@article {pmid33562073,
year = {2021},
author = {Bergner, LM and Mollentze, N and Orton, RJ and Tello, C and Broos, A and Biek, R and Streicker, DG},
title = {Characterizing and Evaluating the Zoonotic Potential of Novel Viruses Discovered in Vampire Bats.},
journal = {Viruses},
volume = {13},
number = {2},
pages = {},
pmid = {33562073},
issn = {1999-4915},
support = {102507/Z/13/A/WT_/Wellcome Trust/United Kingdom ; 217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; Chiroptera/*virology ; Disease Reservoirs/veterinary/virology ; Feces/virology ; Genome, Viral/genetics ; Humans ; Machine Learning ; Metagenomics ; Phylogeny ; Rabies virus/classification/genetics/isolation & purification ; Saliva/virology ; Viruses/classification/genetics/*isolation & purification ; Zoonoses/*virology ; },
abstract = {The contemporary surge in metagenomic sequencing has transformed knowledge of viral diversity in wildlife. However, evaluating which newly discovered viruses pose sufficient risk of infecting humans to merit detailed laboratory characterization and surveillance remains largely speculative. Machine learning algorithms have been developed to address this imbalance by ranking the relative likelihood of human infection based on viral genome sequences, but are not yet routinely applied to viruses at the time of their discovery. Here, we characterized viral genomes detected through metagenomic sequencing of feces and saliva from common vampire bats (Desmodus rotundus) and used these data as a case study in evaluating zoonotic potential using molecular sequencing data. Of 58 detected viral families, including 17 which infect mammals, the only known zoonosis detected was rabies virus; however, additional genomes were detected from the families Hepeviridae, Coronaviridae, Reoviridae, Astroviridae and Picornaviridae, all of which contain human-infecting species. In phylogenetic analyses, novel vampire bat viruses most frequently grouped with other bat viruses that are not currently known to infect humans. In agreement, machine learning models built from only phylogenetic information ranked all novel viruses similarly, yielding little insight into zoonotic potential. In contrast, genome composition-based machine learning models estimated different levels of zoonotic potential, even for closely related viruses, categorizing one out of four detected hepeviruses and two out of three picornaviruses as having high priority for further research. We highlight the value of evaluating zoonotic potential beyond ad hoc consideration of phylogeny and provide surveillance recommendations for novel viruses in a wildlife host which has frequent contact with humans and domestic animals.},
}

Animals
Chiroptera/*virology
Disease Reservoirs/veterinary/virology
Feces/virology
Genome, Viral/genetics
Humans
Machine Learning
Metagenomics
Phylogeny
Rabies virus/classification/genetics/isolation & purification
Saliva/virology
Viruses/classification/genetics/*isolation & purification
Zoonoses/*virology

@article {pmid32972018,
year = {2020},
author = {Hewson, I and Johnson, MR and Tibbetts, IR},
title = {An Unconventional Flavivirus and Other RNA Viruses in the Sea Cucumber (Holothuroidea; Echinodermata) Virome.},
journal = {Viruses},
volume = {12},
number = {9},
pages = {},
pmid = {32972018},
issn = {1999-4915},
mesh = {Animals ; DNA Viruses ; Echinodermata/*virology ; Ecology ; Flavivirus/*classification/genetics ; Genome, Viral ; Metagenome ; Metagenomics ; RNA Viruses/*classification/genetics ; Sea Cucumbers/*virology ; Seawater/virology ; *Virome ; },
abstract = {Sea cucumbers (Holothuroidea; Echinodermata) are ecologically significant constituents of benthic marine habitats. We surveilled RNA viruses inhabiting eight species (representing four families) of holothurian collected from four geographically distinct locations by viral metagenomics, including a single specimen of Apostichopus californicus affected by a hitherto undocumented wasting disease. The RNA virome comprised genome fragments of both single-stranded positive sense and double stranded RNA viruses, including those assigned to the Picornavirales, Ghabrivirales, and Amarillovirales. We discovered an unconventional flavivirus genome fragment which was most similar to a shark virus. Ghabivirales-like genome fragments were most similar to fungal totiviruses in both genome architecture and homology and had likely infected mycobiome constituents. Picornavirales, which are commonly retrieved in host-associated viral metagenomes, were similar to invertebrate transcriptome-derived picorna-like viruses. The greatest number of viral genome fragments was recovered from the wasting A. californicus library compared to the asymptomatic A. californicus library. However, reads from the asymptomatic library recruited to nearly all recovered wasting genome fragments, suggesting that they were present but not well represented in the grossly normal specimen. These results expand the known host range of flaviviruses and suggest that fungi and their viruses may play a role in holothurian ecology.},
}

Animals
DNA Viruses
Echinodermata/*virology
Ecology
Flavivirus/*classification/genetics
Genome, Viral
Metagenome
Metagenomics
RNA Viruses/*classification/genetics
Sea Cucumbers/*virology
Seawater/virology
*Virome

@article {pmid32957679,
year = {2020},
author = {Rossi, A and Treu, L and Toppo, S and Zschach, H and Campanaro, S and Dutilh, BE},
title = {Evolutionary Study of the Crassphage Virus at Gene Level.},
journal = {Viruses},
volume = {12},
number = {9},
pages = {},
pmid = {32957679},
issn = {1999-4915},
mesh = {Bacteriophages/genetics ; Capsid Proteins/genetics ; DNA Viruses/*genetics ; *Evolution, Molecular ; Feces/virology ; Gastrointestinal Microbiome ; Genome, Viral ; Humans ; Metagenome ; Metagenomics ; Phylogeny ; Viral Proteins/genetics ; Viruses/*genetics ; },
abstract = {crAss-like viruses are a putative family of bacteriophages recently discovered. The eponym of the clade, crAssphage, is an enteric bacteriophage estimated to be present in at least half of the human population and it constitutes up to 90% of the sequences in some human fecal viral metagenomic datasets. We focused on the evolutionary dynamics of the genes encoded on the crAssphage genome. By investigating the conservation of the genes, a consistent variation in the evolutionary rates across the different functional groups was found. Gene duplications in crAss-like genomes were detected. By exploring the differences among the functional categories of the genes, we confirmed that the genes encoding capsid proteins were the most ubiquitous, despite their overall low sequence conservation. It was possible to identify a core of proteins whose evolutionary trees strongly correlate with each other, suggesting their genetic interaction. This group includes the capsid proteins, which are thus established as extremely suitable for rebuilding the phylogenetic tree of this viral clade. A negative correlation between the ubiquity and the conservation of viral protein sequences was shown. Together, this study provides an in-depth picture of the evolution of different genes in crAss-like viruses.},
}

Bacteriophages/genetics
Capsid Proteins/genetics
DNA Viruses/*genetics
*Evolution, Molecular
Feces/virology
Gastrointestinal Microbiome
Genome, Viral
Humans
Metagenome
Metagenomics
Phylogeny
Viral Proteins/genetics
Viruses/*genetics

@article {pmid32879395,
year = {2020},
author = {Richard, JC and Leis, E and Dunn, CD and Agbalog, R and Waller, D and Knowles, S and Putnam, J and Goldberg, TL},
title = {Mass mortality in freshwater mussels (Actinonaias pectorosa) in the Clinch River, USA, linked to a novel densovirus.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {14498},
pmid = {32879395},
issn = {2045-2322},
mesh = {Animals ; Biodiversity ; Computational Biology ; Densovirus/*pathogenicity ; Ecosystem ; Environmental Monitoring ; Genome ; Genomics ; Open Reading Frames ; Parvoviridae Infections/mortality/*veterinary ; Phylogeny ; Rivers ; Tennessee ; Unionidae/*virology ; Viral Load ; Virginia ; },
abstract = {Freshwater mussels (order Unionida) are among the world's most biodiverse but imperiled taxa. Recent unionid mass mortality events around the world threaten ecosystem services such as water filtration, nutrient cycling, habitat stabilization, and food web enhancement, but causes have remained elusive. To examine potential infectious causes of these declines, we studied mussels in Clinch River, Virginia and Tennessee, USA, where the endemic and once-predominant pheasantshell (Actinonaias pectorosa) has suffered precipitous declines since approximately 2016. Using metagenomics, we identified 17 novel viruses in Clinch River pheasantshells. However, only one virus, a novel densovirus (Parvoviridae; Densovirinae), was epidemiologically linked to morbidity. Clinch densovirus 1 was 11.2 times more likely to be found in cases (moribund mussels) than controls (apparently healthy mussels from the same or matched sites), and cases had 2.7 (log10) times higher viral loads than controls. Densoviruses cause lethal epidemic disease in invertebrates, including shrimp, cockroaches, crickets, moths, crayfish, and sea stars. Viral infection warrants consideration as a factor in unionid mass mortality events either as a direct cause, an indirect consequence of physiological compromise, or a factor interacting with other biological and ecological stressors to precipitate mortality.},
}

Animals
Biodiversity
Computational Biology
Densovirus/*pathogenicity
Ecosystem
Environmental Monitoring
Genome
Genomics
Open Reading Frames
Parvoviridae Infections/mortality/*veterinary
Phylogeny
Rivers
Tennessee
Unionidae/*virology
Viral Load
Virginia

@article {pmid32545455,
year = {2020},
author = {Klimina, KM and Voroshilova, VN and Poluektova, EU and Veselovsky, VA and Yunes, RA and Kovtun, AS and Kudryavtseva, AV and Kasianov, AS and Danilenko, VN},
title = {Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota.},
journal = {Toxins},
volume = {12},
number = {6},
pages = {},
pmid = {32545455},
issn = {2072-6651},
support = {18-34-00011//Russian Foundation for Basic Research/International ; 19-74-00146//Russian Science Foundation/International ; },
mesh = {Bacteria/classification/*genetics ; Databases, Genetic ; Feces/microbiology ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; Humans ; Intestines/*microbiology ; *Metagenome ; *Metagenomics ; Ribotyping ; Toxin-Antitoxin Systems/*genetics ; },
abstract = {The human gastrointestinal microbiota (HGM) is known for its rich diversity of bacterial species and strains. Yet many studies stop at characterizing the HGM at the family level. This is mainly due to lack of adequate methods for a high-resolution profiling of the HGM. One way to characterize the strain diversity of the HGM is to look for strain-specific functional markers. Here, we propose using type II toxin-antitoxin systems (TAS). To identify TAS systems in the HGM, we previously developed the software TAGMA. This software was designed to detect the TAS systems, MazEF and RelBE, in lactobacilli and bifidobacteria. In this study, we updated the gene catalog created previously and used it to test our software anew on 1346 strains of bacteria, which belonged to 489 species and 49 genera. We also sequenced the genomes of 20 fecal samples and analyzed the results with TAGMA. Although some differences were detected at the strain level, the results showed no particular difference in the bacterial species between our method and other classic analysis software. These results support the use of the updated catalog of genes encoding type II TAS as a useful tool for computer-assisted species and strain characterization of the HGM.},
}

Bacteria/classification/*genetics
Databases, Genetic
Feces/microbiology
*Gastrointestinal Microbiome
Gene Expression Profiling
Humans
Intestines/*microbiology
*Metagenome
*Metagenomics
Ribotyping
Toxin-Antitoxin Systems/*genetics

@article {pmid32293504,
year = {2020},
author = {Raspini, B and Porri, D and De Giuseppe, R and Chieppa, M and Liso, M and Cerbo, RM and Civardi, E and Garofoli, F and Monti, MC and Vacca, M and De Angelis, M and Cena, H},
title = {Prenatal and postnatal determinants in shaping offspring's microbiome in the first 1000 days: study protocol and preliminary results at one month of life.},
journal = {Italian journal of pediatrics},
volume = {46},
number = {1},
pages = {45},
pmid = {32293504},
issn = {1824-7288},
mesh = {Adult ; Child Development/*physiology ; Female ; Fetal Development/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Infant, Newborn ; Italy ; Longitudinal Studies ; Male ; *Maternal Health ; Pregnancy ; Prospective Studies ; },
abstract = {BACKGROUND: Fetal programming during in utero life defines the set point of physiological and metabolic responses that lead into adulthood; events happening in "the first 1,000 days" (from conception to 2-years of age), play a role in the development of non-communicable diseases (NCDs). The infant gut microbiome is a highly dynamic organ, which is sensitive to maternal and environmental factors and is one of the elements driving intergenerational NCDs' transmission. The A.MA.MI (Alimentazione MAmma e bambino nei primi MIlle giorni) project aims at investigating the correlation between several factors, from conception to the first year of life, and infant gut microbiome composition. We described the study design of the A.MA.MI study and presented some preliminary results.

METHODS: A.MA.MI is a longitudinal, prospective, observational study conducted on a group of mother-infant pairs (n = 60) attending the Neonatal Unit, Fondazione IRCCS Policlinico San Matteo, Pavia (Italy). The study was planned to provide data collected at T0, T1, T2 and T3, respectively before discharge, 1,6 and 12 months after birth. Maternal and infant anthropometric measurements were assessed at each time. Other variables evaluated were: pre-pregnancy/gestational weight status (T0), maternal dietary habits/physical activity (T1-T3); infant medical history, type of feeding, antibiotics/probiotics/supplements use, environment exposures (e.g cigarette smoking, pets, environmental temperature) (T1-T3). Infant stool samples were planned to be collected at each time and analyzed using metagenomics 16S ribosomal RNA gene sequence-based methods.

RESULTS: Birth mode (cesarean section vs. vaginal delivery) and maternal pre pregnancy BMI (BMI < 25 Kg/m2 vs. BMI ≥ 25 Kg/m2), significant differences were found at genera and species levels (T0). Concerning type of feeding (breastfed vs. formula-fed), gut microbiota composition differed significantly at genus and species level (T1).

CONCLUSION: These preliminary and explorative results confirmed that pre-pregnancy, mode of delivery and infant factors likely impact infant microbiota composition at different levels.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT04122612.},
}

Adult
Child Development/*physiology
Female
Fetal Development/*physiology
Gastrointestinal Microbiome/*physiology
Humans
Infant
Infant, Newborn
Italy
Longitudinal Studies
Male
*Maternal Health
Pregnancy
Prospective Studies

@article {pmid32200751,
year = {2020},
author = {Quistad, SD and Doulcier, G and Rainey, PB},
title = {Experimental manipulation of selfish genetic elements links genes to microbial community function.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190681},
pmid = {32200751},
issn = {1471-2970},
mesh = {Bacteria/*genetics ; Metagenome ; Metagenomics ; Microbiota/*genetics ; *Repetitive Sequences, Nucleic Acid ; *Soil Microbiology ; },
abstract = {Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}

Bacteria/*genetics
Metagenome
Metagenomics
Microbiota/*genetics
*Repetitive Sequences, Nucleic Acid
*Soil Microbiology

@article {pmid32200748,
year = {2020},
author = {VanInsberghe, D and Arevalo, P and Chien, D and Polz, MF},
title = {How can microbial population genomics inform community ecology?.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190253},
pmid = {32200748},
issn = {1471-2970},
mesh = {Archaea/*genetics ; Bacteria/*genetics ; *Gene Flow ; *Metagenomics ; Microbiota/*genetics ; },
abstract = {Populations are fundamental units of ecology and evolution, but can we define them for bacteria and archaea in a biologically meaningful way? Here, we review why population structure is difficult to recognize in microbes and how recent advances in measuring contemporary gene flow allow us to identify clearly delineated populations among collections of closely related genomes. Such structure can arise from preferential gene flow caused by coexistence and genetic similarity, defining populations based on biological mechanisms. We show that such gene flow units are sufficiently genetically isolated for specific adaptations to spread, making them also ecological units that are differentially adapted compared to their closest relatives. We discuss the implications of these observations for measuring bacterial and archaeal diversity in the environment. We show that operational taxonomic units defined by 16S rRNA gene sequencing have woefully poor resolution for ecologically defined populations and propose monophyletic clusters of nearly identical ribosomal protein genes as an alternative measure for population mapping in community ecological studies employing metagenomics. These population-based approaches have the potential to provide much-needed clarity in interpreting the vast microbial diversity in human and environmental microbiomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}

Archaea/*genetics
Bacteria/*genetics
*Gene Flow
*Metagenomics
Microbiota/*genetics

@article {pmid32200740,
year = {2020},
author = {Garcia, CA and Hagstrom, GI and Larkin, AA and Ustick, LJ and Levin, SA and Lomas, MW and Martiny, AC},
title = {Linking regional shifts in microbial genome adaptation with surface ocean biogeochemistry.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190254},
pmid = {32200740},
issn = {1471-2970},
support = {T32 AI141346/AI/NIAID NIH HHS/United States ; },
mesh = {*Adaptation, Biological ; Atlantic Ocean ; Genome, Microbial/*physiology ; Indian Ocean ; *Metagenome ; Microbiota/*genetics ; Pacific Ocean ; Seawater/*chemistry ; },
abstract = {Linking 'omics measurements with biogeochemical cycles is a widespread challenge in microbial community ecology. Here, we propose applying genomic adaptation as 'biosensors' for microbial investments to overcome nutrient stress. We then integrate this genomic information with a trait-based model to predict regional shifts in the elemental composition of marine plankton communities. We evaluated this approach using metagenomic and particulate organic matter samples from the Atlantic, Indian and Pacific Oceans. We find that our genome-based trait model significantly improves our prediction of particulate C : P (carbon : phosphorus) across ocean regions. Furthermore, we detect previously unrecognized ocean areas of iron, nitrogen and phosphorus stress. In many ecosystems, it can be very challenging to quantify microbial stress. Thus, a carefully calibrated genomic approach could become a widespread tool for understanding microbial responses to environmental changes and the biogeochemical outcomes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}

*Adaptation, Biological
Atlantic Ocean
Genome, Microbial/*physiology
Indian Ocean
*Metagenome
Microbiota/*genetics
Pacific Ocean
Seawater/*chemistry

@article {pmid32200735,
year = {2020},
author = {Rainey, PB and Quistad, SD},
title = {Toward a dynamical understanding of microbial communities.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {375},
number = {1798},
pages = {20190248},
pmid = {32200735},
issn = {1471-2970},
mesh = {Bacteria/*genetics ; *Bacterial Physiological Phenomena/genetics ; *Biological Evolution ; *Gene Transfer, Horizontal ; *Metagenome ; *Microbiota ; },
abstract = {The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.},
}

Bacteria/*genetics
*Bacterial Physiological Phenomena/genetics
*Biological Evolution
*Gene Transfer, Horizontal
*Metagenome
*Microbiota

@article {pmid33597537,
year = {2021},
author = {Jensen, BAH and Holm, JB and Larsen, IS and von Burg, N and Derer, S and Sonne, SB and Pærregaard, SI and Damgaard, MV and Indrelid, SA and Rivollier, A and Agrinier, AL and Sulek, K and Arnoldussen, YJ and Fjære, E and Marette, A and Angell, IL and Rudi, K and Treebak, JT and Madsen, L and Åkesson, CP and Agace, W and Sina, C and Kleiveland, CR and Kristiansen, K and Lea, TE},
title = {Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {1093},
pmid = {33597537},
issn = {2041-1723},
support = {//CIHR/Canada ; },
mesh = {Animals ; Diet ; Forkhead Transcription Factors/immunology/metabolism ; Homeostasis/immunology ; Interleukin-17/immunology/metabolism ; Intestine, Large/*immunology/metabolism/microbiology ; Intestine, Small/*immunology/metabolism/microbiology ; Male ; Methylococcus capsulatus/chemistry/*immunology ; Mice, Inbred C57BL ; Microbiota/*immunology ; Nuclear Receptor Subfamily 1, Group F, Member 3/immunology/metabolism ; Obesity/immunology ; Proteins/*immunology/metabolism ; T-Lymphocytes, Regulatory/*immunology/metabolism ; },
abstract = {Interactions between host and gut microbial communities are modulated by diets and play pivotal roles in immunological homeostasis and health. We show that exchanging the protein source in a high fat, high sugar, westernized diet from casein to whole-cell lysates of the non-commensal bacterium Methylococcus capsulatus Bath is sufficient to reverse western diet-induced changes in the gut microbiota to a state resembling that of lean, low fat diet-fed mice, both under mild thermal stress (T22 °C) and at thermoneutrality (T30 °C). Concomitant with microbiota changes, mice fed the Methylococcus-based western diet exhibit improved glucose regulation, reduced body and liver fat, and diminished hepatic immune infiltration. Intake of the Methylococcu-based diet markedly boosts Parabacteroides abundances in a manner depending on adaptive immunity, and upregulates triple positive (Foxp3+RORγt+IL-17+) regulatory T cells in the small and large intestine. Collectively, these data point to the potential for leveraging the use of McB lysates to improve immunometabolic homeostasis.},
}

Animals
Diet
Forkhead Transcription Factors/immunology/metabolism
Homeostasis/immunology
Interleukin-17/immunology/metabolism
Intestine, Large/*immunology/metabolism/microbiology
Intestine, Small/*immunology/metabolism/microbiology
Male
Methylococcus capsulatus/chemistry/*immunology
Mice, Inbred C57BL
Microbiota/*immunology
Nuclear Receptor Subfamily 1, Group F, Member 3/immunology/metabolism
Obesity/immunology
Proteins/*immunology/metabolism
T-Lymphocytes, Regulatory/*immunology/metabolism

@article {pmid33597514,
year = {2021},
author = {Chen, C and Zhou, Y and Fu, H and Xiong, X and Fang, S and Jiang, H and Wu, J and Yang, H and Gao, J and Huang, L},
title = {Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {1106},
pmid = {33597514},
issn = {2041-1723},
mesh = {Animals ; Bacteria/classification/genetics ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Microbial/genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Phylogeny ; Species Specificity ; Swine ; },
abstract = {Gut microbiota plays an important role in pig health and production. Still, availability of sequenced genomes and functional information for most pig gut microbes remains limited. Here we perform a landscape survey of the swine gut microbiome, spanning extensive sample sources by deep metagenomic sequencing resulting in an expanded gene catalog named pig integrated gene catalog (PIGC), containing 17,237,052 complete genes clustered at 90% protein identity from 787 gut metagenomes, of which 28% are unknown proteins. Using binning analysis, 6339 metagenome-assembled genomes (MAGs) were obtained, which were clustered to 2673 species-level genome bins (SGBs), among which 86% (2309) SGBs are unknown based on current databases. Using the present gene catalog and MAGs, we identified several strain-level differences between the gut microbiome of wild boars and commercial Duroc pigs. PIGC and MAGs provide expanded resources for swine gut microbiome-related research.},
}

Animals
Bacteria/classification/genetics
Female
Gastrointestinal Microbiome/*genetics
Genes, Microbial/genetics
High-Throughput Nucleotide Sequencing/*methods
Metagenome/*genetics
Metagenomics/*methods
Phylogeny
Species Specificity
Swine

@article {pmid33498458,
year = {2021},
author = {Aylward, FO and Moniruzzaman, M},
title = {ViralRecall-A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in 'Omic Data.},
journal = {Viruses},
volume = {13},
number = {2},
pages = {},
pmid = {33498458},
issn = {1999-4915},
mesh = {Amino Acid Sequence ; Biodiversity ; Computational Biology/*methods ; Cytoplasm/*virology ; Eukaryotic Cells/*virology ; Gene Library ; Genome, Viral ; Giant Viruses/*classification/genetics ; *Metagenomics ; Phylogeny ; },
abstract = {Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as nucleo-cytoplasmic large DNA viruses (NCLDVs), these eukaryotic viruses harbor the largest and most complex viral genomes known. Studies have shown that NCLDVs are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDVs is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here, we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in 'omic data. This tool leverages a library of giant virus orthologous groups (GVOGs) to identify sequences that bear signatures of NCLDVs. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall.},
}

Amino Acid Sequence
Biodiversity
Computational Biology/*methods
Cytoplasm/*virology
Eukaryotic Cells/*virology
Gene Library
Genome, Viral
Giant Viruses/*classification/genetics
*Metagenomics
Phylogeny

@article {pmid33124780,
year = {2021},
author = {Chen, BD and Jia, XM and Xu, JY and Zhao, LD and Ji, JY and Wu, BX and Ma, Y and Li, H and Zuo, XX and Pan, WY and Wang, XH and Ye, S and Tsokos, GC and Wang, J and Zhang, X},
title = {An Autoimmunogenic and Proinflammatory Profile Defined by the Gut Microbiota of Patients With Untreated Systemic Lupus Erythematosus.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {73},
number = {2},
pages = {232-243},
doi = {10.1002/art.41511},
pmid = {33124780},
issn = {2326-5205},
mesh = {Actinobacteria ; Actinomyces ; Adult ; Amino Acids, Branched-Chain/biosynthesis ; Animals ; Antirheumatic Agents/therapeutic use ; Autoantibodies/*immunology ; Autoantigens/*immunology ; Bacteroides fragilis ; Case-Control Studies ; Clostridiales ; Clostridium ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/genetics/*immunology ; Humans ; Lipopolysaccharides/biosynthesis ; Lupus Erythematosus, Systemic/drug therapy/immunology/*microbiology/physiopathology ; Male ; Metagenomics ; Mice ; Mice, Inbred MRL lpr ; Molecular Mimicry/*immunology ; Mouth/microbiology ; Polymorphism, Single Nucleotide ; Young Adult ; },
abstract = {OBJECTIVE: Changes in gut microbiota have been linked to systemic lupus erythematosus (SLE), but knowledge is limited. Our study aimed to provide an in-depth understanding of the contribution of gut microbiota to the immunopathogenesis of SLE.

