@article {pmid31548686,
year = {2019},
author = {Zaramela, LS and Martino, C and Alisson-Silva, F and Rees, SD and Diaz, SL and Chuzel, L and Ganatra, MB and Taron, CH and Secrest, P and Zuñiga, C and Huang, J and Siegel, D and Chang, G and Varki, A and Zengler, K},
title = {Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates.},
journal = {Nature microbiology},
volume = {4},
number = {12},
pages = {2082-2089},
doi = {10.1038/s41564-019-0564-9},
pmid = {31548686},
issn = {2058-5276},
support = {R01 GM032373/GM/NIGMS NIH HHS/United States ; T32 EB009380/EB/NIBIB NIH HHS/United States ; T32 GM008806/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/*enzymology ; Bacteroides/enzymology/genetics ; Clostridiales/enzymology/genetics ; Crystallography, X-Ray ; *Diet ; Feces/chemistry/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Neuraminic Acids/*metabolism ; Neuraminidase/*genetics/metabolism ; Polysaccharides/chemistry/*metabolism ; Red Meat/*analysis ; },
abstract = {Dietary habits have been associated with alterations of the human gut resident microorganisms contributing to obesity, diabetes and cancer1. In Western diets, red meat is a frequently eaten food2, but long-term consumption has been associated with increased risk of disease3,4. Red meat is enriched in N-glycolylneuraminic acid (Neu5Gc) that cannot be synthesized by humans5. However, consumption can cause Neu5Gc incorporation into cell surface glycans6, especially in carcinomas4,7. As a consequence, an inflammatory response is triggered when Neu5Gc-containing glycans encounter circulating anti-Neu5Gc antibodies8,9. Although bacteria can use free sialic acids as a nutrient source10-12, it is currently unknown if gut microorganisms contribute to releasing Neu5Gc from food. We found that a Neu5Gc-rich diet induces changes in the gut microbiota, with Bacteroidales and Clostridiales responding the most. Genome assembling of mouse and human shotgun metagenomic sequencing identified bacterial sialidases with previously unobserved substrate preference for Neu5Gc-containing glycans. X-ray crystallography revealed key amino acids potentially contributing to substrate preference. Additionally, we verified that mouse and human sialidases were able to release Neu5Gc from red meat. The release of Neu5Gc from red meat using bacterial sialidases could reduce the risk of inflammatory diseases associated with red meat consumption, including colorectal cancer4 and atherosclerosis13.},
}

Animals
Bacteria/classification/*enzymology
Bacteroides/enzymology/genetics
Clostridiales/enzymology/genetics
Crystallography, X-Ray
*Diet
Feces/chemistry/microbiology
Female
*Gastrointestinal Microbiome
Humans
Male
Metagenomics
Mice
Mice, Inbred C57BL
Neuraminic Acids/*metabolism
Neuraminidase/*genetics/metabolism
Polysaccharides/chemistry/*metabolism
Red Meat/*analysis

@article {pmid31548681,
year = {2019},
author = {Robbins, SJ and Singleton, CM and Chan, CX and Messer, LF and Geers, AU and Ying, H and Baker, A and Bell, SC and Morrow, KM and Ragan, MA and Miller, DJ and Forêt, S and , and Voolstra, CR and Tyson, GW and Bourne, DG},
title = {A genomic view of the reef-building coral Porites lutea and its microbial symbionts.},
journal = {Nature microbiology},
volume = {4},
number = {12},
pages = {2090-2100},
doi = {10.1038/s41564-019-0532-4},
pmid = {31548681},
issn = {2058-5276},
mesh = {Animals ; Anthozoa/metabolism/*microbiology ; Archaea/*genetics ; Bacteria/*genetics ; Coral Reefs ; Dinoflagellida/genetics ; *Genome ; Metagenomics ; Microbiota ; *Symbiosis ; },
abstract = {Corals and the reef ecosystems that they support are in global decline due to increasing anthropogenic pressures such as climate change1. However, effective reef conservation strategies are hampered by a limited mechanistic understanding of coral biology and the functional roles of the diverse microbial communities that underpin coral health2,3. Here, we present an integrated genomic characterization of the coral species Porites lutea and its microbial partners. High-quality genomes were recovered from P. lutea, as well as a metagenome-assembled Cladocopium C15 (the dinoflagellate symbiont) and 52 bacterial and archaeal populations. Comparative genomic analysis revealed that many of the bacterial and archaeal genomes encode motifs that may be involved in maintaining association with the coral host and in supplying fixed carbon, B-vitamins and amino acids to their eukaryotic partners. Furthermore, mechanisms for ammonia, urea, nitrate, dimethylsulfoniopropionate and taurine transformation were identified that interlink members of the holobiont and may be important for nutrient acquisition and retention in oligotrophic waters. Our findings demonstrate the critical and diverse roles that microorganisms play within the coral holobiont and underscore the need to consider all of the components of the holobiont if we are to effectively inform reef conservation strategies.},
}

Animals
Anthozoa/metabolism/*microbiology
Archaea/*genetics
Bacteria/*genetics
Coral Reefs
Dinoflagellida/genetics
*Genome
Metagenomics
Microbiota
*Symbiosis

@article {pmid31307985,
year = {2019},
author = {Burdet, C and Nguyen, TT and Duval, X and Ferreira, S and Andremont, A and Guedj, J and Mentré, F and , },
title = {Impact of Antibiotic Gut Exposure on the Temporal Changes in Microbiome Diversity.},
journal = {Antimicrobial agents and chemotherapy},
volume = {63},
number = {10},
pages = {},
pmid = {31307985},
issn = {1098-6596},
mesh = {Adult ; Anti-Bacterial Agents/*therapeutic use ; Bacteria/drug effects/genetics ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics ; Healthy Volunteers ; Humans ; Male ; Microbiota/*drug effects/*genetics ; Middle Aged ; Moxifloxacin/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Young Adult ; },
abstract = {Although the global deleterious impact of antibiotics on the intestinal microbiota is well known, temporal changes in microbial diversity during and after an antibiotic treatment are still poorly characterized. We used plasma and fecal samples collected frequently during treatment and up to one month after from 22 healthy volunteers assigned to a 5-day treatment by moxifloxacin (n = 14) or no intervention (n = 8). Moxifloxacin concentrations were measured in both plasma and feces, and bacterial diversity was determined in feces by 16S rRNA gene profiling and quantified using the Shannon index and number of operational taxonomic units (OTUs). Nonlinear mixed effect models were used to relate drug pharmacokinetics and bacterial diversity over time. Moxifloxacin reduced bacterial diversity in a concentration-dependent manner, with a median maximal loss of 27.5% of the Shannon index (minimum [min], 17.5; maximum [max], 27.7) and 47.4% of the number of OTUs (min, 30.4; max, 48.3). As a consequence of both the long fecal half-life of moxifloxacin and the susceptibility of the gut microbiota to moxifloxacin, bacterial diversity indices did not return to their pretreatment levels until days 16 and 21, respectively. Finally, the model characterized the effect of moxifloxacin on bacterial diversity biomarkers and provides a novel framework for analyzing antibiotic effects on the intestinal microbiome.},
}

Adult
Anti-Bacterial Agents/*therapeutic use
Bacteria/drug effects/genetics
Feces/microbiology
Female
Gastrointestinal Microbiome/*drug effects/*genetics
Healthy Volunteers
Humans
Male
Microbiota/*drug effects/*genetics
Middle Aged
Moxifloxacin/therapeutic use
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/methods
Young Adult

@article {pmid30995949,
year = {2019},
author = {Fessler, J and Matson, V and Gajewski, TF},
title = {Exploring the emerging role of the microbiome in cancer immunotherapy.},
journal = {Journal for immunotherapy of cancer},
volume = {7},
number = {1},
pages = {108},
pmid = {30995949},
issn = {2051-1426},
support = {F99 CA234946/CA/NCI NIH HHS/United States ; T32 CA009594/CA/NCI NIH HHS/United States ; R35 CA210098/CA/NCI NIH HHS/United States ; F32 CA236296/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/*adverse effects ; Antineoplastic Agents, Immunological/*pharmacology/therapeutic use ; Disease Models, Animal ; Drug Resistance, Neoplasm/immunology ; Gastrointestinal Microbiome/drug effects/*immunology ; Humans ; Immunotherapy/*methods ; Mice ; Neoplasms/immunology/microbiology/mortality/*therapy ; Progression-Free Survival ; },
abstract = {The activity of the commensal microbiota significantly impacts human health and has been linked to the development of many diseases, including cancer. Gnotobiotic animal models have shown that the microbiota has many effects on host physiology, including on the development and regulation of immune responses. More recently, evidence has indicated that the microbiota can more specifically influence the outcome of cancer immunotherapy. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes have shown promise in mouse studies. Ongoing endeavors are translating these pre-clinical findings to early stage clinical testing. In this review we summarize 1) basic methodologies and considerations for studies of host-microbiota interactions; 2) experimental evidence towards a causal link between gut microbiota composition and immunotherapeutic efficacy; 3) possible mechanisms governing the microbiota-mediated impact on immunotherapy efficacy. Moving forward, there is need for a deeper understanding of the underlying biological mechanisms that link specific bacterial strains to host immunity. Integrating microbiome effects with other tumor and host factors regulating immunotherapy responsiveness versus resistance could facilitate optimization of therapeutic outcomes.},
}

Animals
Anti-Bacterial Agents/*adverse effects
Antineoplastic Agents, Immunological/*pharmacology/therapeutic use
Disease Models, Animal
Drug Resistance, Neoplasm/immunology
Gastrointestinal Microbiome/drug effects/*immunology
Humans
Immunotherapy/*methods
Mice
Neoplasms/immunology/microbiology/mortality/*therapy
Progression-Free Survival

@article {pmid32152478,
year = {2020},
author = {Aron-Wisnewsky, J and Vigliotti, C and Witjes, J and Le, P and Holleboom, AG and Verheij, J and Nieuwdorp, M and Clément, K},
title = {Gut microbiota and human NAFLD: disentangling microbial signatures from metabolic disorders.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {17},
number = {5},
pages = {279-297},
doi = {10.1038/s41575-020-0269-9},
pmid = {32152478},
issn = {1759-5053},
mesh = {Animals ; Diabetes Mellitus, Type 2/microbiology ; Digestive System Diseases/microbiology ; Dysbiosis/immunology/microbiology ; Gastrointestinal Microbiome/*immunology ; Humans ; Non-alcoholic Fatty Liver Disease/immunology/*microbiology ; Obesity/microbiology ; Signal Transduction ; },
abstract = {Gut microbiota dysbiosis has been repeatedly observed in obesity and type 2 diabetes mellitus, two metabolic diseases strongly intertwined with non-alcoholic fatty liver disease (NAFLD). Animal studies have demonstrated a potential causal role of gut microbiota in NAFLD. Human studies have started to describe microbiota alterations in NAFLD and have found a few consistent microbiome signatures discriminating healthy individuals from those with NAFLD, non-alcoholic steatohepatitis or cirrhosis. However, patients with NAFLD often present with obesity and/or insulin resistance and type 2 diabetes mellitus, and these metabolic confounding factors for dysbiosis have not always been considered. Patients with different NAFLD severity stages often present with heterogeneous lesions and variable demographic characteristics (including age, sex and ethnicity), which are known to affect the gut microbiome and have been overlooked in most studies. Finally, multiple gut microbiome sequencing tools and NAFLD diagnostic methods have been used across studies that could account for discrepant microbiome signatures. This Review provides a broad insight into microbiome signatures for human NAFLD and explores issues with disentangling these signatures from underlying metabolic disorders. More advanced metagenomics and multi-omics studies using system biology approaches are needed to improve microbiome biomarkers.},
}

