generation sequencing technologies provides powerful tools enabling investigation of such interactions from broader and deeper perspectives. Using metagenomic and metatranscriptomic approaches, this study identified not only changes in microbiome structure of SSIW associated with sprouting but also changes in the gene expression patterns related to the sprouting process in response to Salmonella contamination of alfalfa seeds. This study advances our knowledge on Salmonella-plant (i.e., sprout) interaction.},
}

Agricultural Irrigation
Genes, Bacterial
Medicago sativa/*microbiology
Metagenomics
Microbial Interactions
Microbiota
Salmonella enterica/*genetics
Seedlings/*microbiology
Waste Water/microbiology

@article {pmid32927823,
year = {2020},
author = {Bose, D and Saha, P and Mondal, A and Fanelli, B and Seth, RK and Janulewicz, P and Sullivan, K and Lasley, S and Horner, R and Colwell, RR and Shetty, AK and Klimas, N and Chatterjee, S},
title = {Obesity Worsens Gulf War Illness Symptom Persistence Pathology by Linking Altered Gut Microbiome Species to Long-Term Gastrointestinal, Hepatic, and Neuronal Inflammation in a Mouse Model.},
journal = {Nutrients},
volume = {12},
number = {9},
pages = {},
pmid = {32927823},
issn = {2072-6643},
support = {W81XWH1810374//U.S. Department of Defense/ ; W81XWH-13-2-0072//U.S. Department of Defense/ ; I01 CX001923-01//U.S. Department of Veterans Affairs/ ; },
mesh = {Animals ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Dysbiosis/complications/microbiology/pathology ; Gastroenteritis/complications/microbiology/pathology ; Gastrointestinal Microbiome/*physiology ; Gastrointestinal Tract/microbiology/pathology ; Hepatitis/complications/microbiology/pathology ; Inflammation ; Liver/microbiology/pathology ; Mice ; Neuritis/complications/microbiology/pathology ; Neurons/microbiology/pathology ; Obesity/complications/*microbiology/*pathology ; Persian Gulf Syndrome/complications/*microbiology/*pathology ; },
abstract = {Persistence of Gulf War illness (GWI) pathology among deployed veterans is a clinical challenge even after almost three decades. Recent studies show a higher prevalence of obesity and metabolic disturbances among Gulf War veterans primarily due to the existence of post-traumatic stress disorder (PTSD), chronic fatigue, sedentary lifestyle, and consumption of a high-carbohydrate/high-fat diet. We test the hypothesis that obesity from a Western-style diet alters host gut microbial species and worsens gastrointestinal and neuroinflammatory symptom persistence. We used a 5 month Western diet feeding in mice that received prior Gulf War (GW) chemical exposure to mimic the home phase obese phenotype of the deployed GW veterans. The host microbial profile in the Western diet-fed GWI mice showed a significant decrease in butyrogenic and immune health-restoring bacteria. The altered microbiome was associated with increased levels of IL6 in the serum, Claudin-2, IL6, and IL1β in the distal intestine with concurrent inflammatory lesions in the liver and hyperinsulinemia. Microbial dysbiosis was also associated with frontal cortex levels of increased IL6 and IL1β, activated microglia, decreased levels of brain derived neurotrophic factor (BDNF), and higher accumulation of phosphorylated Tau, an indicator of neuroinflammation-led increased risk of cognitive deficiencies. Mechanistically, serum from Western diet-fed mice with GWI significantly increased microglial activation in transformed microglial cells, increased tyrosyl radicals, and secreted IL6. Collectively, the results suggest that an existing obese phenotype in GWI worsens persistent gastrointestinal and neuronal inflammation, which may contribute to poor outcomes in restoring cognitive function and resolving fatigue, leading to the deterioration of quality of life.},
}

Animals
Diet, High-Fat/adverse effects
Disease Models, Animal
Dysbiosis/complications/microbiology/pathology
Gastroenteritis/complications/microbiology/pathology
Gastrointestinal Microbiome/*physiology
Gastrointestinal Tract/microbiology/pathology
Hepatitis/complications/microbiology/pathology
Inflammation
Liver/microbiology/pathology
Mice
Neuritis/complications/microbiology/pathology
Neurons/microbiology/pathology
Obesity/complications/*microbiology/*pathology
Persian Gulf Syndrome/complications/*microbiology/*pathology

@article {pmid32296425,
year = {2020},
author = {Escobar, MF and Hincapie, MA and Barona, JS},
title = {Immunological Role of the Maternal Uterine Microbiota in Postpartum Hemorrhage.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {504},
pmid = {32296425},
issn = {1664-3224},
mesh = {Animals ; Dysbiosis/*immunology ; Female ; Humans ; Microbiota/*immunology ; Postpartum Hemorrhage/*immunology ; Pregnancy ; Uterus/*immunology/*microbiology ; },
abstract = {Recent metagenomics and microbiology studies have identified microorganisms that are typical of the fetoplacental unit. Considering this emerging evidence, the placenta, uterus, and the amniotic cavity are not sterile and not immune privileged. However, there is evidence for a beneficial interaction between active maternal immune system and the presence of commensal pathogens, which lead to an immune-tolerant state, thereby preventing fetal rejection. Multiple conditions associated with the loss of the normal flora are described (dysbiosis), which could result in perinatal and puerperal adverse events, including, directly or indirectly, postpartum hemorrhage. Altered flora when associated with a severe proinflammatory state and combined with patient's genetic and environmental factors confers a high-risk adverse outcome. Better understanding of the adverse role of dysbiosis in pregnancy outcome will improve maternal outcome.},
}

Animals
Dysbiosis/*immunology
Female
Humans
Microbiota/*immunology
Postpartum Hemorrhage/*immunology
Pregnancy
Uterus/*immunology/*microbiology

@article {pmid31230147,
year = {2020},
author = {Kan, J and Cheng, J and Xu, L and Hood, M and Zhong, D and Cheng, M and Liu, Y and Chen, L and Du, J},
title = {The combination of wheat peptides and fucoidan protects against chronic superficial gastritis and alters gut microbiota: a double-blinded, placebo-controlled study.},
journal = {European journal of nutrition},
volume = {59},
number = {4},
pages = {1655-1666},
doi = {10.1007/s00394-019-02020-6},
pmid = {31230147},
issn = {1436-6215},
mesh = {Adult ; Anti-Ulcer Agents/*pharmacology ; China ; Chronic Disease ; Double-Blind Method ; Feces/microbiology ; Female ; Gastric Mucosa/drug effects/microbiology ; Gastritis/*drug therapy ; Gastrointestinal Microbiome/*drug effects ; Humans ; Male ; Peptides/*pharmacology ; Polysaccharides/*pharmacology ; Surveys and Questionnaires ; *Triticum ; },
abstract = {PURPOSE: Chronic gastritis is observed in almost half world population. Traditional medications against chronic gastritis might produce adverse effects, so alternative nutritional strategies are needed to prevent the aggravation of gastric mucosal damage. The aim of this study is to evaluate the protective effect of the combination of wheat peptides and fucoidan (WPF) on adults diagnosed with chronic superficial gastritis in a randomized, double-blind, placebo-controlled clinical trial.

METHODS: Participants were randomized to receive WPF (N = 53) or placebo (N = 53) once daily for 45 days. Pathological grading of gastric mucosal damage was scored using gastroscopy. Fecal samples were collected for the determination of calprotectin, short chain fatty acids (SCFA) levels and metagenomics analysis. Questionnaires for self-reported gastrointestinal discomforts, life quality and food frequency were collected throughout the study.

RESULTS: WPF intervention reduced gastric mucosal damage in 70% subjects (P < 0.001). Significantly less stomach pain (P < 0.001), belching (P = 0.028), bloating (P < 0.001), acid reflux (P < 0.001), loss of appetite (P = 0.021), increased food intake (P = 0.020), and promoted life quality (P = 0.014) were reported in the WPF group. WPF intervention significantly decreased fecal calprotectin level (P = 0.003) while slightly increased fecal SCFAs level (P = 0.092). In addition, we found altered microbiota composition post-intervention with increased Bifidobacterium pseudocatenulatum (P = 0.032), Eubacterium siraeum (P = 0.036), Bacteroides intestinalis (P = 0.024) and decreased Prevotella copri (P = 0.055).

CONCLUSIONS: WPF intervention could be utilized as a nutritional alternative to mitigate the progression of chronic gastritis. Furthermore, WPF played an important role in altering gut microbial profile and SCFA production, which might benefit the lower gastrointestinal tract.},
}

Adult
Anti-Ulcer Agents/*pharmacology
China
Chronic Disease
Double-Blind Method
Feces/microbiology
Female
Gastric Mucosa/drug effects/microbiology
Gastritis/*drug therapy
Gastrointestinal Microbiome/*drug effects
Humans
Male
Peptides/*pharmacology
Polysaccharides/*pharmacology
Surveys and Questionnaires
*Triticum

@article {pmid33161546,
year = {2021},
author = {Yeoh, YK},
title = {Removing Host-derived DNA Sequences from Microbial Metagenomes via Mapping to Reference Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2232},
number = {},
pages = {147-153},
doi = {10.1007/978-1-0716-1040-4_13},
pmid = {33161546},
issn = {1940-6029},
mesh = {Animals ; Arthropods/microbiology ; Base Sequence/*genetics ; Eukaryota/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota ; Plants/microbiology ; Sequence Analysis, DNA ; Soil Microbiology ; },
abstract = {DNA sequencing has become a common tool in environmental microbial ecology, facilitating characterization of microbial populations as well as complex microbial communities by circumventing culture bottlenecks. However, certain samples especially from host-associated environments (rhizosphere, human tissue) or complex communities (soils) can contain a high degree of DNA sequences derived from hosts (plants, human) or other organisms of non-interest (arthropods, unicellular eukaryotes). This chapter presents a simple in silico method to remove contaminating sequences in metagenomes based on aligning sequences to reference genomes of the target organism.},
}

Animals
Arthropods/microbiology
Base Sequence/*genetics
Eukaryota/genetics
High-Throughput Nucleotide Sequencing/*methods
Humans
Metagenome/*genetics
Metagenomics/*methods
Microbiota
Plants/microbiology
Sequence Analysis, DNA
Soil Microbiology