METHODS: Fecal metagenomes from 117 patients with untreated SLE and 52 SLE patients posttreatment were aligned with 115 matched healthy controls and analyzed by whole-genome profiling. For comparison, we assessed the fecal metagenome of MRL/lpr mice. The oral microbiota origin of the gut species that existed in SLE patients was documented by single-nucleotide polymorphism-based strain-level analyses. Functional validation assays were performed to demonstrate the molecular mimicry of newly found microbial peptides.

RESULTS: Gut microbiota from individuals with SLE displayed significant differences in microbial composition and function compared to healthy controls. Certain species, including the Clostridium species ATCC BAA-442 as well as Atopobium rimae, Shuttleworthia satelles, Actinomyces massiliensis, Bacteroides fragilis, and Clostridium leptum, were enriched in SLE gut microbiota and reduced after treatment. Enhanced lipopolysaccharide biosynthesis aligned with reduced branched chain amino acid biosynthesis was observed in the gut of SLE patients. The findings in mice were consistent with our findings in human subjects. Interestingly, some species with an oral microbiota origin were enriched in the gut of SLE patients. Functional validation assays demonstrated the proinflammatory capacities of some microbial peptides derived from SLE-enriched species.

CONCLUSION: This study provides detailed information on the microbiota of untreated patients with SLE, including their functional signatures, similarities with murine counterparts, oral origin, and the definition of autoantigen-mimicking peptides. Our data demonstrate that microbiome-altering approaches may offer valuable adjuvant therapies in SLE.},
}

Actinobacteria
Actinomyces
Adult
Amino Acids, Branched-Chain/biosynthesis
Animals
Antirheumatic Agents/therapeutic use
Autoantibodies/*immunology
Autoantigens/*immunology
Bacteroides fragilis
Case-Control Studies
Clostridiales
Clostridium
Disease Models, Animal
Female
Gastrointestinal Microbiome/genetics/*immunology
Humans
Lipopolysaccharides/biosynthesis
Lupus Erythematosus, Systemic/drug therapy/immunology/*microbiology/physiopathology
Male
Metagenomics
Mice
Mice, Inbred MRL lpr
Molecular Mimicry/*immunology
Mouth/microbiology
Polymorphism, Single Nucleotide
Young Adult

@article {pmid32512689,
year = {2020},
author = {Iizuka, K and Yabe, D},
title = {The Role of Metagenomics in Precision Nutrition.},
journal = {Nutrients},
volume = {12},
number = {6},
pages = {},
pmid = {32512689},
issn = {2072-6643},
support = {20K11645//Japan Society for the Promotion of Science/ ; 19-049//Suzuken Memorial Foundation/ ; },
mesh = {Gastrointestinal Microbiome ; Humans ; *Metagenomics ; *Nutrigenomics ; *Nutrition Policy ; *Nutritional Status ; *Precision Medicine ; },
abstract = {Conventional recommendations for dietary intervention have been generally based on population groups divided by gender and age [...].},
}

Gastrointestinal Microbiome
Humans
*Metagenomics
*Nutrigenomics
*Nutrition Policy
*Nutritional Status
*Precision Medicine

@article {pmid32482164,
year = {2020},
author = {Costa, OYA and de Hollander, M and Pijl, A and Liu, B and Kuramae, EE},
title = {Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {76},
pmid = {32482164},
issn = {2049-2618},
support = {729.004.003//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/International ; 202496/2015-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/International ; },
mesh = {Bacteria/enzymology/genetics ; Biodegradation, Environmental ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; *Polymers/metabolism ; },
abstract = {BACKGROUND: Cultivation-independent methods, including metagenomics, are tools for the exploration and discovery of biotechnological compounds produced by microbes in natural environments. Glycoside hydrolases (GHs) enzymes are extremely desired and important in the industry of production for goods and biofuel and removal of problematic biofilms and exopolysaccharide (EPS). Biofilms and EPS are complex, requiring a wide range of enzymes for a complete degradation. The aim of this study was to identify potential GH microbial producers and GH genes with biotechnological potential, using EPS-complex structure (WH15EPS) of Acidobacteria Granulicella sp. strain WH15 as an enrichment factor, in cultivation-independent and cultivation-dependent methods. We performed stable isotope probing (SIP) combined with metagenomics on topsoil litter amended with WH15EPS and coupled solid culture-EPS amended medium with metagenomics.

RESULTS: SIP metagenome analysis of the soil litter demonstrated that phyla Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes were the most abundant in WH15EPS amended and unamended treatments. The enrichment cultures in solid culture medium coupled to metagenomics demonstrated an enrichment in Proteobacteria, and the metagenome assembly of this enrichment cultures resulted in 4 metagenome-assembled genomes (MAGs) of microbes with low identity (42-86%) to known microorganisms. Among all carbohydrate-active enzymes (CAZymes) retrieved genes, glycoside transferase (GT) was the most abundant family, either in culture-independent or culture-based metagenome datasets. Within the glycoside hydrolases (GHs), GH13 was the most abundant family in both metagenome datasets. In the "heavy" fraction of the culture-independent metagenome SIP dataset, GH109 (α-N-acetylgalactosaminidases), GH117 (agarases), GH50 (agarases), GH32 (invertases and inulinases), GH17 (endoglucanases), and GH71 (mutanases) families were more abundant in comparison with the controls. Those GH families are affiliated to microorganism that are probably capable to degrade WH15EPS and potentially applicable for biofilm deconstruction. Subsequent in culture-based metagenome, the assembled 4 MAGs (unclassified Proteobacteria) also contained GH families of interest, involving mannosidases, lysozymes, galactosidases, and chitinases.

CONCLUSIONS: We demonstrated that functional diversity induced by the presence of WH15EPS in both culture-independent and culture-dependent approaches was enriched in GHs, such as amylases and endoglucanases that could be applied in chemical, pharmaceutical, and food industrial sectors. Furthermore, WH15EPS may be used for the investigation and isolation of yet unknown taxa, such as unclassified Proteobacteria and Planctomycetes, increasing the number of current cultured bacterial representatives with potential biotechnological traits. Video Abstract.},
}

Bacteria/enzymology/genetics
Biodegradation, Environmental
*Metagenome
Metagenomics
*Microbiota/genetics
*Polymers/metabolism

@article {pmid32438915,
year = {2020},
author = {Zolti, A and Green, SJ and Sela, N and Hadar, Y and Minz, D},
title = {The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {71},
pmid = {32438915},
issn = {2049-2618},
support = {IS- 4662-13//United States - Israel Binational Agricultural Research and Development Fund/International ; M34-011//USAID-MERK/International ; 821-0142-13//Ministry of Agriculture and Rural Development (IL)/International ; },
mesh = {*Biosensing Techniques ; *Host Microbial Interactions ; Metagenomics ; *Microbiota/genetics ; *Plant Roots/microbiology ; Soil Microbiology ; *Stress, Physiological ; },
abstract = {BACKGROUND: Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants.

RESULTS: Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies, provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt.

CONCLUSIONS: We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms. This study is a proof-of-concept for the use of microbial communities as microsensors, with great potential for interrogation of a wide range of host systems. Video Abstract.},
}

*Biosensing Techniques
*Host Microbial Interactions
Metagenomics
*Microbiota/genetics
*Plant Roots/microbiology
Soil Microbiology
*Stress, Physiological

@article {pmid32414415,
year = {2020},
author = {F Escapa, I and Huang, Y and Chen, T and Lin, M and Kokaras, A and Dewhirst, FE and Lemon, KP},
title = {Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {65},
pmid = {32414415},
issn = {2049-2618},
support = {R01 AI101018/AI/NIAID NIH HHS/United States ; R01GM117174//National Institute of General Medical Sciences (US)/International ; R01AI101018//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/International ; R37 DE016937/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; R01DE024468/DE/NIDCR NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; R37DE016937/DE/NIDCR NIH HHS/United States ; },
mesh = {*Bacteria/genetics ; Bayes Theorem ; *Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; Humans ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Species Specificity ; },
abstract = {BACKGROUND: The low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can resolve 16S rRNA gene sequences into high-resolution amplicon sequence variants (ASVs), which represent consistent labels comparable across studies. Assigning these ASVs to species-level taxonomy strengthens the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies and further facilitates data comparison across studies.

RESULTS: To achieve this, we developed a broadly applicable method for constructing high-resolution training sets based on the phylogenic relationships among microbes found in a habitat of interest. When used with the naïve Bayesian Ribosomal Database Project (RDP) Classifier, this training set achieved species/supraspecies-level taxonomic assignment of 16S rRNA gene-derived ASVs. The key steps for generating such a training set are (1) constructing an accurate and comprehensive phylogenetic-based, habitat-specific database; (2) compiling multiple 16S rRNA gene sequences to represent the natural sequence variability of each taxon in the database; (3) trimming the training set to match the sequenced regions, if necessary; and (4) placing species sharing closely related sequences into a training-set-specific supraspecies taxonomic level to preserve subgenus-level resolution. As proof of principle, we developed a V1-V3 region training set for the bacterial microbiota of the human aerodigestive tract using the full-length 16S rRNA gene reference sequences compiled in our expanded Human Oral Microbiome Database (eHOMD). We also overcame technical limitations to successfully use Illumina sequences for the 16S rRNA gene V1-V3 region, the most informative segment for classifying bacteria native to the human aerodigestive tract. Finally, we generated a full-length eHOMD 16S rRNA gene training set, which we used in conjunction with an independent PacBio single molecule, real-time (SMRT)-sequenced sinonasal dataset to validate the representation of species in our training set. This also established the effectiveness of a full-length training set for assigning taxonomy of long-read 16S rRNA gene datasets.

CONCLUSION: Here, we present a systematic approach for constructing a phylogeny-based, high-resolution, habitat-specific training set that permits species/supraspecies-level taxonomic assignment to short- and long-read 16S rRNA gene-derived ASVs. This advancement enhances the ecological and/or clinical relevance of 16S rRNA gene-based microbiota studies. Video Abstract.},
}

*Bacteria/genetics
Bayes Theorem
*Computational Biology/methods
Gastrointestinal Microbiome/genetics
Humans
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Species Specificity

@article {pmid33517034,
year = {2021},
author = {Dou, R and Sun, J and Lu, J and Deng, F and Yang, C and Lu, G and Dang, Z},
title = {Bacterial communities and functional genes stimulated during phenanthrene degradation in soil by bio-microcapsules.},
journal = {Ecotoxicology and environmental safety},
volume = {212},
number = {},
pages = {111970},
doi = {10.1016/j.ecoenv.2021.111970},
pmid = {33517034},
issn = {1090-2414},
mesh = {Bacteria/metabolism ; *Biodegradation, Environmental ; Capsules/metabolism ; Environmental Pollutants/metabolism ; Metagenomics ; Microbiota ; Phenanthrenes/*metabolism ; Polycyclic Aromatic Hydrocarbons/analysis ; Soil/chemistry ; *Soil Microbiology ; Soil Pollutants/analysis/*metabolism ; },
abstract = {In this study, a taxonomic and functional metagenomic method was used to investigate the difference produced between degrading bacteria immobilized in layer-by-layer assembly (LBL) microcapsules or not during the bioremediation of a soil polluted with phenanthrene (PHE). Bioaugmentation with LBL microcapsule immobilized degrading bacteria could result in different changes of native microbial communities, shifting the functional gene constructions of polluted soils. The LBL treatment enhanced PHE degradation (initial concentration of 100 mg kg-1 dry soil) by 60% after 25 d compared to the free bacteria (FB). The enhancing effect of PHE degradation produced by the LBL treatment was found to be significantly associated with some crucial phyla (e.g., Bacteroides, Gemmatimonadetes and Acidobacteria) and genera including Streptomyces, Ramlibacter, Mycobacterium, Phycicoccus, Gemmatirosa, Flavisolibacter, Micromonospora, Acid_Candidatus_Koribacter and Gemmatimonas. The main differences of functional metagenomics between LBL and FB treatments were observed in higher levels in metabolism of aromatic hydrocarbons and its related functions or enzymes in the former, e.g., membrane transport systems, binding, substrate transporter, cleavage enzymes, dehydrogenation, oxidase, esterase and glycosidase, greatly favoring PHE mineralization. Therefore, our results provide useful findings on understanding of how immobilization strategies can influence the taxonomic and functional gene composition in soils, as well as polycyclic aromatic hydrocarbons (PAH) degradation.},
}

Bacteria/metabolism
*Biodegradation, Environmental
Capsules/metabolism
Environmental Pollutants/metabolism
Metagenomics
Microbiota
Phenanthrenes/*metabolism
Polycyclic Aromatic Hydrocarbons/analysis
Soil/chemistry
*Soil Microbiology
Soil Pollutants/analysis/*metabolism

@article {pmid33422963,
year = {2021},
author = {Pérez-Cataluña, A and Cuevas-Ferrando, E and Randazzo, W and Sánchez, G},
title = {Bias of library preparation for virome characterization in untreated and treated wastewaters.},
journal = {The Science of the total environment},
volume = {767},
number = {},
pages = {144589},
doi = {10.1016/j.scitotenv.2020.144589},
pmid = {33422963},
issn = {1879-1026},
mesh = {Gene Library ; Humans ; Metagenomics ; Virome ; *Viruses/genetics ; *Waste Water ; },
abstract = {The use of metagenomics for virome characterization and its implementation for wastewater analyses, including wastewater-based epidemiology, has increased in the last years. However, the lack of standardized methods can led to highly different results. The aim of this work was to analyze virome profiles in upstream and downstream wastewater samples collected from four wastewater treatment plants (WWTPs) using two different library preparation kits. Viral particles were enriched from wastewater concentrates using a filtration and nuclease digestion procedure prior to total nucleic acid (NA) extraction. Sequencing was performed using the ScriptSeq v2 RNA-Seq (LS) and the NEBNext Ultra II RNA (NB) library preparation kits. Cleaned reads and contigs were annotated using a curated in-house database composed by reads assigned to viruses at NCBI. Significant differences in viral families and in the ratio of detection were shown between the two library kits used. The use of LS library showed Virgaviridae, Microviridae and Siphoviridae as the most abundant families; while Ackermannviridae and Helleviridae were highly represented within the NB library. Additionally, the two sequencing libraries produced outcomes that differed in the detection of viral indicators. These results highlighted the importance of library selection for studying viruses in untreated and treated wastewater. Our results underline the need for further studies to elucidate the influence of sequencing procedures in virome profiles in wastewater matrices in order to improve the knowledge of the virome in the water environment.},
}

Gene Library
Humans
Metagenomics
Virome
*Viruses/genetics
*Waste Water

@article {pmid33233680,
year = {2020},
author = {Hewson, I and Aquino, CA and DeRito, CM},
title = {Virome Variation during Sea Star Wasting Disease Progression in Pisaster ochraceus (Asteroidea, Echinodermata).},
journal = {Viruses},
volume = {12},
number = {11},
pages = {},
pmid = {33233680},
issn = {1999-4915},
mesh = {Animals ; Disease Progression ; Genetic Variation ; Longitudinal Studies ; Metagenome ; Metagenomics ; Starfish/*virology ; *Virome ; Viruses/classification/*genetics ; Wasting Syndrome/*veterinary/*virology ; },
abstract = {Sea star wasting disease (SSWD) is a condition that has affected asteroids for over 120 years, yet mechanistic understanding of this wasting etiology remains elusive. We investigated temporal virome variation in two Pisaster ochraceus specimens that wasted in the absence of external stimuli and two specimens that did not experience SSWD for the duration of our study, and compared viromes of wasting lesion margin tissues to both artificial scar margins and grossly normal tissues over time. Global assembly of all SSWD-affected tissue libraries resulted in 24 viral genome fragments represented in >1 library. Genome fragments mostly matched densoviruses and picornaviruses with fewer matching nodaviruses, and a sobemovirus. Picornavirus-like and densovirus-like genome fragments were most similar to viral genomes recovered in metagenomic study of other marine invertebrates. Read recruitment revealed only two picornavirus-like genome fragments that recruited from only SSWD-affected specimens, but neither was unique to wasting lesions. Wasting lesion margin reads recruited to a greater number of viral genotypes (i.e., richness) than did either scar tissue and grossly normal tissue reads. Taken together, these data suggest that no single viral genome fragment was associated with SSWD. Rather, wasting lesion margins may generally support viral proliferation.},
}

Animals
Disease Progression
Genetic Variation
Longitudinal Studies
Metagenome
Metagenomics
Starfish/*virology
*Virome
Viruses/classification/*genetics
Wasting Syndrome/*veterinary/*virology

@article {pmid33121140,
year = {2020},
author = {Gebremedhn, H and Deboutte, W and Schoonvaere, K and Demaeght, P and De Smet, L and Amssalu, B and Matthijnssens, J and de Graaf, DC},
title = {Metagenomic Approach with the NetoVIR Enrichment Protocol Reveals Virus Diversity within Ethiopian Honey Bees (Apis mellifera simensis).},
journal = {Viruses},
volume = {12},
number = {11},
pages = {},
pmid = {33121140},
issn = {1999-4915},
mesh = {Animals ; Bees/*virology ; Ethiopia ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics/*methods ; Phylogeny ; Varroidae/virology ; Virology/*methods ; Virome ; Virus Diseases/transmission/*veterinary ; Viruses/*classification/isolation & purification ; },
abstract = {Metagenomics studies have accelerated the discovery of novel or divergent viruses of the honey bee. However, most of these studies predominantly focused on RNA viruses, and many suffer from the relatively low abundance of viral nucleic acids in the samples (i.e., compared to that of the host). Here, we explored the virome of the Ethiopian honey bee, Apis mellifera simensis, using an unbiased metagenomic approach in which the next-generation sequencing step was preceded by an enrichment protocol for viral particles. Our study revealed five well-known bee viruses and 25 atypical virus species, most of which have never been found in A. mellifera before. The viruses belong to Iflaviridae, Dicistroviridae, Secoviridae, Partitiviridae, Parvoviridae, Potyviridae, and taxonomically unclassified families. Fifteen of these atypical viruses were most likely plant-specific, and the remaining ten were presumed to be insect-specific. Apis mellifera filamentous virus (AmFV) was found in one sampling site out of 10. Two samples contained high read counts of a virus similar to Diatraea saccharales densovirus (DsDNV), which is a virus that causes high mortality in the sugarcane borer. AmFV and the DsDNV-like virus were the only DNA viruses found. Three viruses that primarily infect Drosophila spp. were also discovered: La Jolla virus (LJV), Kilifi virus (KiV), and Thika virus. Our study suggests that phoretic varroa mites are involved in the transmission of LJV and KiV and that both viruses replicate in mites and adult bees. We also found an overwhelming dominance of the deformed wing virus type B variant, which fits well with the apparently harmless infestation by Varroa destructor. It was suggested that Ethiopian bees have developed tolerance against virus infections as the result of natural selection.},
}

Animals
Bees/*virology
Ethiopia
High-Throughput Nucleotide Sequencing
Metagenome
Metagenomics/*methods
Phylogeny
Varroidae/virology
Virology/*methods
Virome
Virus Diseases/transmission/*veterinary
Viruses/*classification/isolation & purification

@article {pmid33110112,
year = {2020},
author = {Kazemian, N and Ramezankhani, M and Sehgal, A and Khalid, FM and Kalkhoran, AHZ and Narayan, A and Wong, GK and Kao, D and Pakpour, S},
title = {The trans-kingdom battle between donor and recipient gut microbiome influences fecal microbiota transplantation outcome.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {18349},
pmid = {33110112},
issn = {2045-2322},
mesh = {Adult ; Bacteroidetes/metabolism ; Clostridiales/metabolism ; Clostridioides/metabolism ; Clostridium Infections/microbiology/therapy ; Desulfovibrio/metabolism ; *Fecal Microbiota Transplantation ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Machine Learning ; Male ; Metagenomics ; Tissue Donors ; Treatment Outcome ; },
abstract = {Fundamental restoration ecology and community ecology theories can help us better understand the underlying mechanisms of fecal microbiota transplantation (FMT) and to better design future microbial therapeutics for recurrent Clostridioides difficile infections (rCDI) and other dysbiosis-related conditions. In this study, stool samples were collected from donors and rCDI patients one week prior to FMT (pre-FMT), as well as from patients one week following FMT (post-FMT). Using metagenomic sequencing and machine learning, our results suggested that FMT outcome is not only dependent on the ecological structure of the recipients, but also the interactions between the donor and recipient microbiomes at the taxonomical and functional levels. We observed that the presence of specific bacteria in donors (Clostridioides spp., Desulfovibrio spp., Odoribacter spp. and Oscillibacter spp.) and the absence of fungi (Yarrowia spp.) and bacteria (Wigglesworthia spp.) in recipients prior to FMT could predict FMT success. Our results also suggested a series of interlocked mechanisms for FMT success, including the repair of the disturbed gut ecosystem by transient colonization of nexus species followed by secondary succession of bile acid metabolizers, sporulators, and short chain fatty acid producers.},
}

Adult
Bacteroidetes/metabolism
Clostridiales/metabolism
Clostridioides/metabolism
Clostridium Infections/microbiology/therapy
Desulfovibrio/metabolism
*Fecal Microbiota Transplantation
Feces/*microbiology
Female
*Gastrointestinal Microbiome/genetics
Humans
Machine Learning
Male
Metagenomics
Tissue Donors
Treatment Outcome

@article {pmid32722579,
year = {2020},
author = {Tsiola, A and Michoud, G and Fodelianakis, S and Karakassis, I and Kotoulas, G and Pavlidou, A and Pavloudi, C and Pitta, P and Simboura, N and Daffonchio, D and Tsapakis, M},
title = {Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone.},
journal = {Viruses},
volume = {12},
number = {8},
pages = {},
pmid = {32722579},
issn = {1999-4915},
mesh = {Bacteria/genetics ; *Ecosystem ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; Seawater/*virology ; Viral Proteins/*genetics ; *Virome ; Viruses/*genetics ; },
abstract = {Viruses interfere with their host's metabolism through the expression of auxiliary metabolic genes (AMGs) that, until now, are mostly studied under large physicochemical gradients. Here, we focus on coastal marine ecosystems and we sequence the viral metagenome (virome) of samples with discrete levels of human-driven disturbances. We aim to describe the relevance of viromics with respect to ecological quality status, defined by the classic seawater trophic index (TRIX). Neither viral (family level) nor bacterial (family level, based on 16S rRNA sequencing) community structure correlated with TRIX. AMGs involved in the Calvin and tricarboxylic acid cycles were found at stations with poor ecological quality, supporting viral lysis by modifying the host's energy supply. AMGs involved in "non-traditional" energy-production pathways (3HP, sulfur oxidation) were found irrespective of ecological quality, highlighting the importance of recognizing the prevalent metabolic paths and their intermediate byproducts. Various AMGs explained the variability between stations with poor vs. good ecological quality. Our study confirms the pivotal role of the virome content in ecosystem functioning, acting as a "pool" of available functions that may be transferred to the hosts. Further, it suggests that AMGs could be used as an ultra-sensitive metric of energy-production pathways with relevance in the vulnerable coastal zone and its ecological quality.},
}

Bacteria/genetics
*Ecosystem
*Metagenomics
RNA, Ribosomal, 16S/genetics
Seawater/*virology
Viral Proteins/*genetics
*Virome
Viruses/*genetics

@article {pmid32718049,
year = {2020},
author = {Altan, E and Delaney, MA and Colegrove, KM and Spraker, TR and Wheeler, EA and Deng, X and Li, Y and Gulland, FMD and Delwart, E},
title = {Complex Virome in a Mesenteric Lymph Node from a Californian Sea Lion (Zalophus Californianus) with Polyserositis and Steatitis.},
journal = {Viruses},
volume = {12},
number = {8},
pages = {},
pmid = {32718049},
issn = {1999-4915},
mesh = {Anelloviridae/classification/isolation & purification ; Animals ; Animals, Wild ; California ; Female ; Inflammation ; Lymph Nodes/*pathology/*virology ; Metagenomics ; Parvovirus/classification/isolation & purification ; Polyomavirus/classification/isolation & purification ; Sea Lions/*virology ; Serositis/*pathology/*veterinary/virology ; Steatitis/*pathology/virology ; *Virome ; },
abstract = {An emaciated subadult free-ranging California sea lion (Csl or Zalophus californianus) died following stranding with lesions similar to 11 other stranded animals characterized by chronic disseminated granulomatous inflammation with necrotizing steatitis and vasculitis, involving visceral adipose tissues in the thoracic and peritoneal cavities. Histologically, affected tissues had extensive accumulations of macrophages with perivascular lymphocytes, plasma cells, and fewer neutrophils. Using viral metagenomics on a mesenteric lymph node six mammalian viruses were identified consisting of novel parvovirus, polyomavirus, rotavirus, anellovirus, and previously described Csl adenovirus 1 and Csl bocavirus 4. The causal or contributory role of these viruses to the gross and histologic lesions of this sea lion remains to be determined.},
}

Anelloviridae/classification/isolation & purification
Animals
Animals, Wild
California
Female
Inflammation
Lymph Nodes/*pathology/*virology
Metagenomics
Parvovirus/classification/isolation & purification
Polyomavirus/classification/isolation & purification
Sea Lions/*virology
Serositis/*pathology/*veterinary/virology
Steatitis/*pathology/virology
*Virome