Animals
Diabetes Mellitus, Type 2/microbiology
Digestive System Diseases/microbiology
Dysbiosis/immunology/microbiology
Gastrointestinal Microbiome/*immunology
Humans
Non-alcoholic Fatty Liver Disease/immunology/*microbiology
Obesity/microbiology
Signal Transduction

@article {pmid31461261,
year = {2019},
author = {Gilmore, SP and Lankiewicz, TS and Wilken, SE and Brown, JL and Sexton, JA and Henske, JK and Theodorou, MK and Valentine, DL and O'Malley, MA},
title = {Top-Down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation.},
journal = {ACS synthetic biology},
volume = {8},
number = {9},
pages = {2174-2185},
doi = {10.1021/acssynbio.9b00271},
pmid = {31461261},
issn = {2161-5063},
mesh = {Anaerobiosis ; Biofuels ; *Biomass ; Lignin/metabolism ; Methane/metabolism ; Methanobacteriaceae/growth & development/*metabolism ; Microbial Consortia ; Piromyces/growth & development/*metabolism ; Spirochaetaceae/growth & development/*metabolism ; },
abstract = {Consortium-based approaches are a promising avenue toward efficient bioprocessing. However, many complex microbial interactions dictate community dynamics and stability that must be replicated in synthetic systems. The rumen and/or hindguts of large mammalian herbivores harbor complex communities of biomass-degrading fungi and bacteria, as well as archaea and protozoa that work collectively to degrade lignocellulose, yet the microbial interactions responsible for stability, resilience, and activity of the community remain largely uncharacterized. In this work, we demonstrate a "top-down" enrichment-based methodology for selecting a minimal but effective lignocellulose-degrading community that produces methane-rich fermentation gas (biogas). The resulting enrichment consortium produced 0.75-1.9-fold more fermentation gas at 1.4-2.1 times the rate compared to a monoculture of fungi from the enrichment. Metagenomic sequencing of the top-down enriched consortium revealed genomes encoding for functional compartmentalization of the community, spread across an anaerobic fungus (Piromyces), a bacterium (Sphaerochaeta), and two methanogenic archaea (Methanosphaera and Methanocorpusculum). Guided by the composition of the top-down enrichment, several synthetic cocultures were formed from the "bottom-up" using previously isolated fungi, Neocallimastix californiae and Anaeromyces robustus paired with the methanogen Methanobacterium bryantii. While cross-feeding occurred in synthetic co-cultures, removal of fungal metabolites by methanogens did not increase the rate of gas production or the rate of substrate deconstruction by the synthetic community relative to fungal monocultures. Metabolomic characterization verified that syntrophy was established within synthetic co-cultures, which generated methane at similar concentrations compared to the enriched consortium but lacked the temporal stability (resilience) seen in the native system. Taken together, deciphering the membership and metabolic potential of an enriched gut consortium enables the design of methanogenic synthetic co-cultures. However, differences in the growth rate and stability of enriched versus synthetic consortia underscore the difficulties in mimicking naturally occurring syntrophy in synthetic systems.},
}

Anaerobiosis
Biofuels
*Biomass
Lignin/metabolism
Methane/metabolism
Methanobacteriaceae/growth & development/*metabolism
Microbial Consortia
Piromyces/growth & development/*metabolism
Spirochaetaceae/growth & development/*metabolism

@article {pmid31310864,
year = {2019},
author = {Roossinck, MJ},
title = {Viruses in the phytobiome.},
journal = {Current opinion in virology},
volume = {37},
number = {},
pages = {72-76},
doi = {10.1016/j.coviro.2019.06.008},
pmid = {31310864},
issn = {1879-6265},
mesh = {Animals ; Bacteria/virology ; Bacteriophages ; Biological Control Agents ; Cuscuta/virology ; Disease Vectors ; Fungal Viruses/pathogenicity ; Host Microbial Interactions ; Insect Vectors ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Nematoda/virology ; Plant Diseases/microbiology/*virology ; *Plant Viruses/growth & development/pathogenicity ; Plants/*virology ; Symbiosis ; },
abstract = {The phytobiome, defined as plants and all the entities that interact with them, is rich in viruses, but with the exception of plant viruses of crop plants, most of the phytobiome viruses remain very understudied. This review focuses on the neglected portions of the phytobiome, including viruses of other microbes interacting with plants, viruses in the soil, viruses of wild plants, and relationships between viruses and the vectors of plant viruses.},
}

Animals
Bacteria/virology
Bacteriophages
Biological Control Agents
Cuscuta/virology
Disease Vectors
Fungal Viruses/pathogenicity
Host Microbial Interactions
Insect Vectors
Metagenomics
*Microbial Interactions
*Microbiota
Nematoda/virology
Plant Diseases/microbiology/*virology
*Plant Viruses/growth & development/pathogenicity
Plants/*virology
Symbiosis

@article {pmid31255903,
year = {2019},
author = {Beller, L and Matthijnssens, J},
title = {What is (not) known about the dynamics of the human gut virome in health and disease.},
journal = {Current opinion in virology},
volume = {37},
number = {},
pages = {52-57},
doi = {10.1016/j.coviro.2019.05.013},
pmid = {31255903},
issn = {1879-6265},
mesh = {Adult ; Anti-Bacterial Agents/adverse effects ; Autoimmune Diseases/virology ; Bacteria/virology ; Bacteriophages/*immunology ; DNA, Viral ; Diet ; Female ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/pathology/*virology ; *Host Microbial Interactions ; Humans ; Infant ; Inflammatory Bowel Diseases/virology ; Intestinal Diseases ; Male ; Microbial Interactions ; Natural Childbirth ; Symbiosis ; Viruses/pathogenicity ; },
abstract = {The human gut virome has an important role in human health but its dynamics remain poorly understood. Few longitudinal studies in healthy adults showed a stable temporal gut virome, with high inter-individual diversity. In contrast, the infant virome shows a high temporal intra-individual diversity. Unfortunately, these virome studies ignore an enormous amount of unknown 'dark matter' sequences, leading to incomplete analyses and possibly incorrect conclusions. Also, the interactions between prokaryotes and bacteriophages in the gut seem to be too complex for currently available models. Therefore, there is a huge need of larger longitudinal cohort studies focusing on both the bacterial and viral component of the microbiome to be able to describe and understand this complex ecosystem.},
}

Adult
Anti-Bacterial Agents/adverse effects
Autoimmune Diseases/virology
Bacteria/virology
Bacteriophages/*immunology
DNA, Viral
Diet
Female
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology/pathology/*virology
*Host Microbial Interactions
Humans
Infant
Inflammatory Bowel Diseases/virology
Intestinal Diseases
Male
Microbial Interactions
Natural Childbirth
Symbiosis
Viruses/pathogenicity

@article {pmid31152018,
year = {2019},
author = {Bertucci, M and Calusinska, M and Goux, X and Rouland-Lefèvre, C and Untereiner, B and Ferrer, P and Gerin, PA and Delfosse, P},
title = {Carbohydrate Hydrolytic Potential and Redundancy of an Anaerobic Digestion Microbiome Exposed to Acidosis, as Uncovered by Metagenomics.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {15},
pages = {},
pmid = {31152018},
issn = {1098-5336},
mesh = {Anaerobiosis ; Bacteria/*metabolism ; Bacteroidetes/metabolism ; Biomass ; Bioreactors/*microbiology ; Carbohydrate Metabolism ; Hydrogen-Ion Concentration ; Hydrolysis ; *Metagenome ; *Microbiota ; },
abstract = {Increased hydrolysis of easily digestible biomass may lead to acidosis of anaerobic reactors and decreased methane production. Previously, it was shown that the structure of microbial communities changed during acidosis; however, once the conditions are back to optimal, biogas (initially CO2) production quickly restarts. This suggests the retention of the community functional redundancy during the process failure. In this study, with the use of metagenomics and downstream bioinformatics analyses, we characterize the carbohydrate hydrolytic potential of the microbial community, with a special focus on acidosis. To that purpose, carbohydrate-active enzymes were identified, and to further link the community hydrolytic potential with key microbes, bacterial genomes were reconstructed. In addition, we characterized biochemically the specificity and activity of selected enzymes, thus verifying the accuracy of the in silico predictions. The results confirm the retention of the community hydrolytic potential during acidosis and indicate Bacteroidetes to be largely involved in biomass degradation. Bacteroidetes showed higher diversity and genomic content of carbohydrate hydrolytic enzymes that might favor the dominance of this phylum over other bacteria in some anaerobic reactors. The combination of bioinformatic analyses and activity tests enabled us to propose a model of acetylated glucomannan degradation by BacteroidetesIMPORTANCE The enzymatic hydrolysis of lignocellulosic biomass is mainly driven by the action of carbohydrate-active enzymes. By characterizing the gene profiles at the different stages of the anaerobic digestion experiment, we showed that the microbiome retains its hydrolytic functional redundancy even during severe acidosis, despite significant changes in taxonomic composition. By analyzing reconstructed bacterial genomes, we demonstrate that Bacteroidetes hydrolytic gene diversity likely favors the abundance of this phylum in some anaerobic digestion systems. Further, we observe genetic redundancy within the Bacteroidetes group, which accounts for the preserved hydrolytic potential during acidosis. This work also uncovers new polysaccharide utilization loci involved in the deconstruction of various biomasses and proposes the model of acetylated glucomannan degradation by Bacteroidetes Acetylated glucomannan-enriched biomass is a common substrate for many industries, including pulp and paper production. Using naturally evolved cocktails of enzymes for biomass pretreatment could be an interesting alternative to the commonly used chemical pretreatments.},
}

Anaerobiosis
Bacteria/*metabolism
Bacteroidetes/metabolism
Biomass
Bioreactors/*microbiology
Carbohydrate Metabolism
Hydrogen-Ion Concentration
Hydrolysis
*Metagenome
*Microbiota