@article {pmid32755703,
year = {2020},
author = {Zhang, X and Zhao, S and He, Y and Zheng, N and Yan, X and Wang, J},
title = {Substitution of residues in UreG to investigate UreE interactions and nickel binding in a predominant urease gene cluster from the ruminal metagenome.},
journal = {International journal of biological macromolecules},
volume = {161},
number = {},
pages = {1591-1601},
doi = {10.1016/j.ijbiomac.2020.07.260},
pmid = {32755703},
issn = {1879-0003},
mesh = {Amino Acid Sequence ; Animals ; Binding Sites ; Gene Expression ; *Metagenome ; *Metagenomics/methods ; *Microbiota ; *Multigene Family ; Nickel/*chemistry ; Phylogeny ; Protein Binding ; Recombinant Proteins ; Ruminants/*microbiology ; Urease/*chemistry/genetics ; },
abstract = {Microbial ureases catalyze the hydrolysis of urea to ammonia, and inhibition of these enzymes in rumen has the potential to improve urea utilization efficiency and reduce urinary nitrogen excretion. Urease activity is catalyzed by a protein complex encoded by a gene cluster, and its accessory proteins (especially UreE and UreG) play important roles in transferring nickel to the active site for urease maturation. In this study, a predominant urease gene cluster (5290 bp) from the ruminal microbial metagenome was identified. Isothermal titration calorimetry (ITC) and analytical ultracentrifugation (AUC) analyses showed that the reaction of identified UreE with UreG was endothermic, and was dominated by a hydrophobic interaction, in which each UreE dimer bound 2 M equivalents of UreG monomer to form a UreE2-2UreG complex. Mutagenesis analyses showed that the UreG residues Glu-23, Asp-41, Glu-46, Glu-66, Cys-70, His-72, Asp-78, and Asp-118 were involved in the GTPase activity of UreG. Furthermore, variants of Cys-70 and His-72 involved in CPH motif of UreG, as well as the nearby Glu-66 and Asp-78, not only prevented interactions with UreE, but also prevented nickel binding. These data provide additional information regarding UreG residues that may be targeted for the design of new urease inhibitors.},
}

Amino Acid Sequence
Animals
Binding Sites
Gene Expression
*Metagenome
*Metagenomics/methods
*Microbiota
*Multigene Family
Nickel/*chemistry
Phylogeny
Protein Binding
Recombinant Proteins
Ruminants/*microbiology
Urease/*chemistry/genetics

@article {pmid32477320,
year = {2020},
author = {Sharma, P and Rani, J and Chauhan, C and Kumari, S and Tevatiya, S and Das De, T and Savargaonkar, D and Pandey, KC and Dixit, R},
title = {Altered Gut Microbiota and Immunity Defines Plasmodium vivax Survival in Anopheles stephensi.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {609},
pmid = {32477320},
issn = {1664-3224},
mesh = {Animals ; Anopheles/immunology/microbiology/*parasitology ; Gastrointestinal Microbiome/*physiology ; Plasmodium vivax/*growth & development ; RNA-Seq ; Symbiosis ; },
abstract = {Blood-feeding enriched gut-microbiota boosts mosquitoes' anti-Plasmodium immunity. Here, we ask how Plasmodium vivax alters gut-microbiota, anti-Plasmodial immunity, and impacts tripartite Plasmodium-mosquito-microbiota interactions in the gut lumen. We used a metagenomics and RNAseq strategy to address these questions. In naïve mosquitoes, Elizabethkingia meningitis and Pseudomonas spp. are the dominant bacteria and blood-feeding leads to a heightened detection of Elizabethkingia, Pseudomonas and Serratia 16S rRNA. A parallel RNAseq analysis of blood-fed midguts also shows the presence of Elizabethkingia-related transcripts. After, P. vivax infected blood-meal, however, we do not detect bacterial 16S rRNA until circa 36 h. Intriguingly, the transcriptional expression of a selected array of antimicrobial arsenal cecropins 1-2, defensin-1, and gambicin remained low during the first 36 h-a time frame when ookinetes/early oocysts invaded the gut. We conclude during the preinvasive phase, P. vivax outcompetes midgut-microbiota. This microbial suppression likely negates the impact of mosquito immunity which in turn may enhance the survival of P. vivax. Detection of sequences matching to mosquito-associated Wolbachia opens a new inquiry for its exploration as an agent for "paratransgenesis-based" mosquito control.},
}

Animals
Anopheles/immunology/microbiology/*parasitology
Gastrointestinal Microbiome/*physiology
Plasmodium vivax/*growth & development
RNA-Seq
Symbiosis

@article {pmid31600845,
year = {2020},
author = {Zeng, Y and Chen, S and Fu, Y and Wu, W and Chen, T and Chen, J and Yang, B and Ou, Q},
title = {Gut microbiota dysbiosis in patients with hepatitis B virus-induced chronic liver disease covering chronic hepatitis, liver cirrhosis and hepatocellular carcinoma.},
journal = {Journal of viral hepatitis},
volume = {27},
number = {2},
pages = {143-155},
doi = {10.1111/jvh.13216},
pmid = {31600845},
issn = {1365-2893},
mesh = {Adult ; Bacteria/classification ; Carcinoma, Hepatocellular/*virology ; Case-Control Studies ; Dysbiosis/etiology/*genetics ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatitis B virus/pathogenicity ; Hepatitis B, Chronic/*microbiology ; Humans ; Liver Cirrhosis/*virology ; Liver Neoplasms/*virology ; Male ; Metagenomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The information regarding the effect of hepatitis B virus (HBV) infection on gut microbiota and the relationship between gut microbiota dysbiosis and hepatitis B virus-induced chronic liver disease (HBVCLD) is limited. In this study, we aimed at characterizing the gut microbiota composition in the three different stages of hepatitis B virus-induced chronic liver disease patients and healthy individuals. Faecal samples and clinical data were collected from HBVCLD patients and healthy individuals. The 16S rDNA gene amplification products were sequenced. Bioinformatic analysis including alpha diversity and PICRUSt was performed. A total of 19 phyla, 43 classes, 72 orders, 126 families and 225 genera were detected. The beta-diversity showed a separate clustering of healthy controls and HBVCLD patients covering chronic hepatitis (CHB), liver cirrhosis (LC) and hepatocellular carcinoma (HCC); and gut microbiota of healthy controls was more consistent, whereas those of CHB, LC and HCC varied substantially. The abundance of Firmicutes was lower, and Bacteroidetes was higher in patients with CHB, LC and HCC than in healthy controls. Predicted metagenomics of microbial communities showed an increase in glycan biosynthesis and metabolism-related genes and lipid metabolism-related genes in HBVCLD than in healthy individuals. Our study suggested that HBVCLD is associated with gut dysbiosis, with characteristics including, a gain in potential bacteria and a loss in potential beneficial bacteria or genes. Further study of CHB, LC and HCC based on microbiota may provide a novel insight into the pathogenesis of HBVCLD as well as a novel treatment strategy.},
}

Adult
Bacteria/classification
Carcinoma, Hepatocellular/*virology
Case-Control Studies
Dysbiosis/etiology/*genetics
Feces/microbiology
Female
*Gastrointestinal Microbiome
Hepatitis B virus/pathogenicity
Hepatitis B, Chronic/*microbiology
Humans
Liver Cirrhosis/*virology
Liver Neoplasms/*virology
Male
Metagenomics
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid32746696,
year = {2021},
author = {Baker, BJ and Appler, KE and Gong, X},
title = {New Microbial Biodiversity in Marine Sediments.},
journal = {Annual review of marine science},
volume = {13},
number = {},
pages = {161-175},
doi = {10.1146/annurev-marine-032020-014552},
pmid = {32746696},
issn = {1941-0611},
mesh = {Archaea/*classification/genetics ; Bacteria/*classification/genetics ; Biodiversity ; Datasets as Topic ; Geologic Sediments/*microbiology ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; Seawater/*microbiology ; },
abstract = {Microbes in marine sediments represent a large portion of the biosphere, and resolving their ecology is crucial for understanding global ocean processes. Single-gene diversity surveys have revealed several uncultured lineages that are widespread in ocean sediments and whose ecological roles are unknown, and advancements in the computational analysis of increasingly large genomic data sets have made it possible to reconstruct individual genomes from complex microbial communities. Using these metagenomic approaches to characterize sediments is transforming our view of microbial communities on the ocean floor and the biodiversity of the planet. In recent years, marine sediments have been a prominent source of new lineages in the tree of life. The incorporation of these lineages into existing phylogenies has revealed that many belong to distinct phyla, including archaeal phyla that are advancing our understanding of the origins of cellular complexity and eukaryotes. Detailed comparisons of the metabolic potentials of these new lineages have made it clear that uncultured bacteria and archaea are capable of mediating key previously undescribed steps in carbon and nutrient cycling.},
}

Archaea/*classification/genetics
Bacteria/*classification/genetics
Biodiversity
Datasets as Topic
Geologic Sediments/*microbiology
*Metagenome
Metagenomics
Microbiota/*genetics
Phylogeny
Seawater/*microbiology

@article {pmid33597039,
year = {2021},
author = {Li, Z and Xia, J and Jiang, L and Tan, Y and An, Y and Zhu, X and Ruan, J and Chen, Z and Zhen, H and Ma, Y and Jie, Z and Xiao, L and Yang, H and Wang, J and Kristiansen, K and Xu, X and Jin, L and Nie, C and Krutmann, J and Liu, X and Wang, J},
title = {Characterization of the human skin resistome and identification of two microbiota cutotypes.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {47},
pmid = {33597039},
issn = {2049-2618},
mesh = {Adult ; Aged ; Anti-Bacterial Agents/pharmacology ; China/ethnology ; Drug Resistance, Microbial/drug effects/genetics ; Ethnic Groups ; Female ; Genes, Bacterial/drug effects ; Humans ; Male ; Metagenomics ; *Microbiota/drug effects/genetics ; Middle Aged ; Moraxella/drug effects/*genetics/*isolation & purification ; North America/ethnology ; Propionibacteriaceae/drug effects/*genetics/*isolation & purification ; Skin/*microbiology ; Staphylococcus/drug effects/genetics/isolation & purification ; Symbiosis ; Young Adult ; },
abstract = {BACKGROUND: The human skin microbiota is considered to be essential for skin homeostasis and barrier function. Comprehensive analyses of its function would substantially benefit from a catalog of reference genes derived from metagenomic sequencing. The existing catalog for the human skin microbiome is based on samples from limited individuals from a single cohort on reference genomes, which limits the coverage of global skin microbiome diversity.