@article {pmid33149234,
year = {2020},
author = {Siddiqui, S and Bao, D and Doyle-Meyers, L and Dufour, J and Wu, Y and Liu, YZ and Ling, B},
title = {Alterations of the gut bacterial microbiota in rhesus macaques with SIV infection and on short- or long-term antiretroviral therapy.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {19056},
pmid = {33149234},
issn = {2045-2322},
support = {R01 MH102144/MH/NIMH NIH HHS/United States ; P51 OD011104/OD/NIH HHS/United States ; R01 MH116844/MH/NIMH NIH HHS/United States ; R01 AI093307/AI/NIAID NIH HHS/United States ; R01 NS104016/NS/NINDS NIH HHS/United States ; },
mesh = {Animals ; Antiretroviral Therapy, Highly Active ; Biodiversity ; Biomarkers ; Duration of Therapy ; Dysbiosis/*etiology/immunology ; Gastrointestinal Microbiome/*drug effects/immunology ; Lipopolysaccharides/blood/metabolism ; Macaca mulatta ; Metagenome ; Metagenomics ; Simian Acquired Immunodeficiency Syndrome/*drug therapy/immunology/virology ; *Simian Immunodeficiency Virus/drug effects/immunology ; },
abstract = {Gut dysbiosis and microbial translocation are associated with chronic systemic immune activation and inflammation in HIV-1 infection. However, the extent of restoration of gut microbiota in HIV-1 patients with short or long-term antiretroviral therapy (ART) is unclear. To understand the impact of ART on the gut microbiota, we used the rhesus macaque model of SIV infection to characterize and compare the gut microbial community upon SIV infection and during ART. We observed altered taxonomic compositions of gut microbiota communities upon SIV infection and at different time points of ART. SIV-infected animals showed decreased diversity of gut microbiome composition, while the ART group appeared to recover towards the diversity level of the healthy control. Animals undergoing ART for various lengths of time were observed to have differential gut bacterial abundance across different time points. In addition, increased blood lipopolysaccharide (LPS) levels during SIV infection were reduced to near normal upon ART, indicating that microbial translocation and immune activation can be improved during therapy. In conclusion, while short ART may be related to transient increase of certain pathogenic bacterial microbiome, ART may promote microbiome diversity compromised by SIV infection, improve the gut microbiota towards the healthy compositions and alleviate immune activation.},
}

Animals
Antiretroviral Therapy, Highly Active
Biodiversity
Biomarkers
Duration of Therapy
Dysbiosis/*etiology/immunology
Gastrointestinal Microbiome/*drug effects/immunology
Lipopolysaccharides/blood/metabolism
Macaca mulatta
Metagenome
Metagenomics
Simian Acquired Immunodeficiency Syndrome/*drug therapy/immunology/virology
*Simian Immunodeficiency Virus/drug effects/immunology

@article {pmid32645241,
year = {2020},
author = {Liu, Y and Jin, X and Hong, HG and Xiang, L and Jiang, Q and Ma, Y and Chen, Z and Cheng, L and Jian, Z and Wei, Z and Ai, J and Qi, S and Sun, Q and Li, H and Li, Y and Wang, K},
title = {The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {34},
number = {8},
pages = {11200-11214},
doi = {10.1096/fj.202000786R},
pmid = {32645241},
issn = {1530-6860},
mesh = {Animals ; Bacteria/genetics ; Calcium Oxalate/*metabolism ; Case-Control Studies ; Fatty Acids, Volatile/*metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Kidney/*metabolism ; Kidney Calculi/*metabolism/*microbiology ; Male ; Metagenomics/methods ; Middle Aged ; Nephrolithiasis/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; },
abstract = {The relationship of gut microbiota and calcium oxalate stone has been limited investigated, especially with no study of gut microbiota and short chain fatty acids (SCFAs) in nephrolithiasis. We provided Sprague Dawley rats of renal calcium oxalate stones with antibiotics and examined the renal crystals deposition. We also performed a case-control study by analyzing 16S rRNA microbial profiling, shotgun metagenomics and SCFAs in 153 fecal samples from non-kidney stone (NS) controls, patients with occasional renal calcium oxalate stones (OS) and patients with recurrent stones (RS). Antibiotics reduced bacterial load in feces and could promote the formation of renal calcium crystals in model rats. In addition, both OS and RS patients exhibited higher fecal microbial diversity than NS controls. Several SCFAs-producing gut bacteria, as well as metabolic pathways associated with SCFAs production, were considerably lower in the gut microbiota among the kidney stone patients compared with the NS controls. Representation of genes involved in oxalate degradation showed no significance difference among groups. However, fecal acetic acid concentration was the highest in RS patients with high level of urinary oxalate, which was positively correlated with genes involvement in oxalate synthesis. Administration of SCFAs reduced renal crystals. These results shed new light on bacteria and SCFAs, which may promote the development of treatment strategy in nephrolithiasis.},
}

Animals
Bacteria/genetics
Calcium Oxalate/*metabolism
Case-Control Studies
Fatty Acids, Volatile/*metabolism
Feces/microbiology
Gastrointestinal Microbiome/genetics/*physiology
Humans
Kidney/*metabolism
Kidney Calculi/*metabolism/*microbiology
Male
Metagenomics/methods
Middle Aged
Nephrolithiasis/metabolism/microbiology
RNA, Ribosomal, 16S/genetics
Rats
Rats, Sprague-Dawley

@article {pmid33246225,
year = {2021},
author = {Yu, Y and Lu, J and Sun, L and Lyu, X and Chang, XY and Mi, X and Hu, MG and Wu, C and Chen, X},
title = {Akkermansia muciniphila: A potential novel mechanism of nuciferine to improve hyperlipidemia.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {133},
number = {},
pages = {111014},
doi = {10.1016/j.biopha.2020.111014},
pmid = {33246225},
issn = {1950-6007},
mesh = {Akkermansia/drug effects/genetics/growth & development ; Animals ; Anti-Bacterial Agents/pharmacology ; Aporphines/*pharmacology ; Bacteroides/drug effects/genetics/growth & development ; Biomarkers/blood ; Diet, High-Fat ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Hyperlipidemias/blood/*drug therapy/microbiology ; Hypolipidemic Agents/*pharmacology ; Intestines/*microbiology ; Lipids/*blood ; Male ; Metagenome ; Metagenomics ; Mice, Inbred C57BL ; Non-alcoholic Fatty Liver Disease/blood/microbiology/prevention & control ; Obesity/blood/microbiology/prevention & control ; RNA-Seq ; },
abstract = {BACKGROUND: Intestinal microbiota is a novel drug target of metabolic diseases, especially for those with poor oral bioavailability. Nuciferine, with poor bioavailability, has an anti-hyperlipidemic effect at low dosages.

PURPOSE: In the present study, we aimed to explore the role of intestinal microbiota in the anti-hyperlipidemic function of nuciferine and identify the key bacterial targets that might confer the therapeutic actions.

METHODS: The contribution of gut microbes in the anti-hyperlipidemic effect of nuciferine was evaluated by conventional and antibiotic-established pseudo-sterile mice. Whole-metagenome shotgun sequencing was used to characterize the changes in microbial communities by various agents.

RESULTS: Nuciferine exhibited potent anti-hyperlipidemic and liver steatosis-alleviating effects at the doses of 7.5-30 mg/kg. The beneficial effects of nuciferine were substantially abolished when combined with antibiotics. Metagenomic analysis showed that nuciferine significantly shifted the microbial structure, and the enrichment of Akkermansia muciniphila was closely related to the therapeutic effect of nuciferine.

CONCLUSIONS: Our results revealed that gut microbiota played an essential role in the anti-hyperlipidemic effect of nuciferine, and enrichment of Akkermansia muciniphila represented a key mechanism through which nuciferine exerted its therapeutic effects.},
}

Akkermansia/drug effects/genetics/growth & development
Animals
Anti-Bacterial Agents/pharmacology
Aporphines/*pharmacology
Bacteroides/drug effects/genetics/growth & development
Biomarkers/blood
Diet, High-Fat
Disease Models, Animal
Gastrointestinal Microbiome/*drug effects
Hyperlipidemias/blood/*drug therapy/microbiology
Hypolipidemic Agents/*pharmacology
Intestines/*microbiology
Lipids/*blood
Male
Metagenome
Metagenomics
Mice, Inbred C57BL
Non-alcoholic Fatty Liver Disease/blood/microbiology/prevention & control
Obesity/blood/microbiology/prevention & control
RNA-Seq

@article {pmid32930660,
year = {2020},
author = {Dar, D and Thomashow, LS and Weller, DM and Newman, DK},
title = {Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {32930660},
issn = {2050-084X},
support = {R01 AI127850/AI/NIAID NIH HHS/United States ; W911NF-17-1-0024//Army Research Office/International ; 1R01AI127850-01A1/NH/NIH HHS/United States ; },
mesh = {Agriculture ; Biodegradation, Environmental ; Crops, Agricultural/*microbiology ; Gammaproteobacteria/physiology ; *Metagenomics ; *Microbiota ; Phenazines/*metabolism ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants/*metabolism ; Species Specificity ; Up-Regulation ; Zea mays/microbiology ; },
abstract = {Phenazines are natural bacterial antibiotics that can protect crops from disease. However, for most crops it is unknown which producers and specific phenazines are ecologically relevant, and whether phenazine biodegradation can counter their effects. To better understand their ecology, we developed and environmentally-validated a quantitative metagenomic approach to mine for phenazine biosynthesis and biodegradation genes, applying it to >800 soil and plant-associated shotgun-metagenomes. We discover novel producer-crop associations and demonstrate that phenazine biosynthesis is prevalent across habitats and preferentially enriched in rhizospheres, whereas biodegrading bacteria are rare. We validate an association between maize and Dyella japonica, a putative producer abundant in crop microbiomes. D. japonica upregulates phenazine biosynthesis during phosphate limitation and robustly colonizes maize seedling roots. This work provides a global picture of phenazines in natural environments and highlights plant-microbe associations of agricultural potential. Our metagenomic approach may be extended to other metabolites and functional traits in diverse ecosystems.},
}

Agriculture
Biodegradation, Environmental
Crops, Agricultural/*microbiology
Gammaproteobacteria/physiology
*Metagenomics
*Microbiota
Phenazines/*metabolism
Soil/*chemistry
*Soil Microbiology
Soil Pollutants/*metabolism
Species Specificity
Up-Regulation
Zea mays/microbiology

@article {pmid32824037,
year = {2020},
author = {Šimić, I and Zorec, TM and Lojkić, I and Krešić, N and Poljak, M and Cliquet, F and Picard-Meyer, E and Wasniewski, M and Zrnčić, V and Ćukušić, A and Bedeković, T},
title = {Viral Metagenomic Profiling of Croatian Bat Population Reveals Sample and Habitat Dependent Diversity.},
journal = {Viruses},
volume = {12},
number = {8},
pages = {},
pmid = {32824037},
issn = {1999-4915},
mesh = {Animals ; Chiroptera/*virology ; Croatia ; Disease Reservoirs/*veterinary/virology ; *Ecosystem ; Feces/virology ; High-Throughput Nucleotide Sequencing ; Insect Viruses/classification ; *Metagenome ; Metagenomics ; Phylogeny ; Saliva/virology ; Sequence Analysis, DNA ; Virome/*genetics ; Virus Diseases/*veterinary ; Viruses/classification/isolation & purification ; Zoonoses/virology ; },
abstract = {To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown. Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (Myotis myotis, Miniopterus schreibersii, Rhinolophus ferrumequinum, Eptesicus serotinus, Myotis blythii, Myotis nattereri and Myotis emarginatus) conducted in Mediterranean and continental Croatia. Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing. The presence of 63 different viral families representing all seven Baltimore groups were confirmed, most commonly insect viruses likely reflecting the diet of insectivorous bats. Virome compositions of our samples were largely impacted by the sample type: invertebrate-infecting viruses were most frequently found in feces, bacterial viruses in guano, whereas vertebrate-infecting viruses were most common in swabs. Most vertebrate-infecting virus sequences were assigned to retroviruses, parvoviruses, iridoviruses, and poxviruses. We further report the complete genome sequence of a novel adeno-associated virus, densovirus and a near complete length genome sequence of a novel iflavirus. Additionally, one of the most interesting findings in this study was the difference in viromes between two contrasting habitats, the continental and Mediterranean Croatia.},
}

Animals
Chiroptera/*virology
Croatia
Disease Reservoirs/*veterinary/virology
*Ecosystem
Feces/virology
High-Throughput Nucleotide Sequencing
Insect Viruses/classification
*Metagenome
Metagenomics
Phylogeny
Saliva/virology
Sequence Analysis, DNA
Virome/*genetics
Virus Diseases/*veterinary
Viruses/classification/isolation & purification
Zoonoses/virology

@article {pmid32630711,
year = {2020},
author = {Williams, SH and Levy, A and Yates, RA and Somaweera, N and Neville, PJ and Nicholson, J and Lindsay, MDA and Mackenzie, JS and Jain, K and Imrie, A and Smith, DW and Lipkin, WI},
title = {The Diversity and Distribution of Viruses Associated with Culex annulirostris Mosquitoes from the Kimberley Region of Western Australia.},
journal = {Viruses},
volume = {12},
number = {7},
pages = {},
pmid = {32630711},
issn = {1999-4915},
support = {U19AI109761/NH/NIH HHS/United States ; },
mesh = {Animals ; Culex/*virology ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; Mosquito Vectors/*virology ; *Virome ; Viruses/*classification/isolation & purification ; Western Australia ; },
abstract = {Metagenomics revealed an impressive breadth of previously unrecognized viruses. Here, we report the virome of the Culex annulirostris Skuse mosquito, an important vector of pathogenic arboviruses in Australia. Mosquitoes were collected from three sites in the Kimberley region of Western Australia. Unbiased high-throughput sequencing (HTS) revealed the presence of 16 novel viral sequences that share less than 90% identity with known viruses. None were closely related to pathogenic arboviruses. Viruses were distributed unevenly across sites, indicating a heterogeneous Cx. annulirostris virome. Polymerase chain reaction assays confirmed HTS data and identified marked variation between the virus prevalence identified at each site.},
}

Animals
Culex/*virology
High-Throughput Nucleotide Sequencing
*Metagenomics
Mosquito Vectors/*virology
*Virome
Viruses/*classification/isolation & purification
Western Australia

@article {pmid32487781,
year = {2020},
author = {Ma, S and Qin, J and Hao, Y and Fu, L},
title = {Association of gut microbiota composition and function with an aged rat model of senile osteoporosis using 16S rRNA and metagenomic sequencing analysis.},
journal = {Aging},
volume = {12},
number = {11},
pages = {10795-10808},
pmid = {32487781},
issn = {1945-4589},
mesh = {Animals ; Bone Density ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Metabolic Networks and Pathways ; Metagenomics ; Osteoporosis/*microbiology ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; },
abstract = {Recently, more interest has been paid to the association between bone mass and gut microecological dysbiosis. The results of clinical studies comparing gut microbiota (GM) in osteoporosis patients have been inconsistent due to different inclusion and exclusion criteria. To date, the association between the GM and senile osteoporosis remains poorly understood. Here, we utilized an aged rat model (22 months old) of senile osteoporosis to study the association of the composition and function of the GM with osteoporosis by 16S rRNA and metagenomic sequencing. The results showed that there was a significant reduction in alpha diversity and the F/B (Firmicutes/Bacteroidetes) ratio in aged rats. At the genus level, the enrichment of Helicobacter was potentially related to osteoporosis as a risk factor. Metagenomics results based on two databases indicated that shifts in the GM contribute to senile osteoporosis through metabolic pathways and subsequent immune disorders. In conclusion, our study reveals the association of gut microbiota composition and function with senile osteoporosis in an aged rat model in a brand new way, and variations in the GM might contribute to senile osteoporosis through metabolic pathways.},
}

Animals
Bone Density
Female
*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Metabolic Networks and Pathways
Metagenomics
Osteoporosis/*microbiology
RNA, Ribosomal, 16S/genetics
Rats
Rats, Sprague-Dawley

@article {pmid32484785,
year = {2020},
author = {Ma, S and Qin, J and Hao, Y and Shi, Y and Fu, L},
title = {Structural and functional changes of gut microbiota in ovariectomized rats and their correlations with altered bone mass.},
journal = {Aging},
volume = {12},
number = {11},
pages = {10736-10753},
pmid = {32484785},
issn = {1945-4589},
mesh = {Animals ; Biomechanical Phenomena ; Bone Development/*physiology ; Bone and Bones/*metabolism ; Disease Models, Animal ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Osteoporosis, Postmenopausal/*metabolism ; Ovariectomy ; RNA, Ribosomal, 16S/analysis ; Rats ; Rats, Sprague-Dawley ; Ruminococcus/isolation & purification ; },
abstract = {As a critical factor involved in the maintenance of physiological homeostasis, the gut microbiota (GM) reportedly plays a key role in bone development. To date, the association between the GM and steroid deficiency-induced osteoporosis remains poorly understood. Forty female Sprague Dawley rats were divided into an ovariectomy (OVX) or control group. We performed 16S rRNA and metagenome sequencing, to compare diversity, taxonomic differences, and functional genes. The GM composition did not change in the control group and the number of operational taxonomic units increased significantly following ovariectomy. Alpha diversity, determined by ACE estimator, CHAO estimator, the Shannon index, and the Simpson index showed an increasing trend after ovariectomy. Samples in the OVX group were well clustered both pre- and post-ovariectomy, as demonstrated by principal coordinate 1 (PC1) and PC2. Functional genes of GM, including those involved in synthesis and metabolism of carbohydrates and nucleotides, microbial structure, and heme, as well as hemin uptake and utilization, increased at the early stage of osteoporosis. We observed that Ruminococcus flavefaciens exhibited the greatest variation in abundance among the GM and this was also associated with osteoclastic indicators and the estrobolome. Specific changes in fecal microbiota are associated with the pathogenesis of steroid deficiency-induced osteoporosis.},
}

Animals
Biomechanical Phenomena
Bone Development/*physiology
Bone and Bones/*metabolism
Disease Models, Animal
Feces/microbiology
Female
Gastrointestinal Microbiome/*physiology
Humans
Osteoporosis, Postmenopausal/*metabolism
Ovariectomy
RNA, Ribosomal, 16S/analysis
Rats
Rats, Sprague-Dawley
Ruminococcus/isolation & purification

@article {pmid32424436,
year = {2020},
author = {Zemskaya, TI and Cabello-Yeves, PJ and Pavlova, ON and Rodriguez-Valera, F},
title = {Microorganisms of Lake Baikal-the deepest and most ancient lake on Earth.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {14},
pages = {6079-6090},
pmid = {32424436},
issn = {1432-0614},
support = {"VIREVO" CGL2016-76273-P [MCI/AEI/FEDER, EU]//Ministerio de Ciencia e Innovación (ES)/ ; "HIDRAS3" PROMETEO/2019/009//Generalitat Valenciana/ ; APOSTD/2019/009 Post-Doctoral fellowship//Generalitat Valenciana/ ; 0345-2019-0007//Ministry of Education and Science of the Russian Federation/ ; Ofi-m 17-29-05040//Российский Фонд Фундаментальных Исследований (РФФИ)/ ; },
mesh = {Climate ; Geography ; In Situ Hybridization, Fluorescence ; Lakes/chemistry/*microbiology ; Metagenomics ; Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; *Water Microbiology ; },
abstract = {Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments. KEY POINTS: • The chemical composition and limnic features of the deepest lake on Earth determine the vital activity of microorganisms. • The diversity, ecology, and role of individual taxa of microorganisms were studied using cultivation and molecular methods. • Data of large metagenomic datasets in the epipelagic and bathypelagic layers of the water column in southern Baikal were discussed.},
}

Climate
Geography
In Situ Hybridization, Fluorescence
Lakes/chemistry/*microbiology
Metagenomics
Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
Russia
*Water Microbiology

@article {pmid33074097,
year = {2020},
author = {Mobegi, FM and Leong, LE and Thompson, F and Taylor, SM and Harriss, LR and Choo, JM and Taylor, SL and Wesselingh, SL and McDermott, R and Ivey, KL and Rogers, GB},
title = {Intestinal microbiology shapes population health impacts of diet and lifestyle risk exposures in Torres Strait Islander communities.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {33074097},
issn = {2050-084X},
support = {GNT0631947//National Health and Medical Research Council/International ; },
mesh = {Adult ; Aged ; *Diet ; Female ; *Gastrointestinal Microbiome ; Humans ; *Life Style ; Male ; Middle Aged ; Oceanic Ancestry Group/*statistics & numerical data ; Population Health/*statistics & numerical data ; Young Adult ; },
abstract = {Poor diet and lifestyle exposures are implicated in substantial global increases in non-communicable disease burden in low-income, remote, and Indigenous communities. This observational study investigated the contribution of the fecal microbiome to influence host physiology in two Indigenous communities in the Torres Strait Islands: Mer, a remote island where a traditional diet predominates, and Waiben a more accessible island with greater access to takeaway food and alcohol. Counterintuitively, disease markers were more pronounced in Mer residents. However, island-specific differences in disease risk were explained, in part, by microbiome traits. The absence of Alistipes onderdonkii, for example, significantly (p=0.014) moderated island-specific patterns of systolic blood pressure in multivariate-adjusted models. We also report mediatory relationships between traits of the fecal metagenome, disease markers, and risk exposures. Understanding how intestinal microbiome traits influence response to disease risk exposures is critical for the development of strategies that mitigate the growing burden of cardiometabolic disease in these communities.},
}

Adult
Aged
*Diet
Female
*Gastrointestinal Microbiome
Humans
*Life Style
Male
Middle Aged
Oceanic Ancestry Group/*statistics & numerical data
Population Health/*statistics & numerical data
Young Adult

@article {pmid32252812,
year = {2020},
author = {Zhou, Y and Coventry, DR and Gupta, VVSR and Fuentes, D and Merchant, A and Kaiser, BN and Li, J and Wei, Y and Liu, H and Wang, Y and Gan, S and Denton, MD},
title = {The preceding root system drives the composition and function of the rhizosphere microbiome.},
journal = {Genome biology},
volume = {21},
number = {1},
pages = {89},
pmid = {32252812},
issn = {1474-760X},
mesh = {Cicer/microbiology ; Genes, Microbial ; Metagenome ; Metagenomics ; *Microbiota ; Molecular Sequence Annotation ; Plant Roots/growth & development/microbiology ; *Rhizosphere ; Soil/chemistry ; *Soil Microbiology ; Symbiosis ; Triticum/microbiology ; },
abstract = {BACKGROUND: The soil environment is responsible for sustaining most terrestrial plant life, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. Understanding the microbial metagenome of the detritusphere, and how it responds to agricultural management such as crop rotations and soil tillage, is vital for improving global food production.

RESULTS: This study establishes an in-depth soil microbial gene catalogue based on the living-decaying rhizosphere niches in a cropping soil. The detritusphere microbiome regulates the composition and function of the rhizosphere microbiome to a greater extent than plant type: rhizosphere microbiomes of wheat and chickpea were homogenous (65-87% similarity) in the presence of decaying root (DR) systems but were heterogeneous (3-24% similarity) where DR was disrupted by tillage. When the microbiomes of the rhizosphere and the detritusphere interact in the presence of DR, there is significant degradation of plant root exudates by the rhizosphere microbiome, and genes associated with membrane transporters, carbohydrate and amino acid metabolism are enriched.

CONCLUSIONS: The study describes the diversity and functional capacity of a high-quality soil microbial metagenome. The results demonstrate the contribution of the detritusphere microbiome in determining the metagenome of developing root systems. Modifications in root microbial function through soil management can ultimately govern plant health, productivity and food security.},
}

Cicer/microbiology
Genes, Microbial
Metagenome
Metagenomics
*Microbiota
Molecular Sequence Annotation
Plant Roots/growth & development/microbiology
*Rhizosphere
Soil/chemistry
*Soil Microbiology
Symbiosis
Triticum/microbiology

@article {pmid33321431,
year = {2021},
author = {Misery, B and Legendre, P and Rue, O and Bouchart, V and Guichard, H and Laplace, JM and Cretenet, M},
title = {Diversity and dynamics of bacterial and fungal communities in cider for distillation.},
journal = {International journal of food microbiology},
volume = {339},
number = {},
pages = {108987},
doi = {10.1016/j.ijfoodmicro.2020.108987},
pmid = {33321431},
issn = {1879-3460},
mesh = {Alcoholic Beverages/*microbiology ; Bacteria/genetics ; *Bacterial Physiological Phenomena ; *Biodiversity ; DNA, Ribosomal Spacer/genetics ; *Distillation ; Fermentation ; Fungi/*physiology ; Malus ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Bacterial and fungal population dynamics in cider for distillation have so far been explored by culture-dependant methods. Cider for distillation can be produced by the spontaneous fermentation of apples that do not undergo any intervention during the process. In this study, cider microbiomes extracted from six tanks containing ciders for distillation from four producers in Normandy were characterized at three main stages of the fermentation process: fermentation Initiation (I), end of the alcoholic Fermentation (F) and end of the Maturation period (M). Cider samples were subjected to Illumina MiSeq sequencing (rRNA 16S V1-V3 and ITS1 region targeting) to determine bacterial and fungal communities. Yeasts (YGC), Zymomonas (mZPP) and lactic acid bacteria selective media (mMRS, mMLO, mPSM) were also used to collect 807 isolates. Alcoholic levels, glycerol, sugar content (glucose, fructose and sucrose), pH, total and volatile acidity, nitrogen, malic and lactic acid contents were determined at all sampling points. Alpha diversity indexes show significant differences (p < 0.05) in microbial populations between I, F and M. Fungal communities were characterized by microorganisms from the environment and phytopathogens at I followed by the association of yearsts with alcoholic fermentation like Saccharomyces and non-Saccharomyces yeasts (Hanseniaspora, Candida). A maturation period for cider leads to an increase of the Dekkera/Brettanomyces population, which is responsible for off-flavors in cider for all producers. Among bacterial communities, the genera community associated to malolactic fermentation (Lactobacillus sp., Leuconostoc sp., Oenococcus sp.) was the most abundant at F and M. Acetic acid bacteria such as Acetobacter sp., Komagataeibacter sp. and Gluconobacter sp. were also detected during the process. Significant differences (p < 0.05) were found in fungal and bacterial populations between the four producers and during the fermentation process. The development of microorganisms associated with cider spoilage such as Zymomonas mobilis, Lactobacillus collinoides or Brettanomyces/Dekkera sp. was anticipated by a metagenomic approach. The monitoring of microbial diversity via high throughput sequencing combined with physical-chemical analysis is an interesting approach to improve the fermentation performance of cider for distillation and therefore, the quality of Calvados.},
}

Alcoholic Beverages/*microbiology
Bacteria/genetics
*Bacterial Physiological Phenomena
*Biodiversity
DNA, Ribosomal Spacer/genetics
*Distillation
Fermentation
Fungi/*physiology
Malus
RNA, Ribosomal, 16S/genetics

@article {pmid33228639,
year = {2020},
author = {Liu, C and Ponsero, AJ and Armstrong, DG and Lipsky, BA and Hurwitz, BL},
title = {The dynamic wound microbiome.},
journal = {BMC medicine},
volume = {18},
number = {1},
pages = {358},
pmid = {33228639},
issn = {1741-7015},
mesh = {Diabetic Foot/*microbiology ; Female ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Male ; Metabolomics/*methods ; Microbiota/*physiology ; },
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) account for the majority of all limb amputations and hospitalizations due to diabetes complications. With 30 million cases of diabetes in the USA and 500,000 new diagnoses each year, DFUs are a growing health problem. Diabetes patients with limb amputations have high postoperative mortality, a high rate of secondary amputation, prolonged inpatient hospital stays, and a high incidence of re-hospitalization. DFU-associated amputations constitute a significant burden on healthcare resources that cost more than 10 billion dollars per year. Currently, there is no way to identify wounds that will heal versus those that will become severely infected and require amputation.