@article {pmid31152014,
year = {2019},
author = {Liang, R and Lau, M and Vishnivetskaya, T and Lloyd, KG and Wang, W and Wiggins, J and Miller, J and Pfiffner, S and Rivkina, EM and Onstott, TC},
title = {Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost.},
journal = {Applied and environmental microbiology},
volume = {85},
number = {15},
pages = {},
pmid = {31152014},
issn = {1098-5336},
mesh = {Bacteria, Anaerobic/*metabolism ; Geologic Sediments/*microbiology ; *Microbiota ; Permafrost/*microbiology ; Phylogeny ; Siberia ; },
abstract = {The prevalence of microbial life in permafrost up to several million years (Ma) old has been well documented. However, the long-term survivability, evolution, and metabolic activity of the entombed microbes over this time span remain underexplored. We integrated aspartic acid (Asp) racemization assays with metagenomic sequencing to characterize the microbial activity, phylogenetic diversity, and metabolic functions of indigenous microbial communities across a ∼0.01- to 1.1-Ma chronosequence of continuously frozen permafrost from northeastern Siberia. Although Asp in the older bulk sediments (0.8 to 1.1 Ma) underwent severe racemization relative to that in the youngest sediment (∼0.01 Ma), the much lower d-Asp/l-Asp ratio (0.05 to 0.14) in the separated cells from all samples suggested that indigenous microbial communities were viable and metabolically active in ancient permafrost up to 1.1 Ma. The microbial community in the youngest sediment was the most diverse and was dominated by the phyla Actinobacteria and Proteobacteria In contrast, microbial diversity decreased dramatically in the older sediments, and anaerobic, spore-forming bacteria within Firmicutes became overwhelmingly dominant. In addition to the enrichment of sporulation-related genes, functional genes involved in anaerobic metabolic pathways such as fermentation, sulfate reduction, and methanogenesis were more abundant in the older sediments. Taken together, the predominance of spore-forming bacteria and associated anaerobic metabolism in the older sediments suggest that a subset of the original indigenous microbial community entrapped in the permafrost survived burial over geological time.IMPORTANCE Understanding the long-term survivability and associated metabolic traits of microorganisms in ancient permafrost frozen millions of years ago provides a unique window into the burial and preservation processes experienced in general by subsurface microorganisms in sedimentary deposits because of permafrost's hydrological isolation and exceptional DNA preservation. We employed aspartic acid racemization modeling and metagenomics to determine which microbial communities were metabolically active in the 1.1-Ma permafrost from northeastern Siberia. The simultaneous sequencing of extracellular and intracellular genomic DNA provided insight into the metabolic potential distinguishing extinct from extant microorganisms under frozen conditions over this time interval. This in-depth metagenomic sequencing advances our understanding of the microbial diversity and metabolic functions of extant microbiomes from early Pleistocene permafrost. Therefore, these findings extend our knowledge of the survivability of microbes in permafrost from 33,000 years to 1.1 Ma.},
}

Bacteria, Anaerobic/*metabolism
Geologic Sediments/*microbiology
*Microbiota
Permafrost/*microbiology
Phylogeny
Siberia

@article {pmid30223687,
year = {2019},
author = {Lin, H and He, QY and Shi, L and Sleeman, M and Baker, MS and Nice, EC},
title = {Proteomics and the microbiome: pitfalls and potential.},
journal = {Expert review of proteomics},
volume = {16},
number = {6},
pages = {501-511},
doi = {10.1080/14789450.2018.1523724},
pmid = {30223687},
issn = {1744-8387},
mesh = {Animals ; Biomarkers/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome/physiology ; Humans ; Microbiota/*physiology ; Precision Medicine ; Proteomics/*methods ; },
abstract = {Introduction: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics, and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyze its relationship with the human body. Fecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and Therapeutic Goods Administration (TGA)-approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.},
}

Animals
Biomarkers/metabolism
Feces/microbiology
Gastrointestinal Microbiome/physiology
Humans
Microbiota/*physiology
Precision Medicine
Proteomics/*methods

@article {pmid32605604,
year = {2020},
author = {Hou, J and Sievert, SM and Wang, Y and Seewald, JS and Natarajan, VP and Wang, F and Xiao, X},
title = {Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys.},
journal = {Microbiome},
volume = {8},
number = {1},
pages = {102},
doi = {10.1186/s40168-020-00851-8},
pmid = {32605604},
issn = {2049-2618},
support = {DY135-B2-12//China Ocean Mineral Resources Research and Development Association (CN)/ ; 91751205//National Natural Science Foundation of China/ ; 41530967//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; KEXUE2019GZ06//Senior User Project of RV KEXUE/ ; OCE-1136727//US National Science Foundation/ ; },
abstract = {BACKGROUND: Deep-sea hydrothermal vents are highly productive biodiversity hotspots in the deep ocean supported by chemosynthetic microorganisms. Prominent features of these systems are sulfide chimneys emanating high-temperature hydrothermal fluids. While several studies have investigated the microbial diversity in both active and inactive sulfide chimneys that have been extinct for up to thousands of years, little is known about chimneys that have ceased activity more recently, as well as the microbial succession occurring during the transition from active to inactive chimneys.

RESULTS: Genome-resolved metagenomics was applied to an active and a recently extinct (~ 7 years) sulfide chimney from the 9-10° N hydrothermal vent field on the East Pacific Rise. Full-length 16S rRNA gene and a total of 173 high-quality metagenome assembled genomes (MAGs) were retrieved for comparative analysis. In the active chimney (L-vent), sulfide- and/or hydrogen-oxidizing Campylobacteria and Aquificae with the potential for denitrification were identified as the dominant community members and primary producers, fixing carbon through the reductive tricarboxylic acid (rTCA) cycle. In contrast, the microbiome of the recently extinct chimney (M-vent) was largely composed of heterotrophs from various bacterial phyla, including Delta-/Beta-/Alphaproteobacteria and Bacteroidetes. Gammaproteobacteria were identified as the main primary producers, using the oxidation of metal sulfides and/or iron oxidation coupled to nitrate reduction to fix carbon through the Calvin-Benson-Bassham (CBB) cycle. Further analysis revealed a phylogenetically distinct Nitrospirae cluster that has the potential to oxidize sulfide minerals coupled to oxygen and/or nitrite reduction, as well as for sulfate reduction, and that might serve as an indicator for the early stages of chimneys after venting has ceased.

CONCLUSIONS: This study sheds light on the composition, metabolic functions, and succession of microbial communities inhabiting deep-sea hydrothermal vent sulfide chimneys. Collectively, microbial succession during the life span of a chimney could be described to proceed from a "fluid-shaped" microbial community in newly formed and actively venting chimneys supported by the oxidation of reductants in the hydrothermal fluid to a "mineral-shaped" community supported by the oxidation of minerals after hydrothermal activity has ceased. Remarkably, the transition appears to occur within the first few years, after which the communities stay stable for thousands of years. Video Abstract.},
}

@article {pmid31116375,
year = {2019},
author = {Ma, A and Sun, M and McDermaid, A and Liu, B and Ma, Q},
title = {MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {21},
pages = {4474-4477},
pmid = {31116375},
issn = {1367-4811},
support = {UL1 TR002733/TR/NCATS NIH HHS/United States ; },
mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Metagenomics ; Transcriptome ; },
abstract = {MOTIVATION: Metagenomic and metatranscriptomic analyses can provide an abundance of information related to microbial communities. However, straightforward analysis of this data does not provide optimal results, with a required integration of data types being needed to thoroughly investigate these microbiomes and their environmental interactions.

RESULTS: Here, we present MetaQUBIC, an integrated biclustering-based computational pipeline for gene module detection that integrates both metagenomic and metatranscriptomic data. Additionally, we used this pipeline to investigate 735 paired DNA and RNA human gut microbiome samples, resulting in a comprehensive hybrid gene expression matrix of 2.3 million cross-species genes in the 735 human fecal samples and 155 functional enriched gene modules. We believe both the MetaQUBIC pipeline and the generated comprehensive human gut hybrid expression matrix will facilitate further investigations into multiple levels of microbiome studies.

The package is freely available at https://github.com/OSU-BMBL/metaqubic.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

Feces
*Gastrointestinal Microbiome
Humans
*Metagenome
Metagenomics
Transcriptome

@article {pmid30927646,
year = {2019},
author = {Rong, H and Xie, XH and Zhao, J and Lai, WT and Wang, MB and Xu, D and Liu, YH and Guo, YY and Xu, SX and Deng, WF and Yang, QF and Xiao, L and Zhang, YL and He, FS and Wang, S and Liu, TB},
title = {Similarly in depression, nuances of gut microbiota: Evidences from a shotgun metagenomics sequencing study on major depressive disorder versus bipolar disorder with current major depressive episode patients.},
journal = {Journal of psychiatric research},
volume = {113},
number = {},
pages = {90-99},
doi = {10.1016/j.jpsychires.2019.03.017},
pmid = {30927646},
issn = {1879-1379},
mesh = {Adult ; Bipolar Disorder/*microbiology ; Depressive Disorder, Major/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Metagenomics/*methods/statistics & numerical data ; },
abstract = {BACKGROUND: To probe the differences of gut microbiota among major depressive disorder (MDD), bipolar disorder with current major depressive episode (BPD) and health participants.

METHODS: Thirty one MDD patients, thirty BPD patients, and thirty healthy controls (HCs) were recruited. All the faecal samples were analyzed by shotgun metagenomics sequencing. Except for routine analyses of alpha diversity, we specially designed a new indicator, the Gm coefficient, to evaluate the inequality of relative abundances of microbiota for each participant.

RESULTS: The Gm coefficients are significant decreased in both MDD and BPD groups. The relative abundances of increased phyla Firmicutes and Actinobacteria and decreased Bacteroidetes were significantly in the MDD and BPD groups. At genus level, four of top five enriched genera (Bacteroides, Clostridium, Bifidobacterium, Oscillibacter and Streptococcus) were found increased significantly in the MDD and BPD groups compared with HCs. The genera Escherichia and Klebsiella showed significant changes in abundances only between the BPD and HC groups. At the species level, compared with BPD patients, MDD patients had a higher abundance of Prevotellaceae including Prevotella denticola F0289, Prevotella intermedia 17, Prevotella ruminicola, and Prevotella intermedia. Furthermore, the abundance of Fusobacteriaceae, Escherichia blattae DSM 4481 and Klebsiella oxytoca were significantly increased, whereas the Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 was significantly reduced in BPD group compared with MDD group.