RESULTS: In the present study, we have used shotgun metagenomics to newly sequence 822 skin samples from Han Chinese, which were subsequently combined with 538 previously sequenced North American samples to construct an integrated Human Skin Microbial Gene Catalog (iHSMGC). The iHSMGC comprised 10,930,638 genes with the detection of 4,879,024 new genes. Characterization of the human skin resistome based on iHSMGC confirmed that skin commensals, such as Staphylococcus spp, are an important reservoir of antibiotic resistance genes (ARGs). Further analyses of skin microbial ARGs detected microbe-specific and skin site-specific ARG signatures. Of note, the abundance of ARGs was significantly higher in Chinese than Americans, while multidrug-resistant bacteria ("superbugs") existed on the skin of both Americans and Chinese. A detailed analysis of microbial signatures identified Moraxella osloensis as a species specific for Chinese skin. Importantly, Moraxella osloensis proved to be a signature species for one of two robust patterns of microbial networks present on Chinese skin, with Cutibacterium acnes indicating the second one. Each of such "cutotypes" was associated with distinct patterns of data-driven marker genes, functional modules, and host skin properties. The two cutotypes markedly differed in functional modules related to their metabolic characteristics, indicating that host-dependent trophic chains might underlie their development.

CONCLUSIONS: The development of the iHSMGC will facilitate further studies on the human skin microbiome. In the present study, it was used to further characterize the human skin resistome. It also allowed to discover the existence of two cutotypes on the human skin. The latter finding will contribute to a better understanding of the interpersonal complexity of the skin microbiome. Video abstract.},
}

Adult
Aged
Anti-Bacterial Agents/pharmacology
China/ethnology
Drug Resistance, Microbial/drug effects/genetics
Ethnic Groups
Female
Genes, Bacterial/drug effects
Humans
Male
Metagenomics
*Microbiota/drug effects/genetics
Middle Aged
Moraxella/drug effects/*genetics/*isolation & purification
North America/ethnology
Propionibacteriaceae/drug effects/*genetics/*isolation & purification
Skin/*microbiology
Staphylococcus/drug effects/genetics/isolation & purification
Symbiosis
Young Adult

@article {pmid33347881,
year = {2021},
author = {Iliev, ID and Cadwell, K},
title = {Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases.},
journal = {Gastroenterology},
volume = {160},
number = {4},
pages = {1050-1066},
pmid = {33347881},
issn = {1528-0012},
support = {UL1 TR001445/TR/NCATS NIH HHS/United States ; P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK093668/DK/NIDDK NIH HHS/United States ; R01 HL125816/HL/NHLBI NIH HHS/United States ; R01 AI140754/AI/NIAID NIH HHS/United States ; R01 AI130945/AI/NIAID NIH HHS/United States ; R01 AI121244/AI/NIAID NIH HHS/United States ; R56 AI137157/AI/NIAID NIH HHS/United States ; R01 DK121977/DK/NIDDK NIH HHS/United States ; R21 AI146957/AI/NIAID NIH HHS/United States ; R01 DK113136/DK/NIDDK NIH HHS/United States ; R01 HL123340/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; COVID-19/complications ; Fecal Microbiota Transplantation ; Gastrointestinal Microbiome/*physiology ; Humans ; Immunity/*immunology ; Inflammatory Bowel Diseases/*etiology ; Lectins, C-Type/physiology ; Mycobiome/*physiology ; SARS-CoV-2 ; Th1 Cells/immunology ; Virome/*physiology ; },
abstract = {The intestinal microbiota comprises diverse fungal and viral components, in addition to bacteria. These microbes interact with the immune system and affect human physiology. Advances in metagenomics have associated inflammatory and autoimmune diseases with alterations in fungal and viral species in the gut. Studies of animal models have found that commensal fungi and viruses can activate host-protective immune pathways related to epithelial barrier integrity, but can also induce reactions that contribute to events associated with inflammatory bowel disease. Changes in our environment associated with modernization and the COVID-19 pandemic have exposed humans to new fungi and viruses, with unknown consequences. We review the lessons learned from studies of animal viruses and fungi commonly detected in the human gut and how these might affect health and intestinal disease.},
}

Animals
COVID-19/complications
Fecal Microbiota Transplantation
Gastrointestinal Microbiome/*physiology
Humans
Immunity/*immunology
Inflammatory Bowel Diseases/*etiology
Lectins, C-Type/physiology
Mycobiome/*physiology
SARS-CoV-2
Th1 Cells/immunology
Virome/*physiology

@article {pmid32578244,
year = {2020},
author = {Sun, Y and Fu, X and Li, Y and Yuan, Q and Ou, Z and Lindgren, T and Deng, Y and Norbäck, D},
title = {Shotgun metagenomics of dust microbiome from flight deck and cabin in civil aviation aircraft.},
journal = {Indoor air},
volume = {30},
number = {6},
pages = {1199-1212},
doi = {10.1111/ina.12707},
pmid = {32578244},
issn = {1600-0668},
mesh = {*Air Microbiology ; Air Pollution, Indoor ; *Aircraft ; Aviation ; Comamonadaceae ; Dust/*analysis ; Environmental Monitoring ; Floors and Floorcoverings ; Humans ; *Metagenomics ; Microbiota ; },
abstract = {Microbial exposure is related to the health of passengers on commercial aircraft, but no studies characterized the microbial composition at the species level and identified their ecological determinants. We collected vacuum dust from floor and seat surfaces in flight decks and cabins of 18 aircraft, and amplification-free shotgun metagenomics was conducted to characterize the microbial composition. In total, 7437 microbial taxa were identified. The relative abundance for bacteria, eukaryote, viruses, and archaea was 96.9%, 1.8%, 0.3%, and 0.03%, respectively. The top bacterial species mainly derived from outdoor air and human skin included Sphingomonas, Corynebacterium, Micrococcus luteus, Variovorax paradoxus, Paracoccus dentrificans, and Propionibacterium acnes. The abundance of NIAID-defined pathogens was low, accounted for only 0.23% of total microbes. The microbial species and functional composition were structured by the indoor surface type (R2 = 0.38, Adonis), followed by the manufacturer of the aircraft (R2 = 0.12) and flight duration (R2 = 0.07). Indoor surfaces affected species derived from different habitats; the abundance of dry skin and desiccated species was higher on textile surfaces, whereas the abundance of moist and oily skin species was higher on leather surfaces. The growth rates for most microbes were stopped and almost stopped.},
}

*Air Microbiology
Air Pollution, Indoor
*Aircraft
Aviation
Comamonadaceae
Dust/*analysis
Environmental Monitoring
Floors and Floorcoverings
Humans
*Metagenomics
Microbiota

@article {pmid32492369,
year = {2020},
author = {Sorbara, MT and Littmann, ER and Fontana, E and Moody, TU and Kohout, CE and Gjonbalaj, M and Eaton, V and Seok, R and Leiner, IM and Pamer, EG},
title = {Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity.},
journal = {Cell host & microbe},
volume = {28},
number = {1},
pages = {134-146.e4},
pmid = {32492369},
issn = {1934-6069},
support = {P30 CA008748/CA/NCI NIH HHS/United States ; R01 AI042135/AI/NIAID NIH HHS/United States ; R01 AI095706/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; },
mesh = {Clostridiales/*classification/*genetics ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; *Genetic Variation ; Genome, Bacterial ; Humans ; Metabolic Networks and Pathways/*genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Whole Genome Sequencing ; },
abstract = {Bacteria belonging to the Lachnospiraceae family are abundant, obligate anaerobic members of the microbiota in healthy humans. Lachnospiraceae impact their hosts by producing short-chain fatty acids, converting primary to secondary bile acids, and facilitating colonization resistance against intestinal pathogens. To increase our understanding of genomic and functional diversity between members of this family, we cultured 273 Lachnospiraceae isolates representing 11 genera and 27 species from human donors and performed whole-genome sequencing assembly and annotation. This analysis revealed substantial inter- and intra-species diversity in pathways that likely influence an isolate's ability to impact host health. These differences are likely to impact colonization resistance through lantibiotic expression or intestinal acidification, influence host mucosal immune cells and enterocytes via butyrate production, or contribute to synergism within a consortium by heterogenous polysaccharide metabolism. Identification of these specific functions could facilitate development of probiotic bacterial consortia that drive and/or restore in vivo microbiome functions.},
}

Clostridiales/*classification/*genetics
Feces/microbiology
Gastrointestinal Microbiome/*genetics
*Genetic Variation
Genome, Bacterial
Humans
Metabolic Networks and Pathways/*genetics
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Whole Genome Sequencing

@article {pmid32265914,
year = {2020},
author = {Pan, X and Zhang, D and Nguyen, DN and Wei, W and Yu, X and Gao, F and Sangild, PT},
title = {Postnatal Gut Immunity and Microbiota Development Is Minimally Affected by Prenatal Inflammation in Preterm Pigs.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {420},
pmid = {32265914},
issn = {1664-3224},
mesh = {Animals ; Animals, Newborn ; *Chorioamnionitis ; Female ; Gastrointestinal Microbiome/*physiology ; Inflammation/immunology/microbiology ; Intestines/*immunology/*microbiology ; Pregnancy ; Premature Birth ; Swine ; },
abstract = {Chorioamnionitis (CA), resulting from intra-amniotic inflammation, is a frequent cause of preterm birth and exposes the immature intestine to bacterial toxins and/or inflammatory mediators before birth via fetal swallowing. This may affect intestinal immune development, interacting with the effects of enteral feeding and gut microbiota colonization just after birth. Using preterm pigs as model for preterm infants, we hypothesized that prenatal exposure to gram-negative endotoxin influences postnatal bacterial colonization and gut immune development. Pig fetuses were given intra-amniotic lipopolysaccharide (LPS) 3 days before preterm delivery by cesarean section and were compared with littermate controls (CON) at birth and after 5 days of formula feeding and spontaneous bacterial colonization. Amniotic fluid was collected for analysis of leukocyte counts and cytokines, and the distal small intestine was analyzed for endotoxin level, morphology, and immune cell counts. Intestinal gene expression and microbiota were analyzed by transcriptomics and metagenomics, respectively. At birth, LPS-exposed pigs showed higher intestinal endotoxin, neutrophil/macrophage density, and shorter villi. About 1.0% of intestinal genes were affected at birth, and DMBT1, a regulator of mucosal immune defense, was identified as the hub gene in the co-expression network. Genes related to innate immune response (TLR2, LBP, CD14, C3, SFTPD), neutrophil chemotaxis (C5AR1, CSF3R, CCL5), and antigen processing (MHC II genes and CD4) were also affected, and expression levels correlated with intestinal neutrophil/macrophage density and amniotic fluid cytokine levels. On day 5, LPS and CON pigs showed similar sensitivity to necrotizing enterocolitis, endotoxin levels, morphology, immune cell counts, gene expressions, and microbiota composition (except for difference in some low-abundant species). Our results show that CA markedly affects intestinal genes at preterm birth, including genes related to immune cell infiltration. However, a few days later, following the physiological adaptations to preterm birth, CA had limited effects on intestinal structure, function, gene expression, bacterial colonization, and necrotizing enterocolitis sensitivity. We conclude that short-term, prenatal intra-amniotic inflammation is unlikely to exert marked effects on intestinal immune development in preterm neonates beyond the immediate neonatal period.},
}