MAIN BODY: Accurate identification of causative pathogens in diabetic foot ulcers is a critical component of effective treatment. Compared to traditional culture-based methods, advanced sequencing technologies provide more comprehensive and unbiased profiling on wound microbiome with a higher taxonomic resolution, as well as functional annotation such as virulence and antibiotic resistance. In this review, we summarize the latest developments in defining the microbiology of diabetic foot ulcers that have been unveiled by sequencing technologies and discuss both the future promises and current limitations of these approaches. In particular, we highlight the temporal patterns and system dynamics in the diabetic foot microbiome monitored and measured during wound progression and medical intervention, and explore the feasibility of molecular diagnostics in clinics.

CONCLUSION: Molecular tests conducted during weekly office visits to clean and examine DFUs would allow clinicians to offer personalized treatment and antibiotic therapy. Personalized wound management could reduce healthcare costs, improve quality of life for patients, and recoup lost productivity that is important not only to the patient, but also to healthcare payers and providers. These efforts could also improve antibiotic stewardship and control the rise of "superbugs" vital to global health.},
}

Diabetic Foot/*microbiology
Female
High-Throughput Nucleotide Sequencing/*methods
Humans
Male
Metabolomics/*methods
Microbiota/*physiology

@article {pmid33152902,
year = {2020},
author = {Dalal, N and Jalandra, R and Sharma, M and Prakash, H and Makharia, GK and Solanki, PR and Singh, R and Kumar, A},
title = {Omics technologies for improved diagnosis and treatment of colorectal cancer: Technical advancement and major perspectives.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {131},
number = {},
pages = {110648},
doi = {10.1016/j.biopha.2020.110648},
pmid = {33152902},
issn = {1950-6007},
mesh = {Colorectal Neoplasms/*diagnosis/genetics/metabolism/*therapy ; Gastrointestinal Microbiome ; Humans ; Metabolomics ; Metagenomics ; Proteomics ; Transcriptome ; },
abstract = {Colorectal cancer (CRC) ranks third among the most commonly occurring cancers worldwide, and it causes half a million deaths annually. Alongside mechanistic study for CRC detection and treatment by conventional techniques, new technologies have been developed to study CRC. These technologies include genomics, transcriptomics, proteomics, and metabolomics which elucidate DNA markers, RNA transcripts, protein and, metabolites produced inside the colon and rectum part of the gut. All these approaches form the omics arena, which presents a remarkable opportunity for the discovery of novel prognostic, diagnostic and therapeutic biomarkers and also delineate the underlying mechanism of CRC causation, which may further help in devising treatment strategies. This review also mentions the latest developments in metagenomics and culturomics as emerging evidence suggests that metagenomics of gut microbiota has profound implications in the causation, prognosis, and treatment of CRC. A majority of bacteria cannot be studied as they remain unculturable, so culturomics has also been strengthened to develop culture conditions suitable for the growth of unculturable bacteria and identify unknown bacteria. The overall purpose of this review is to succinctly evaluate the application of omics technologies in colorectal cancer research for improving the diagnosis and treatment strategies.},
}

Colorectal Neoplasms/*diagnosis/genetics/metabolism/*therapy
Gastrointestinal Microbiome
Humans
Metabolomics
Metagenomics
Proteomics
Transcriptome

@article {pmid32633011,
year = {2020},
author = {Meijnikman, AS and Aydin, O and Prodan, A and Tremaroli, V and Herrema, H and Levin, E and Acherman, Y and Bruin, S and Gerdes, VE and Backhed, F and Groen, AK and Nieuwdorp, M},
title = {Distinct differences in gut microbial composition and functional potential from lean to morbidly obese subjects.},
journal = {Journal of internal medicine},
volume = {288},
number = {6},
pages = {699-710},
doi = {10.1111/joim.13137},
pmid = {32633011},
issn = {1365-2796},
mesh = {Adult ; Amino Acids/metabolism ; Body Mass Index ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Machine Learning ; Metabolic Networks and Pathways ; Metagenomics ; Middle Aged ; Obesity, Morbid/metabolism/*microbiology ; Thinness/metabolism/*microbiology ; },
abstract = {INTRODUCTION: The gut microbiome may contribute to the development of obesity. So far, the extent of microbiome variation in people with obesity has not been determined in large cohorts and for a wide range of body mass index (BMI). Here, we aimed to investigate whether the faecal microbial metagenome can explain the variance in several clinical phenotypes associated with morbid obesity.

METHODS: Caucasian subjects were recruited at our hospital. Blood pressure and anthropometric measurements were taken. Dietary intake was determined using questionnaires. Shotgun metagenomic sequencing was performed on faecal samples from 177 subjects.

RESULTS: Subjects without obesity (n = 82, BMI 24.7 ± 2.9 kg m-2) and subjects with obesity (n = 95, BMI 38.6 ± 5.1 kg m-2) could be clearly distinguished based on microbial composition and microbial metabolic pathways. A total number of 52 bacterial species differed significantly in people with and without obesity. Independent of dietary intake, we found that microbial pathways involved in biosynthesis of amino acids were enriched in subjects with obesity, whereas pathways involved in the degradation of amino acids were depleted. Machine learning models showed that more than half of the variance in body fat composition followed by BMI could be explained by the gut microbiome, composition and microbial metabolic pathways, compared with 6% of variation explained in triglycerides and 9% in HDL.

CONCLUSION: Based on the faecal microbiota composition, we were able to separate subjects with and without obesity. In addition, we found strong associations between gut microbial amino acid metabolism and specific microbial species in relation to clinical features of obesity.},
}

Adult
Amino Acids/metabolism
Body Mass Index
Feces/microbiology
*Gastrointestinal Microbiome
Humans
Machine Learning
Metabolic Networks and Pathways
Metagenomics
Middle Aged
Obesity, Morbid/metabolism/*microbiology
Thinness/metabolism/*microbiology

@article {pmid32492805,
year = {2020},
author = {Haudum, C and Lindheim, L and Ascani, A and Trummer, C and Horvath, A and Münzker, J and Obermayer-Pietsch, B},
title = {Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics.},
journal = {Nutrients},
volume = {12},
number = {6},
pages = {},
pmid = {32492805},
issn = {2072-6643},
support = {W1241//Austrian Science Fund/ ; FFG844609//Österreichische Forschungsförderungsgesellschaft/ ; },
mesh = {Adult ; Equol/metabolism ; Female ; Gastrointestinal Microbiome/*physiology ; Glucose/metabolism ; Humans ; Isoflavones/metabolism/*pharmacology/*therapeutic use ; *Metagenomics ; *Phytotherapy ; Polycystic Ovary Syndrome/*drug therapy/etiology/metabolism/*microbiology ; Receptors, Estrogen/metabolism ; Soy Milk ; Young Adult ; },
abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) affects 5-20% of women of reproductive age worldwide and is associated with disorders of glucose metabolism. Hormone and metabolic signaling may be influenced by phytoestrogens, such as isoflavones. Their endocrine effects may modify symptom penetrance in PCOS. Equol is one of the most active isoflavone metabolites, produced by intestinal bacteria, and acts as a selective estrogen receptor modulator.

METHOD: In this interventional study of clinical and biochemical characterization, urine isoflavone levels were measured in PCOS and control women before and three days after a defined isoflavone intervention via soy milk. In this interventional study, bacterial equol production was evaluated using the log(equol: daidzein ratio) and microbiome, metabolic, and predicted metagenome analyses were performed.

RESULTS: After isoflavone intervention, predicted stool metagenomic pathways, microbial alpha diversity, and glucose homeostasis in PCOS improved resembling the profile of the control group at baseline. In the whole cohort, larger equol production was associated with lower androgen as well as fertility markers.

CONCLUSION: The dynamics in our metabolic, microbiome, and predicted metagenomic profiles underline the importance of external phytohormones on PCOS characteristics and a potential therapeutic approach or prebiotic in the future.},
}

Adult
Equol/metabolism
Female
Gastrointestinal Microbiome/*physiology
Glucose/metabolism
Humans
Isoflavones/metabolism/*pharmacology/*therapeutic use
*Metagenomics
*Phytotherapy
Polycystic Ovary Syndrome/*drug therapy/etiology/metabolism/*microbiology
Receptors, Estrogen/metabolism
Soy Milk
Young Adult

@article {pmid32375386,
year = {2020},
author = {Li, Y and Gordon, E and Idle, A and Altan, E and Seguin, MA and Estrada, M and Deng, X and Delwart, E},
title = {Virome of a Feline Outbreak of Diarrhea and Vomiting Includes Bocaviruses and a Novel Chapparvovirus.},
journal = {Viruses},
volume = {12},
number = {5},
pages = {},
pmid = {32375386},
issn = {1999-4915},
mesh = {Animals ; Bocavirus/classification/genetics/*isolation & purification/physiology ; British Columbia/epidemiology ; Cat Diseases/epidemiology/*virology ; Cats ; Diarrhea/epidemiology/*veterinary/virology ; Disease Outbreaks ; Feces/virology ; Female ; Genome, Viral ; Male ; Parvovirinae/classification/genetics/*isolation & purification/physiology ; Phylogeny ; *Virome ; Vomiting/epidemiology/*veterinary/virology ; },
abstract = {An unexplained outbreak of feline diarrhea and vomiting, negative for common enteric viral and bacterial pathogens, was subjected to viral metagenomics and PCR. We characterized from fecal samples the genome of a novel chapparvovirus we named fechavirus that was shed by 8/17 affected cats and identified three different feline bocaviruses shed by 9/17 cats. Also detected were nucleic acids from attenuated vaccine viruses, members of the normal feline virome, viruses found in only one or two cases, and viruses likely derived from ingested food products. Epidemiological investigation of disease signs, time of onset, and transfers of affected cats between three facilities support a possible role for this new chapparvovirus in a highly contagious feline diarrhea and vomiting disease.},
}

Animals
Bocavirus/classification/genetics/*isolation & purification/physiology
British Columbia/epidemiology
Cat Diseases/epidemiology/*virology
Cats
Diarrhea/epidemiology/*veterinary/virology
Disease Outbreaks
Feces/virology
Female
Genome, Viral
Male
Parvovirinae/classification/genetics/*isolation & purification/physiology
Phylogeny
*Virome
Vomiting/epidemiology/*veterinary/virology

@article {pmid32283670,
year = {2020},
author = {Bolatti, EM and Zorec, TM and Montani, ME and Hošnjak, L and Chouhy, D and Viarengo, G and Casal, PE and Barquez, RM and Poljak, M and Giri, AA},
title = {A Preliminary Study of the Virome of the South American Free-Tailed Bats (Tadarida brasiliensis) and Identification of Two Novel Mammalian Viruses.},
journal = {Viruses},
volume = {12},
number = {4},
pages = {},
pmid = {32283670},
issn = {1999-4915},
mesh = {Animals ; Argentina ; Chiroptera/*virology ; Gene Order ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Open Reading Frames ; Papillomaviridae/classification/genetics ; Phylogeny ; Sequence Analysis, DNA ; *Virome ; Whole Genome Sequencing ; Workflow ; },
abstract = {Bats provide important ecosystem services as pollinators, seed dispersers, and/or insect controllers, but they have also been found harboring different viruses with zoonotic potential. Virome studies in bats distributed in Asia, Africa, Europe, and North America have increased dramatically over the past decade, whereas information on viruses infecting South American species is scarce. We explored the virome of Tadarida brasiliensis, an insectivorous New World bat species inhabiting a maternity colony in Rosario (Argentina), by a metagenomic approach. The analysis of five pooled oral/anal swab samples indicated the presence of 43 different taxonomic viral families infecting a wide range of hosts. By conventional nucleic acid detection techniques and/or bioinformatics approaches, the genomes of two novel viruses were completely covered clustering into the Papillomaviridae (Tadarida brasiliensis papillomavirus type 1, TbraPV1) and Genomoviridae (Tadarida brasiliensis gemykibivirus 1, TbGkyV1) families. TbraPV1 is the first papillomavirus type identified in this host and the prototype of a novel genus. TbGkyV1 is the first genomovirus reported in New World bats and constitutes a new species within the genus Gemykibivirus. Our findings extend the knowledge about oral/anal viromes of a South American bat species and contribute to understand the evolution and genetic diversity of the novel characterized viruses.},
}

Animals
Argentina
Chiroptera/*virology
Gene Order
Genome, Viral
High-Throughput Nucleotide Sequencing
*Metagenome
*Metagenomics/methods
Open Reading Frames
Papillomaviridae/classification/genetics
Phylogeny
Sequence Analysis, DNA
*Virome
Whole Genome Sequencing
Workflow

@article {pmid32271249,
year = {2020},
author = {Li, Y and Altan, E and Pilcher, C and Hartogensis, W and Hecht, FM and Deng, X and Delwart, E},
title = {Semen virome of men with HIV on or off antiretroviral treatment.},
journal = {AIDS (London, England)},
volume = {34},
number = {6},
pages = {827-832},
doi = {10.1097/QAD.0000000000002497},
pmid = {32271249},
issn = {1473-5571},
mesh = {Anelloviridae/isolation & purification ; Anti-HIV Agents/*therapeutic use ; Antiretroviral Therapy, Highly Active ; Blood/virology ; CD4 Lymphocyte Count ; Cytomegalovirus/isolation & purification ; DNA, Viral/genetics/isolation & purification ; Genotype ; HIV Infections/diagnosis/*drug therapy/*virology ; HIV-1/genetics/*isolation & purification ; Humans ; Male ; Metagenomics ; RNA, Viral ; San Francisco ; Semen/*virology ; *Virome ; Virus Shedding ; },
abstract = {OBJECTIVES: Improving immune status of people living with HIV through antiretroviral therapy (ART) may also reduce shedding of other viruses in semen. We characterized the seminal fluid virome of men with HIV and tested potential associations between viruses present and CD4 T-cell count, HIV viremia, and antiretroviral therapy (ART) status.

DESIGN AND METHODS: Metagenomics was used to enrich and sequence viral nucleic acids from the seminal fluid of 55 semen samples from 42 men living with HIV from San Francisco with a median age of 33 (IQR, 28.7-45) and median CD4 T-cell counts of 837 cells/μl (IQR, 258-1571 cells/μl). All samples were collected between 2005 and 2015, and ART status was ascertained from medical records.

RESULTS: Anelloviruses, cytomegalovirus (CMV), and multiple genotypes of human papillomaviruses were detected. Participants shed from 0 to 4 distinct human viruses. Longitudinally collected seminal fluid samples showed changes in the viruses shed. Viruses were more frequently shed by individuals with detectable HIV viremia (43.7 vs. 15.4%, P = 0.042). A trend was seen for increased shedding by individuals who were not on ART (42.8 vs. 17.8%, P = 0.082) or with CD4 T-cell count less than 350 cells/μl (35.3 vs. 20%, P = 0.27).

CONCLUSION: Seminal fluid from men with HIV from San Francisco contains nucleic acids from three different DNA viral families. A greater number of viruses, particularly CMV, were shed by participants with detectable HIV viremia (18.9 vs. 0%, P = 0.022). Control of viremia through ART may lower shedding of other viruses in semen in addition to HIV.},
}

Anelloviridae/isolation & purification
Anti-HIV Agents/*therapeutic use
Antiretroviral Therapy, Highly Active
Blood/virology
CD4 Lymphocyte Count
Cytomegalovirus/isolation & purification
DNA, Viral/genetics/isolation & purification
Genotype
HIV Infections/diagnosis/*drug therapy/*virology
HIV-1/genetics/*isolation & purification
Humans
Male
Metagenomics
RNA, Viral
San Francisco
Semen/*virology
*Virome
Virus Shedding

@article {pmid32121094,
year = {2020},
author = {Faizah, AN and Kobayashi, D and Isawa, H and Amoa-Bosompem, M and Murota, K and Higa, Y and Futami, K and Shimada, S and Kim, KS and Itokawa, K and Watanabe, M and Tsuda, Y and Minakawa, N and Miura, K and Hirayama, K and Sawabe, K},
title = {Deciphering the Virome of Culex vishnui Subgroup Mosquitoes, the Major Vectors of Japanese Encephalitis, in Japan.},
journal = {Viruses},
volume = {12},
number = {3},
pages = {},
pmid = {32121094},
issn = {1999-4915},
mesh = {Animals ; Biodiversity ; Culex/classification/*virology ; Encephalitis Viruses, Japanese/*physiology ; Encephalitis, Japanese/epidemiology/*transmission/*virology ; Genome, Viral ; Geography, Medical ; Japan/epidemiology ; Metagenome ; Metagenomics/methods ; Mosquito Vectors/classification/*virology ; Phylogeny ; Public Health Surveillance ; *Virome ; Viruses/classification/genetics ; },
abstract = {Japanese encephalitis (JE) remains a public health concern in several countries, and the Culex mosquito plays a central role in its transmission cycle. Culex mosquitoes harbor a wide range of viruses, including insect-specific viruses (ISVs), and can transmit a variety of arthropod-borne viruses (arboviruses) that cause human and animal diseases. The current trend of studies displays enhanced efforts to characterize the mosquito virome through bulk RNA sequencing due to possible arbovirus-ISV interactions; however, the extent of viral diversity in the mosquito taxon is still poorly understood, particularly in some disease vectors. In this study, arboviral screening and RNA virome analysis of Culex tritaeniorhynchus and C. pseudovishnui, which are part of the Culex vishnui subgroup mosquitoes, were performed. Results from these two mosquito species, known as the major vectors of JE virus (JEV) in Asia, collected in three prefectures in Japan were also compared with the sympatric species C. inatomii. A total of 27 viruses, including JEV, were detected from these Culex mosquitoes. Molecular and phylogenetic analyses of the detected viruses classified 15 of the 27 viruses as novel species, notably belonging to the Flaviviridae, Rhabdoviridae, Totiviridae, and Iflaviridae families. The successful isolation of JEV genotype I confirmed its continuous presence in Japan, suggesting the need for periodic surveillance. Aside from JEV, this study has also reported the diversity of the RNA virome of disease vectors and broadened the knowledge on mosquito virome profiles containing both arbovirus and ISV. Mosquito taxon seemed to contribute largely to the virome structure (e.g., virome composition, diversity, and abundance) as opposed to the geographical location of the mosquito species. This study therefore offers notable insights into the ecology and evolution of each identified virus and viral family. To the authors' knowledge, this is the first study to characterize the viromes of the major JE vectors in Japan.},
}

Animals
Biodiversity
Culex/classification/*virology
Encephalitis Viruses, Japanese/*physiology
Encephalitis, Japanese/epidemiology/*transmission/*virology
Genome, Viral
Geography, Medical
Japan/epidemiology
Metagenome
Metagenomics/methods
Mosquito Vectors/classification/*virology
Phylogeny
Public Health Surveillance
*Virome
Viruses/classification/genetics

@article {pmid31838792,
year = {2020},
author = {Chang, DH and Shin, J and Rhee, MS and Park, KR and Cho, BK and Lee, SK and Kim, BC},
title = {Vaginal Microbiota Profiles of Native Korean Women and Associations with High-Risk Pregnancy.},
journal = {Journal of microbiology and biotechnology},
volume = {30},
number = {2},
pages = {248-258},
doi = {10.4014/jmb.1908.08016},
pmid = {31838792},
issn = {1738-8872},
mesh = {Abortion, Spontaneous/etiology ; Adult ; Bacterial Load ; Biomarkers ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Polymerase Chain Reaction ; Pregnancy ; Pregnancy Outcome ; *Pregnancy, High-Risk ; Premature Birth/etiology ; Prevalence ; Public Health Surveillance ; RNA, Ribosomal, 16S ; Republic of Korea/epidemiology ; Sequence Analysis, DNA ; Vagina/*microbiology ; Young Adult ; },
abstract = {The vaginal microbiota may be important for pregnancy prognosis because vaginal dysbiosis during pregnancy appears to be related to preterm birth (PTB) or pregnancy loss. Previous reports have indicated that a Lactobacillus-poor microbial flora in the vagina and intrauterine infection by diverse anaerobes ascending from the vagina are associated with undesirable delivery outcomes. However, no research has involved the use of pyrosequencing analysis to examine vaginal microbiota profiles or their potential associations with high-risk pregnancy in Korean women. Vaginal swabs were collected from 500 Korean women for the identification of community state types (CSTs). Of these, 137 samples were further analyzed using a Roche/454 GS Junior pyrosequencer. Three distinct CSTs were identified based on the dominant vaginal microbes: CST I (Lactobacillus crispatus dominated), CST III (Lactobacillus iners dominated), and CST IV (with diverse species of anaerobes). Twelve of the 67 pregnant women had undesirable pregnancy outcomes (four miscarriages and eight PTBs). The dominant microbe in the vaginal microbiota of women who gave birth at full-term was L. crispatus. In contrast, L. iners was the dominant vaginal microbe in women who miscarried. Most (n = 6/8) vaginal microbiota profiles of women who experienced PTB could be classified as CST IV, with diverse bacteria, including anaerobic vaginal species. The present study provides valuable information regarding the characteristics of the vaginal microbiota of Korean women related to high-risk pregnancy. Investigation of the vaginal microbiotic structure in pregnant Korean women is necessary to enable better prediction of adverse pregnancy outcomes.},
}

Abortion, Spontaneous/etiology
Adult
Bacterial Load
Biomarkers
Female
High-Throughput Nucleotide Sequencing
Humans
Metagenome
Metagenomics/methods
*Microbiota
Middle Aged
Polymerase Chain Reaction
Pregnancy
Pregnancy Outcome
*Pregnancy, High-Risk
Premature Birth/etiology
Prevalence
Public Health Surveillance
RNA, Ribosomal, 16S
Republic of Korea/epidemiology
Sequence Analysis, DNA
Vagina/*microbiology
Young Adult

@article {pmid31635444,
year = {2020},
author = {Wu, M and Li, P and Li, J and An, Y and Wang, M and Zhong, G},
title = {The Differences between Luminal Microbiota and Mucosal Microbiota in Mice.},
journal = {Journal of microbiology and biotechnology},
volume = {30},
number = {2},
pages = {287-295},
doi = {10.4014/jmb.1908.08037},
pmid = {31635444},
issn = {1738-8872},
mesh = {Animals ; Bacteria/classification/genetics ; Biodiversity ; Colon/microbiology ; Computational Biology/methods ; Duodenum/microbiology ; High-Throughput Nucleotide Sequencing ; Intestinal Mucosa/microbiology ; Metagenome ; Metagenomics/methods ; Mice ; *Microbiota ; Mucous Membrane/*microbiology ; Organ Specificity ; },
abstract = {The differences between luminal microbiota (LM) and mucosal microbiota (MAM) were little known, especially in duodenum. In this study, LM and MAM in colon and duodenum of mice were investigated through 16S rRNA high-throughput sequencing. The lowest bacterial diversity and evenness were observed in duodenal LM (D_LM), followed by duodenal MAM (D_MAM). Meanwhile, the bacterial diversity and evenness were obviously increased in D_MAM than these in D_LM, while no significant difference was observed between colonic MAM (C_MAM) and colonic LM (C_LM). PCoA analysis also showed that bacterial communities of LM and MAM in duodenum were completely separated, while these in colon overlapped partly. The ratio of Firmicutes to Bacteroidetes (F/B) in D_MAM was significantly higher than that in D_LM. Lactobacillus was largely enriched and was the characteristic bacteria in D_LM. The characteristic bacteria in D_MAM were Turicibacter, Parasutterella, Marvinbryantia and Bifidobacterium, while in C_LM they were Ruminiclostridium_6, Ruminiclostridium_9, Ruminococcaceae_UCG_007 and Lachnospiraceae_UCG_010, and in C_MAM they were Lachnospiraceae_NK4A136, Mucispirillum, Alistipes, Ruminiclostridium and Odoribacter. The networks showed that more interactions existed in colonic microbiota (24 nodes and 74 edges) than in duodenal microbiota (17 nodes and 29 edges). The 16S rDNA function prediction results indicated that bigger differences of function exist between LM and MAM in duodenum than these in colon. In conclusion, microbiota from intestinal luminal content and mucosa were different both in colon and in duodenum, and bacteria in colon interacted with each other much more closely than those in duodenum.},
}

Animals
Bacteria/classification/genetics
Biodiversity
Colon/microbiology
Computational Biology/methods
Duodenum/microbiology
High-Throughput Nucleotide Sequencing
Intestinal Mucosa/microbiology
Metagenome
Metagenomics/methods
Mice
*Microbiota
Mucous Membrane/*microbiology
Organ Specificity

@article {pmid33609137,
year = {2021},
author = {Neal, AL and McLaren, T and Campolino, ML and Hughes, D and Coelho, AM and Lana, UGP and Gomes, EA and de Sousa, SM},
title = {Crop type exerts greater influence upon rhizosphere phosphohydrolase gene abundance and phylogenetic diversity than phosphorus fertilization.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiab033},
pmid = {33609137},
issn = {1574-6941},
abstract = {Rock phosphate is an alternative form of phosphorus (P) fertilizer, however there is no information regarding the influence of P fertilizer sources in Brazilian Cerrado soils upon microbial genes coding for phosphohydrolase enzymes in crop rhizospheres. Here, we analyse a field experiment comparing maize and sorghum grown under different P fertilization (rock phosphate and triple superphosphate) upon crop performance, phosphatase activity and rhizosphere microbiomes at three levels of diversity: small subunit rRNA marker genes of bacteria, archaea and fungi; a suite of alkaline and acid phosphatase and phytase genes; and ecotypes of individual genes. We showed no significant difference in crop performance between the fertilizer sources, but the accumulation of fertilizer P into pools of organic soil P differed. Phosphatase activity was the only biological parameter influenced by P fertilization. Differences in rhizosphere microbiomes were observed at all levels of biodiversity due to crop type, but not fertilization. Inspection of phosphohydrolase gene ecotypes responsible for differences between the crops suggests a role for lateral genetic transfer in establishing ecotype distributions. Moreover, they were not reflected in microbial community composition, suggesting that they confer competitive advantage to individual cells rather than species in the sorghum rhizosphere.},
}

@article {pmid33597026,
year = {2021},
author = {de Nies, L and Lopes, S and Busi, SB and Galata, V and Heintz-Buschart, A and Laczny, CC and May, P and Wilmes, P},
title = {PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {49},
pmid = {33597026},
issn = {2049-2618},
support = {CORE/BM/11333923//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; PRIDE/11823097//Fonds National de la Recherche Luxembourg/ ; 14701//Michael J. Fox Foundation/ ; ERC-CoG 863664//H2020 European Research Council/ ; },
abstract = {BACKGROUND: Pathogenic microorganisms cause disease by invading, colonizing, and damaging their host. Virulence factors including bacterial toxins contribute to pathogenicity. Additionally, antimicrobial resistance genes allow pathogens to evade otherwise curative treatments. To understand causal relationships between microbiome compositions, functioning, and disease, it is essential to identify virulence factors and antimicrobial resistance genes in situ. At present, there is a clear lack of computational approaches to simultaneously identify these factors in metagenomic datasets.