CONCLUSIONS: Our study suggested that gut microbiota may be involved in the pathogenesis of both MDD and BPD patients, and the nuances of bacteria may have the potentiality of being the biomarkers of MDD and BPD.},
}

Adult
Bipolar Disorder/*microbiology
Depressive Disorder, Major/*microbiology
Feces/microbiology
Female
Gastrointestinal Microbiome/*physiology
Humans
Male
Metagenomics/*methods/statistics & numerical data

@article {pmid31049590,
year = {2019},
author = {Butina, TV and Bukin, YS and Krasnopeev, AS and Belykh, OI and Tupikin, AE and Kabilov, MR and Sakirko, МV and Belikov, SI},
title = {Estimate of the diversity of viral and bacterial assemblage in the coastal water of Lake Baikal.},
journal = {FEMS microbiology letters},
volume = {366},
number = {9},
pages = {},
doi = {10.1093/femsle/fnz094},
pmid = {31049590},
issn = {1574-6968},
mesh = {Bacteria/*classification ; *Biodiversity ; DNA, Bacterial/isolation & purification ; DNA, Viral/isolation & purification ; High-Throughput Nucleotide Sequencing ; Lakes/*microbiology/*virology ; Metagenomics ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Russia ; Viruses/*classification ; },
abstract = {In this study, we analysed the diversity and composition of double-stranded DNA viral and bacterial communities within the sample of surface coastal water of Southern Baikal through metagenomics and deep sequencing of the 16S ribosomal RNA gene, respectively. The 16S rRNA gene analysis has revealed 14 phyla and dominance of the 'Actinobacteria' (43.6%), 'Proteobacteria' (25.2%) and 'Bacteroidetes' (11.5%). The bacterial composition was similar to that obtained previously in Lake Baikal littoral zone. Out of 1 030 169 processed virome reads, 37.4% of sequences (385 421) were identified as viral; 15.1% were identified as nonviral and related to the domains Eukarya, Bacteria and Archaea; and 47.5% had no matches in the databases. The identified virotypes belonged to different families and were predicted to infect a wide range of organisms, from bacteria to mammals. Six families (Myoviridae, Poxviridae, Mimiviridae, Siphoviridae, Phycodnaviridae and Podoviridae) were dominant accounting for more than 90% of the identified sequences (48.3%, 17.4%, 8.3%, 6.8%, 5.8% and 4.1%, respectively). In contrast to other freshwater systems, high percentage of the Poxviridae and Mimiviridae was recorded in the water sample of Lake Baikal.},
}

Bacteria/*classification
*Biodiversity
DNA, Bacterial/isolation & purification
DNA, Viral/isolation & purification
High-Throughput Nucleotide Sequencing
Lakes/*microbiology/*virology
Metagenomics
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
Russia
Viruses/*classification

@article {pmid30649386,
year = {2019},
author = {Van Gompel, L and Luiken, REC and Sarrazin, S and Munk, P and Knudsen, BE and Hansen, RB and Bossers, A and Aarestrup, FM and Dewulf, J and Wagenaar, JA and Mevius, DJ and Schmitt, H and Heederik, DJJ and Dorado-García, A and Smit, LAM and , },
title = {The antimicrobial resistome in relation to antimicrobial use and biosecurity in pig farming, a metagenome-wide association study in nine European countries.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {74},
number = {4},
pages = {865-876},
doi = {10.1093/jac/dky518},
pmid = {30649386},
issn = {1460-2091},
mesh = {Animal Husbandry/*methods ; Animals ; Anti-Infective Agents/*therapeutic use ; Biota/*drug effects ; Computational Biology ; Cross-Sectional Studies ; *Drug Resistance, Bacterial ; Drug Utilization/*statistics & numerical data ; Europe ; Feces/*microbiology ; *Genes, Bacterial ; Metagenomics ; Swine ; },
abstract = {OBJECTIVES: Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe.

METHODS: A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM).

RESULTS: Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models.

CONCLUSIONS: Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions.},
}

Animal Husbandry/*methods
Animals
Anti-Infective Agents/*therapeutic use
Biota/*drug effects
Computational Biology
Cross-Sectional Studies
*Drug Resistance, Bacterial
Drug Utilization/*statistics & numerical data
Europe
Feces/*microbiology
*Genes, Bacterial
Metagenomics
Swine

@article {pmid30554770,
year = {2019},
author = {Cordier, T and Lanzén, A and Apothéloz-Perret-Gentil, L and Stoeck, T and Pawlowski, J},
title = {Embracing Environmental Genomics and Machine Learning for Routine Biomonitoring.},
journal = {Trends in microbiology},
volume = {27},
number = {5},
pages = {387-397},
doi = {10.1016/j.tim.2018.10.012},
pmid = {30554770},
issn = {1878-4380},
mesh = {Bacteria/*classification ; DNA Barcoding, Taxonomic ; Ecosystem ; Environmental Microbiology ; Environmental Monitoring/*methods ; Genetic Variation ; *Machine Learning ; *Metagenomics ; Microbiota ; },
abstract = {Genomics is fast becoming a routine tool in medical diagnostics and cutting-edge biotechnologies. Yet, its use for environmental biomonitoring is still considered a futuristic ideal. Until now, environmental genomics was mainly used as a replacement of the burdensome morphological identification, to screen known morphologically distinguishable bioindicator taxa. While prokaryotic and eukaryotic microbial diversity is of key importance in ecosystem functioning, its implementation in biomonitoring programs is still largely unappreciated, mainly because of difficulties in identifying microbes and limited knowledge of their ecological functions. Here, we argue that the combination of massive environmental genomics microbial data with machine learning algorithms can be extremely powerful for biomonitoring programs and pave the way to fill important gaps in our understanding of microbial ecology.},
}

Bacteria/*classification
DNA Barcoding, Taxonomic
Ecosystem
Environmental Microbiology
Environmental Monitoring/*methods
Genetic Variation
*Machine Learning
*Metagenomics
Microbiota

@article {pmid31174953,
year = {2019},
author = {Pietrucci, D and Cerroni, R and Unida, V and Farcomeni, A and Pierantozzi, M and Mercuri, NB and Biocca, S and Stefani, A and Desideri, A},
title = {Dysbiosis of gut microbiota in a selected population of Parkinson's patients.},
journal = {Parkinsonism & related disorders},
volume = {65},
number = {},
pages = {124-130},
doi = {10.1016/j.parkreldis.2019.06.003},
pmid = {31174953},
issn = {1873-5126},
mesh = {Aged ; Dysbiosis/*diagnosis/physiopathology ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Male ; Middle Aged ; Parkinson Disease/*diagnosis/*microbiology/physiopathology ; },
abstract = {INTRODUCTION: In recent years the hypothesis that gut microbiota associates with Parkinson's disease (PD) has gained importance, although it has not been possible to define a specific microbiota composition as a predictive biomarker of this disease. We have investigated dysbiosis of gut microbiota in a selected population of PD patients from Central Italy, and examined the weight of specific confounders and predictors, in order to identify potential correlations with clinical phenotypes.

METHODS: 152 fecal samples were collected from 80 patients and 72 healthy controls. Patients were enrolled according to tight inclusion criteria. Microbiota composition was studied through 16s ribosomal RNA gene amplicon sequencing analysis in combination with data on dietary/life habits. Age, loss of weight, and sex were recognized as confounding factors, whereas PD-status, age, Body Mass Index, "eat cereals", "gain of weigth" and "physical activity" as predictors. The presence of Lactobacillaceae, Enterobacteriaceae and Enterococcaceae families was significantly higher in feces from PD patients compared to healthy controls, while Lachnospiraceae were significantly reduced. Lower levels of Lachnospiraceae and higher levels of Enterobacteriaceae families also correlated with increased disease severity and motor impairment (Hoehn & Yahr stage, MDS-UPDRS Part III). Predictive metagenomics indicated a significant variation of genes involved in the metabolism of short chain fatty acids and amino acids, and in lipopolysaccharide biosynthesis.

CONCLUSIONS: PD showed a distinctive microbiota composition. Functional predictions suggest changes in pathways favoring a pro-inflammatory environment in the gastrointestinal tract, and a reduction in the biosynthesis of amino acids acting as precursors of physiological transmitters.},
}

Aged
Dysbiosis/*diagnosis/physiopathology
Feces/microbiology
Female
Gastrointestinal Microbiome/*physiology
Humans
Male
Middle Aged
Parkinson Disease/*diagnosis/*microbiology/physiopathology

@article {pmid31423298,
year = {2019},
author = {Casaburi, G and Duar, RM and Vance, DP and Mitchell, R and Contreras, L and Frese, SA and Smilowitz, JT and Underwood, MA},
title = {Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria.},
journal = {Antimicrobial resistance and infection control},
volume = {8},
number = {},
pages = {131},
pmid = {31423298},
issn = {2047-2994},
support = {S10 OD018174/OD/NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/*pharmacology ; Bacteria/*classification/drug effects/isolation & purification ; Bifidobacterium longum subspecies infantis/physiology ; Breast Feeding ; Case-Control Studies ; *Drug Resistance, Microbial ; Feces/microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Humans ; Infant, Newborn ; Metagenomics/*methods ; Microbial Sensitivity Tests ; Probiotics/*administration & dosage ; Whole Genome Sequencing ; beta-Lactamases/genetics ; },
abstract = {Background: Antibiotic-resistant (AR) bacteria are a global threat. AR bacteria can be acquired in early life and have long-term sequelae. Limiting the spread of antibiotic resistance without triggering the development of additional resistance mechanisms is of immense clinical value. Here, we show how the infant gut microbiome can be modified, resulting in a significant reduction of AR genes (ARGs) and the potentially pathogenic bacteria that harbor them.

Methods: The gut microbiome was characterized using shotgun metagenomics of fecal samples from two groups of healthy, term breastfed infants. One group was fed B. infantis EVC001 in addition to receiving lactation support (n = 29, EVC001-fed), while the other received lactation support alone (n = 31, controls). Coliforms were isolated from fecal samples and genome sequenced, as well as tested for minimal inhibitory concentrations against clinically relevant antibiotics.

Results: Infants fed B. infantis EVC001 exhibited a change to the gut microbiome, resulting in a 90% lower level of ARGs compared to controls. ARGs that differed significantly between groups were predicted to confer resistance to beta lactams, fluoroquinolones, or multiple drug classes, the majority of which belonged to Escherichia, Clostridium, and Staphylococcus. Minimal inhibitory concentration assays confirmed the resistance phenotypes among isolates with these genes. Notably, we found extended-spectrum beta lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics.

Conclusions: Colonization of the gut of breastfed infants by a single strain of B. longum subsp. infantis had a profound impact on the fecal metagenome, including a reduction in ARGs. This highlights the importance of developing novel approaches to limit the spread of these genes among clinically relevant bacteria. Future studies are needed to determine whether colonization with B. infantis EVC001 decreases the incidence of AR infections in breastfed infants.