Animals
Animals, Newborn
*Chorioamnionitis
Female
Gastrointestinal Microbiome/*physiology
Inflammation/immunology/microbiology
Intestines/*immunology/*microbiology
Pregnancy
Premature Birth
Swine

@article {pmid32256492,
year = {2020},
author = {Okamura, Y and Morimoto, N and Ikeda, D and Mizusawa, N and Watabe, S and Miyanishi, H and Saeki, Y and Takeyama, H and Aoki, T and Kinoshita, M and Kono, T and Sakai, M and Hikima, JI},
title = {Interleukin-17A/F1 Deficiency Reduces Antimicrobial Gene Expression and Contributes to Microbiome Alterations in Intestines of Japanese medaka (Oryzias latipes).},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {425},
pmid = {32256492},
issn = {1664-3224},
mesh = {Animals ; Fish Proteins/*immunology ; Gastrointestinal Microbiome/*immunology ; Gene Expression ; Immunity, Mucosal/*immunology ; Interleukin-17/deficiency/*immunology ; Oryzias/*immunology ; },
abstract = {In mammals, interleukin (IL)-17A and F are hallmark inflammatory cytokines that play key roles in protection against infection and intestinal mucosal immunity. In the gastrointestinal tract (GI), the induction of antimicrobial peptide (AMP) production via Paneth cells is a fundamental role of IL-17A and F in maintaining homeostasis of the GI microbiome and health. Although mammalian IL-17A and F homologs (referred to as IL-17A/F1-3) have been identified in several fish species, their function in the intestine is poorly understood. Additionally, the fish intestine lacks Paneth cells, and its GI structure is very different from that of mammals. Therefore, the GI microbiome modulatory mechanism via IL-17A/F genes has not been fully elucidated. In this study, Japanese medaka (Oryzias latipes) were used as a teleost model, and IL-17A/F1-knockout (IL-17A/F1-KO) medaka were established using the CRISPR/Cas9 genome editing technique. Furthermore, two IL-17A/F1-deficient medaka strains were generated, including one strain containing a 7-bp deletion (-7) and another with an 11-bp addition (+11). After establishing F2 homozygous KO medaka, transcriptome analysis (RNA-seq) was conducted to elucidate IL-17A/F1-dependent gene induction in the intestine. Results of RNA-seq and real-time PCR (qPCR) demonstrated down-regulation of immune-related genes, including interleukin-1β (IL-1β), complement 1q subunit C (C1qc), transferrin a (Tfa), and G-type lysozyme (LyzG), in IL-17A/F1-KO medaka. Interestingly, protein and lipid digestive enzyme genes, including phospholipase A2, group IB (pla2g1b), and elastase-1-like (CELA1), were also downregulated in the intestines of IL-17A/F1-KO medaka. Furthermore, to reveal the influence of these downregulated genes on the gut microbiome in IL-17A/F1-KO, 16S rRNA-based metagenomic sequencing analysis was conducted to analyze the microbiome constitution. Under a non-exposed state, the intestinal microbiome of IL-17A/F1-KO medaka differed at the phylum level from wild-type, with significantly higher levels of Verrucomicrobia and Planctomycetes. Additionally, at the operational taxonomic unit (OTU) level of the human and fish pathogens, the Enterobacteriaceae Plesiomonas shigelloides was the dominant species in IL-17A/F1-KO medaka. These findings suggest that IL-17A/F1 is involved in the maintenance of a healthy gut microbiome.},
}

Animals
Fish Proteins/*immunology
Gastrointestinal Microbiome/*immunology
Gene Expression
Immunity, Mucosal/*immunology
Interleukin-17/deficiency/*immunology
Oryzias/*immunology

@article {pmid33736375,
year = {2021},
author = {Macedo, G and van Veelen, HPJ and Hernandez-Leal, L and van der Maas, P and Heederik, D and Mevius, D and Bossers, A and Schmitt, H},
title = {Targeted metagenomics reveals inferior resilience of farm soil resistome compared to soil microbiome after manure application.},
journal = {The Science of the total environment},
volume = {770},
number = {},
pages = {145399},
doi = {10.1016/j.scitotenv.2021.145399},
pmid = {33736375},
issn = {1879-1026},
mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Farms ; Genes, Bacterial ; *Manure ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S ; Soil ; Soil Microbiology ; },
abstract = {Application of animal manure to soils results in the introduction of manure-derived bacteria and their antimicrobial resistance genes (ARGs) into soils. ResCap is a novel targeted-metagenomic approach that allows the detection of minority components of the resistome gene pool without the cost-prohibitive coverage depths and can provide a valuable tool to study the spread of antimicrobial resistance (AMR) in the environment. We used high-throughput sequencing and qPCR for 16S rRNA gene fragments as well as ResCap to explore the dynamics of bacteria, and ARGs introduced to soils and adjacent water ditches, both at community and individual scale, over a period of three weeks. The soil bacteriome and resistome showed strong resilience to the input of manure, as manuring did not impact the overall structure of the bacteriome, and its effects on the resistome were transient. Initially, manure application resulted in a substantial increase of ARGs in soils and adjacent waters, while not affecting the overall bacterial community composition. Still, specific families increased after manure application, either through the input of manure (e.g., Dysgonomonadaceae) or through enrichment after manuring (e.g., Pseudomonadaceae). Depending on the type of ARG, manure application resulted mostly in an increase (e.g., aph(6)-Id), but occasionally also in a decrease (e.g., dfrB3) of the absolute abundance of ARG clusters (FPKM/kg or L). This study shows that the structures of the bacteriome and resistome are shaped by different factors, where the bacterial community composition could not explain the changes in ARG diversity or abundances. Also, it highlights the potential of applying targeted metagenomic techniques, such as ResCap, to study the fate of AMR in the environment.},
}

Animals
Anti-Bacterial Agents/pharmacology
Drug Resistance, Microbial/genetics
Farms
Genes, Bacterial
*Manure
Metagenomics
*Microbiota/genetics
RNA, Ribosomal, 16S
Soil
Soil Microbiology

@article {pmid33097506,
year = {2020},
author = {Silvaraju, S and Menon, N and Fan, H and Lim, K and Kittelmann, S},
title = {Phylotype-Level Characterization of Complex Communities of Lactobacilli Using a High-Throughput, High-Resolution Phenylalanyl-tRNA Synthetase (pheS) Gene Amplicon Sequencing Approach.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {1},
pages = {},
pmid = {33097506},
issn = {1098-5336},
mesh = {*Genes, Bacterial ; High-Throughput Nucleotide Sequencing/*methods ; Lactobacillus/classification/enzymology/*genetics ; Microbiota/*genetics ; Pediococcus/classification/enzymology/*genetics ; Phenylalanine-tRNA Ligase/*genetics ; },
abstract = {The lactobacilli identified to date encompass more than 270 closely related species that were recently reclassified into 26 genera. Because of their relevance to industry, there is a need to distinguish between closely related and yet metabolically and regulatory distinct species, e.g., during monitoring of biotechnological processes or screening of samples of unknown composition. Current available methods, such as shotgun metagenomics or rRNA gene-based amplicon sequencing, have significant limitations (high cost, low resolution, etc.). Here, we generated a phylogeny of lactobacilli based on phenylalanyl-tRNA synthetase (pheS) genes and, from it, developed a high-resolution taxonomic framework which allows for comprehensive and confident characterization of the community diversity and structure of lactobacilli at the species level. This framework is based on a total of 445 pheS gene sequences, including sequences of 276 validly described species and subspecies (of a total of 282, including the proposed L. timonensis species and the reproposed L. zeae species; coverage of 98%), and allows differentiation between 265 species-level clades of lactobacilli and the subspecies of L. sakei The methodology was validated through next-generation sequencing of mock communities. At a sequencing depth of ∼30,000 sequences, the minimum level of detection was approximately 0.02 pg per μl DNA (equaling approximately 10 genome copies per μl template DNA). The pheS approach, along with parallel sequencing of partial 16S rRNA genes, revealed considerable diversity of lactobacilli and distinct community structures across a broad range of samples from different environmental niches. This novel complementary approach may be applicable to industry and academia alike.IMPORTANCE Species formerly classified within the genera Lactobacillus and Pediococcus have been studied extensively at the genomic level. To accommodate their exceptional functional diversity, the over 270 species were recently reclassified into 26 distinct genera. Despite their relevance to both academia and industry, methods that allow detailed exploration of their ecology are still limited by low resolution, high cost, or copy number variations. The approach described here makes use of a single-copy marker gene which outperforms other markers with regard to species-level resolution and availability of reference sequences (98% coverage). The tool was validated against a mock community and used to address diversity of lactobacilli and community structure in various environmental matrices. Such analyses can now be performed at a broader scale to assess and monitor the assembly, structure, and function of communities of lactobacilli at the species level (and, in some cases, even at the subspecies level) across a wide range of academic and commercial applications.},
}

*Genes, Bacterial
High-Throughput Nucleotide Sequencing/*methods
Lactobacillus/classification/enzymology/*genetics
Microbiota/*genetics
Pediococcus/classification/enzymology/*genetics
Phenylalanine-tRNA Ligase/*genetics