RESULTS: Here, we present PathoFact, a tool for the contextualized prediction of virulence factors, bacterial toxins, and antimicrobial resistance genes with high accuracy (0.921, 0.832 and 0.979, respectively) and specificity (0.957, 0.989 and 0.994). We evaluate the performance of PathoFact on simulated metagenomic datasets and perform a comparison to two other general workflows for the analysis of metagenomic data. PathoFact outperforms all existing workflows in predicting virulence factors and toxin genes. It performs comparably to one pipeline regarding the prediction of antimicrobial resistance while outperforming the others. We further demonstrate the performance of PathoFact on three publicly available case-control metagenomic datasets representing an actual infection as well as chronic diseases in which either pathogenic potential or bacterial toxins are hypothesized to play a role. In each case, we identify virulence factors and AMR genes which differentiated between the case and control groups, thereby revealing novel gene associations with the studied diseases.

CONCLUSION: PathoFact is an easy-to-use, modular, and reproducible pipeline for the identification of virulence factors, bacterial toxins, and antimicrobial resistance genes in metagenomic data. Additionally, our tool combines the prediction of these pathogenicity factors with the identification of mobile genetic elements. This provides further depth to the analysis by considering the genomic context of the pertinent genes. Furthermore, PathoFact's modules for virulence factors, toxins, and antimicrobial resistance genes can be applied independently, thereby making it a flexible and versatile tool. PathoFact, its models, and databases are freely available at https://pathofact.lcsb.uni.lu . Video abstract.},
}

@article {pmid33277434,
year = {2020},
author = {Reysenbach, AL and St John, E and Meneghin, J and Flores, GE and Podar, M and Dombrowski, N and Spang, A and L'Haridon, S and Humphris, SE and de Ronde, CEJ and Caratori Tontini, F and Tivey, M and Stucker, VK and Stewart, LC and Diehl, A and Bach, W},
title = {Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {117},
number = {51},
pages = {32627-32638},
doi = {10.1073/pnas.2019021117},
pmid = {33277434},
issn = {1091-6490},
mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Hydrogen-Ion Concentration ; Hydrothermal Vents/*microbiology ; Metagenome ; Microbial Consortia/*physiology ; New Zealand ; Oxidation-Reduction ; Pacific Ocean ; Phylogeny ; Seawater/*microbiology ; Sulfides/chemistry ; *Volcanic Eruptions ; },
abstract = {Hydrothermally active submarine volcanoes are mineral-rich biological oases contributing significantly to chemical fluxes in the deep sea, yet little is known about the microbial communities inhabiting these systems. Here we investigate the diversity of microbial life in hydrothermal deposits and their metagenomics-inferred physiology in light of the geological history and resulting hydrothermal fluid paths in the subsurface of Brothers submarine volcano north of New Zealand on the southern Kermadec arc. From metagenome-assembled genomes we identified over 90 putative bacterial and archaeal genomic families and nearly 300 previously unknown genera, many potentially endemic to this submarine volcanic environment. While magmatically influenced hydrothermal systems on the volcanic resurgent cones of Brothers volcano harbor communities of thermoacidophiles and diverse members of the superphylum "DPANN," two distinct communities are associated with the caldera wall, likely shaped by two different types of hydrothermal circulation. The communities whose phylogenetic diversity primarily aligns with that of the cone sites and magmatically influenced hydrothermal systems elsewhere are characterized predominately by anaerobic metabolisms. These populations are probably maintained by fluids with greater magmatic inputs that have interacted with different (deeper) previously altered mineral assemblages. However, proximal (a few meters distant) communities with gene-inferred aerobic, microaerophilic, and anaerobic metabolisms are likely supported by shallower seawater-dominated circulation. Furthermore, mixing of fluids from these two distinct hydrothermal circulation systems may have an underlying imprint on the high microbial phylogenomic diversity. Collectively our results highlight the importance of considering geologic evolution and history of subsurface processes in studying microbial colonization and community dynamics in volcanic environments.},
}

Archaea/genetics
Bacteria/genetics
Biodiversity
Hydrogen-Ion Concentration
Hydrothermal Vents/*microbiology
Metagenome
Microbial Consortia/*physiology
New Zealand
Oxidation-Reduction
Pacific Ocean
Phylogeny
Seawater/*microbiology
Sulfides/chemistry
*Volcanic Eruptions

@article {pmid32846980,
year = {2020},
author = {Kubacki, J and Flacio, E and Qi, W and Guidi, V and Tonolla, M and Fraefel, C},
title = {Viral Metagenomic Analysis of Aedes albopictus Mosquitos from Southern Switzerland.},
journal = {Viruses},
volume = {12},
number = {9},
pages = {},
pmid = {32846980},
issn = {1999-4915},
mesh = {Aedes/*virology ; Animals ; Female ; Flavivirus/classification/genetics/isolation & purification ; Male ; Metagenomics ; Phylogeny ; Switzerland ; Virome/*genetics ; Viruses/classification/genetics/isolation & purification ; },
abstract = {A metagenomic study was performed on 498 female and 40 male Aedes albopictus mosquitos collected in August and September 2019 in Ticino, a region in southern Switzerland, to address the question regarding the risk of the local transmission of zoonotic viruses. A total of 13 viruses from seven different virus families and several unclassified viral taxa were identified. Reads of insect-specific flaviviruses were present in all pools, and a complete genome of aedes flavivirus was assembled and phylogenetically analysed. The most abundant virus was Wenzhou sobemo-like virus, assembled from 1.3 × 105 to 3.6 × 106 reads in each pool. In a pool of male mosquitos, a complete genome of aedes Iflavi-like virus was detected and phylogenetically analysed. Most importantly, genomes of human pathogenic viruses were not found. This is the first study to determine the virome of Ae. albopictus from Switzerland and forms a baseline for future longitudinal investigations concerning the potential role of Ae. albopictus as a vector of clinically relevant viruses.},
}

Aedes/*virology
Animals
Female
Flavivirus/classification/genetics/isolation & purification
Male
Metagenomics
Phylogeny
Switzerland
Virome/*genetics
Viruses/classification/genetics/isolation & purification

@article {pmid32400083,
year = {2020},
author = {Piñar, G and Tafer, H and Schreiner, M and Miklas, H and Sterflinger, K},
title = {Decoding the biological information contained in two ancient Slavonic parchment codices: an added historical value.},
journal = {Environmental microbiology},
volume = {22},
number = {8},
pages = {3218-3233},
pmid = {32400083},
issn = {1462-2920},
support = {//(FWF)/International ; P29892//Austrian Science Fund/International ; },
mesh = {Animals ; Biodegradation, Environmental ; Conservation of Natural Resources ; *DNA, Ancient/isolation & purification ; Europe, Eastern ; History, Ancient ; Humans ; Manuscripts as Topic/*history ; *Microbiota ; Saccharopolyspora ; Skin/microbiology ; },
abstract = {This study provides an example in the emerging field of biocodicology showing how metagenomics can help answer relevant questions that may contribute to a better understanding of the history of ancient manuscripts. To this end, two Slavonic codices dating from the 11th century were investigated through shotgun metagenomics. Endogenous DNA enabled to infer the animal origin of the skins used in the manufacture of the two codices, while nucleic sequences recovered from viruses were investigated for the first time in this material, opening up new possibilities in the field of biocodicology. In addition, the microbiomes colonizing the surface of the parchments served to determine their conservation status and their latent risk of deterioration. The saline environment provided by the parchments selected halophilic and halotolerant microorganisms, which are known to be responsible for the biodegradation of parchment. Species of Nocardiopsis, Gracilibacillus and Saccharopolyspora, but also members of the Aspergillaceae family were detected in this study, all possessing enzymatic capabilities for the biodeterioration of this material. Finally, a relative abundance of microorganisms originating from the human skin microbiome were identified, most probably related to the intensive manipulation of the manuscripts throughout the centuries, which should be taken with caution as they can be potential pathogens.},
}

Animals
Biodegradation, Environmental
Conservation of Natural Resources
*DNA, Ancient/isolation & purification
Europe, Eastern
History, Ancient
Humans
Manuscripts as Topic/*history
*Microbiota
Saccharopolyspora
Skin/microbiology

@article {pmid32155753,
year = {2020},
author = {Ottati, S and Chiapello, M and Galetto, L and Bosco, D and Marzachì, C and Abbà, S},
title = {New Viral Sequences Identified in the Flavescence Dorée Phytoplasma Vector Scaphoideus titanus.},
journal = {Viruses},
volume = {12},
number = {3},
pages = {},
pmid = {32155753},
issn = {1999-4915},
mesh = {Amino Acid Sequence ; Animals ; Base Sequence ; Hemiptera/*microbiology/*virology ; *Metagenome ; *Metagenomics/methods ; Phylogeny ; Phytoplasma ; RNA Viruses/genetics ; RNA, Double-Stranded ; *Virome ; },
abstract = {The leafhopper Scaphoideus titanus is the primary vector of Flavescence dorée phytoplasma (FDp) in European vineyards. Flavescence dorée is one of the most severely damaging diseases of Vitis vinifera and, consequently, a major threat to grape and wine production in several European countries. Control measures are compulsory, but they mainly involve large-scale insecticide treatments, with detrimental impacts on the environment. One possible solution is to exploit the largely unexplored genetic diversity of viruses infecting S. titanus as highly specific and environmentally benign tools for biological control. (2)Methods: A metatranscriptomic approach was adopted to identify viruses that may infect individuals caught in the wild in both its native (United States) and invasive (Europe) areas. Reverse transcription PCR was used to confirm their presence in RNA pools and explore their prevalence. (3)Results: We described nine new RNA viruses, including members of "Picorna-Calici", "Permutotetra", "Bunya-Arena", "Reo", "Partiti-Picobirna", "Luteo-Sobemo" and "Toti-Chryso" clades. A marked difference in the diversity and abundance of the viral species was observed between the US population and the European ones. (4)Conclusions: This work represents the first survey to assess the viral community of a phytoplasma insect vector. The possibility to exploit these naturally occurring viruses as specific and targeted biocontrol agents of S. titanus could be the answer to increasing demand for a more sustainable viticulture.},
}

Amino Acid Sequence
Animals
Base Sequence
Hemiptera/*microbiology/*virology
*Metagenome
*Metagenomics/methods
Phylogeny
Phytoplasma
RNA Viruses/genetics
RNA, Double-Stranded
*Virome

@article {pmid32121402,
year = {2020},
author = {Birnberg, L and Temmam, S and Aranda, C and Correa-Fiz, F and Talavera, S and Bigot, T and Eloit, M and Busquets, N},
title = {Viromics on Honey-Baited FTA Cards as a New Tool for the Detection of Circulating Viruses in Mosquitoes.},
journal = {Viruses},
volume = {12},
number = {3},
pages = {},
pmid = {32121402},
issn = {1999-4915},
mesh = {Animals ; Culicidae/*virology ; *Environmental Microbiology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Honey ; Metagenomics/*methods ; Mosquito Vectors/virology ; Phylogeny ; Polymerase Chain Reaction ; RNA, Viral ; Sequence Analysis, DNA ; Spain ; *Virome ; Virus Diseases/transmission ; Viruses/classification/genetics ; },
abstract = {Worldwide, emerging and re-emerging infectious diseases (EIDs) are a major burden on public and animal health. Arthropod vectors, with mosquitoes being the main contributors of global disease, transmit more than 70% of the recognized EIDs. To assess new alternatives for arthropod-borne viral diseases surveillance, and for the detection of new viruses, honey-baited Flinders Technology Associates (FTA) cards were used as sugar bait in mosquito traps during entomological surveys at the Llobregat River Delta (Catalonia, Spain). Next generation sequencing (NGS) metagenomics analysis was applied on honey-baited FTA cards, which had been exposed to field-captured mosquitoes to characterize their associated virome. Arthropod- and plant-infecting viruses governed the virome profile on FTA cards. Twelve near-complete viral genomes were successfully obtained, suggesting good quality preservation of viral RNAs. Mosquito pools linked to the FTA cards were screened for the detection of mosquito-associated viruses by specific RT-PCRs to confirm the presence of these viruses. The circulation of viruses related to Alphamesonivirus, Quaranjavirus and unclassified Bunyavirales was detected in mosquitoes, and phylogenetic analyses revealed their similarities to viruses previously reported in other continents. To the best our knowledge, our findings constitute the first distribution record of these viruses in European mosquitoes and the first hint of insect-specific viruses in mosquitoes' saliva in field conditions, demonstrating the feasibility of this approach to monitor the transmissible fraction of the mosquitoes' virome. In conclusion, this pilot viromics study on honey-baited FTA cards was shown to be a valid approach for the detection of viruses circulating in mosquitoes, thereby setting up an alternative tool for arbovirus surveillance and control programs.},
}

Animals
Culicidae/*virology
*Environmental Microbiology
Genome, Viral
High-Throughput Nucleotide Sequencing
*Honey
Metagenomics/*methods
Mosquito Vectors/virology
Phylogeny
Polymerase Chain Reaction
RNA, Viral
Sequence Analysis, DNA
Spain
*Virome
Virus Diseases/transmission
Viruses/classification/genetics

@article {pmid33097978,
year = {2021},
author = {Forouzan, S and Hoffman, KL and Kosten, TA},
title = {Methamphetamine exposure and its cessation alter gut microbiota and induce depressive-like behavioral effects on rats.},
journal = {Psychopharmacology},
volume = {238},
number = {1},
pages = {281-292},
pmid = {33097978},
issn = {1432-2072},
mesh = {Animals ; Anxiety/*chemically induced/microbiology ; Anxiety Disorders/chemically induced/microbiology ; Behavior, Animal/*drug effects ; Brain/drug effects ; Central Nervous System Stimulants/administration & dosage/*toxicity ; Depression/chemically induced/microbiology ; Dose-Response Relationship, Drug ; Dysbiosis/microbiology ; Feces/microbiology ; Gastrointestinal Microbiome/*drug effects ; Male ; Methamphetamine/administration & dosage/*toxicity ; RNA, Ribosomal, 16S/genetics ; Rats ; Rats, Sprague-Dawley ; Swimming ; },
abstract = {RATIONALE: Methamphetamine is a highly abused psychostimulant drug and its use remains a major public health concern worldwide with limited effective treatment options. Accumulative evidence reveals the influence of gut microbiota on the brain, behavior, and health as a part of the gut-brain axis but its involvement in modulating this substance use disorder remains poorly understood.

OBJECTIVE: We sought to determine whether methamphetamine exposure and cessation or withdrawal alter the intestinal gut microbiota as well as characterize cessation-induced behavioral changes.

METHODS: Male, Sprague-Dawley rats were administered methamphetamine (2 mg/kg; s.c.) or vehicle (n = 8 per group) twice per day for 14 consecutive days. On various days before, during, and after administration, fecal samples were collected and tests of anxiety- and depressive-like behaviors were conducted.

RESULTS: Methamphetamine administration and cessation did not alter the relative abundance of bacteria but significantly changed the composition of gut bacteria through 16S rRNA sequencing. These changes were normalized after 7 days of methamphetamine cessation. Moreover, acute methamphetamine cessation induced depressive-like behavior, with an increase in immobility in the forced swim test but did not alter anxiety-like behaviors in tests of open field test or elevated plus maze.

CONCLUSIONS: These findings provide direct evidence that methamphetamine and its cessation cause gut dysbiosis and that the latter associates with depressive-like behavior in rodents. Our observation will contribute to a better understanding of the function of gut microbiota in the process of substance use disorders and guide the choice of target therapeutics.},
}

Animals
Anxiety/*chemically induced/microbiology
Anxiety Disorders/chemically induced/microbiology
Behavior, Animal/*drug effects
Brain/drug effects
Central Nervous System Stimulants/administration & dosage/*toxicity
Depression/chemically induced/microbiology
Dose-Response Relationship, Drug
Dysbiosis/microbiology
Feces/microbiology
Gastrointestinal Microbiome/*drug effects
Male
Methamphetamine/administration & dosage/*toxicity
RNA, Ribosomal, 16S/genetics
Rats
Rats, Sprague-Dawley
Swimming

@article {pmid32482258,
year = {2020},
author = {Chu, W and Han, Q and Xu, J and Wang, J and Sun, Y and Li, W and Chen, ZJ and Du, Y},
title = {Metagenomic analysis identified microbiome alterations and pathological association between intestinal microbiota and polycystic ovary syndrome.},
journal = {Fertility and sterility},
volume = {113},
number = {6},
pages = {1286-1298.e4},
doi = {10.1016/j.fertnstert.2020.01.027},
pmid = {32482258},
issn = {1556-5653},
mesh = {Adult ; Bacteria/classification/*genetics ; Case-Control Studies ; Cross-Sectional Studies ; Dysbiosis ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*genetics ; Humans ; Intestines/*microbiology ; Metagenomics ; Polycystic Ovary Syndrome/diagnosis/*microbiology/physiopathology ; Young Adult ; },
abstract = {OBJECTIVE: To identify different microbial species in women with polycystic ovary syndrome (PCOS) and reveal a possible relationship between gut dysbiosis and pathological changes.

DESIGN: Cross-sectional study.

SETTING: Academic institution.

PATIENT(S): Reproductive-aged women with PCOS (n = 14) and controls (n = 14) from the Centre for Reproductive Medicine.

INTERVENTION(S): Shotgun metagenomic sequencing on fecal samples from patients, and clinical parameters (including body mass index, endocrine hormone levels, and glycemia level) gathered for correlation analysis.

MAIN OUTCOME MEASURE(S): Identification of different gut microbial strains and relativity between microbiota and clinical parameters.

RESULT(S): We found several microbial strains were statistically significantly more abundant in the PCOS group, including Parabacteroides merdae, Bacteroides fragilis, and strains of Escherichia and Shigella, whereas Faecalibacterium prausnitzii was enriched in the control group. Metagenomic species (MGS) analysis revealed that the microbes of the PCOS group were negatively correlated with those of the control group. Of note, we observed a positive correlation between MGS relevant to PCOS and endocrine disorders, including body mass index and elevated levels of serum testosterone, luteinizing hormone, and antimüllerian hormone. Functional alterations, reflected by Kyoto Encyclopedia of Genes and Genomes orthologues, could imply potential mechanisms of microbial involvement in the developmental progress of PCOS.

CONCLUSION(S): Our findings suggest an intimate association and potential mechanisms linking microbial dysbiosis and the pathophysiologic changes of PCOS. We address the importance of monitoring and modulating microbial composition and functional shifts in future clinical practice.},
}

Adult
Bacteria/classification/*genetics
Case-Control Studies
Cross-Sectional Studies
Dysbiosis
Feces/microbiology
Female
Gastrointestinal Microbiome/*genetics
Humans
Intestines/*microbiology
Metagenomics
Polycystic Ovary Syndrome/diagnosis/*microbiology/physiopathology
Young Adult

@article {pmid32075887,
year = {2020},
author = {Meslier, V and Laiola, M and Roager, HM and De Filippis, F and Roume, H and Quinquis, B and Giacco, R and Mennella, I and Ferracane, R and Pons, N and Pasolli, E and Rivellese, A and Dragsted, LO and Vitaglione, P and Ehrlich, SD and Ercolini, D},
title = {Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake.},
journal = {Gut},
volume = {69},
number = {7},
pages = {1258-1268},
pmid = {32075887},
issn = {1468-3288},
mesh = {Adult ; Cholesterol/*blood ; *Diet, Mediterranean ; Energy Intake ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; *Metabolome ; Obesity/blood/*diet therapy/microbiology ; Overweight/blood/*diet therapy/microbiology ; },
abstract = {OBJECTIVES: This study aimed to explore the effects of an isocaloric Mediterranean diet (MD) intervention on metabolic health, gut microbiome and systemic metabolome in subjects with lifestyle risk factors for metabolic disease.

DESIGN: Eighty-two healthy overweight and obese subjects with a habitually low intake of fruit and vegetables and a sedentary lifestyle participated in a parallel 8-week randomised controlled trial. Forty-three participants consumed an MD tailored to their habitual energy intakes (MedD), and 39 maintained their regular diets (ConD). Dietary adherence, metabolic parameters, gut microbiome and systemic metabolome were monitored over the study period.

RESULTS: Increased MD adherence in the MedD group successfully reprogrammed subjects' intake of fibre and animal proteins. Compliance was confirmed by lowered levels of carnitine in plasma and urine. Significant reductions in plasma cholesterol (primary outcome) and faecal bile acids occurred in the MedD compared with the ConD group. Shotgun metagenomics showed gut microbiome changes that reflected individual MD adherence and increase in gene richness in participants who reduced systemic inflammation over the intervention. The MD intervention led to increased levels of the fibre-degrading Faecalibacterium prausnitzii and of genes for microbial carbohydrate degradation linked to butyrate metabolism. The dietary changes in the MedD group led to increased urinary urolithins, faecal bile acid degradation and insulin sensitivity that co-varied with specific microbial taxa.

CONCLUSION: Switching subjects to an MD while maintaining their energy intake reduced their blood cholesterol and caused multiple changes in their microbiome and metabolome that are relevant in future strategies for the improvement of metabolic health.},
}

Adult
Cholesterol/*blood
*Diet, Mediterranean
Energy Intake
Female
*Gastrointestinal Microbiome
Humans
Male
*Metabolome
Obesity/blood/*diet therapy/microbiology
Overweight/blood/*diet therapy/microbiology

@article {pmid32580987,
year = {2020},
author = {Volery, M and Scherz, V and Jakob, W and Bandeira, D and Deggim-Messmer, V and Lauber-Biason, A and Wildhaber, J and Falquet, L and Curtis, N and Zimmermann, P},
title = {Study protocol for the ABERRANT study: antibiotic-induced disruption of the maternal and infant microbiome and adverse health outcomes - a prospective cohort study among children born at term.},
journal = {BMJ open},
volume = {10},
number = {6},
pages = {e036275},
pmid = {32580987},
issn = {2044-6055},
abstract = {INTRODUCTION: There is compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome. Antibiotics cause profound changes in the microbiome. However, the effect of intrapartum and early-life antibiotics on the maternal intestinal and breast milk microbiome, and the infant oral and intestinal microbiome, and whether effects are only short term or persist long term remain uncertain.

METHODS AND ANALYSES: In this prospective cohort study, we will use metagenomic sequencing to determine: (1) the effect of intrapartum antibiotics on the composition of the breast milk, and the infant oral and intestinal microbiome, including the development and persistence of antibiotic resistance; (2) the effect of antibiotic exposure in the first year of life on the composition of the infant oral and intestinal microbiome, including the development and persistence of antibiotic resistance; (3) the effect of disruption of the infant oral and intestinal microbiome on health outcomes and (4) the compositional overlap between the maternal intestinal microbiome, the breast milk microbiome and the infant oral and intestinal microbiome.