Trial registration: This clinical trial was registered at ClinicalTrials.gov, NCT02457338.},
}

Anti-Bacterial Agents/*pharmacology
Bacteria/*classification/drug effects/isolation & purification
Bifidobacterium longum subspecies infantis/physiology
Breast Feeding
Case-Control Studies
*Drug Resistance, Microbial
Feces/microbiology
Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
Humans
Infant, Newborn
Metagenomics/*methods
Microbial Sensitivity Tests
Probiotics/*administration & dosage
Whole Genome Sequencing
beta-Lactamases/genetics

@article {pmid31407303,
year = {2019},
author = {Kröber, E and Eyice, Ö},
title = {Profiling of Active Microorganisms by Stable Isotope Probing-Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2046},
number = {},
pages = {151-161},
doi = {10.1007/978-1-4939-9721-3_12},
pmid = {31407303},
issn = {1940-6029},
mesh = {Cluster Analysis ; Ecosystem ; Isotope Labeling/methods ; Metabolic Networks and Pathways/genetics ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/*genetics/physiology ; Software ; },
abstract = {Stable isotope probing (SIP) provides researchers a culture-independent method to retrieve nucleic acids from active microbial populations performing a specific metabolic activity in complex ecosystems. In recent years, the use of the SIP method in microbial ecology studies has been accelerated. This is partly due to the advances in sequencing and bioinformatics tools, which enable fast and reliable analysis of DNA and RNA from the SIP experiments. One of these sequencing tools, metagenomics, has contributed significantly to the body of knowledge by providing data not only on taxonomy but also on the key functional genes in specific metabolic pathways and their relative abundances. In this chapter, we provide a general background on the application of the SIP-metagenomics approach in microbial ecology and a workflow for the analysis of metagenomic datasets using the most up-to-date bioinformatics tools.},
}

Cluster Analysis
Ecosystem
Isotope Labeling/methods
Metabolic Networks and Pathways/genetics
Metagenome/*genetics
Metagenomics/*methods
Microbiota/*genetics/physiology
Software

@article {pmid31885873,
year = {2019},
author = {Pareek, S and Kurakawa, T and Das, B and Motooka, D and Nakaya, S and Rongsen-Chandola, T and Goyal, N and Kayama, H and Dodd, D and Okumura, R and Maeda, Y and Fujimoto, K and Nii, T and Ogawa, T and Iida, T and Bhandari, N and Kida, T and Nakamura, S and Nair, GB and Takeda, K},
title = {Comparison of Japanese and Indian intestinal microbiota shows diet-dependent interaction between bacteria and fungi.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {},
pages = {37},
pmid = {31885873},
issn = {2055-5008},
support = {K08 DK110335/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Bacteria/classification/*growth & development/*metabolism ; Diet/*methods ; Feces/microbiology ; Fungi/classification/*growth & development/*metabolism ; *Gastrointestinal Microbiome ; Humans ; India ; Japan ; Mice ; *Microbial Interactions ; Models, Animal ; Polysaccharides/metabolism ; },
abstract = {The bacterial species living in the gut mediate many aspects of biological processes such as nutrition and activation of adaptive immunity. In addition, commensal fungi residing in the intestine also influence host health. Although the interaction of bacterium and fungus has been shown, its precise mechanism during colonization of the human intestine remains largely unknown. Here, we show interaction between bacterial and fungal species for utilization of dietary components driving their efficient growth in the intestine. Next generation sequencing of fecal samples from Japanese and Indian adults revealed differential patterns of bacterial and fungal composition. In particular, Indians, who consume more plant polysaccharides than Japanese, harbored increased numbers of Prevotella and Candida. Candida spp. showed strong growth responses to the plant polysaccharide arabinoxylan in vitro. Furthermore, the culture supernatants of Candida spp. grown with arabinoxylan promoted rapid proliferation of Prevotella copri. Arabinose was identified as a potential growth-inducing factor in the Candida culture supernatants. Candida spp. exhibited a growth response to xylose, but not to arabinose, whereas P. copri proliferated in response to both xylose and arabinose. Candida spp., but not P. copri, colonized the intestine of germ-free mice. However, P. copri successfully colonized mouse intestine already harboring Candida. These findings demonstrate a proof of concept that fungal members of gut microbiota can facilitate a colonization of the intestine by their bacterial counterparts, potentially mediated by a dietary metabolite.},
}

Animals
Bacteria/classification/*growth & development/*metabolism
Diet/*methods
Feces/microbiology
Fungi/classification/*growth & development/*metabolism
*Gastrointestinal Microbiome
Humans
India
Japan
Mice
*Microbial Interactions
Models, Animal
Polysaccharides/metabolism

@article {pmid31632686,
year = {2019},
author = {Koo, H and Hakim, JA and Crossman, DK and Kumar, R and Lefkowitz, EJ and Morrow, CD},
title = {Individualized recovery of gut microbial strains post antibiotics.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {},
pages = {30},
pmid = {31632686},
issn = {2055-5008},
mesh = {Anti-Bacterial Agents/*administration & dosage ; *Biological Variation, Individual ; Gastrointestinal Microbiome/*drug effects ; Gastrointestinal Tract/*microbiology ; Humans ; Metagenomics ; },
abstract = {To further understand the impact of antibiotics on the gastrointestinal tract microbial community, the intra-individual recovery pattern of specific microbial strains was determined using metagenomic sequencing coupled with strain-tracking analyses. In a study where 18 individuals were administered a single antibiotic (cefprozil), new microbial genomic variants (herein strains) were transiently detected in 15 individuals, while in a second study that used a cocktail of three antibiotics (meropenem, gentamicin, and vancomycin), all 12 participants had either permanent or transient strain changes. The presence of distinct microbial genomic variants indicates a pattern of strain recovery that is intra-individual specific following disruption of the human gastrointestinal tract with antibiotics.},
}

Anti-Bacterial Agents/*administration & dosage
*Biological Variation, Individual
Gastrointestinal Microbiome/*drug effects
Gastrointestinal Tract/*microbiology
Humans
Metagenomics

@article {pmid31556231,
year = {2019},
author = {Liu, B and Yang, L and Cui, Z and Zheng, J and Huang, J and Zhao, Q and Su, Z and Wang, M and Zhang, W and Liu, J and Wang, T and Li, Q and Lu, H},
title = {Anti-TNF-α therapy alters the gut microbiota in proteoglycan-induced ankylosing spondylitis in mice.},
journal = {MicrobiologyOpen},
volume = {8},
number = {12},
pages = {e927},
pmid = {31556231},
issn = {2045-8827},
mesh = {Animals ; Antirheumatic Agents/pharmacology ; Disease Models, Animal ; Etanercept/*pharmacology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Intestinal Mucosa/drug effects/metabolism/microbiology/pathology ; Metagenomics/methods ; Mice ; Permeability ; Proteoglycans/*adverse effects ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Spondylitis, Ankylosing/diagnosis/drug therapy/*etiology/*metabolism ; Tight Junction Proteins/metabolism ; Tumor Necrosis Factor-alpha/*antagonists & inhibitors ; },
abstract = {Ankylosing spondylitis is a chronic, progressive disease, and its treatment is relevant to the gut microbiota. Anti-tumor necrosis factor-alpha (anti-TNF-α) therapy alters the gut microbiota in many diseases, including inflammatory bowel disease. However, little is known about the effect of TNF-α blocker treatment on the gut microbiota in ankylosing spondylitis. Herein, the effect of a TNF-α blocker on the gut microbiota in proteoglycan-induced arthritis was investigated. Proteoglycan-induced mice were treated with an rhTNFR:Fc solution of etanercept (5 µg/g) for 4 weeks. rhTNFR:Fc treatment attenuated the arthritis incidence and severity of arthritis in the proteoglycan-induced mice and decreased inflammation in the ankle joints and ameliorated ileal tissue destruction. Moreover, high gut permeability occurred, and zonula occludens-1 and occludin protein levels were reduced in proteoglycan-induced mice. These levels were significantly restored by the administration of rhTNFR:Fc. The serum TNF-α and IL-17 levels were also decreased. In addition, flora analysis via 16S rDNA high-throughput sequencing revealed that rhTNFR:Fc treatment restored the gut microbiota composition to a composition similar to that in control mice. In conclusion, anti-TNF-α therapy attenuated proteoglycan-induced arthritis progression and modulated the gut microbiota and intestinal barrier function. These results provide new insights for anti-TNF-α therapy strategies via regulating the gut microbiota in ankylosing spondylitis.},
}

Animals
Antirheumatic Agents/pharmacology
Disease Models, Animal
Etanercept/*pharmacology
Female
Gastrointestinal Microbiome/*drug effects
Humans
Intestinal Mucosa/drug effects/metabolism/microbiology/pathology
Metagenomics/methods
Mice
Permeability
Proteoglycans/*adverse effects
RNA, Ribosomal, 16S/genetics
Severity of Illness Index
Spondylitis, Ankylosing/diagnosis/drug therapy/*etiology/*metabolism
Tight Junction Proteins/metabolism
Tumor Necrosis Factor-alpha/*antagonists & inhibitors

@article {pmid31552140,
year = {2019},
author = {Shah, TM and Patel, JG and Gohil, TP and Blake, DP and Joshi, CG},
title = {Host transcriptome and microbiome interaction modulates physiology of full-sibs broilers with divergent feed conversion ratio.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {},
pages = {24},
pmid = {31552140},
issn = {2055-5008},
mesh = {*Animal Feed ; Animals ; Chickens/*growth & development ; *Gastrointestinal Microbiome ; Gene Expression Profiling ; *Host Microbial Interactions ; Intestines ; Liver ; Siblings ; *Weight Gain ; },
abstract = {Efficient livestock production relies on effective conversion of feed into body weight gain (BWG). High levels of feed conversion are especially important in production of broiler chickens, birds reared for meat, where economic margins are tight. Traits associated with improved broiler growth and feed efficiency have been subjected to intense genetic selection, but measures such as feed conversion ratio (FCR) remain variable, even between full siblings (sibs). Non-genetic factors such as the composition and function of microbial populations within different enteric compartments have been recognized to influence FCR, although the extent of interplay between hosts and their microbiomes is unclear. To examine host-microbiome interactions we investigated variation in the composition and functions of host intestinal-hepatic transcriptomes and the intestinal microbiota of full-sib broilers with divergent FCR. Progeny from 300 broiler families were assessed for divergent FCR set against shared genetic backgrounds and exposure to the same environmental factors. The seven most divergent full-sib pairs were chosen for analysis, exhibiting marked variation in transcription of genes as well as gut microbial diversity. Examination of enteric microbiota in low FCR sibs revealed variation in microbial community structure and function with no difference in feed intake compared to high FCR sibs. Gene transcription in low and high FCR sibs was significantly associated with the abundance of specific microbial taxa. Highly intertwined interactions between host transcriptomes and enteric microbiota are likely to modulate complex traits like FCR and may be amenable to selective modification with relevance to improving intestinal homeostasis and health.},
}