@article {pmid33067200,
year = {2020},
author = {Mori, JF and Kanaly, RA},
title = {Multispecies Diesel Fuel Biodegradation and Niche Formation Are Ignited by Pioneer Hydrocarbon-Utilizing Proteobacteria in a Soil Bacterial Consortium.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {1},
pages = {},
pmid = {33067200},
issn = {1098-5336},
mesh = {Biodegradation, Environmental ; *Gasoline ; Hydrocarbons/*metabolism ; *Microbial Consortia ; Proteobacteria/*metabolism ; *Soil Microbiology ; },
abstract = {A soil bacterial consortium that was grown on diesel fuel and consisted of more than 10 members from different genera was maintained through repetitive subculturing and was utilized as a practical model to investigate a bacterial community that was continuously exposed to petroleum hydrocarbons. Through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification which supported the linkage of genomic data and functionality, two pioneering genera, Sphingobium and Pseudomonas, whose catabolic capabilities were differentiated, were found to be responsible for the creation of specialized ecological niches that were apparently occupied by other bacterial members for survival within the consortium. Coexisting genera Achromobacter and Cupriavidus maintained their existence in the consortium through metabolic dependencies by utilizing hydrocarbon biotransformation products of pioneer metabolism, which was confirmed through growth tests and identification of biotransformation products of the isolated strains. Pioneering Sphingobium and Pseudomonas spp. utilized relatively water-insoluble hydrocarbon parent compounds and facilitated the development of a consortium community structure that resulted in the creation of niches in response to diesel fuel exposure which were created through the production of more-water-soluble biotransformation products available to cocolonizers. That these and other organisms were still present in the consortium after multiple transfers spanning 15 years provided evidence for these ecological niches. Member survival through occupation of these niches led to robustness of each group within the multispecies bacterial community. Overall, these results contribute to our understanding of the complex ecological relationships that may evolve during prokaryotic hydrocarbon pollutant biodegradation.IMPORTANCE There are few metagenome studies that have explored soil consortia maintained on a complex hydrocarbon substrate after the community interrelationships were formed. A soil bacterial consortium maintained on diesel fuel was utilized as a practical model to investigate bacterial community relationships through metagenomics analyses, consortium member isolation, growth assays, and metabolite identification, which supported the linkage of genomic data and functionality. Two pioneering genera were responsible for the biodegradation of aromatics and alkanes by initiating biotransformation and thereby created specialized niches that were populated by other members. A model that represents these relationships was constructed, which contributes to our understanding of the complex ecological relationships that evolve during prokaryotic hydrocarbon pollutant biodegradation.},
}

Biodegradation, Environmental
*Gasoline
Hydrocarbons/*metabolism
*Microbial Consortia
Proteobacteria/*metabolism
*Soil Microbiology

@article {pmid32210237,
year = {2020},
author = {Long, S and Yang, Y and Shen, C and Wang, Y and Deng, A and Qin, Q and Qiao, L},
title = {Metaproteomics characterizes human gut microbiome function in colorectal cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {6},
number = {1},
pages = {14},
pmid = {32210237},
issn = {2055-5008},
mesh = {Bacteria/*classification/isolation & purification/metabolism ; Bacterial Proteins/*analysis ; Case-Control Studies ; Chromatography, Liquid ; Colorectal Neoplasms/*microbiology ; DNA Replication ; Feces/microbiology ; Female ; Gastrointestinal Microbiome ; Humans ; Iron/metabolism ; Male ; Oxidative Stress ; Phylogeny ; Proteomics/*methods ; Tandem Mass Spectrometry ; },
abstract = {Pathogenesis of colorectal cancer (CRC) is associated with alterations in gut microbiome. Previous studies have focused on the changes of taxonomic abundances by metagenomics. Variations of the function of intestinal bacteria in CRC patients compared to healthy crowds remain largely unknown. Here we collected fecal samples from CRC patients and healthy volunteers and characterized their microbiome using quantitative metaproteomic method. We have identified and quantified 91,902 peptides, 30,062 gut microbial protein groups, and 195 genera of microbes. Among the proteins, 341 were found significantly different in abundance between the CRC patients and the healthy volunteers. Microbial proteins related to iron intake/transport; oxidative stress; and DNA replication, recombination, and repair were significantly alternated in abundance as a result of high local concentration of iron and high oxidative stress in the large intestine of CRC patients. Our study shows that metaproteomics can provide functional information on intestinal microflora that is of great value for pathogenesis research, and can help guide clinical diagnosis in the future.},
}

Bacteria/*classification/isolation & purification/metabolism
Bacterial Proteins/*analysis
Case-Control Studies
Chromatography, Liquid
Colorectal Neoplasms/*microbiology
DNA Replication
Feces/microbiology
Female
Gastrointestinal Microbiome
Humans
Iron/metabolism
Male
Oxidative Stress
Phylogeny
Proteomics/*methods
Tandem Mass Spectrometry

@article {pmid33373390,
year = {2020},
author = {Hull, JJA and Qi, M and Montmayeur, AM and Kumar, D and Velasquez, DE and Moon, SS and Magaña, LC and Betrapally, N and Ng, TFF and Jiang, B and Marthaler, D},
title = {Metagenomic sequencing generates the whole genomes of porcine rotavirus A, C, and H from the United States.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0244498},
pmid = {33373390},
issn = {1932-6203},
mesh = {Animals ; Evolution, Molecular ; Genome, Viral/*genetics ; Metagenomics ; Phylogeny ; Rotavirus/*genetics/isolation & purification ; Rotavirus Infections/diagnosis/prevention & control/*veterinary/virology ; Sus scrofa/*virology ; Swine ; Swine Diseases/diagnosis/prevention & control/*virology ; United States ; Virome/genetics ; Whole Genome Sequencing ; },
abstract = {The genus Rotavirus comprises eight species, designated A to H, and two recently identified tentative species I in dogs and J in bats. Species Rotavirus A, B, C and H (RVA, RVB, RVC and RVH) have been detected in humans and animals. While human and animal RVA are well characterized and defined, complete porcine genome sequences in the GenBank are limited compared to human strains. Here, we used a metagenomic approach to sequence the 11 segments of RVA, RVC and RVH strains from piglets in the United States (US) and explore the evolutionary relations of these RV species. Metagenomics identified Astroviridae, Picornaviridae, Caliciviridae, Coronoviridae in samples MN9.65 and OK5.68 while Picobirnaviridae and Arteriviridae were only identified in sample OK5.68. Whole genome sequencing and phylogenetic analyses identified multiple genotypes with the RVA of strain MN9.65 and OK5.68, with the genome constellation of G5/G9-P[7]/P[13]-I5/I5- R1/R1-C1-M1-A8-N1-T7-E1/E1-H1 and G5/G9-P[6]/P[7]-I5-R1/R1-C1-M1-A8-N1-T1/T7-E1/E1-H1, respectively. The RVA strains had a complex evolutionary relationship with other mammalian strains. The RVC strain OK5.68 had a genome constellation of G9-P[6]-I1-R1-C5-M6-A5-N1-T1-E1-H1, and shared an evolutionary relationship with porcine strains from the US. The RVH strains MN9.65 and OK5.68 had the genome constellation of G5-P1-I1-R1-C1-M1-A5-N1-T1-E4-H1 and G5-P1-I1-R1-C1-M1-A5-N1-T1-E1-H1, indicating multiple RVH genome constellations are circulating in the US. These findings allow us to understand the complexity of the enteric virome, develop improved screening methods for RVC and RVH strains, facilitate expanded rotavirus surveillance in pigs, and increase our understanding of the origin and evolution of rotavirus species.},
}

Animals
Evolution, Molecular
Genome, Viral/*genetics
Metagenomics
Phylogeny
Rotavirus/*genetics/isolation & purification
Rotavirus Infections/diagnosis/prevention & control/*veterinary/virology
Sus scrofa/*virology
Swine
Swine Diseases/diagnosis/prevention & control/*virology
United States
Virome/genetics
Whole Genome Sequencing

@article {pmid32127450,
year = {2020},
author = {Lima, LFO and Weissman, M and Reed, M and Papudeshi, B and Alker, AT and Morris, MM and Edwards, RA and de Putron, SJ and Vaidya, NK and Dinsdale, EA},
title = {Modeling of the Coral Microbiome: the Influence of Temperature and Microbial Network.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32127450},
issn = {2150-7511},
mesh = {Animals ; Anthozoa/*microbiology ; Bermuda ; Metagenomics ; Microbial Interactions ; *Microbiota ; *Models, Theoretical ; Mucus/microbiology ; *Temperature ; },
abstract = {Host-associated microbial communities are shaped by extrinsic and intrinsic factors to the holobiont organism. Environmental factors and microbe-microbe interactions act simultaneously on the microbial community structure, making the microbiome dynamics challenging to predict. The coral microbiome is essential to the health of coral reefs and sensitive to environmental changes. Here, we develop a dynamic model to determine the microbial community structure associated with the surface mucus layer (SML) of corals using temperature as an extrinsic factor and microbial network as an intrinsic factor. The model was validated by comparing the predicted relative abundances of microbial taxa to the relative abundances of microbial taxa from the sample data. The SML microbiome from Pseudodiploria strigosa was collected across reef zones in Bermuda, where inner and outer reefs are exposed to distinct thermal profiles. A shotgun metagenomics approach was used to describe the taxonomic composition and the microbial network of the coral SML microbiome. By simulating the annual temperature fluctuations at each reef zone, the model output is statistically identical to the observed data. The model was further applied to six scenarios that combined different profiles of temperature and microbial network to investigate the influence of each of these two factors on the model accuracy. The SML microbiome was best predicted by model scenarios with the temperature profile that was closest to the local thermal environment, regardless of the microbial network profile. Our model shows that the SML microbiome of P. strigosa in Bermuda is primarily structured by seasonal fluctuations in temperature at a reef scale, while the microbial network is a secondary driver.IMPORTANCE Coral microbiome dysbiosis (i.e., shifts in the microbial community structure or complete loss of microbial symbionts) caused by environmental changes is a key player in the decline of coral health worldwide. Multiple factors in the water column and the surrounding biological community influence the dynamics of the coral microbiome. However, by including only temperature as an external factor, our model proved to be successful in describing the microbial community associated with the surface mucus layer (SML) of the coral P. strigosa The dynamic model developed and validated in this study is a potential tool to predict the coral microbiome under different temperature conditions.},
}

Animals
Anthozoa/*microbiology
Bermuda
Metagenomics
Microbial Interactions
*Microbiota
*Models, Theoretical
Mucus/microbiology
*Temperature

@article {pmid33593429,
year = {2021},
author = {Moshkelgosha, S and Verhasselt, HL and Masetti, G and Covelli, D and Biscarini, F and Horstmann, M and Daser, A and Westendorf, AM and Jesenek, C and Philipp, S and Diaz-Cano, S and Banga, JP and Michael, D and Plummer, S and Marchesi, JR and Eckstein, A and Ludgate, M and Berchner-Pfannschmidt, U and , },
title = {Modulating gut microbiota in a mouse model of Graves' orbitopathy and its impact on induced disease.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {45},
pmid = {33593429},
issn = {2049-2618},
mesh = {Animals ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; *Gastrointestinal Microbiome ; Graves Ophthalmopathy/immunology/metabolism/*microbiology/pathology ; Humans ; Mice ; Mice, Inbred BALB C ; },
abstract = {BACKGROUND: Graves' disease (GD) is an autoimmune condition in which autoantibodies to the thyrotropin receptor (TSHR) cause hyperthyroidism. About 50% of GD patients also have Graves' orbitopathy (GO), an intractable disease in which expansion of the orbital contents causes diplopia, proptosis and even blindness. Murine models of GD/GO, developed in different centres, demonstrated significant variation in gut microbiota composition which correlated with TSHR-induced disease heterogeneity. To investigate whether correlation indicates causation, we modified the gut microbiota to determine whether it has a role in thyroid autoimmunity. Female BALB/c mice were treated with either vancomycin, probiotic bacteria, human fecal material transfer (hFMT) from patients with severe GO or ddH2O from birth to immunization with TSHR-A subunit or beta-galactosidase (βgal; age ~ 6 weeks). Incidence and severity of GD (TSHR autoantibodies, thyroid histology, thyroxine level) and GO (orbital fat and muscle histology), lymphocyte phenotype, cytokine profile and gut microbiota were analysed at sacrifice (~ 22 weeks).