ETHICS AND DISSEMINATION: The ABERRANT study has been approved by the commission cantonale d'éthique de la recherche sur l'être humain (CER-VD) du Canton de Vaud (#2019-01567). Outcomes will be disseminated through publication and will be presented at scientific conferences.

TRIAL REGISTRATION NUMBER: NCT04091282.},
}

@article {pmid32516966,
year = {2020},
author = {Tilocca, B and Pieroni, L and Soggiu, A and Britti, D and Bonizzi, L and Roncada, P and Greco, V},
title = {Gut-Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization.},
journal = {International journal of molecular sciences},
volume = {21},
number = {11},
pages = {},
pmid = {32516966},
issn = {1422-0067},
abstract = {Recent advances in the field of meta-omics sciences and related bioinformatics tools have allowed a comprehensive investigation of human-associated microbiota and its contribution to achieving and maintaining the homeostatic balance. Bioactive compounds from the microbial community harboring the human gut are involved in a finely tuned network of interconnections with the host, orchestrating a wide variety of physiological processes. These includes the bi-directional crosstalk between the central nervous system, the enteric nervous system, and the gastrointestinal tract (i.e., gut-brain axis). The increasing accumulation of evidence suggest a pivotal role of the composition and activity of the gut microbiota in neurodegeneration. In the present review we aim to provide an overview of the state-of-the-art of meta-omics sciences including metagenomics for the study of microbial genomes and taxa strains, metatranscriptomics for gene expression, metaproteomics and metabolomics to identify and/or quantify microbial proteins and metabolites, respectively. The potential and limitations of each discipline were highlighted, as well as the advantages of an integrated approach (multi-omics) to predict microbial functions and molecular mechanisms related to human diseases. Particular emphasis is given to the latest results obtained with these approaches in an attempt to elucidate the link between the gut microbiota and the most common neurodegenerative diseases, such as multiple sclerosis (MS), Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS).},
}

@article {pmid32354152,
year = {2020},
author = {Reider, SJ and Moosmang, S and Tragust, J and Trgovec-Greif, L and Tragust, S and Perschy, L and Przysiecki, N and Sturm, S and Tilg, H and Stuppner, H and Rattei, T and Moschen, AR},
title = {Prebiotic Effects of Partially Hydrolyzed Guar Gum on the Composition and Function of the Human Microbiota-Results from the PAGODA Trial.},
journal = {Nutrients},
volume = {12},
number = {5},
pages = {},
pmid = {32354152},
issn = {2072-6643},
support = {17605//Oesterreichische Nationalbank/ ; CD Laboratory for Mucosal Immunology//Christian Doppler Forschungsgesellschaft/ ; },
abstract = {(1) Background: Alterations in the structural composition of the human gut microbiota have been identified in various disease entities along with exciting mechanistic clues by reductionist gnotobiotic modeling. Improving health by beneficially modulating an altered microbiota is a promising treatment approach. Prebiotics, substrates selectively used by host microorganisms conferring a health benefit, are broadly used for dietary and clinical interventions. Herein, we sought to investigate the microbiota-modelling effects of the soluble fiber, partially hydrolyzed guar gum (PHGG). (2) Methods: We performed a 9 week clinical trial in 20 healthy volunteers that included three weeks of a lead-in period, followed by three weeks of an intervention phase, wherein study subjects received 5 g PHGG up to three times per day, and concluding with a three-week washout period. A stool diary was kept on a daily basis, and clinical data along with serum/plasma and stool samples were collected on a weekly basis. PHGG-induced alterations of the gut microbiota were studied by 16S metagenomics of the V1-V3 and V3-V4 regions. To gain functional insight, we further studied stool metabolites using nuclear magnetic resonance (NMR) spectroscopy. (3) Results: In healthy subjects, PHGG had significant effects on stool frequency and consistency. These effects were paralleled by changes in α- (species evenness) and β-diversity (Bray-Curtis distances), along with increasing abundances of metabolites including butyrate, acetate and various amino acids. On a taxonomic level, PHGG intake was associated with a bloom in Ruminococcus, Fusicatenibacter, Faecalibacterium and Bacteroides and a reduction in Roseburia, Lachnospiracea and Blautia. The majority of effects disappeared after stopping the prebiotic and most effects tended to be more pronounced in male participants. (4) Conclusions: Herein, we describe novel aspects of the prebiotic PHGG on compositional and functional properties of the healthy human microbiota.},
}

@article {pmid32056780,
year = {2020},
author = {Madan, A and Thompson, D and Fowler, JC and Ajami, NJ and Salas, R and Frueh, BC and Bradshaw, MR and Weinstein, BL and Oldham, JM and Petrosino, JF},
title = {The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness.},
journal = {Journal of affective disorders},
volume = {264},
number = {},
pages = {98-106},
doi = {10.1016/j.jad.2019.12.020},
pmid = {32056780},
issn = {1573-2517},
abstract = {BACKGROUND: Emerging evidence implicates the gut microbiota in central nervous system functioning via its effects on inflammation, the hypothalamic-pituitary axis, and/or neurotransmission. Our understanding of the cellular underpinnings of the brain-gut relationship is based almost exclusively on animal models with some small-scale human studies. This study examined the relationship between the gut microbiota and psychiatric symptom severity and treatment response among inpatients with serious mental illness.

METHOD: We collected data from adult inpatients (N = 111). Measures of diagnoses, suicide severity, trauma, depression, and anxiety were collected shortly after admission, while self-collected fecal swabs were collected early in the course of hospitalization and processed using 16S rRNA gene sequencing and whole genome shotgun sequencing methods.

RESULTS: Results indicate that depression and anxiety severity shortly after admission were negatively associated with bacterial richness and alpha diversity. Additional analyses revealed a number of bacterial taxa associated with depression and anxiety severity. Gut microbiota richness and alpha diversity early in the course of hospitalization was a significant predictor of depression remission at discharge.

CONCLUSIONS: This study is among the first to demonstrate a gut microbiota relationship with symptom severity among psychiatric inpatients as well as a relationship to remission of depression post-treatment. These findings are consistent with animal models and limited human studies as well as with the broader literature implicating inflammation in the pathophysiology of depression. These findings offer the foundation for further studies of novel therapeutic approaches to the treatment, prevention of, or recurrence of serious mental illness.},
}

@article {pmid32270658,
year = {2020},
author = {Ku, HJ and Kim, YT and Lee, JH},
title = {Microbiome Study of Initial Gut Microbiota from Newborn Infants to Children Reveals that Diet Determines Its Compositional Development.},
journal = {Journal of microbiology and biotechnology},
volume = {30},
number = {7},
pages = {1067-1071},
doi = {10.4014/jmb.2002.02042},
pmid = {32270658},
issn = {1738-8872},
mesh = {*Breast Feeding ; Child, Preschool ; *Diet ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Infant ; Infant, Newborn ; Klebsiella ; Male ; Milk, Human/*microbiology ; Serratia ; },
abstract = {To understand the formation of initial gut microbiota, three initial fecal samples were collected from two groups of two breast milk-fed (BM1) and seven formula milk-fed (FM1) infants, and the compositional changes in gut microbiota were determined using metagenomics. Compositional change analysis during week one showed that Bifidobacterium increased from the first to the third fecal samples in the BM1 group (1.3% to 35.1%), while Klebsiella and Serratia were detected in the third fecal sample of the FM1 group (4.4% and 34.2%, respectively), suggesting the beneficial effect of breast milk intake. To further understand the compositional changes during progression from infancy to childhood (i.e., from three weeks to five years of age), additional fecal samples were collected from four groups of two breast milk-fed infants (BM2), one formula milk-fed toddler (FM2), three weaning food-fed toddlers (WF), and three solid food-fed children (SF). Subsequent compositional change analysis and principal coordinates analysis (PCoA) revealed that the composition of the gut microbiota changed from an infant-like composition to an adult-like one in conjunction with dietary changes. Interestingly, overall gut microbiota composition analyses during the period of progression from infancy to childhood suggested increasing complexity of gut microbiota as well as emergence of a new species of bacteria capable of digesting complex carbohydrates in WF and SF groups, substantiating that diet type is a key factor in determining the composition of gut microbiota. Consequently, this study may be useful as a guide to understanding the development of initial gut microbiota based on diet.},
}

*Breast Feeding
Child, Preschool
*Diet
Feces/microbiology
Female
Gastrointestinal Microbiome/*physiology
Humans
Infant
Infant, Newborn
Klebsiella
Male
Milk, Human/*microbiology
Serratia

@article {pmid32000795,
year = {2020},
author = {Mohammad, HA and Madi, NM and Al-Nakib, W},
title = {Analysis of viral diversity in stool samples from infants and children with acute gastroenteritis in Kuwait using Metagenomics approach.},
journal = {Virology journal},
volume = {17},
number = {1},
pages = {10},
pmid = {32000795},
issn = {1743-422X},
mesh = {Acute Disease ; Child ; Child, Preschool ; Diarrhea/virology ; Feces/*virology ; Female ; Gastroenteritis/*virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Kuwait ; Male ; *Metagenomics ; RNA, Viral/genetics ; Real-Time Polymerase Chain Reaction ; *Virome ; Viruses/*classification/genetics ; },
abstract = {BACKGROUND: Current molecular target-dependent methods are used to detect only known viruses. However, metagenomics based on next-generation sequencing (NGS) technique is a target-independent assay that enables simultaneous detection and genomic characterisation of all microorganisms present in a sample. In this study, we aimed to develop a metagenomics approach using NGS to identify and characterise viruses in stool samples from infants and children with Acute Gastroenteritis (AGE) in Kuwait.

METHODS: We have investigated 84 stool samples from infants and children aged one month to ten years old with signs and symptoms of gastroenteritis who attended Mubarak Al-Kabeer and Al-Amiri hospitals in Kuwait from January to December 2017. A metagenomics approach using NGS to characterise viruses in clinical samples was used. Also, the commercial Real-Time PCR assay was used to detect viruses causing gastroenteritis.

RESULTS: Metagenomics analysis revealed an average of 280,768 reads in which 5% of the reads were derived from viruses. The analysis of viral sequences verified that single infection of human adenovirus was the leading cause of gastroenteritis among infants and children, which was detected in 23.2% of the patients, followed by a mixed infection of human adenovirus and other viruses, which was detected in 20.9% of patients. Also, the newly discovered viruses known to cause gastroenteritis were detected, such as astrovirus MLB2, primate bocaparvovirus-1, Aichivirus A, cardiovirus, parechovirus A, astrovirus VA4, cosavirus-F, and bufavirus-3. Our results showed 71% agreement (k = 0.445, P = 0.000) between multiplex Real-Time PCR, which is used as a routine diagnostic test and metagenomics approach in the detection of viruses causing gastroenteritis in clinical samples.

CONCLUSION: Despite the difficulties in sample preparation and analysis process, we showed that metagenomics approach is a powerful and promising tool for the detection and characterisation of different viruses in clinical samples.},
}

Acute Disease
Child
Child, Preschool
Diarrhea/virology
Feces/*virology
Female
Gastroenteritis/*virology
Genome, Viral
High-Throughput Nucleotide Sequencing
Humans
Infant
Kuwait
Male
*Metagenomics
RNA, Viral/genetics
Real-Time Polymerase Chain Reaction
*Virome
Viruses/*classification/genetics

@article {pmid33270717,
year = {2020},
author = {Skarżyńska, M and Leekitcharoenphon, P and Hendriksen, RS and Aarestrup, FM and Wasyl, D},
title = {A metagenomic glimpse into the gut of wild and domestic animals: Quantification of antimicrobial resistance and more.},
journal = {PloS one},
volume = {15},
number = {12},
pages = {e0242987},
pmid = {33270717},
issn = {1932-6203},
mesh = {Animal Feed ; Animals ; Animals, Wild ; Drug Resistance, Bacterial/*genetics ; Foxes/microbiology ; Gastrointestinal Microbiome/*genetics ; *Metagenome ; Plasmids ; Poland ; Poultry/*microbiology ; Rodentia/microbiology ; Sus scrofa/microbiology ; },
abstract = {Antimicrobial resistance (AMR) in bacteria is a complex subject, why one need to look at this phenomenon from a wider and holistic perspective. The extensive use of the same antimicrobial classes in human and veterinary medicine as well as horticulture is one of the main drivers for the AMR selection. Here, we applied shotgun metagenomics to investigate the AMR epidemiology in several animal species including farm animals, which are often exposed to antimicrobial treatment opposed to an unique set of wild animals that seems not to be subjected to antimicrobial pressure. The comparison of the domestic and wild animals allowed to investigate the possible anthropogenic impact on AMR spread. Inclusion of animals with different feeding behaviors (carnivores, omnivores) enabled to further assess which AMR genes that thrives within the food chain. We tested fecal samples not only of intensively produced chickens, turkeys, and pigs, but also of wild animals such as wild boars, red foxes, and rodents. A multi-directional approach mapping obtained sequences to several databases provided insight into the occurrence of the different AMR genes. The method applied enabled also analysis of other factors that may influence AMR of intestinal microbiome such as diet. Our findings confirmed higher levels of AMR in farm animals than in wildlife. The results also revealed the potential of wildlife in the AMR dissemination. Particularly in red foxes, we found evidence of several AMR genes conferring resistance to critically important antimicrobials like quinolones and cephalosporins. In contrast, the lowest abundance of AMR was observed in rodents originating from natural environment with presumed limited exposure to antimicrobials. Shotgun metagenomics enabled us to demonstrate that discrepancies between AMR profiles found in the intestinal microbiome of various animals probably resulted from the different antimicrobial exposure, habitats, and behavior of the tested animal species.},
}

Animal Feed
Animals
Animals, Wild
Drug Resistance, Bacterial/*genetics
Foxes/microbiology
Gastrointestinal Microbiome/*genetics
*Metagenome
Plasmids
Poland
Poultry/*microbiology
Rodentia/microbiology
Sus scrofa/microbiology

@article {pmid33183813,
year = {2021},
author = {Coutinho, FH and von Meijenfeldt, FAB and Walter, JM and Haro-Moreno, JM and Lopéz-Pérez, M and van Verk, MC and Thompson, CC and Cosenza, CAN and Appolinario, L and Paranhos, R and Cabral, A and Dutilh, BE and Thompson, FL},
title = {Ecogenomics and metabolic potential of the South Atlantic Ocean microbiome.},
journal = {The Science of the total environment},
volume = {765},
number = {},
pages = {142758},
doi = {10.1016/j.scitotenv.2020.142758},
pmid = {33183813},
issn = {1879-1026},
mesh = {Archaea/genetics ; Atlantic Ocean ; Metagenome ; Metagenomics ; *Microbiota ; *Seawater ; },
abstract = {The unique combination of depth, salinity, and water masses make the South Atlantic Ocean an ecosystem of special relevance within the global ocean. Yet, the microbiome of this ecosystem has received less attention than other regions of the global Ocean. This has hampered our understanding of the diversity and metabolic potential of the microorganisms that dwell in this habitat. To fill this knowledge gap, we analyzed a collection of 31 metagenomes from the Atlantic Ocean that spanned the epipelagic, mesopelagic and bathypelagic zones (surface to 4000 m). Read-centric and gene-centric analysis revealed the unique taxonomic and functional composition of metagenomes from each depth zone, which was driven by differences in physical and chemical parameters. In parallel, a total of 40 metagenome-assembled genomes were obtained, which recovered one third of the total community. Phylogenomic reconstruction revealed that many of these genomes are derived from poorly characterized taxa of Bacteria and Archaea. Genomes derived from heterotrophic bacteria of the aphotic zone displayed a large apparatus of genes suited for the utilization of recalcitrant organic compounds such as cellulose, chitin and alkanes. In addition, we found genomic evidence suggesting that mixotrophic bacteria from the bathypelagic zone could perform carbon fixation through the Calvin-Benson-Bassham cycle, fueled by sulfur oxidation. Finally, we found that the viral communities shifted throughout the water column regarding their targeted hosts and virus-to-microbe ratio, in response to shifts in the composition and functioning their microbial counterparts. Our findings shed light on the microbial and viral drivers of important biogeochemical processes that take place in the South Atlantic Ocean.},
}

Archaea/genetics
Atlantic Ocean
Metagenome
Metagenomics
*Microbiota
*Seawater

@article {pmid32690973,
year = {2021},
author = {Almeida, A and Nayfach, S and Boland, M and Strozzi, F and Beracochea, M and Shi, ZJ and Pollard, KS and Sakharova, E and Parks, DH and Hugenholtz, P and Segata, N and Kyrpides, NC and Finn, RD},
title = {A unified catalog of 204,938 reference genomes from the human gut microbiome.},
journal = {Nature biotechnology},
volume = {39},
number = {1},
pages = {105-114},
pmid = {32690973},
issn = {1546-1696},
support = {BB/N018354/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Bacteria/classification/genetics ; *Databases, Genetic ; Gastrointestinal Microbiome/*genetics ; Genome, Bacterial/*genetics ; Humans ; Metagenome/*genetics ; Metagenomics ; Phenotype ; Phylogeny ; },
abstract = {Comprehensive, high-quality reference genomes are required for functional characterization and taxonomic assignment of the human gut microbiota. We present the Unified Human Gastrointestinal Genome (UHGG) collection, comprising 204,938 nonredundant genomes from 4,644 gut prokaryotes. These genomes encode >170 million protein sequences, which we collated in the Unified Human Gastrointestinal Protein (UHGP) catalog. The UHGP more than doubles the number of gut proteins in comparison to those present in the Integrated Gene Catalog. More than 70% of the UHGG species lack cultured representatives, and 40% of the UHGP lack functional annotations. Intraspecies genomic variation analyses revealed a large reservoir of accessory genes and single-nucleotide variants, many of which are specific to individual human populations. The UHGG and UHGP collections will enable studies linking genotypes to phenotypes in the human gut microbiome.},
}

Bacteria/classification/genetics
*Databases, Genetic
Gastrointestinal Microbiome/*genetics
Genome, Bacterial/*genetics
Humans
Metagenome/*genetics
Metagenomics
Phenotype
Phylogeny

@article {pmid32382536,
year = {2020},
author = {Kibegwa, FM and Bett, RC and Gachuiri, CK and Stomeo, F and Mujibi, FD},
title = {A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle.},
journal = {BioMed research international},
volume = {2020},
number = {},
pages = {2348560},
pmid = {32382536},
issn = {2314-6141},
mesh = {Animals ; *Archaea/classification/genetics ; *Bacteria/classification/genetics ; Cattle/*microbiology ; Computational Biology ; Feces/*microbiology ; *Metagenome ; Metagenomics ; Microbiota/*genetics ; },
abstract = {Analysis of shotgun metagenomic data generated from next generation sequencing platforms can be done through a variety of bioinformatic pipelines. These pipelines employ different sets of sophisticated bioinformatics algorithms which may affect the results of this analysis. In this study, we compared two commonly used pipelines for shotgun metagenomic analysis: MG-RAST and Kraken 2, in terms of taxonomic classification, diversity analysis, and usability using their primarily default parameters. Overall, the two pipelines detected similar abundance distributions in the three most abundant taxa Proteobacteria, Firmicutes, and Bacteroidetes. Within bacterial domain, 497 genera were identified by both pipelines, while an additional 694 and 98 genera were solely identified by Kraken 2 and MG-RAST, respectively. 933 species were detected by the two algorithms. Kraken 2 solely detected 3550 species, while MG-RAST identified 557 species uniquely. For archaea, Kraken 2 generated 105 and 236 genera and species, respectively, while MG-RAST detected 60 genera and 88 species. 54 genera and 72 species were commonly detected by the two methods. Kraken 2 had a quicker analysis time (~4 hours) while MG-RAST took approximately 2 days per sample. This study revealed that Kraken 2 and MG-RAST generate comparable results and that a reliable high-level overview of sample is generated irrespective of the pipeline selected. However, Kraken 2 generated a more accurate taxonomic identification given the higher number of "Unclassified" reads in MG-RAST. The observed variations at the genus level show that a main restriction is using different databases for classification of the metagenomic data. The results of this research indicate that a more inclusive and representative classification of microbiomes may be achieved through creation of the combined pipelines.},
}

Animals
*Archaea/classification/genetics
*Bacteria/classification/genetics
Cattle/*microbiology
Computational Biology
Feces/*microbiology
*Metagenome
Metagenomics
Microbiota/*genetics

@article {pmid33564113,
year = {2021},
author = {Tran, PQ and Bachand, SC and McIntyre, PB and Kraemer, BM and Vadeboncoeur, Y and Kimirei, IA and Tamatamah, R and McMahon, KD and Anantharaman, K},
title = {Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {33564113},
issn = {1751-7370},
support = {CGSD3 - 532474 - 2019//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; DEB-1030242//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-0842253//NSF | BIO | Division of Environmental Biology (DEB)/ ; DEB-1344254//NSF | BIO | Division of Environmental Biology (DEB)/ ; },
abstract = {Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth's surface. LT's mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT's 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.},
}

@article {pmid32345639,
year = {2020},
author = {Neugent, ML and Hulyalkar, NV and Nguyen, VH and Zimmern, PE and De Nisco, NJ},
title = {Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection.},
journal = {mBio},
volume = {11},
number = {2},
pages = {},
pmid = {32345639},
issn = {2150-7511},
mesh = {Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; *Microbiota/drug effects/genetics ; Probiotics/therapeutic use ; Urinary Tract/*microbiology ; *Urinary Tract Infections/diagnosis/microbiology/prevention & control/therapy ; Urine/microbiology ; },
abstract = {Recent advances in the analysis of microbial communities colonizing the human body have identified a resident microbial community in the human urinary tract (UT). Compared to many other microbial niches, the human UT harbors a relatively low biomass. Studies have identified many genera and species that may constitute a core urinary microbiome. However, the contribution of the UT microbiome to urinary tract infection (UTI) and recurrent UTI (rUTI) pathobiology is not yet clearly understood. Evidence suggests that commensal species within the UT and urogenital tract (UGT) microbiomes, such as Lactobacillus crispatus, may act to protect against colonization with uropathogens. However, the mechanisms and fundamental biology of the urinary microbiome-host relationship are not understood. The ability to measure and characterize the urinary microbiome has been enabled through the development of next-generation sequencing and bioinformatic platforms that allow for the unbiased detection of resident microbial DNA. Translating technological advances into clinical insight will require further study of the microbial and genomic ecology of the urinary microbiome in both health and disease. Future diagnostic, prognostic, and therapeutic options for the management of UTI may soon incorporate efforts to measure, restore, and/or preserve the native, healthy ecology of the urinary microbiomes.},
}

Female
High-Throughput Nucleotide Sequencing
Humans
Male
Metagenomics
*Microbiota/drug effects/genetics
Probiotics/therapeutic use
Urinary Tract/*microbiology
*Urinary Tract Infections/diagnosis/microbiology/prevention & control/therapy
Urine/microbiology

@article {pmid32179121,
year = {2020},
author = {Maleki, M and Shahraki, MF and Kavousi, K and Ariaeenejad, S and Hosseini Salekdeh, G},
title = {A novel thermostable cellulase cocktail enhances lignocellulosic bioconversion and biorefining in a broad range of pH.},
journal = {International journal of biological macromolecules},
volume = {154},
number = {},
pages = {349-360},
doi = {10.1016/j.ijbiomac.2020.03.100},
pmid = {32179121},
issn = {1879-0003},
mesh = {Animals ; Bacteria/*enzymology ; Beta vulgaris/metabolism ; Camelus ; Cellulases/*chemistry ; *Gastrointestinal Microbiome ; Hydrolysis ; Kinetics ; Lignin/*metabolism ; Oryza/metabolism ; Recombinant Proteins ; Rumen/*microbiology ; },
abstract = {Lignocellulose is the most abundant biomass in nature, and the effective biorefining of them is dependent upon enzymes with high catalytic activity and stability in extreme pH and high temperatures. Due to the molecular constraints for a single enzyme, obtaining a more excellent active pH range can be more easily achievable through the simultaneous activity of two or more enzymes in a cocktail. To address this, we attempted to develop a cocktail of novel thermostable cellulases with high hydrolytic ability and stability. Two cellulases were mined, identified, cloned, and expressed from the camel rumen microbiota. The PersiCel1 demonstrated its maximum relative activity at the pH of 8, and the temperature of 60 °C and the PersiCel2 was optimally active at the pH of 5 and the temperature of 50 °C. Furthermore, utilization of the enzyme cocktail implies the synergistic relationship and significantly increased the saccharification yield of lignocellulosic substrates up to 71.7% for sugar-beet pulp (active pH range of 4-9) and 138.7% for rice-straw (active pH range of 5-8), compared to maximum hydrolysis of Persicel1 or PersiCel2 separately at 55 °C. Our results indicate the probable applicability of PersiCel1, PersiCel2, and their cocktail in numerous industries, specifically biorefineries and lignocellulose bioconversion based technologies.},
}

Animals
Bacteria/*enzymology
Beta vulgaris/metabolism
Camelus
Cellulases/*chemistry
*Gastrointestinal Microbiome
Hydrolysis
Kinetics
Lignin/*metabolism
Oryza/metabolism
Recombinant Proteins
Rumen/*microbiology

@article {pmid33454531,
year = {2021},
author = {Lu, H and Wang, J and Huang, L and Wang, X and Zhou, J and Wang, J},
title = {Effect of immobilized anthraquinone-2-sulfonate on antibiotic resistance genes and microbial community in biofilms of anaerobic reactors.},
journal = {Journal of environmental management},
volume = {282},
number = {},
pages = {111967},
doi = {10.1016/j.jenvman.2021.111967},
pmid = {33454531},
issn = {1095-8630},
mesh = {Anaerobiosis ; Anthraquinones ; *Anti-Bacterial Agents/pharmacology ; Biofilms ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; },
abstract = {Quinone compounds could significantly accelerate anaerobic biotransformation of refractory pollutants. However, the effect of quinone compounds application on the propagation of antibiotic resistance genes (ARGs) in the bio-treatment of these pollutants-containing wastewater is not available. In this study, the catalytic performance of anthraquinone-2-sulfonate immobilized on polyurethane foam (AQS-PUF), changes of ARGs, mobile gene elements (MGEs) and microbial community structure attached on AQS-PUF and PUF in the up-flow anaerobic bioreactors were investigated. The results showed that AQS-PUF could significantly accelerate the decolorization of azo dye RR X-3B. Meanwhile, metagenomics analysis showed that the total absolute abundance of ARGs increased in the presence of the immobilized AQS. Among ARGs, the number of the efflux pump-encoding ARGs in the biofilm of AQS-PUF accounted for 35.7% of the total ARGs, which was slightly higher than that of PUF (32.1%) due to the presence of the immobilized AQS. The relative abundances of ARGs conferring resistance to MLS (macrolide, lincosamide and streptogramin), tetracycline and sulfonamide, which were deeply concerned, reduced 10%, 21.7% and 7.3% in the presence of the immobilized AQS, respectively. Moreover, the immobilized AQS resulted in the decreased relative abundance of plasmids, transposons and class I integrons. Among the detected 31 ARG subtypes located in MGEs, the relative abundances of only lnuF, msrE and mphD in the biofilm of AQS-PUF were over 2-fold higher compared with those in the biofilm of PUF. However, the three ARGs and their host Gammaproteobacteria was not dominant in microbial community. The relative abundances of more ARGs including MLS (lnuB and EreA), tetracycline (tetH) resistance genes located in MGEs decreased, which was attributed to the decreased relative abundance of their hosts. These studies showed that the addition of the immobilized AQS (around 0.25 mM) had a beneficial effect on reducing the spread of ARGs during dyeing wastewater bio-treatment.},
}

Anaerobiosis
Anthraquinones
*Anti-Bacterial Agents/pharmacology
Biofilms
Drug Resistance, Microbial/genetics
Genes, Bacterial
*Microbiota

@article {pmid32334626,
year = {2020},
author = {Liu, Q and Wang, H and Ling, Y and Yang, SX and Wang, XC and Zhou, R and Xiao, YQ and Chen, X and Yang, J and Fu, WG and Zhang, W and Qi, GL},
title = {Viral metagenomics revealed diverse CRESS-DNA virus genomes in faeces of forest musk deer.},
journal = {Virology journal},
volume = {17},
number = {1},
pages = {61},
pmid = {32334626},
issn = {1743-422X},
mesh = {Animals ; China ; DNA Viruses/*classification/genetics ; DNA, Viral/genetics ; Deer/*virology ; Feces/*virology ; Metagenomics ; Phylogeny ; *Virome ; },
abstract = {BACKGROUND: Musk deer can produce musk which has high medicinal value and is closely related to human health. Viruses in forest musk deer both threaten the health of forest musk deer and human beings.