*Animal Feed
Animals
Chickens/*growth & development
*Gastrointestinal Microbiome
Gene Expression Profiling
*Host Microbial Interactions
Intestines
Liver
Siblings
*Weight Gain

@article {pmid31544365,
year = {2019},
author = {Pootakham, W and Mhuantong, W and Yoocha, T and Putchim, L and Jomchai, N and Sonthirod, C and Naktang, C and Kongkachana, W and Tangphatsornruang, S},
title = {Heat-induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea.},
journal = {MicrobiologyOpen},
volume = {8},
number = {12},
pages = {e935},
pmid = {31544365},
issn = {2045-8827},
mesh = {Animals ; Anthozoa/*microbiology ; *Biodiversity ; Coral Reefs ; DNA Barcoding, Taxonomic ; Ecosystem ; *Hot Temperature ; Metagenomics/methods ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Rhodobacteraceae ; *Stress, Physiological ; },
abstract = {The coral holobiont is a complex ecosystem consisting of coral animals and a highly diverse consortium of associated microorganisms including algae, fungi, and bacteria. Several studies have highlighted the importance of coral-associated bacteria and their potential roles in promoting the host fitness and survival. Recently, dynamics of coral-associated microbiomes have been demonstrated to be linked to patterns of coral heat tolerance. Here, we examined the effect of elevated seawater temperature on the structure and diversity of bacterial populations associated with Porites lutea, using full-length 16S rRNA sequences obtained from Pacific Biosciences circular consensus sequencing. We observed a significant increase in alpha diversity indices and a distinct shift in microbiome composition during thermal stress. There was a marked decline in the apparent relative abundance of Gammaproteobacteria family Endozoicomonadaceae after P. lutea had been exposed to elevated seawater temperature. Concomitantly, the bacterial community structure shifted toward the predominance of Alphaproteobacteria family Rhodobacteraceae. Interestingly, we did not observe an increase in relative abundance of Vibrio-related sequences in our heat-stressed samples even though the appearance of Vibrio spp. has often been detected in parallel with the increase in the relative abundance of Rhodobacteraceae during thermal bleaching in other coral species. The ability of full-length 16S rRNA sequences in resolving taxonomic uncertainty of associated bacteria at a species level enabled us to identify 24 robust indicator bacterial species for thermally stressed corals. It is worth noting that the majority of those indicator species were members of the family Rhodobacteraceae. The comparison of bacterial community structure and diversity between corals in ambient water temperature and thermally stressed corals may provide a better understanding on how bacteria symbionts contribute to the resilience of their coral hosts to ocean warming.},
}

Animals
Anthozoa/*microbiology
*Biodiversity
Coral Reefs
DNA Barcoding, Taxonomic
Ecosystem
*Hot Temperature
Metagenomics/methods
*Microbiota
RNA, Ribosomal, 16S/genetics
*Rhodobacteraceae
*Stress, Physiological

@article {pmid31496126,
year = {2019},
author = {Yang, Q and Huang, X and Wang, P and Yan, Z and Sun, W and Zhao, S and Gun, S},
title = {Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age-related dietary changes.},
journal = {MicrobiologyOpen},
volume = {8},
number = {12},
pages = {e923},
pmid = {31496126},
issn = {2045-8827},
mesh = {Age Factors ; *Animal Feed ; Animals ; Biodiversity ; Biomarkers ; Computational Biology/methods ; Diarrhea/*microbiology ; Dysbiosis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Male ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Swine ; Symbiosis ; Weaning ; },
abstract = {Diarrhea is one of the most common enteric diseases in young piglets. Diverse factors such as an unstable gut microenvironment, immature intestinal immune system, early supplementary feeding, and weaning often induce dysfunction of gut microbiota, thus leading to a continuing high incidence of diarrhea in piglets. However, few studies have characterized the gut microbiota of diarrheic piglets following changes in diet and during the development of intestinal physiology. In this study, we used 16S rRNA gene sequencing to analyze the dynamic establishment of fecal microbiota in six healthy piglets in response to age-related changes in the diet: sow-reared, early supplementary creep-feeding (sow-reared + starter diet), and weaning (solid nursery diet). We compared the gut microbiota of these six healthy piglets with those of diarrheic piglets during each of the three dietary stages (n = 10 sow-reared, n = 10 early supplementary creep-feeding, and n = 5 weaning). We found that weaning (solid nursery feeding) was the primary factor leading to dynamic colonization by microbiota in healthy piglets, and diarrhea primarily affected the microbial communities of piglets before weaning. Healthy piglets showed a continuous decrease in Lactobacillus and Escherichia, as well as a gradual increase in Prevotella with the transition to solid food. An altered relationship between Prevotella and Escherichia may be the main cause of diarrhea in preweaned piglets, whereas reduced numbers of Bacteroides, Ruminococcus, Bulleidia, and Treponema that are responsible for the digestion and utilization of solid feeds may be related to the onset of postweaning piglet diarrhea. The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) functional analysis indicated that a reduction in genes involved in carbohydrate metabolism induced by intestinal dysbacteriosis in diarrheic piglets was one of the major causes of diarrhea at the three dietary stages. These findings provide insights into developing an intervention strategy for better management of diarrhea in piglets.},
}

Age Factors
*Animal Feed
Animals
Biodiversity
Biomarkers
Computational Biology/methods
Diarrhea/*microbiology
Dysbiosis
Feces/microbiology
Female
*Gastrointestinal Microbiome
Male
Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Swine
Symbiosis
Weaning

@article {pmid31482697,
year = {2019},
author = {Wang, X and Liu, X and Lu, S and Liu, C and Gu, Z and Zeng, X and Ni, Q},
title = {Culture of attached and suspended Rhodopseudomonas faecalis in the presence of decomposing fish feed.},
journal = {MicrobiologyOpen},
volume = {8},
number = {12},
pages = {e924},
pmid = {31482697},
issn = {2045-8827},
mesh = {Animal Feed/*microbiology ; Animals ; Biomass ; *Fermentation ; *Fishes ; Metagenome ; Metagenomics/methods ; Microbiota ; Photosynthesis ; Rhodopseudomonas/growth & development/*metabolism ; Water Microbiology ; },
abstract = {An approach to culturing attached and suspended forms of Rhodopseudomonas faecalis by using compound fish feed with tap water in transparent containers is reported in this study. The ratio of fish feed to tap water was 14.3-50.8 g/L, and no other inoculum or substances were added during the culture process. When the ratio of fish feed to tap water was 14.3 g/L, the highest total nitrogen, total phosphorus, and total dissolved carbon content recorded in the water in the containers were approximately 730 mg/L, 356 mg/L, and 1,620 mg/L, respectively, during the process of feed decay. Comamonas, Rhodopseudomonas, and Clostridium successively dominated during the culture process. Rhodopseudomonas was the most common dominant genus in both the attached and suspended forms when the water was dark red, and the relative operational taxonomic unit abundance reached 80-89% and 24.8%, respectively. The dominant species was R. faecalis. The maximum thickness of attached bacteria and the biomass of attached Rhodopseudomonas reached up to 0.56 mm and 7.5 mg/cm2 , respectively. This study provides a method for the mass culture of Rhodopseudomonas by using the fermentation of aquatic compound fish feed.},
}

Animal Feed/*microbiology
Animals
Biomass
*Fermentation
*Fishes
Metagenome
Metagenomics/methods
Microbiota
Photosynthesis
Rhodopseudomonas/growth & development/*metabolism
Water Microbiology

@article {pmid31337439,
year = {2019},
author = {Zheng, Y and Wang, T and Tu, X and Huang, Y and Zhang, H and Tan, D and Jiang, W and Cai, S and Zhao, P and Song, R and Li, P and Qin, N and Fang, W},
title = {Gut microbiome affects the response to anti-PD-1 immunotherapy in patients with hepatocellular carcinoma.},
journal = {Journal for immunotherapy of cancer},
volume = {7},
number = {1},
pages = {193},
pmid = {31337439},
issn = {2051-1426},
mesh = {Antibodies, Monoclonal, Humanized/*administration & dosage/pharmacology ; Bacteria/*classification/drug effects/genetics/isolation & purification ; Carcinoma, Hepatocellular/*drug therapy/microbiology ; Clinical Decision-Making ; Gastrointestinal Microbiome/drug effects ; Humans ; Immunotherapy ; Liver Neoplasms/*drug therapy/microbiology ; Metabolic Networks and Pathways ; Metagenomics/*methods ; Phylogeny ; Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Sequence Analysis, DNA ; Treatment Outcome ; },
abstract = {BACKGROUND: Checkpoint-blockade immunotherapy targeting programmed cell death protein 1 (PD-1) has recently shown promising efficacy in hepatocellular carcinoma (HCC). However, the factors affecting and predicting the response to anti-PD-1 immunotherapy in HCC are still unclear. Herein, we report the dynamic variation characteristics and specificities of the gut microbiome during anti-PD-1 immunotherapy in HCC using metagenomic sequencing.

RESULTS: Fecal samples from patients responding to immunotherapy showed higher taxa richness and more gene counts than those of non-responders. For dynamic analysis during anti-PD-1 immunotherapy, the dissimilarity of beta diversity became prominent across patients as early as Week 6. In non-responders, Proteobacteria increased from Week 3, and became predominant at Week 12. Twenty responder-enriched species, including Akkermansia muciniphila and Ruminococcaceae spp., were further identified. The related functional genes and metabolic pathway analysis, such as carbohydrate metabolism and methanogenesis, verified the potential bioactivities of responder-enriched species.