RESULTS: In ddH2O-TSHR mice, 84% had pathological autoantibodies, 67% elevated thyroxine, 77% hyperplastic thyroids and 70% orbital pathology. Firmicutes were increased, and Bacteroidetes reduced relative to ddH2O-βgal; CCL5 was increased. The random forest algorithm at the genus level predicted vancomycin treatment with 100% accuracy but 74% and 70% for hFMT and probiotic, respectively. Vancomycin significantly reduced gut microbiota richness and diversity compared with all other groups; the incidence and severity of both GD and GO also decreased; reduced orbital pathology correlated positively with Akkermansia spp. whilst IL-4 levels increased. Mice receiving hFMT initially inherited their GO donors' microbiota, and the severity of induced GD increased, as did the orbital brown adipose tissue volume in TSHR mice. Furthermore, genus Bacteroides, which is reduced in GD patients, was significantly increased by vancomycin but reduced in hFMT-treated mice. Probiotic treatment significantly increased CD25+ Treg cells in orbital draining lymph nodes but exacerbated induced autoimmune hyperthyroidism and GO.

CONCLUSIONS: These results strongly support a role for the gut microbiota in TSHR-induced disease. Whilst changes to the gut microbiota have a profound effect on quantifiable GD endocrine and immune factors, the impact on GO cellular changes is more nuanced. The findings have translational potential for novel, improved treatments. Video abstract.},
}

Animals
Disease Models, Animal
Fecal Microbiota Transplantation
Female
*Gastrointestinal Microbiome
Graves Ophthalmopathy/immunology/metabolism/*microbiology/pathology
Humans
Mice
Mice, Inbred BALB C

@article {pmid33583433,
year = {2021},
author = {Raimundo, I and Silva, R and Meunier, L and Valente, SM and Lago-Lestón, A and Keller-Costa, T and Costa, R},
title = {Functional metagenomics reveals differential chitin degradation and utilization features across free-living and host-associated marine microbiomes.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {43},
pmid = {33583433},
issn = {2049-2618},
mesh = {Animals ; Anthozoa/microbiology ; Aquatic Organisms/*microbiology ; Bacteria/enzymology/genetics/*metabolism ; Chitin/*metabolism ; Chitinases/genetics/metabolism ; Geologic Sediments/*microbiology ; *Metagenomics ; *Microbiota/genetics ; Oceans and Seas ; Phylogeny ; Porifera/microbiology ; Seawater/*microbiology ; Symbiosis ; },
abstract = {BACKGROUND: Chitin ranks as the most abundant polysaccharide in the oceans yet knowledge of shifts in structure and diversity of chitin-degrading communities across marine niches is scarce. Here, we integrate cultivation-dependent and -independent approaches to shed light on the chitin processing potential within the microbiomes of marine sponges, octocorals, sediments, and seawater.

RESULTS: We found that cultivatable host-associated bacteria in the genera Aquimarina, Enterovibrio, Microbulbifer, Pseudoalteromonas, Shewanella, and Vibrio were able to degrade colloidal chitin in vitro. Congruent with enzymatic activity bioassays, genome-wide inspection of cultivated symbionts revealed that Vibrio and Aquimarina species, particularly, possess several endo- and exo-chitinase-encoding genes underlying their ability to cleave the large chitin polymer into oligomers and dimers. Conversely, Alphaproteobacteria species were found to specialize in the utilization of the chitin monomer N-acetylglucosamine more often. Phylogenetic assessments uncovered a high degree of within-genome diversification of multiple, full-length endo-chitinase genes for Aquimarina and Vibrio strains, suggestive of a versatile chitin catabolism aptitude. We then analyzed the abundance distributions of chitin metabolism-related genes across 30 Illumina-sequenced microbial metagenomes and found that the endosymbiotic consortium of Spongia officinalis is enriched in polysaccharide deacetylases, suggesting the ability of the marine sponge microbiome to convert chitin into its deacetylated-and biotechnologically versatile-form chitosan. Instead, the abundance of endo-chitinase and chitin-binding protein-encoding genes in healthy octocorals leveled up with those from the surrounding environment but was found to be depleted in necrotic octocoral tissue. Using cultivation-independent, taxonomic assignments of endo-chitinase encoding genes, we unveiled previously unsuspected richness and divergent structures of chitinolytic communities across host-associated and free-living biotopes, revealing putative roles for uncultivated Gammaproteobacteria and Chloroflexi symbionts in chitin processing within sessile marine invertebrates.

CONCLUSIONS: Our findings suggest that differential chitin degradation pathways, utilization, and turnover dictate the processing of chitin across marine micro-niches and support the hypothesis that inter-species cross-feeding could facilitate the co-existence of chitin utilizers within marine invertebrate microbiomes. We further identified chitin metabolism functions which may serve as indicators of microbiome integrity/dysbiosis in corals and reveal putative novel chitinolytic enzymes in the genus Aquimarina that may find applications in the blue biotechnology sector. Video abstract.},
}

Animals
Anthozoa/microbiology
Aquatic Organisms/*microbiology
Bacteria/enzymology/genetics/*metabolism
Chitin/*metabolism
Chitinases/genetics/metabolism
Geologic Sediments/*microbiology
*Metagenomics
*Microbiota/genetics
Oceans and Seas
Phylogeny
Porifera/microbiology
Seawater/*microbiology
Symbiosis

@article {pmid33517011,
year = {2021},
author = {Jin, L and Huang, Y and Yang, S and Wu, D and Li, C and Deng, W and Zhao, K and He, Y and Li, B and Zhang, G and Xiong, Y and Wei, R and Li, G and Wu, H and Zhang, H and Zou, L},
title = {Diet, habitat environment and lifestyle conversion affect the gut microbiomes of giant pandas.},
journal = {The Science of the total environment},
volume = {770},
number = {},
pages = {145316},
doi = {10.1016/j.scitotenv.2021.145316},
pmid = {33517011},
issn = {1879-1026},
mesh = {Animals ; Diet ; Ecosystem ; *Gastrointestinal Microbiome ; Life Style ; *Ursidae ; },
abstract = {Gut microbiota (GM) are important for the health of giant pandas (GPs), in addition to the utilization of bamboo in their diets. However, it is not fully understood how diet, habitat environment and lifestyle contribute to the composition of GM in GP. Consequently, we evaluated how dietary changes, habitat environment conversions and lifestyle shifts influence the GM of GPs using high-throughput sequencing and genome-resolved metagenomics. The GM of GPs were more similar when their hosts exhibited the same diet. High fiber diets significantly increased the diversity and decreased the richness of gut bacterial communities alone or interacted with the age factor (p < 0.05). The abundances of Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium significantly increased during diet conversion process (Non-parametric factorial Kruskal-Wallis sum-rank test, LDA > 4). Reconstruction of 60 metagenome-assembled-genomes (MAGs) indicated that these bacteria were likely responsible for bamboo digestion via gene complements involved in cellulose, hemicellulose, and lignin degradation. While habitat environment may play a more important role in shaping the GM of GP, lifestyle can also greatly affect bacterial communities. The GM structure in reintroduced GPs notably converged to that of wild pandas. Importantly, the main bacterial genera of wild GPs could aid in lignin degradation, while those of reintroduced GPs were related to cellulose and hemicellulose digestion. Streptococcus, Pseudomonas, Enterococcus, Lactococcus, Acinetobacter, and Clostridium may contribute to lignocellulose digestion in GP. The results revealed that diet conversion, habitat environment and lifestyle could remarkably influence the GM of GP. In addition, results suggested that increasing the ability of lignin degradation with GM may aid to change the GM of reintroduced pandas to resemble those of wild pandas.},
}

Animals
Diet
Ecosystem
*Gastrointestinal Microbiome
Life Style
*Ursidae

@article {pmid33293686,
year = {2020},
author = {West, KM and Richards, ZT and Harvey, ES and Susac, R and Grealy, A and Bunce, M},
title = {Under the karst: detecting hidden subterranean assemblages using eDNA metabarcoding in the caves of Christmas Island, Australia.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {21479},
pmid = {33293686},
issn = {2045-2322},
mesh = {Animals ; Australia ; *Biodiversity ; Cell Nucleus/genetics ; *DNA Barcoding, Taxonomic/methods ; Environmental DNA/*genetics ; Eukaryota/genetics ; Indian Ocean ; *Metagenomics/methods ; Mitochondria/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Subterranean ecosystems are understudied and challenging to conventionally survey given the inaccessibility of underground voids and networks. In this study, we conducted a eukaryotic environmental DNA (eDNA) metabarcoding survey across the karst landscape of Christmas Island, (Indian Ocean, Australia) to evaluate the utility of this non-invasive technique to detect subterranean aquatic 'stygofauna' assemblages. Three metabarcoding assays targeting the mitochondrial 16S rRNA and nuclear 18S genes were applied to 159 water and sediment samples collected from 23 caves and springs across the island. Taken together, our assays detected a wide diversity of chordates, cnidarians, porifera, arthropods, molluscs, annelids and bryozoans from 71 families across 60 orders. We report a high level of variation between cave and spring subterranean community compositions which are significantly influenced by varying levels of salinity. Additionally, we show that dissolved oxygen and longitudinal gradients significantly affect biotic assemblages within cave communities. Lastly, we combined eDNA-derived community composition and environmental (water quality) data to predict potential underground interconnectivity across Christmas Island. We identified three cave and spring groups that showed a high degree of biotic and abiotic similarity indicating likely local connectivity. This study demonstrates the applicability of eDNA metabarcoding to detect subterranean eukaryotic communities and explore underground interconnectivity.},
}