METHODS: Using viral metagenomics we investigated the virome in 85 faeces samples collected from forest musk deer.

RESULTS: In this article, eight novel CRESS-DNA viruses were characterized, whole genomes were 2148 nt-3852 nt in length. Phylogenetic analysis indicated that some viral genomes were part of four different groups of CRESS-DNA virus belonging in the unclassified CRESS-DNA virus, Smacoviridae, pCPa-like virus and pPAPh2-like virus. UJSL001 (MN621482), UJSL003 (MN621469) and UJSL017 (MN621476) fall into the branch of unclassified CRESS-DNA virus (CRESSV1-2), UJSL002 (MN621468), UJSL004 (MN621481) and UJSL007 (MN621470) belong to the cluster of Smacoviridae, UJSL005 (MN604398) showing close relationship with pCPa-like (pCRESS4-8) clusters and UJSL006 (MN621480) clustered into the branch of pPAPh2-like (pCRESS9) virus, respectively.

CONCLUSION: The virome in faeces samples of forest musk deer from Chengdu, Sichuan province, China was revealed, which further characterized the diversity of viruses in forest musk deer intestinal tract.},
}

Animals
China
DNA Viruses/*classification/genetics
DNA, Viral/genetics
Deer/*virology
Feces/*virology
Metagenomics
Phylogeny
*Virome

@article {pmid32170201,
year = {2020},
author = {Alneberg, J and Bennke, C and Beier, S and Bunse, C and Quince, C and Ininbergs, K and Riemann, L and Ekman, M and Jürgens, K and Labrenz, M and Pinhassi, J and Andersson, AF},
title = {Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.},
journal = {Communications biology},
volume = {3},
number = {1},
pages = {119},
pmid = {32170201},
issn = {2399-3642},
mesh = {Aquatic Organisms/*genetics ; Archaea/genetics ; Bacteria/genetics ; Base Sequence ; Ecology ; *Ecosystem ; *Genome, Archaeal ; *Genome, Bacterial ; Machine Learning ; *Metagenome ; Metagenomics/*methods ; Phylogeny ; Plankton/microbiology ; Sequence Analysis, DNA/methods ; },
abstract = {The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.},
}

Aquatic Organisms/*genetics
Archaea/genetics
Bacteria/genetics
Base Sequence
Ecology
*Ecosystem
*Genome, Archaeal
*Genome, Bacterial
Machine Learning
*Metagenome
Metagenomics/*methods
Phylogeny
Plankton/microbiology
Sequence Analysis, DNA/methods

@article {pmid32962897,
year = {2020},
author = {Albaugh, VL},
title = {Comment on: Fecal metagenomics and metabolomics reveal gut microbial changes after bariatric surgery.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {16},
number = {11},
pages = {1782-1783},
doi = {10.1016/j.soard.2020.08.006},
pmid = {32962897},
issn = {1878-7533},
mesh = {*Bariatric Surgery ; Feces ; *Gastrointestinal Microbiome ; Humans ; Metabolomics ; Metagenomics ; },
}

*Bariatric Surgery
Feces
*Gastrointestinal Microbiome
Humans
Metabolomics
Metagenomics

@article {pmid32909146,
year = {2020},
author = {Punyapwar, S and Mutnuri, S},
title = {Diversity and functional annotation of microorganisms in French vertical flow constructed wetland treating greywater.},
journal = {World journal of microbiology & biotechnology},
volume = {36},
number = {10},
pages = {148},
doi = {10.1007/s11274-020-02923-1},
pmid = {32909146},
issn = {1573-0972},
mesh = {Bacteria/*classification/genetics/*metabolism ; *Biodiversity ; Biological Oxygen Demand Analysis ; Carbon/metabolism ; Ecosystem ; Metagenomics ; Nitrogen/analysis ; Phosphorus/metabolism ; Proteobacteria ; *Soil Microbiology ; Waste Disposal, Fluid ; Waste Water/*microbiology ; Water Purification/*methods ; *Wetlands ; Xenobiotics/metabolism ; },
abstract = {Constructed wetlands form a unique ecosystem having plants, soil, microbes in which microorganisms play a vital role in the transformation and degradation of pollutants from wastewater. In the present study, French type two-stage vertical flow constructed wetland (VFCW) was used for the treatment of single household greywater (GW). Pilot-scale VFCW having sand and gravel as the filter substrate was constructed with Canna indica plantation for treating GW. To understand the pollutant removal mechanism in VFCW, microbial diversity and functional annotation was carried out by metagenomics analysis of sequences obtained from illumina platform. Efficiency of VFCW was measured with respect to water quality parameters like COD, BOD5, Total Nitrogen, Nitrate, Nitrite, Ammoniacal-N, ortho-phosphate and TOC from inlet and outlet of system. The removal efficiency was 90%, 93%, 34%, 26%, 89%, 68%, 80%, and 80% for COD, BOD5, Total Nitrogen, Nitrate, Nitrite, Ammoniacal-N, ortho-phosphate and TOC respectively. Microbial diversity was much more diversified and unique in VFCW compared to GW. Metagenomes exhibited Proteobacteria and Bacteroidetes as major phyla in GW whereas Actinobacteria, Proteobacteria, Nitrospirae abundance in VFCW layers. Total of 809 and 695 genus were found in VFCW and GW respectively with minimum abundance of 10 hits. From functional annotation of sequences, VFCW microbes have the potential to transform various aromatic and xenobiotic compounds along with the removal of pollutants present in the form of Carbon, Nitrogen, and Phosphorus. These data reveal French type VFCW can efficiently treat GW and with its own unique, variable habitat VFCW harbours diverse community of microorganisms that transform and degrade the pollutants in GW.},
}

Bacteria/*classification/genetics/*metabolism
*Biodiversity
Biological Oxygen Demand Analysis
Carbon/metabolism
Ecosystem
Metagenomics
Nitrogen/analysis
Phosphorus/metabolism
Proteobacteria
*Soil Microbiology
Waste Disposal, Fluid
Waste Water/*microbiology
Water Purification/*methods
*Wetlands
Xenobiotics/metabolism

@article {pmid32495495,
year = {2020},
author = {Rodriguez-R, LM and Tsementzi, D and Luo, C and Konstantinidis, KT},
title = {Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences.},
journal = {Environmental microbiology},
volume = {22},
number = {8},
pages = {3394-3412},
doi = {10.1111/1462-2920.15112},
pmid = {32495495},
issn = {1462-2920},
support = {1241046//National Science Foundation/International ; 1759831//National Science Foundation/International ; },
mesh = {Chloroflexi/*classification/genetics/*isolation & purification ; Databases, Genetic ; Genome, Bacterial/*genetics ; Lakes/*microbiology ; Metagenome/genetics ; Metagenomics ; Microbiota/genetics ; },
abstract = {Recent advances in sequencing technology and bioinformatic pipelines have allowed unprecedented access to the genomes of yet-uncultivated microorganisms from diverse environments. However, the catalogue of freshwater genomes remains limited, and most genome recovery attempts in freshwater ecosystems have only targeted specific taxa. Here, we present a genome recovery pipeline incorporating iterative subtractive binning, and apply it to a time series of 100 metagenomic datasets from seven connected lakes and estuaries along the Chattahoochee River (Southeastern USA). Our set of metagenome-assembled genomes (MAGs) represents >400 yet-unnamed genomospecies, substantially increasing the number of high-quality MAGs from freshwater lakes. We propose names for two novel species: 'Candidatus Elulimicrobium humile' ('Ca. Elulimicrobiota', 'Patescibacteria') and 'Candidatus Aquidulcis frankliniae' ('Chloroflexi'). Collectively, our MAGs represented about half of the total microbial community at any sampling point. To evaluate the prevalence of these genomospecies in the chronoseries, we introduce methodologies to estimate relative abundance and habitat preference that control for uneven genome quality and sample representation. We demonstrate high degrees of habitat-specialization and endemicity for most genomospecies in the Chattahoochee lakes. Wider ecological ranges characterized smaller genomes with higher coding densities, indicating an overall advantage of smaller, more compact genomes for cosmopolitan distributions.},
}

Chloroflexi/*classification/genetics/*isolation & purification
Databases, Genetic
Genome, Bacterial/*genetics
Lakes/*microbiology
Metagenome/genetics
Metagenomics
Microbiota/genetics

@article {pmid32294307,
year = {2020},
author = {Goller, CC and Ott, LE},
title = {Evolution of an 8-week upper-division metagenomics course: Diagramming a learning path from observational to quantitative microbiome analysis.},
journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology},
volume = {48},
number = {4},
pages = {391-403},
doi = {10.1002/bmb.21349},
pmid = {32294307},
issn = {1539-3429},
mesh = {Bacteria/classification/*genetics/isolation & purification ; Computational Biology/*methods ; Genome, Bacterial ; Humans ; Metagenomics/*education/methods ; *Microbiota ; Problem-Based Learning/*methods ; RNA, Bacterial/*analysis/genetics ; RNA, Ribosomal, 16S/*analysis/genetics ; Soil Microbiology ; Students ; },
abstract = {Metagenomics is a tool that enables researchers to study genetic material recovered directly from microbial communities or microbiomes. Fueled by advances in sequencing technologies, bioinformatics tools, and sample processing, metagenomics studies promise to expand our understanding of human health and the use of microorganisms for agriculture and industry. Therefore, teaching students about metagenomics is crucial to prepare them for modern careers in the life sciences. However, the increasing number of different approaches makes teaching metagenomics to students a challenge. This 8-week metagenomics laboratory course has the objective of introducing upper-level undergraduate and graduate students to strategies for designing, executing, and analyzing microbiome investigations. The laboratory component begins with sample processing, library preparation, and submission for high-throughput sequencing before transitioning to computer-based activities, which include an introduction to several fundamental computational metagenomics tools. Students analyze their sequencing results and deposit findings in sequence databases. The laboratory component is complemented by a weekly lecture, where active learning sessions promote retrieval practice and allow students to reflect on and diagram processes performed in the laboratory. Attainment of student learning outcomes was assessed through the completion of various course assignments: laboratory reports, presentations, and a cumulative final exam. Further, students' perceptions of their gains relevant to the learning outcomes were evaluated using pre- and postcourse surveys. Collectively, these data demonstrate that this course results in the attainment of the learning outcomes and that this approach provides an adaptable way to expose students to the cutting-edge field of metagenomics.},
}

Bacteria/classification/*genetics/isolation & purification
Computational Biology/*methods
Genome, Bacterial
Humans
Metagenomics/*education/methods
*Microbiota
Problem-Based Learning/*methods
RNA, Bacterial/*analysis/genetics
RNA, Ribosomal, 16S/*analysis/genetics
Soil Microbiology
Students

@article {pmid32232443,
year = {2020},
author = {Bartolomaeus, H and Avery, EG and Bartolomaeus, TUP and Kozhakhmetov, S and Zhumadilov, Z and Müller, DN and Wilck, N and Kushugulova, A and Forslund, SK},
title = {Blood pressure changes correlate with short-chain fatty acid production potential shifts under a synbiotic intervention.},
journal = {Cardiovascular research},
volume = {116},
number = {7},
pages = {1252-1253},
doi = {10.1093/cvr/cvaa083},
pmid = {32232443},
issn = {1755-3245},
mesh = {Bacteria/genetics/*metabolism ; *Blood Pressure ; Databases, Genetic ; Fatty Acids/*blood ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Syndrome/blood/*diet therapy/microbiology/physiopathology ; Metagenomics ; Randomized Controlled Trials as Topic ; Synbiotics/*administration & dosage ; Treatment Outcome ; },
}

Bacteria/genetics/*metabolism
*Blood Pressure
Databases, Genetic
Fatty Acids/*blood
*Gastrointestinal Microbiome/genetics
Humans
Metabolic Syndrome/blood/*diet therapy/microbiology/physiopathology
Metagenomics
Randomized Controlled Trials as Topic
Synbiotics/*administration & dosage
Treatment Outcome

@article {pmid33540579,
year = {2021},
author = {Conti, A and Corte, L and Casagrande Pierantoni, D and Robert, V and Cardinali, G},
title = {What Is the Best Lens? Comparing the Resolution Power of Genome-Derived Markers and Standard Barcodes.},
journal = {Microorganisms},
volume = {9},
number = {2},
pages = {},
doi = {10.3390/microorganisms9020299},
pmid = {33540579},
issn = {2076-2607},
abstract = {Fungal species delimitation was traditionally carried out with multicopy ribosomal RNA (rRNA) genes, principally for their ease of amplification. Since the efficacy of these markers has been questioned, single-copy protein-encoding genes have been proposed alone or in combination for Multi-Locus Sequence Typing (MLST). In this context, the role of the many sequences obtained with Next-Generation Sequencing (NGS) techniques, in both genomics and metagenomics, further pushes toward an analysis of the efficacy of NGS-derived markers and of the metrics to evaluate the marker efficacy in discriminating fungal species. This paper aims at proposing MeTRe (Mean Taxonomic Resolution), a novel index that could be used both for measuring marker efficacy and for assessing the actual resolution (i.e., the level of separation) between species obtained with different markers or their combinations. In this paper, we described and then employed this index to compare the efficacy of two rRNAs and four single-copy markers obtained from public databases as both an amplicon-based approach and genome-derived sequences. Two different groups of species were used, one with a pathogenic species of Candida that was characterized by relatively well-separated taxa, whereas the other, comprising some relevant species of the sensu stricto group of the genus Saccharomyces, included close species and interspecific hybrids. The results showed the ability of MeTRe to evaluate marker efficacy in general and genome-derived markers specifically.},
}

@article {pmid32466241,
year = {2020},
author = {Li, Z and Tian, J and Lai, Y and Lee, CH and Cai, Z and Yu, CF},
title = {Puffer Fish Gut Microbiota Studies Revealed Unique Bacterial Co-Occurrence Patterns and New Insights on Tetrodotoxin Producers.},
journal = {Marine drugs},
volume = {18},
number = {5},
pages = {},
pmid = {32466241},
issn = {1660-3397},
support = {UGC/FDS25/M03/15//Hong Kong Research Grants Council/ ; R201907/R201711//Research grants of Beijing Normal University - Hong Kong Baptist University United International College/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/analysis ; Symbiosis ; *Tetraodontiformes ; Tetrodotoxin/*metabolism ; },
abstract = {Tetrodotoxin (TTX) is a potent neurotoxin isolated mainly from toxic puffer fish. To date, the TTX biosynthetic mechanism inside its hosts remains unresolved. Here, we hypothesize the TTX synthesis relies on the host gut microbiota, including the neglected non-culturable bacteria. In these studies, we collected the gut contents from 5 puffer fish species of the genus Takifugu including one suspected hybrid species for gut microbiota study by 16S rRNA amplicon metagenomics approach. Their gut samples were divided into toxic and non-toxic groups based on the TTX concentrations in the livers detected by LC-MS/MS. Bacterial diversity studies showed that gut microbiota structures were significantly different between toxic and non-toxic species. Vibrio and Cyanobacteria centered at the gut bacterial co-occurrence network, suggesting their importance in TTX biosynthesis. The results of PICRUSt2 metagenomic prediction and gene set enrichment analysis provided new support of arginine-precursor required in TTX biosynthesis. This is the first study to profile the gut microbiota in toxic and non-toxic puffer fish species by 16S rRNA amplicon metagenomic approach, defining significant microbial co-occurrence patterns in their gut environment. Our data supported the proposed biosynthesis of TTX inside the hosts by their gut bacterial symbionts using arginine as a precursor.},
}

Animals
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/analysis
Symbiosis
*Tetraodontiformes
Tetrodotoxin/*metabolism

@article {pmid33537012,
year = {2020},
author = {Zhu, XY and Liu, J and Xue, CX and Tian, J and Zhang, XH},
title = {Shift and Metabolic Potentials of Microbial Eukaryotic Communities Across the Full Depths of the Mariana Trench.},
journal = {Frontiers in microbiology},
volume = {11},
number = {},
pages = {603692},
doi = {10.3389/fmicb.2020.603692},
pmid = {33537012},
issn = {1664-302X},
abstract = {Microbial eukaryotes are widespread and play important roles in marine ecosystems. However, their ecological characteristics in the deep sea (>1,000 m), especially hadal trenches, were largely unknown. Here, we investigated the diversity and metabolic potentials of microbial eukaryotes along the whole water column of the Mariana Trench by metagenomics. Our results showed clear depth-related distribution of microbial eukaryotic community and associated metabolic potentials. Surface seawater was dominated by phototrophic/mixotrophic groups (e.g., Dinoflagellata) and genes involved in biosynthesis (photosynthesis and fatty acid biosynthesis), while deep (bathypelagic and/or hadal) seawaters were enriched with heterotrophic groups (e.g., Bicoecea) and genes related to digestion (lysosomal enzymes and V-type ATPase) and carbohydrate metabolism. Co-occurrence analysis revealed high intra-domain connectivity, indicating that microbial eukaryotic composition was more influenced by microbial eukaryotes themselves than bacteria. Increased abundance of genes associated with unsaturated fatty acid biosynthesis likely plays a role in resisting high hydrostatic pressure. Top1 and hupB genes, responsible for the formation and stabilization of DNA structure, were unique and abundant in the hadal zone and thus may be helpful to stabilize DNA structure in the deep sea. Overall, our results provide insights into the distribution and potential adaptability of microbial eukaryotes in the hadal zone.},
}

@article {pmid32499497,
year = {2020},
author = {Van Rossum, T and Ferretti, P and Maistrenko, OM and Bork, P},
title = {Diversity within species: interpreting strains in microbiomes.},
journal = {Nature reviews. Microbiology},
volume = {18},
number = {9},
pages = {491-506},
doi = {10.1038/s41579-020-0368-1},
pmid = {32499497},
issn = {1740-1534},
mesh = {Bacteria/genetics ; Evolution, Molecular ; Metagenomics/*methods ; Microbiota/*genetics ; },
abstract = {Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.},
}

Bacteria/genetics
Evolution, Molecular
Metagenomics/*methods
Microbiota/*genetics

@article {pmid32398126,
year = {2020},
author = {Xue, MY and Sun, HZ and Wu, XH and Liu, JX and Guan, LL},
title = {Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {64},
pmid = {32398126},
issn = {2049-2618},
mesh = {Animals ; Cattle ; Dairying ; Female ; *Lactation ; *Metabolome ; *Microbiota ; *Milk ; Prevotella/isolation & purification/metabolism ; Rumen/*microbiology ; },
abstract = {BACKGROUND: Recently, we reported that some dairy cows could produce high amounts of milk with high amounts of protein (defined as milk protein yield [MPY]) when a population was raised under the same nutritional and management condition, a potential new trait that can be used to increase high-quality milk production. It is unknown to what extent the rumen microbiome and its metabolites, as well as the host metabolism, contribute to MPY. Here, analysis of rumen metagenomics and metabolomics, together with serum metabolomics was performed to identify potential regulatory mechanisms of MPY at both the rumen microbiome and host levels.

RESULTS: Metagenomics analysis revealed that several Prevotella species were significantly more abundant in the rumen of high-MPY cows, contributing to improved functions related to branched-chain amino acid biosynthesis. In addition, the rumen microbiome of high-MPY cows had lower relative abundances of organisms with methanogen and methanogenesis functions, suggesting that these cows may produce less methane. Metabolomics analysis revealed that the relative concentrations of rumen microbial metabolites (mainly amino acids, carboxylic acids, and fatty acids) and the absolute concentrations of volatile fatty acids were higher in the high-MPY cows. By associating the rumen microbiome with the rumen metabolome, we found that specific microbial taxa (mainly Prevotella species) were positively correlated with ruminal microbial metabolites, including the amino acids and carbohydrates involved in glutathione, phenylalanine, starch, sucrose, and galactose metabolism. To detect the interactions between the rumen microbiome and host metabolism, we associated the rumen microbiome with the host serum metabolome and found that Prevotella species may affect the host's metabolism of amino acids (including glycine, serine, threonine, alanine, aspartate, glutamate, cysteine, and methionine). Further analysis using the linear mixed effect model estimated contributions to the variation in MPY based on different omics and revealed that the rumen microbial composition, functions, and metabolites, and the serum metabolites contributed 17.81, 21.56, 29.76, and 26.78%, respectively, to the host MPY.

CONCLUSIONS: These findings provide a fundamental understanding of how the microbiome-dependent and host-dependent mechanisms contribute to varied individualized performance in the milk production quality of dairy cows under the same management condition. This fundamental information is vital for the development of potential manipulation strategies to improve milk quality and production through precision feeding. Video Abstract.},
}

Animals
Cattle
Dairying
Female
*Lactation
*Metabolome
*Microbiota
*Milk
Prevotella/isolation & purification/metabolism
Rumen/*microbiology

@article {pmid32375874,
year = {2020},
author = {Rifkin, RF and Vikram, S and Ramond, JB and Rey-Iglesia, A and Brand, TB and Porraz, G and Val, A and Hall, G and Woodborne, S and Le Bailly, M and Potgieter, M and Underdown, SJ and Koopman, JE and Cowan, DA and Van de Peer, Y and Willerslev, E and Hansen, AJ},
title = {Multi-proxy analyses of a mid-15th century Middle Iron Age Bantu-speaker palaeo-faecal specimen elucidates the configuration of the 'ancestral' sub-Saharan African intestinal microbiome.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {62},
pmid = {32375874},
issn = {2049-2618},
mesh = {Africa South of the Sahara ; *Archaeology ; Feces/*microbiology ; *Gastrointestinal Microbiome ; History, 15th Century ; Humans ; Metagenomics ; },
abstract = {BACKGROUND: The archaeological incidence of ancient human faecal material provides a rare opportunity to explore the taxonomic composition and metabolic capacity of the ancestral human intestinal microbiome (IM). Here, we report the results of the shotgun metagenomic analyses of an ancient South African palaeo-faecal specimen.

METHODS: Following the recovery of a single desiccated palaeo-faecal specimen from Bushman Rock Shelter in Limpopo Province, South Africa, we applied a multi-proxy analytical protocol to the sample. The extraction of ancient DNA from the specimen and its subsequent shotgun metagenomic sequencing facilitated the taxonomic and metabolic characterisation of this ancient human IM.

RESULTS: Our results indicate that the distal IM of the Neolithic 'Middle Iron Age' (c. AD 1460) Bantu-speaking individual exhibits features indicative of a largely mixed forager-agro-pastoralist diet. Subsequent comparison with the IMs of the Tyrolean Iceman (Ötzi) and contemporary Hadza hunter-gatherers, Malawian agro-pastoralists and Italians reveals that this IM precedes recent adaptation to 'Western' diets, including the consumption of coffee, tea, chocolate, citrus and soy, and the use of antibiotics, analgesics and also exposure to various toxic environmental pollutants.