CONCLUSIONS: Gut microbiome may have a critical impact on the responses of HCC patients treated with anti-PD-1 immunotherapy. The dynamic variation characteristics of the gut microbiome may provide early predictions of the outcomes of immunotherapy in HCC, which is critical for disease-monitoring and treatment decision-making.},
}

Antibodies, Monoclonal, Humanized/*administration & dosage/pharmacology
Bacteria/*classification/drug effects/genetics/isolation & purification
Carcinoma, Hepatocellular/*drug therapy/microbiology
Clinical Decision-Making
Gastrointestinal Microbiome/drug effects
Humans
Immunotherapy
Liver Neoplasms/*drug therapy/microbiology
Metabolic Networks and Pathways
Metagenomics/*methods
Phylogeny
Programmed Cell Death 1 Receptor/antagonists & inhibitors
Sequence Analysis, DNA
Treatment Outcome

@article {pmid31263569,
year = {2019},
author = {Tan, SM and Yung, PYM and Hutchinson, PE and Xie, C and Teo, GH and Ismail, MH and Drautz-Moses, DI and Little, PFR and Williams, RBH and Cohen, Y},
title = {Primer-free FISH probes from metagenomics/metatranscriptomics data permit the study of uncharacterised taxa in complex microbial communities.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {},
pages = {17},
pmid = {31263569},
issn = {2055-5008},
mesh = {Bacteria/*classification/*genetics ; DNA, Bacterial/genetics ; DNA, Ribosomal/genetics ; In Situ Hybridization, Fluorescence/*methods ; Metagenomics/*methods ; *Microbiota ; Optical Imaging/*methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; },
abstract = {Methods for the study of member species in complex microbial communities remain a high priority, particularly for rare and/or novel member species that might play an important ecological role. Specifically, methods that link genomic information of member species with its spatial structure are lacking. This study adopts an integrative workflow that permits the characterisation of previously unclassified bacterial taxa from microbiomes through: (1) imaging of the spatial structure; (2) taxonomic classification and (3) genome recovery. Our study attempts to bridge the gaps between metagenomics/metatranscriptomics and high-resolution biomass imaging methods by developing new fluorescence in situ hybridisation (FISH) probes-termed as R-Probes-from shotgun reads that harbour hypervariable regions of the 16S rRNA gene. The sample-centric design of R-Probes means that probes can directly hybridise to OTUs as detected in shotgun sequencing surveys. The primer-free probe design captures larger microbial diversity as compared to canonical probes. R-Probes were designed from deep-sequenced RNA-Seq datasets for both FISH imaging and FISH-Fluorescence activated cell sorting (FISH-FACS). FISH-FACS was used for target enrichment of previously unclassified bacterial taxa prior to downstream multiple displacement amplification (MDA), genomic sequencing and genome recovery. After validation of the workflow on an axenic isolate of Thauera species, the techniques were applied to investigate two previously uncharacterised taxa from a tropical full-scale activated sludge community. In some instances, probe design on the hypervariable region allowed differentiation to the species level. Collectively, the workflow can be readily applied to microbiomes for which shotgun nucleic acid survey data is available.},
}

Bacteria/*classification/*genetics
DNA, Bacterial/genetics
DNA, Ribosomal/genetics
In Situ Hybridization, Fluorescence/*methods
Metagenomics/*methods
*Microbiota
Optical Imaging/*methods
Phylogeny
RNA, Ribosomal, 16S/genetics
Sewage/microbiology

@article {pmid30774969,
year = {2019},
author = {Santillan, E and Seshan, H and Constancias, F and Drautz-Moses, DI and Wuertz, S},
title = {Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {},
pages = {8},
pmid = {30774969},
issn = {2055-5008},
mesh = {Bioreactors/*microbiology ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; *Environmental Exposure ; Environmental Pollutants/*toxicity ; Metagenome ; Microbiota/*drug effects ; Models, Theoretical ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sewage/*microbiology ; },
abstract = {Disturbance is known to affect the ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, assembly, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors operated in daily cycles were subjected to eight different frequency levels of augmentation with a toxic pollutant, from never (undisturbed) to every day (press-disturbed), for 35 days. Microbial communities were assessed by combining distance-based methods, general linear multivariate models, α-diversity indices, and null model analyses on metagenomics and 16S rRNA gene amplicon data. A stronger temporal decrease in α-diversity at the extreme, undisturbed and press-disturbed, ends of the disturbance range led to a hump-backed pattern, with the highest diversity found at intermediate levels of disturbance. Undisturbed and press-disturbed levels displayed the highest community and functional similarity across replicates, suggesting deterministic processes were dominating. The opposite was observed amongst intermediately disturbed levels, indicating stronger stochastic assembly mechanisms. Trade-offs were observed in the ecosystem function between organic carbon removal and both nitrification and biomass productivity, as well as between diversity and these functions. Hence, not every ecosystem function was favoured by higher community diversity. Our results show that the assessment of changes in diversity, along with the underlying stochastic-deterministic assembly processes, is essential to understanding the impact of disturbance in complex microbial communities.},
}

Bioreactors/*microbiology
Cluster Analysis
DNA, Ribosomal/chemistry/genetics
*Environmental Exposure
Environmental Pollutants/*toxicity
Metagenome
Microbiota/*drug effects
Models, Theoretical
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Sewage/*microbiology

@article {pmid30701077,
year = {2019},
author = {Lindefeldt, M and Eng, A and Darban, H and Bjerkner, A and Zetterström, CK and Allander, T and Andersson, B and Borenstein, E and Dahlin, M and Prast-Nielsen, S},
title = {The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {},
pages = {5},
pmid = {30701077},
issn = {2055-5008},
support = {R01 GM124312/GM/NIGMS NIH HHS/United States ; },
mesh = {Adolescent ; Bacteria/*classification/genetics ; Child ; Child, Preschool ; *Diet, Ketogenic ; Epilepsy/*therapy ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Male ; Metagenomics ; Microbiota/*drug effects ; },
abstract = {The gut microbiota has been linked to various neurological disorders via the gut-brain axis. Diet influences the composition of the gut microbiota. The ketogenic diet (KD) is a high-fat, adequate-protein, low-carbohydrate diet established for treatment of therapy-resistant epilepsy in children. Its efficacy in reducing seizures has been confirmed, but the mechanisms remain elusive. The diet has also shown positive effects in a wide range of other diseases, including Alzheimer's, depression, autism, cancer, and type 2 diabetes. We collected fecal samples from 12 children with therapy-resistant epilepsy before starting KD and after 3 months on the diet. Parents did not start KD and served as diet controls. Applying shotgun metagenomic DNA sequencing, both taxonomic and functional profiles were established. Here we report that alpha diversity is not changed significantly during the diet, but differences in both taxonomic and functional composition are detected. Relative abundance of bifidobacteria as well as E. rectale and Dialister is significantly diminished during the intervention. An increase in relative abundance of E. coli is observed on KD. Functional analysis revealed changes in 29 SEED subsystems including the reduction of seven pathways involved in carbohydrate metabolism. Decomposition of these shifts indicates that bifidobacteria and Escherichia are important contributors to the observed functional shifts. As relative abundance of health-promoting, fiber-consuming bacteria becomes less abundant during KD, we raise concern about the effects of the diet on the gut microbiota and overall health. Further studies need to investigate whether these changes are necessary for the therapeutic effect of KD.},
}

Adolescent
Bacteria/*classification/genetics
Child
Child, Preschool
*Diet, Ketogenic
Epilepsy/*therapy
Feces/microbiology
Female
Gastrointestinal Microbiome/*drug effects
Humans
Infant
Male
Metagenomics
Microbiota/*drug effects

@article {pmid30675371,
year = {2019},
author = {Layeghifard, M and Li, H and Wang, PW and Donaldson, SL and Coburn, B and Clark, ST and Caballero, JD and Zhang, Y and Tullis, DE and Yau, YCW and Waters, V and Hwang, DM and Guttman, DS},
title = {Microbiome networks and change-point analysis reveal key community changes associated with cystic fibrosis pulmonary exacerbations.},
journal = {NPJ biofilms and microbiomes},
volume = {5},
number = {},
pages = {4},
pmid = {30675371},
issn = {2055-5008},
support = {//CIHR/Canada ; },
mesh = {Bacteria/*classification/genetics ; Canada ; Child ; Cystic Fibrosis/*complications ; Humans ; Longitudinal Studies ; Metagenomics ; *Microbiota ; Pneumonia/*microbiology ; Sputum/*microbiology ; },
abstract = {Over 90% of cystic fibrosis (CF) patients die due to chronic lung infections leading to respiratory failure. The decline in CF lung function is greatly accelerated by intermittent and progressively severe acute pulmonary exacerbations (PEs). Despite their clinical impact, surprisingly few microbiological signals associated with PEs have been identified. Here we introduce an unsupervised, systems-oriented approach to identify key members of the microbiota. We used two CF sputum microbiome data sets that were longitudinally collected through periods spanning baseline health and PEs. Key taxa were defined based on three strategies: overall relative abundance, prevalence, and co-occurrence network interconnectedness. We measured the association between changes in the abundance of the key taxa and changes in patient clinical status over time via change-point detection, and found that taxa with the highest level of network interconnectedness tracked changes in patient health significantly better than taxa with the highest abundance or prevalence. We also cross-sectionally stratified all samples into the clinical states and identified key taxa associated with each state. We found that network interconnectedness most strongly delineated the taxa among clinical states, and that anaerobic bacteria were over-represented during PEs. Many of these anaerobes are oropharyngeal bacteria that have been previously isolated from the respiratory tract, and/or have been studied for their role in CF. The observed shift in community structure, and the association of anaerobic taxa and PEs lends further support to the growing consensus that anoxic conditions and the subsequent growth of anaerobic microbes are important predictors of PEs.},
}

Bacteria/*classification/genetics
Canada
Child
Cystic Fibrosis/*complications
Humans
Longitudinal Studies
Metagenomics
*Microbiota
Pneumonia/*microbiology
Sputum/*microbiology

@article {pmid30867308,
year = {2019},
author = {Chong, R and Shi, M and Grueber, CE and Holmes, EC and Hogg, CJ and Belov, K and Barrs, VR},
title = {Fecal Viral Diversity of Captive and Wild Tasmanian Devils Characterized Using Virion-Enriched Metagenomics and Metatranscriptomics.},
journal = {Journal of virology},
volume = {93},
number = {11},
pages = {},
pmid = {30867308},
issn = {1098-5514},
mesh = {Animals ; Animals, Wild ; Animals, Zoo ; Australia ; Endangered Species ; Feces/*virology ; Gene Expression Profiling/methods ; Marsupialia/*virology ; Metagenomics/methods ; Transcriptome/genetics ; Virion ; },
abstract = {The Tasmanian devil is an endangered carnivorous marsupial threatened by devil facial tumor disease (DFTD). While research on DFTD has been extensive, little is known about viruses in devils and whether any are of potential conservation relevance for this endangered species. Using both metagenomics based on virion enrichment and sequence-independent amplification (virion-enriched metagenomics) and metatranscriptomics based on bulk RNA sequencing, we characterized and compared the fecal viromes of captive and wild devils. A total of 54 fecal samples collected from two captive and four wild populations were processed for virome characterization using both approaches. In total, 24 novel marsupial-related viruses, comprising a sapelovirus, astroviruses, rotaviruses, picobirnaviruses, parvoviruses, papillomaviruses, polyomaviruses, and a gammaherpesvirus, were identified, as well as known mammalian pathogens such as rabbit hemorrhagic disease virus 2. Captive devils showed significantly lower viral diversity than wild devils. Comparison of the two virus discovery approaches revealed substantial differences in the number and types of viruses detected, with metatranscriptomics better suited for RNA viruses and virion-enriched metagenomics largely identifying more DNA viruses. Thus, the viral communities revealed by virion-enriched metagenomics and metatranscriptomics were not interchangeable and neither approach was able to detect all viruses present. An integrated approach using both virion-enriched metagenomics and metatranscriptomics constitutes a powerful tool for obtaining a complete overview of both the taxonomic and functional profiles of viral communities within a sample.IMPORTANCE The Tasmanian devil is an iconic Australian marsupial that has suffered an 80% population decline due to a contagious cancer, devil facial tumor disease, along with other threats. Until now, viral discovery in this species has been confined to one gammaherpesvirus (dasyurid herpesvirus 2 [DaHV-2]), for which captivity was identified as a significant risk factor. Our discovery of 24 novel marsupial-associated RNA and DNA viruses, and that viral diversity is lower in captive than in wild devils, has greatly expanded our knowledge of gut-associated viruses in devils and provides important baseline information that will contribute to the conservation and captive management of this endangered species. Our results also revealed that a combination of virion-enriched metagenomics and metatranscriptomics may be a more comprehensive approach for virome characterization than either method alone. Our results thus provide a springboard for continuous improvements in the way we study complex viral communities.},
}