Animals
Australia
*Biodiversity
Cell Nucleus/genetics
*DNA Barcoding, Taxonomic/methods
Environmental DNA/*genetics
Eukaryota/genetics
Indian Ocean
*Metagenomics/methods
Mitochondria/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid32439449,
year = {2020},
author = {Yao, H and Wang, L and Tang, X and Yang, Z and Li, H and Sun, C and Wu, X and Xu, D},
title = {Two novel polysaccharides from Solanum nigrum L. exert potential prebiotic effects in an in vitro fermentation model.},
journal = {International journal of biological macromolecules},
volume = {159},
number = {},
pages = {648-658},
doi = {10.1016/j.ijbiomac.2020.05.121},
pmid = {32439449},
issn = {1879-0003},
mesh = {Chromatography, Gas ; Fatty Acids, Volatile/biosynthesis ; Feces/chemistry/microbiology ; *Fermentation ; Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics/methods ; Molecular Weight ; Monosaccharides/chemistry ; Polysaccharides/*chemistry/isolation & purification ; *Prebiotics ; Solanum nigrum/*chemistry ; },
abstract = {In this research, two novel polysaccharides (S1 and S2) from Solanum nigrum L were extracted and purified. Then homogeneity, molecular weights, major chemical contents and monosaccharide compositions of S1 and S2 were determined. Then, the effects of S1 and S2 on human faecal microbial community and short-chain fatty acid production were investigated using an in vitro fermentation model. Results showed that S1 and S2 have different impacts on human gut microbiota in vitro. S1 selectively promoted the abundance of 9 genera and the production of propionic acid, butyric acid, isobutyric acid, valeric acid and isovaleric acid; while S2 selectively promoted the abundance of 8 genera and the production of acetic acid, propionic acid, butyric acid, isobutyric acid, valeric acid, isovaleric acid and succinic acid. Also, S1 group had higher abundance of genera Butyricimonas and Megamonas and higher levels of lactic acid than S2; while S2 group had higher abundance of Megaphaera and higher levels of butyric acid, valeric acid, isobutyric acid, isovaleric acid and succinic acid comparably. We concluded that S1 and S2 may have potential prebiotic functions.},
}

Chromatography, Gas
Fatty Acids, Volatile/biosynthesis
Feces/chemistry/microbiology
*Fermentation
Gastrointestinal Microbiome
Humans
Metagenome
Metagenomics/methods
Molecular Weight
Monosaccharides/chemistry
Polysaccharides/*chemistry/isolation & purification
*Prebiotics
Solanum nigrum/*chemistry

@article {pmid32188747,
year = {2020},
author = {Zuo, K and Yin, X and Li, K and Zhang, J and Wang, P and Jiao, J and Liu, Z and Liu, X and Liu, J and Li, J and Yang, X},
title = {Different Types of Atrial Fibrillation Share Patterns of Gut Microbiota Dysbiosis.},
journal = {mSphere},
volume = {5},
number = {2},
pages = {},
pmid = {32188747},
issn = {2379-5042},
mesh = {Aged ; Atrial Fibrillation/classification/*etiology ; Cohort Studies ; Dysbiosis/metabolism/*microbiology ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; },
abstract = {Dysbiotic gut microbiota (GM) and disordered metabolic patterns are known to be involved in the clinical expression of atrial fibrillation (AF). However, little evidence has been reported in characterizing the specific changes in fecal microbiota in paroxysmal AF (PAF) and persistent AF (psAF). To provide a comprehensive understanding of GM dysbiosis in AF types, we assessed the GM signatures of 30 PAF patients, 20 psAF patients, and 50 non-AF controls based on metagenomic and metabolomic analyses. Compared with control subjects, similar changes of GM were identified in PAF and psAF patients, with elevated microbial diversity and similar alteration in the microbiota composition. PAF and psAF patients shared the majority of differential taxa compared with non-AF controls. Moreover, the similarity was also illuminated in microbial function and associated metabolic alterations. Additionally, minor disparity was observed in PAF compared with psAF. Several distinctive taxa between PAF and psAF were correlated with certain metabolites and atrial diameter, which might play a role in the pathogenesis of atrial remodeling. Our findings characterized the presence of many common features in GM shared by PAF and psAF, which occurred at the self-terminating PAF. Preventative and therapeutic measures targeting GM for early intervention to postpone the progression of AF are highly warranted.IMPORTANCE Atrial fibrillation has been identified to be associated with disordered gut microbiota. Notably, atrial fibrillation is a progressive disease and could be categorized as paroxysmal and persistent based on the duration of the episodes. The persistent atrial fibrillation patients are accompanied by higher risk of stroke and lower success rate of rhythm control. However, the microbial signatures of different categories of atrial fibrillation patients remain unknown. We sought to determine whether disordered gut microbiota occurs in the self-terminating PAF or intestinal flora develops dynamically during atrial fibrillation progression. We found that different types of atrial fibrillation show a limited degree of gut microbiota shift. Gut microbiota dysbiosis has already occurred in mild stages of atrial fibrillation, which might act as an early modulator of disease, and therefore may be regarded as a potential target to postpone atrial fibrillation progression.},
}

Aged
Atrial Fibrillation/classification/*etiology
Cohort Studies
Dysbiosis/metabolism/*microbiology
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Male
Metabolomics
Metagenomics
Middle Aged

@article {pmid31734341,
year = {2020},
author = {Liu, F and Wang, Y and Gao, GF and Zhu, B},
title = {Metagenomic analysis reveals the abundance and diversity of ARGs in children's respiratory tract microbiomes.},
journal = {The Journal of infection},
volume = {80},
number = {2},
pages = {232-254},
doi = {10.1016/j.jinf.2019.11.002},
pmid = {31734341},
issn = {1532-2742},
mesh = {Anti-Bacterial Agents ; Child ; Genes, Bacterial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota ; Respiratory System ; },
}

Anti-Bacterial Agents
Child
Genes, Bacterial
Humans
Metagenome
*Metagenomics
*Microbiota
Respiratory System

@article {pmid32591010,
year = {2020},
author = {Leung, MHY and Tong, X and Bastien, P and Guinot, F and Tenenhaus, A and Appenzeller, BMR and Betts, RJ and Mezzache, S and Li, J and Bourokba, N and Breton, L and Clavaud, C and Lee, PKH},
title = {Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {100},
pmid = {32591010},
issn = {2049-2618},
mesh = {Adult ; China ; Cities ; Environmental Monitoring ; Environmental Pollutants/administration & dosage/*pharmacology ; Female ; Humans ; Microbiota/*drug effects ; Middle Aged ; Polycyclic Aromatic Hydrocarbons/administration & dosage/*pharmacology ; Skin/*drug effects/*microbiology ; },
abstract = {BACKGROUND: Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous microbiota. Given the roles of the skin microbiota have on healthy and undesirable skin phenotypes and the relationships between PAHs and skin properties, we hypothesize that exposure of PAHs may be associated with changes in the cutaneous microbiota. In this study, the skin microbiota of over two hundred Chinese individuals from two cities in China with varying exposure levels of PAHs were characterized by bacterial and fungal amplicon and shotgun metagenomics sequencing.

RESULTS: Skin site and city were strong parameters in changing microbial communities and their assembly processes. Reductions of bacterial-fungal microbial network structural integrity and stability were associated with skin conditions (acne and dandruff). Multivariate analysis revealed associations between abundances of Propionibacterium and Malassezia with host properties and pollutant exposure levels. Shannon diversity increase was correlated to exposure levels of PAHs in a dose-dependent manner. Shotgun metagenomics analysis of samples (n = 32) from individuals of the lowest and highest exposure levels of PAHs further highlighted associations between the PAHs quantified and decrease in abundances of skin commensals and increase in oral bacteria. Functional analysis identified associations between levels of PAHs and abundance of microbial genes of metabolic and other pathways with potential importance in host-microbe interactions as well as degradation of aromatic compounds.

CONCLUSIONS: The results in this study demonstrated the changes in composition and functional capacities of the cutaneous microbiota associated with chronic exposure levels of PAHs. Findings from this study will aid the development of strategies to harness the microbiota in protecting the skin against pollutants. Video Abstract.},
}

Adult
China
Cities
Environmental Monitoring
Environmental Pollutants/administration & dosage/*pharmacology
Female
Humans
Microbiota/*drug effects
Middle Aged
Polycyclic Aromatic Hydrocarbons/administration & dosage/*pharmacology
Skin/*drug effects/*microbiology

@article {pmid32576288,
year = {2020},
author = {Hosoda, S and Nishijima, S and Fukunaga, T and Hattori, M and Hamada, M},
title = {Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {95},
pmid = {32576288},
issn = {2049-2618},
mesh = {Bacteria/classification/genetics/isolation & purification ; Butyrates/metabolism ; Datasets as Topic ; Gastrointestinal Microbiome/*genetics ; Humans ; *Latent Class Analysis ; *Metagenome ; },
abstract = {BACKGROUND: The human gut microbiome has been suggested to affect human health and thus has received considerable attention. To clarify the structure of the human gut microbiome, clustering methods are frequently applied to human gut taxonomic profiles. Enterotypes, i.e., clusters of individuals with similar microbiome composition, are well-studied and characterized. However, only a few detailed studies on assemblages, i.e., clusters of co-occurring bacterial taxa, have been conducted. Particularly, the relationship between the enterotype and assemblage is not well-understood.

RESULTS: In this study, we detected gut microbiome assemblages using a latent Dirichlet allocation (LDA) method. We applied LDA to a large-scale human gut metagenome dataset and found that a 4-assemblage LDA model could represent relationships between enterotypes and assemblages with high interpretability. This model indicated that each individual tends to have several assemblages, three of which corresponded to the three classically recognized enterotypes. Conversely, the fourth assemblage corresponded to no enterotypes and emerged in all enterotypes. Interestingly, the dominant genera of this assemblage (Clostridium, Eubacterium, Faecalibacterium, Roseburia, Coprococcus, and Butyrivibrio) included butyrate-producing species such as Faecalibacterium prausnitzii. Indeed, the fourth assemblage significantly positively correlated with three butyrate-producing functions.

CONCLUSIONS: We conducted an assemblage analysis on a large-scale human gut metagenome dataset using LDA. The present study revealed that there is an enterotype-independent assemblage. Video Abstract.},
}

Bacteria/classification/genetics/isolation & purification
Butyrates/metabolism
Datasets as Topic
Gastrointestinal Microbiome/*genetics
Humans
*Latent Class Analysis
*Metagenome

@article {pmid32534596,
year = {2020},
author = {Doane, MP and Morris, MM and Papudeshi, B and Allen, L and Pande, D and Haggerty, JM and Johri, S and Turnlund, AC and Peterson, M and Kacev, D and Nosal, A and Ramirez, D and Hovel, K and Ledbetter, J and Alker, A and Avalos, J and Baker, K and Bhide, S and Billings, E and Byrum, S and Clemens, M and Demery, AJ and Lima, LFO and Gomez, O and Gutierrez, O and Hinton, S and Kieu, D and Kim, A and Loaiza, R and Martinez, A and McGhee, J and Nguyen, K and Parlan, S and Pham, A and Price-Waldman, R and Edwards, RA and Dinsdale, EA},
title = {The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {93},
pmid = {32534596},
issn = {2049-2618},
support = {1323809//National Science Foundation/International ; 1330800//National Science Foundation/International ; },
mesh = {Animals ; Bacteria/genetics/isolation & purification ; Elasmobranchii/*microbiology ; Fishes/*microbiology ; Integumentary System/*microbiology ; *Metagenomics ; Microbiota/*genetics ; *Phylogeny ; *Symbiosis ; },
abstract = {BACKGROUND: The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes.