CONCLUSIONS: Our analyses reveal some of the causes and means by which current human IMs are likely to have responded to recent dietary changes, prescription medications and environmental pollutants, providing rare insight into human IM evolution following the advent of the Neolithic c. 12,000 years ago. Video Abtract.},
}

Africa South of the Sahara
*Archaeology
Feces/*microbiology
*Gastrointestinal Microbiome
History, 15th Century
Humans
Metagenomics

@article {pmid32317019,
year = {2020},
author = {Guibert, I and Lecellier, G and Torda, G and Pochon, X and Berteaux-Lecellier, V},
title = {Metabarcoding reveals distinct microbiotypes in the giant clam Tridacna maxima.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {57},
pmid = {32317019},
issn = {2049-2618},
mesh = {Animals ; *Anthozoa/microbiology/physiology ; Bacteria/classification/growth & development ; *Bivalvia/microbiology/physiology ; *Coral Reefs ; *DNA Barcoding, Taxonomic ; Dinoflagellida/classification/growth & development ; *Microbiota ; Symbiosis ; Temperature ; },
abstract = {BACKGROUND: Giant clams and scleractinian (reef-building) corals are keystone species of coral reef ecosystems. The basis of their ecological success is a complex and fine-tuned symbiotic relationship with microbes. While the effect of environmental change on the composition of the coral microbiome has been heavily studied, we know very little about the composition and sensitivity of the microbiome associated with clams. Here, we explore the influence of increasing temperature on the microbial community (bacteria and dinoflagellates from the family Symbiodiniaceae) harbored by giant clams, maintained either in isolation or exposed to other reef species. We created artificial benthic assemblages using two coral species (Pocillopora damicornis and Acropora cytherea) and one giant clam species (Tridacna maxima) and studied the microbial community in the latter using metagenomics.

RESULTS: Our results led to three major conclusions. First, the health status of giant clams depended on the composition of the benthic species assemblages. Second, we discovered distinct microbiotypes in the studied T. maxima population, one of which was disproportionately dominated by Vibrionaceae and directly linked to clam mortality. Third, neither the increase in water temperature nor the composition of the benthic assemblage had a significant effect on the composition of the Symbiodiniaceae and bacterial communities of T. maxima.

CONCLUSIONS: Altogether, our results suggest that at least three microbiotypes naturally exist in the studied clam populations, regardless of water temperature. These microbiotypes plausibly provide similar functions to the clam host via alternate molecular pathways as well as microbiotype-specific functions. This redundancy in functions among microbiotypes together with their specificities provides hope that giant clam populations can tolerate some levels of environmental variation such as increased temperature. Importantly, the composition of the benthic assemblage could make clams susceptible to infections by Vibrionaceae, especially when water temperature increases. Video abstract.},
}

Animals
*Anthozoa/microbiology/physiology
Bacteria/classification/growth & development
*Bivalvia/microbiology/physiology
*Coral Reefs
*DNA Barcoding, Taxonomic
Dinoflagellida/classification/growth & development
*Microbiota
Symbiosis
Temperature

@article {pmid32084485,
year = {2020},
author = {Lei, S and Li, X and Liu, L and Zheng, M and Chang, Q and Zhang, Y and Zeng, H},
title = {Effect of lotus seed resistant starch on tolerance of mice fecal microbiota to bile salt.},
journal = {International journal of biological macromolecules},
volume = {151},
number = {},
pages = {384-393},
doi = {10.1016/j.ijbiomac.2020.02.197},
pmid = {32084485},
issn = {1879-0003},
mesh = {Animals ; Bile Acids and Salts/*chemistry ; Biodiversity ; Cluster Analysis ; Feces/*microbiology ; *Gastrointestinal Microbiome/drug effects ; Lotus/*chemistry ; Metagenomics/methods ; Mice ; Seeds/*chemistry ; Starch/*chemistry ; },
abstract = {We investigated the effect of lotus seed resistant starch (LRS) on mice fecal microbiota tolerance to bile salt by culturing organisms compared to inulin (INU) glucose (GLU) and waxy corn starch (WAX). Operational taxonomic units (OTUs) and diversity indices in LRS and INU groups were increased in the presence of 0.03% to 0.3% bile salt, while they were decreased in GLU, and OTUs were decreased in WAX. Specifically, LRS promoted proliferation of Lactobacillus, which potentially used bile acid, and inhibited growth of the potentially harmful bacteria Enterococcus and Staphylococcus. Moreover, Lactobacillus was negatively correlated with Salinicoccus and Granulicatella in GLU, LRS and INU groups at 1.5% bile salt. With LRS, amino acid metabolic pathways were increased while pathogens causing certain diseases were decreased. LRS increased the tolerance of mice fecal microbiota to bile salt by promoting the proliferation of bacteria utilizing bile acid and inhibiting the growth of harmful bacteria.},
}

Animals
Bile Acids and Salts/*chemistry
Biodiversity
Cluster Analysis
Feces/*microbiology
*Gastrointestinal Microbiome/drug effects
Lotus/*chemistry
Metagenomics/methods
Mice
Seeds/*chemistry
Starch/*chemistry

@article {pmid33531031,
year = {2021},
author = {Liem, M and Regensburg-Tuïnk, T and Henkel, C and Jansen, H and Spaink, H},
title = {Microbial diversity characterization of seawater in a pilot study using Oxford Nanopore Technologies long-read sequencing.},
journal = {BMC research notes},
volume = {14},
number = {1},
pages = {42},
pmid = {33531031},
issn = {1756-0500},
abstract = {OBJECTIVE: Currently the majority of non-culturable microbes in sea water are yet to be discovered, Nanopore offers a solution to overcome the challenging tasks to identify the genomes and complex composition of oceanic microbiomes. In this study we evaluate the utility of Oxford Nanopore Technologies (ONT) sequencing to characterize microbial diversity in seawater from multiple locations. We compared the microbial species diversity of retrieved environmental samples from two different locations and time points.

RESULTS: With only three ONT flow cells we were able to identify thousands of organisms, including bacteriophages, from which a large part at species level. It was possible to assemble genomes from environmental samples with Flye. In several cases this resulted in > 1 Mbp contigs and in the particular case of a Thioglobus singularis species it even produced a near complete genome. k-mer analysis reveals that a large part of the data represents species of which close relatives have not yet been deposited to the database. These results show that our approach is suitable for scalable genomic investigations such as monitoring oceanic biodiversity and provides a new platform for education in biodiversity.},
}

@article {pmid31953225,
year = {2020},
author = {Xiao, D and Yang, G and Wang, Z and Khalique, A and Zhu, Z and Xiong, L and Li, J and Yuan, X and Ni, X and Zeng, D and Zhang, D and Pan, K},
title = {Efficacy of Bacillus methylotrophicus SY200 strain as feed additive against experimental Salmonella typhimurium infection in mice.},
journal = {Microbial pathogenesis},
volume = {141},
number = {},
pages = {103978},
doi = {10.1016/j.micpath.2020.103978},
pmid = {31953225},
issn = {1096-1208},
mesh = {Animal Feed ; Animals ; *Antibiosis ; Bacillus/*physiology ; Bacterial Load ; Gastrointestinal Microbiome ; Leukocyte Count ; Male ; Metagenomics ; Mice ; Neutrophils ; Phylogeny ; Salmonella Infections, Animal/blood/*microbiology/prevention & control ; Salmonella typhimurium/*physiology ; },
abstract = {To investigate the effects of Bacillus methylotrophicus SY200 on Salmonella typhimurium (STM) infection in mice, a total of 36 three-week-old male mice were selected and randomly divided into 3 equal groups (N = 12). Group A and group B were fed with basal diet while group C was fed the basal diet supplemented with 0.1% (w/w) B. methylotrophicus SY200 during the 21 days experimental period. On the 14th day of the experiment, mice of group A were intragastrically administered with 0.5 ml of normal saline, group B and C were orally administered with 0.5 ml of STM suspension. On the first day and seventh day after STM challenge, the number of total white blood cells (WBCs) and neutrophils, relative weight of visceral organs, the number of Salmonella spp., Escherichia coli, Lactobacillus spp. and Bifidobacterium spp. in ileum and cecum, and diversity of cecal microflora were measured. The results showed that: on the first day and seventh day after STM challenge, the number of WBCs and neutrophils in the blood of the mice was the highest in group B, then followed by group C, and group A. On the first day after STM challenge, the relative weight of spleen in group C was significantly higher than that in group B (p < 0.05), moreover, compared with group B, B. methylotrophicus SY200 significantly reduced the number of Salmonella spp. and E. coli (p < 0.05), and increased the number of Lactobacillus spp. and Bifidobacterium spp. (p < 0.05) in the intestines of mice, and improved the Shannon-Wiener diversity (H), Simpson (E) and richness (S) indices of cecal flora of mice (p < 0.05). The results indicated that B. methylotrophicus SY200 could alleviate the inflammatory reaction after STM infection and resist the adverse effects of STM infection on mice intestinal flora.},
}

Animal Feed
Animals
*Antibiosis
Bacillus/*physiology
Bacterial Load
Gastrointestinal Microbiome
Leukocyte Count
Male
Metagenomics
Mice
Neutrophils
Phylogeny
Salmonella Infections, Animal/blood/*microbiology/prevention & control
Salmonella typhimurium/*physiology

@article {pmid31536813,
year = {2020},
author = {Alma, L and Kram, KE and Holtgrieve, GW and Barbarino, A and Fiamengo, CJ and Padilla-Gamiño, JL},
title = {Ocean acidification and warming effects on the physiology, skeletal properties, and microbiome of the purple-hinge rock scallop.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {240},
number = {},
pages = {110579},
doi = {10.1016/j.cbpa.2019.110579},
pmid = {31536813},
issn = {1531-4332},
mesh = {Acclimatization ; Acids/*chemistry ; Animal Shells ; Animals ; Bone and Bones/*metabolism ; Carbon Dioxide/*analysis ; Global Warming ; Homeostasis ; Hydrogen-Ion Concentration ; *Microbiota ; Pectinidae/microbiology/*physiology ; Seawater/*microbiology ; *Temperature ; },
abstract = {Ocean acidification and increased ocean temperature from elevated atmospheric carbon dioxide can significantly influence the physiology, growth and survival of marine organisms. Despite increasing research efforts, there are still many gaps in our knowledge of how these stressors interact to affect economically and ecologically important species. This project is the first to explore the physiological effects of high pCO2 and temperature on the acclimation potential of the purple-hinge rock scallop (Crassadoma gigantea), a widely distributed marine bivalve, important reef builder, and potential aquaculture product. Scallops were exposed to two pCO2 (365 and 1050 μatm) and temperature (14 and 21.5 °C) conditions in a two-factor experimental design. Simultaneous exposure to high temperature and high pCO2 reduced shell strength, decreased outer shell density and increased total lipid content. Despite identical diets, scallops exposed to high pCO2 had higher content of saturated fatty acids, and lower content of polyunsaturated fatty acids suggesting reorganization of fatty acid chains to sustain basic metabolic functions under high pCO2. Metagenomic sequencing of prokaryotes in scallop tissue revealed treatment differences in community composition between treatments and in the presence of genes associated with microbial cell regulation, signaling, and pigmentation. Results from this research highlight the complexity of physiological responses for calcifying species under global change related stress and provide the first insights for understanding the response of a bivalve's microbiome under multiple stressors.},
}

Acclimatization
Acids/*chemistry
Animal Shells
Animals
Bone and Bones/*metabolism
Carbon Dioxide/*analysis
Global Warming
Homeostasis
Hydrogen-Ion Concentration
*Microbiota
Pectinidae/microbiology/*physiology
Seawater/*microbiology
*Temperature

@article {pmid33461660,
year = {2021},
author = {Urban, L and Holzer, A and Baronas, JJ and Hall, MB and Braeuninger-Weimer, P and Scherm, MJ and Kunz, DJ and Perera, SN and Martin-Herranz, DE and Tipper, ET and Salter, SJ and Stammnitz, MR},
title = {Freshwater monitoring by nanopore sequencing.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {33461660},
issn = {2050-084X},
support = {Graduate Student Fellowship//Gates Cambridge Trust/International ; OPP1144//Bill and Melinda Gates Foundation/International ; OpenPlant Fund (BBSRC BB/L014130/1)/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Public Engagement Starter Grant (RCUK Catalyst Seed Fund)//University of Cambridge/International ; Graduate Student Fellowship//European Bioinformatics Institute/International ; Graduate Student Fellowship (203828/Z/16/A, 203828/Z/16/Z)/WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship (102453/Z/13/Z)/WT_/Wellcome Trust/United Kingdom ; Graduate Student Fellowship//Oliver Gatty Studentship/International ; Standard Grant (NE/P011659/1)//Natural Environment Research Council/International ; },
mesh = {Bacteria/classification/genetics ; Base Sequence ; Cluster Analysis ; Computational Biology/methods ; Environmental Monitoring/methods ; Fresh Water/*microbiology ; Geography ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Nanopore Sequencing/*methods ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Sequence Homology, Nucleic Acid ; Species Specificity ; United Kingdom ; *Water Microbiology ; },
abstract = {While traditional microbiological freshwater tests focus on the detection of specific bacterial indicator species, including pathogens, direct tracing of all aquatic DNA through metagenomics poses a profound alternative. Yet, in situ metagenomic water surveys face substantial challenges in cost and logistics. Here, we present a simple, fast, cost-effective and remotely accessible freshwater diagnostics workflow centred around the portable nanopore sequencing technology. Using defined compositions and spatiotemporal microbiota from surface water of an example river in Cambridge (UK), we provide optimised experimental and bioinformatics guidelines, including a benchmark with twelve taxonomic classification tools for nanopore sequences. We find that nanopore metagenomics can depict the hydrological core microbiome and fine temporal gradients in line with complementary physicochemical measurements. In a public health context, these data feature relevant sewage signals and pathogen maps at species level resolution. We anticipate that this framework will gather momentum for new environmental monitoring initiatives using portable devices.},
}

Bacteria/classification/genetics
Base Sequence
Cluster Analysis
Computational Biology/methods
Environmental Monitoring/methods
Fresh Water/*microbiology
Geography
Metagenome/*genetics
Metagenomics/*methods
Microbiota/*genetics
Nanopore Sequencing/*methods
RNA, Ribosomal, 16S/genetics
Rivers/microbiology
Sequence Homology, Nucleic Acid
Species Specificity
United Kingdom
*Water Microbiology

@article {pmid33176699,
year = {2020},
author = {Li, Z and Wei, J and Zhang, Y and Li, G and Zhu, H and Lei, N and He, Q and Geng, Y and Zhu, J},
title = {Risk factors for Keshan disease: a prospective cohort study protocol of gut flora.},
journal = {BMC cardiovascular disorders},
volume = {20},
number = {1},
pages = {481},
pmid = {33176699},
issn = {1471-2261},
support = {81870298//the National Natural Science Foundation of China/International ; },
mesh = {Adolescent ; Adult ; Aged ; Bacteria/classification/*genetics/*metabolism ; Big Data ; Biomarkers/*metabolism ; Cardiomyopathies/diagnosis/*microbiology/virology ; Case-Control Studies ; Enterovirus Infections/diagnosis/*microbiology/virology ; Female ; *Gastrointestinal Microbiome ; Humans ; Intestines/*microbiology ; Male ; *Metabolomics ; *Metagenomics ; Middle Aged ; Prospective Studies ; Research Design ; Young Adult ; },
abstract = {BACKGROUND: Keshan disease is an endemic cardiomyopathy of undefined causes. Being involved in the unclear pathogenesis of Keshan disease, a clear diagnosis, and effective treatment cannot be initiated. However, the rapid development of gut flora in cardiovascular disease combined with omics and big data platforms may promote the discovery of new diagnostic markers and provide new therapeutic options. This study aims to identify biomarkers for the early diagnosis and further explore new therapeutic targets for Keshan disease.

METHODS: This cohort study consists of two parts. Though the first part includes 300 participants, however, recruiting will be continued for the eligible participants. After rigorous screening, the blood samples, stools, electrocardiograms, and ultrasonic cardiogram data would be collected from participants to elucidate the relationship between gut flora and host. The second part includes a prospective follow-up study for every 6 months within 2 years. Finally, deep mining of big data and rapid machine learning will be employed to analyze the baseline data, experimental data, and clinical data to seek out the new biomarkers to predict the pathogenesis of Keshan disease.

DISCUSSION: Our study will clarify the distribution of gut flora in patients with Keshan disease and the abundance and population changes of gut flora in different stages of the disease. Through the big data platform analyze the relationship between environmental factors, clinical factors, and gut flora, the main factors affecting the occurrence of Keshan disease were identified, and the changed molecular pathways of gut flora were predicted. Finally, the specific gut flora and molecular pathways affecting Keshan disease were identified by metagenomics combined with metabonomic analysis.

TRIAL REGISTRATION: ChiCTR1900026639. Registered on 16 October 2019.},
}

Adolescent
Adult
Aged
Bacteria/classification/*genetics/*metabolism
Big Data
Biomarkers/*metabolism
Cardiomyopathies/diagnosis/*microbiology/virology
Case-Control Studies
Enterovirus Infections/diagnosis/*microbiology/virology
Female
*Gastrointestinal Microbiome
Humans
Intestines/*microbiology
Male
*Metabolomics
*Metagenomics
Middle Aged
Prospective Studies
Research Design
Young Adult

@article {pmid32479018,
year = {2020},
author = {Asad, F and Anwar, H and Yassine, HM and Ullah, MI and Rahman, A and Kamran, Z and Sohail, MU},
title = {White Button Mushroom, Agaricus bisporus (Agaricomycetes), and a Probiotics Mixture Supplementation Correct Dyslipidemia without Influencing the Colon Microbiome Profile in Hypercholesterolemic Rats.},
journal = {International journal of medicinal mushrooms},
volume = {22},
number = {3},
pages = {235-244},
doi = {10.1615/IntJMedMushrooms.2020033807},
pmid = {32479018},
issn = {1940-4344},
mesh = {*Agaricus ; Animals ; Bacteria/classification/isolation & purification ; Cholesterol/blood ; Diet, High-Fat ; *Dietary Supplements ; Dyslipidemias/*therapy ; Female ; *Gastrointestinal Microbiome ; Hypercholesterolemia/*therapy ; Male ; Metagenomics ; Oxidative Stress ; Phylogeny ; Probiotics/*therapeutic use ; Rats ; Rats, Wistar ; Triglycerides/blood ; },
abstract = {Consumption of foods rich in dietary fiber has attracted considerable attention for lowering blood cholesterol and triglycerides through attenuation of gut microbiome. Diets rich in fiber may provide substrates for microbes to digest and proliferate. In response, products of microbial digestion enter systemic circulation and support host energy homeostasis. In the present study, rats with hypercholesterolemia (HC) were supplemented with probiotics (PB) and Agaricus bisporus mushroom to examine the antidyslipidemia effects. Forty adult rats were divided into five treatment groups. The rats in the control group were fed only a chow maintenance diet (CON; n = 8), whereas an atherogenic diet (chow diet supplemented with 1.5% cholesterol and 0.5% cholic acid) was offered to the remaining rats to induce hypercholesterolemia (HC group; n = 32). Rats developed HC following a 24-day continuous supplementation with the atherogenic diet. From day 25 onward, the HC group was further divided into HC-CON, HC-PB (supplemented with PB at 1 mg/rat/day), HC-AB (supplemented with A. bisporus at 5% of diet), and HC-AB.PB (supplemented with both A. bisporus and PB). After 6 weeks of supplementation, rats were killed to collect blood to determine serum lipid profile, oxidative stress, and for metagenomics analysis of colon contents. Results showed that all supplementations corrected HC-induced oxidative stress. Furthermore, A. bisporus supplementation corrected HC-induced dyslipidemia (P ≤ .05). Blautia and Bifidobacterium were the most dominant bacterial genera in HC-AB and HC-PB groups, respectively. Phylum Firmicutes and class Clostridia predominantly occupied the gut microbiome in all groups. However, no significant differences were observed in microbiome diversity and clustering patterns among study groups. In conclusion, supplementation of A. bisporus mushroom and probiotics can lower oxidative stress and dyslipidemia with partial effects on the phylogenetic makeup in the gut microbiome.},
}

*Agaricus
Animals
Bacteria/classification/isolation & purification
Cholesterol/blood
Diet, High-Fat
*Dietary Supplements
Dyslipidemias/*therapy
Female
*Gastrointestinal Microbiome
Hypercholesterolemia/*therapy
Male
Metagenomics
Oxidative Stress
Phylogeny
Probiotics/*therapeutic use
Rats
Rats, Wistar
Triglycerides/blood

@article {pmid32019901,
year = {2020},
author = {Mancini, N and Peri, F and Rescigno, M and Zanoni, I},
title = {Microbiome studies in the medical sciences and the need for closer multidisciplinary interplay.},
journal = {Science signaling},
volume = {13},
number = {617},
pages = {},
doi = {10.1126/scisignal.aba9911},
pmid = {32019901},
issn = {1937-9145},
mesh = {Bacteria/classification/*genetics ; Gastrointestinal Microbiome/*genetics ; Gastrointestinal Tract/*microbiology ; High-Throughput Nucleotide Sequencing/*methods ; Humans ; Metabolic Syndrome/*genetics/metabolism/microbiology ; Metabolomics/methods ; Metagenomics/methods ; Proteomics/methods ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Next-generation sequencing techniques have enabled identification of the microorganisms colonizing mucosal tissues. The International Congress "MicrobiotaMi 2020" (Milan, February 2020) will focus on the mechanisms of microbiota-related functions in health and disease and their clinical application.},
}

Bacteria/classification/*genetics
Gastrointestinal Microbiome/*genetics
Gastrointestinal Tract/*microbiology
High-Throughput Nucleotide Sequencing/*methods
Humans
Metabolic Syndrome/*genetics/metabolism/microbiology
Metabolomics/methods
Metagenomics/methods
Proteomics/methods
RNA, Ribosomal, 16S/*genetics

@article {pmid32600361,
year = {2020},
author = {Moskowitz, JE and Doran, AG and Lei, Z and Busi, SB and Hart, ML and Franklin, CL and Sumner, LW and Keane, TM and Amos-Landgraf, JM},
title = {Integration of genomics, metagenomics, and metabolomics to identify interplay between susceptibility alleles and microbiota in adenoma initiation.},
journal = {BMC cancer},
volume = {20},
number = {1},
pages = {600},
pmid = {32600361},
issn = {1471-2407},
support = {U42 OD010918/OD/NIH HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; },
mesh = {Adenoma/*genetics/metabolism/microbiology ; Adenomatous Polyposis Coli Protein/genetics ; Alleles ; Animals ; Colorectal Neoplasms/*genetics/metabolism/microbiology ; Disease Models, Animal ; Female ; Gastrointestinal Microbiome/*physiology ; *Genetic Predisposition to Disease ; Humans ; Male ; Metabolomics ; Metagenomics ; Mice ; Mutation ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is a multifactorial disease resulting from both genetic predisposition and environmental factors including the gut microbiota (GM), but deciphering the influence of genetic variants, environmental variables, and interactions with the GM is exceedingly difficult. We previously observed significant differences in intestinal adenoma multiplicity between C57BL/6 J-ApcMin (B6-Min/J) from The Jackson Laboratory (JAX), and original founder strain C57BL/6JD-ApcMin (B6-Min/D) from the University of Wisconsin.

METHODS: To resolve genetic and environmental interactions and determine their contributions we utilized two genetically inbred, independently isolated ApcMin mouse colonies that have been separated for over 20 generations. Whole genome sequencing was used to identify genetic variants unique to the two substrains. To determine the influence of genetic variants and the impact of differences in the GM on phenotypic variability, we used complex microbiota targeted rederivation to generate two Apc mutant mouse colonies harboring complex GMs from two different sources (GMJAX originally from JAX or GMHSD originally from Envigo), creating four ApcMin groups. Untargeted metabolomics were used to characterize shifts in the fecal metabolite profile based on genetic variation and differences in the GM.

RESULTS: WGS revealed several thousand high quality variants unique to the two substrains. No homozygous variants were present in coding regions, with the vast majority of variants residing in noncoding regions. Host genetic divergence between Min/J and Min/D and the complex GM additively determined differential adenoma susceptibility. Untargeted metabolomics revealed that both genetic lineage and the GM collectively determined the fecal metabolite profile, and that each differentially regulates bile acid (BA) metabolism. Metabolomics pathway analysis facilitated identification of a functionally relevant private noncoding variant associated with the bile acid transporter Fatty acid binding protein 6 (Fabp6). Expression studies demonstrated differential expression of Fabp6 between Min/J and Min/D, and the variant correlates with adenoma multiplicity in backcrossed mice.

CONCLUSIONS: We found that both genetic variation and differences in microbiota influences the quantitiative adenoma phenotype in ApcMin mice. These findings demonstrate how the use of metabolomics datasets can aid as a functional genomic tool, and furthermore illustrate the power of a multi-omics approach to dissect complex disease susceptibility of noncoding variants.},
}

Adenoma/*genetics/metabolism/microbiology
Adenomatous Polyposis Coli Protein/genetics
Alleles
Animals
Colorectal Neoplasms/*genetics/metabolism/microbiology
Disease Models, Animal
Female
Gastrointestinal Microbiome/*physiology
*Genetic Predisposition to Disease
Humans
Male
Metabolomics
Metagenomics
Mice
Mutation