RESULTS: We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes.

CONCLUSION: Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales. Video abstract.},
}

Animals
Bacteria/genetics/isolation & purification
Elasmobranchii/*microbiology
Fishes/*microbiology
Integumentary System/*microbiology
*Metagenomics
Microbiota/*genetics
*Phylogeny
*Symbiosis

@article {pmid33602336,
year = {2021},
author = {Bashir, AK and Wink, L and Duller, S and Schwendner, P and Cockell, C and Rettberg, P and Mahnert, A and Beblo-Vranesevic, K and Bohmeier, M and Rabbow, E and Gaboyer, F and Westall, F and Walter, N and Cabezas, P and Garcia-Descalzo, L and Gomez, F and Malki, M and Amils, R and Ehrenfreund, P and Monaghan, E and Vannier, P and Marteinsson, V and Erlacher, A and Tanski, G and Strauss, J and Bashir, M and Riedo, A and Moissl-Eichinger, C},
title = {Taxonomic and functional analyses of intact microbial communities thriving in extreme, astrobiology-relevant, anoxic sites.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {50},
pmid = {33602336},
issn = {2049-2618},
mesh = {Anaerobiosis ; Bacteria/classification/genetics/isolation & purification ; *Exobiology ; *Extreme Environments ; Metagenome ; Microbiota/genetics/*physiology ; },
abstract = {BACKGROUND: Extreme terrestrial, analogue environments are widely used models to study the limits of life and to infer habitability of extraterrestrial settings. In contrast to Earth's ecosystems, potential extraterrestrial biotopes are usually characterized by a lack of oxygen.

METHODS: In the MASE project (Mars Analogues for Space Exploration), we selected representative anoxic analogue environments (permafrost, salt-mine, acidic lake and river, sulfur springs) for the comprehensive analysis of their microbial communities. We assessed the microbiome profile of intact cells by propidium monoazide-based amplicon and shotgun metagenome sequencing, supplemented with an extensive cultivation effort.

RESULTS: The information retrieved from microbiome analyses on the intact microbial community thriving in the MASE sites, together with the isolation of 31 model microorganisms and successful binning of 15 high-quality genomes allowed us to observe principle pathways, which pinpoint specific microbial functions in the MASE sites compared to moderate environments. The microorganisms were characterized by an impressive machinery to withstand physical and chemical pressures. All levels of our analyses revealed the strong and omnipresent dependency of the microbial communities on complex organic matter. Moreover, we identified an extremotolerant cosmopolitan group of 34 poly-extremophiles thriving in all sites.

CONCLUSIONS: Our results reveal the presence of a core microbiome and microbial taxonomic similarities between saline and acidic anoxic environments. Our work further emphasizes the importance of the environmental, terrestrial parameters for the functionality of a microbial community, but also reveals a high proportion of living microorganisms in extreme environments with a high adaptation potential within habitability borders. Video abstract.},
}

Anaerobiosis
Bacteria/classification/genetics/isolation & purification
*Exobiology
*Extreme Environments
Metagenome
Microbiota/genetics/*physiology

@article {pmid32660640,
year = {2020},
author = {Adegoke, A and Neff, E and Geary, A and Husser, MC and Wilson, K and Norris, SM and Dharmarajan, G and Karim, S},
title = {Laboratory colonization by Dirofilaria immitis alters the microbiome of female Aedes aegypti mosquitoes.},
journal = {Parasites & vectors},
volume = {13},
number = {1},
pages = {349},
pmid = {32660640},
issn = {1756-3305},
mesh = {*Aedes/microbiology/parasitology ; Animals ; Bacteria/genetics/isolation & purification ; Cat Diseases/parasitology/transmission ; Cats ; DNA, Bacterial ; *Dirofilaria immitis ; Dirofilariasis/transmission ; Dog Diseases/parasitology/transmission ; Dogs ; Female ; Klebsiella oxytoca/genetics/isolation & purification ; Metagenome ; Metagenomics ; *Microbiota ; Mosquito Vectors/microbiology/parasitology ; Phylogeny ; RNA, Ribosomal, 16S ; Symbiosis ; },
abstract = {BACKGROUND: The ability of blood-feeding arthropods to successfully acquire and transmit pathogens of medical and veterinary importance has been shown to be interfered with, or enhanced by, the arthropod's native microbiome. Mosquitoes transmit viruses, protozoan and filarial nematodes, the majority of which contribute to the 17% of infectious disease cases worldwide. Dirofilaria immitis, a mosquito-transmitted filarial nematodes of dogs and cats, is vectored by several mosquito species including Aedes aegypti.

METHODS: In this study, we investigated the impact of D. immitis colonization on the microbiome of laboratory reared female Ae. aegypti. Metagenomic analysis of the V3-V4 variable region of the microbial 16S RNA gene was used for identification of the microbial differences down to species level.

RESULTS: We generated a total of 1068 OTUs representing 16 phyla, 181 genera and 271 bacterial species. Overall, in order of abundance, Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the most represented phylum with D. immitis-infected mosquitoes having more of Proteobacteria (71%) than uninfected mosquitoes (56.9%). An interesting finding in this study is the detection of Klebsiella oxytoca in relatively similar abundance in infected and uninfected mosquitoes, suggesting a possible endosymbiotic relationship, and has been previously shown to indirectly compete for nutrients with fungi on domestic housefly eggs and larvae. While D. immitis colonization has no effect on the overall species richness, we identified significant differences in the composition of selected bacterial genera and phyla between the two groups. We also reported distinct compositional and phylogenetic differences in the individual bacterial species when commonly identified bacteria were compared.

CONCLUSIONS: To the best of our knowledge, this is the first study to understand the impact of a filarial infection on the microbiome of its mosquito vector. Further studies are required to identify bacteria species that could play an important role in the mosquito biology. While the microbiome composition of Ae. aegypti mosquito have been previously reported, our study shows that in an effort to establish itself, a filarial nematode modifies and alters the overall microbial diversity within its mosquito host.},
}

*Aedes/microbiology/parasitology
Animals
Bacteria/genetics/isolation & purification
Cat Diseases/parasitology/transmission
Cats
DNA, Bacterial
*Dirofilaria immitis
Dirofilariasis/transmission
Dog Diseases/parasitology/transmission
Dogs
Female
Klebsiella oxytoca/genetics/isolation & purification
Metagenome
Metagenomics
*Microbiota
Mosquito Vectors/microbiology/parasitology
Phylogeny
RNA, Ribosomal, 16S
Symbiosis

@article {pmid33717447,
year = {2021},
author = {Meucci, S and Schulte, L and Zimmermann, HH and Stoof-Leichsenring, KR and Epp, L and Bronken Eidesen, P and Herzschuh, U},
title = {Holocene chloroplast genetic variation of shrubs (Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses.},
journal = {Ecology and evolution},
volume = {11},
number = {5},
pages = {2173-2193},
doi = {10.1002/ece3.7183},
pmid = {33717447},
issn = {2045-7758},
abstract = {Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.},
}

@article {pmid33637740,
year = {2021},
author = {Goyal, A and Wang, T and Dubinkina, V and Maslov, S},
title = {Ecology-guided prediction of cross-feeding interactions in the human gut microbiome.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {1335},
pmid = {33637740},
issn = {2041-1723},
mesh = {Algorithms ; Computational Biology/methods ; *Ecology ; Gastrointestinal Microbiome/*genetics/*physiology ; Humans ; Intestines/*microbiology ; Machine Learning ; Metabolome ; Metabolomics ; Metagenomics ; Models, Biological ; },
abstract = {Understanding a complex microbial ecosystem such as the human gut microbiome requires information about both microbial species and the metabolites they produce and secrete. These metabolites are exchanged via a large network of cross-feeding interactions, and are crucial for predicting the functional state of the microbiome. However, till date, we only have information for a part of this network, limited by experimental throughput. Here, we propose an ecology-based computational method, GutCP, using which we predict hundreds of new experimentally untested cross-feeding interactions in the human gut microbiome. GutCP utilizes a mechanistic model of the gut microbiome with the explicit exchange of metabolites and their effects on the growth of microbial species. To build GutCP, we combine metagenomic and metabolomic measurements from the gut microbiome with optimization techniques from machine learning. Close to 65% of the cross-feeding interactions predicted by GutCP are supported by evidence from genome annotations, which we provide for experimental testing. Our method has the potential to greatly improve existing models of the human gut microbiome, as well as our ability to predict the metabolic profile of the gut.},
}

Algorithms
Computational Biology/methods
*Ecology
Gastrointestinal Microbiome/*genetics/*physiology
Humans
Intestines/*microbiology
Machine Learning
Metabolome
Metabolomics
Metagenomics
Models, Biological

@article {pmid33115864,
year = {2021},
author = {Li, Y and Altan, E and Reyes, G and Halstead, B and Deng, X and Delwart, E},
title = {Virome of Bat Guano from Nine Northern California Roosts.},
journal = {Journal of virology},
volume = {95},
number = {3},
pages = {},
pmid = {33115864},
issn = {1098-5514},
mesh = {Animals ; California ; Chiroptera/*virology ; Feces/*virology ; *Genome, Viral ; *Metagenome ; Phylogeny ; *Virome ; Viruses/classification/*genetics ; },
abstract = {Bats are hosts to a large variety of viruses, including many capable of cross-species transmissions to other mammals, including humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and from a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Nearly complete or complete genomes of a novel parvovirus, astrovirus, nodavirus, circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses, and densoviruses, and more partial genomes of a novel alphacoronavirus and a bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found, likely reflecting their wide distribution among different bats. Unexpectedly, a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR; these possibly originated from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent, indicating that numerous viruses still remain to be characterized, even from such a heavily investigated order as Chiroptera.IMPORTANCE Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using an unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species, likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected, whose presence are likely the result of contamination from defecation and urination atop guano and which reflect the close interaction of these mammals in the wild.},
}

Animals
California
Chiroptera/*virology
Feces/*virology
*Genome, Viral
*Metagenome
Phylogeny
*Virome
Viruses/classification/*genetics