Animals
Animals, Wild
Animals, Zoo
Australia
Endangered Species
Feces/*virology
Gene Expression Profiling/methods
Marsupialia/*virology
Metagenomics/methods
Transcriptome/genetics
Virion

@article {pmid30517025,
year = {2019},
author = {Bazin, A and Debroas, D and Mephu Nguifo, E},
title = {A De Novo Robust Clustering Approach for Amplicon-Based Sequence Data.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {26},
number = {6},
pages = {618-624},
doi = {10.1089/cmb.2018.0170},
pmid = {30517025},
issn = {1557-8666},
mesh = {Algorithms ; Cluster Analysis ; Computational Biology/methods ; Metagenomics/methods ; Microbiota/*genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/*methods ; },
abstract = {When analyzing microbial communities, an active and computational challenge concerns the categorization of 16S rRNA gene sequences into operational taxonomic units (OTUs). Established clustering tools use a one pass algorithm to tackle high number of gene sequences and produce OTUs in reasonable time. However, all of the current tools are based on a crisp clustering approach, where a gene sequence is assigned to one cluster. The weak quality of the output compared with more complex clustering algorithms forces the user to postprocess the obtained OTUs. Providing a membership degree when assigning a gene sequence to an OTU will help the user during the postprocessing task. Moreover it is possible to use this membership degree to automatically evaluate the quality of the obtained OTUs. So the goal of this study is to propose a new clustering approach that takes into account uncertainty when producing OTUs, and improves both the quality and the presentation of the OTU results.},
}

Algorithms
Cluster Analysis
Computational Biology/methods
Metagenomics/methods
Microbiota/*genetics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/*methods

@article {pmid32345218,
year = {2020},
author = {Loo, EXL and Zain, A and Yap, GC and Purbojati, RW and Drautz-Moses, DI and Koh, YQ and Chong, YS and Tan, KH and Gluckman, PD and Yap, F and Eriksson, JG and Tham, E and Shek, LP and Kjelleberg, S and Schuster, SC and Banerjee, R and Lee, BW},
title = {Longitudinal assessment of antibiotic resistance gene profiles in gut microbiomes of infants at risk of eczema.},
journal = {BMC infectious diseases},
volume = {20},
number = {1},
pages = {312},
doi = {10.1186/s12879-020-05000-y},
pmid = {32345218},
issn = {1471-2334},
support = {(R-178-000-222-511)//NMRC/ ; NMRC/TCR/004-NUS/2008; NMRC/TCR/012-NUHS/2014.//NMRC/ ; },
mesh = {Aminoglycosides/pharmacology ; Anti-Bacterial Agents/*pharmacology ; Bacterial Proteins/genetics/metabolism ; Drug Resistance, Bacterial/*genetics ; Eczema/*diagnosis/etiology ; Escherichia coli/drug effects/enzymology/isolation & purification ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects ; Humans ; Infant ; Infant, Newborn ; Klebsiella pneumoniae/drug effects/enzymology/isolation & purification ; Longitudinal Studies ; Male ; Risk ; beta-Lactamases/genetics/metabolism ; beta-Lactams/pharmacology ; },
abstract = {BACKGROUND: While there is increasing knowledge about the gut microbiome, the factors influencing and the significance of the gut resistome are still not well understood. Infant gut commensals risk transferring multidrug-resistant antibiotic resistance genes (ARGs) to pathogenic bacteria. The rapid spread of multidrug-resistant pathogenic bacteria is a worldwide public health concern. Better understanding of the naïve infant gut resistome may build the evidence base for antimicrobial stewardship in both humans and in the food industry. Given the high carriage rate of extended spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in Asia, we aimed to evaluate community prevalence, dynamics, and longitudinal changes in antibiotic resistance gene (ARG) profiles and prevalence of ESBL-producing E. coli and K. pneumoniae in the intestinal microbiome of infants participating in the Growing Up in Singapore Towards Healthy Outcomes (GUSTO) study, a longitudinal cohort study of pregnant women and their infants.

METHODS: We analysed ARGs in the first year of life among 75 infants at risk of eczema who had stool samples collected at multiple timepoints using metagenomics.

RESULTS: The mean number of ARGs per infant increased with age. The most common ARGs identified confer resistance to aminoglycoside, beta-lactam, macrolide and tetracycline antibiotics; all infants harboured these antibiotic resistance genes at some point in the first year of life. Few ARGs persisted throughout the first year of life. Beta-lactam resistant Escherichia coli and Klebsiella pneumoniae were detected in 4 (5.3%) and 32 (42.7%) of subjects respectively.

CONCLUSION: In this longitudinal cohort study of infants living in a region with high endemic antibacterial resistance, we demonstrate that majority of the infants harboured several antibiotic resistance genes in their gut and showed that the infant gut resistome is diverse and dynamic over the first year of life.},
}

Aminoglycosides/pharmacology
Anti-Bacterial Agents/*pharmacology
Bacterial Proteins/genetics/metabolism
Drug Resistance, Bacterial/*genetics
Eczema/*diagnosis/etiology
Escherichia coli/drug effects/enzymology/isolation & purification
Feces/microbiology
Female
Gastrointestinal Microbiome/*drug effects
Humans
Infant
Infant, Newborn
Klebsiella pneumoniae/drug effects/enzymology/isolation & purification
Longitudinal Studies
Male
Risk
beta-Lactamases/genetics/metabolism
beta-Lactams/pharmacology

@article {pmid32208434,
year = {2020},
author = {Jangid, A and Fukuda, S and Seki, M and Horiuchi, T and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T},
title = {Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0228358},
pmid = {32208434},
issn = {1932-6203},
mesh = {Adaptor Protein Complex 1/*deficiency/*genetics ; Animals ; Colitis/complications/*genetics/*microbiology ; Dysbiosis/complications/*microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Mice ; },
abstract = {Inflammatory bowel disease results from alterations in the immune system and intestinal microbiota. The role of intestinal epithelial cells (IECs) in maintaining gut homeostasis is well known and its perturbation often causes gastrointestinal disorders including IBD. The epithelial specific adaptor protein (AP)-1B is involved in the establishment of the polarity of IECs. Deficiency of the AP-1B μ subunit (Ap1m2-/-) leads to the development of chronic colitis in mice. However, how this deficiency affects the gut microbes and its potential functions remains elusive. To gain insights into the gut microbiome of Ap1m2-/- mice having the colitis phenotype, we undertook shotgun metagenomic sequencing analysis of knockout mice. We found important links to the microbial features involved in altering various physiological pathways, including carbohydrate metabolism, nutrient transportation, oxidative stress, and bacterial pathogenesis (cell motility). In addition, an increased abundance of sulfur-reducing and lactate-producing bacteria has been observed which may aggravate the colitis condition.},
}

Adaptor Protein Complex 1/*deficiency/*genetics
Animals
Colitis/complications/*genetics/*microbiology
Dysbiosis/complications/*microbiology
*Gastrointestinal Microbiome
Metagenomics
Mice

@article {pmid32182280,
year = {2020},
author = {Ivanova, AA and Zhelezova, AD and Chernov, TI and Dedysh, SN},
title = {Linking ecology and systematics of acidobacteria: Distinct habitat preferences of the Acidobacteriia and Blastocatellia in tundra soils.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0230157},
pmid = {32182280},
issn = {1932-6203},
mesh = {*Acidobacteria/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Carbon/analysis ; Classification ; DNA, Bacterial ; Ecosystem ; Metagenomics ; Nitrogen/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Soil Microbiology ; *Tundra ; },
abstract = {The Acidobacteria is one of the major bacterial phyla in soils and peatlands. The currently explored diversity within this phylum is assigned to 15 class-level units, five of which contain described members. The ecologically relevant traits of acidobacteria from different classes remain poorly understood. Here, we compared the patterns of acidobacterial diversity in sandy soils of tundra, along a gradient of increasing vegetation-unfixed aeolian sand, semi-fixed surfaces with mosses and lichens, and mature soil under fully developed plant cover. The Acidobacteria-affiliated 16S rRNA gene sequences retrieved from these soils comprised 11 to 33% of total bacterial reads and belonged mostly to members of the classes Acidobacteriia and Blastocatellia, which displayed opposite habitat preferences. The relative abundance of the Blastocatellia was maximal in unfixed sands and declined in soils of vegetated plots, showing positive correlation with soil pH and negative correlation with carbon and nitrogen availability. An opposite tendency was characteristic for the Acidobacteriia. Most Blastocatellia-affiliated reads belonged to as-yet-undescribed members of the family Arenimicrobiaceae, which appears to be characteristic for dry, depleted in organic matter soil habitats. The pool of Acidobacteriia-affiliated sequences, apart from Acidobacteriaceae- and Bryobacteraceae-related reads, had a large proportion of sequences from as-yet-undescribed families, which seem to specialize in degrading plant-derived organic matter. This analysis reveals sandy soils of tundra as a source of novel acidobacterial diversity and provides an insight into the ecological preferences of different taxonomic groups within this phylum.},
}

*Acidobacteria/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Biodiversity
Carbon/analysis
Classification
DNA, Bacterial
Ecosystem
Metagenomics
Nitrogen/analysis
Phylogeny
RNA, Ribosomal, 16S/genetics
Soil/chemistry
*Soil Microbiology
*Tundra

@article {pmid32182269,
year = {2020},
author = {Herren, GL and Habraken, J and Waeyenberge, L and Haegeman, A and Viaene, N and Cougnon, M and Reheul, D and Steel, H and Bert, W},
title = {Effects of synthetic fertilizer and farm compost on soil nematode community in long-term crop rotation plots: A morphological and metabarcoding approach.},
journal = {PloS one},
volume = {15},
number = {3},
pages = {e0230153},
pmid = {32182269},
issn = {1932-6203},
mesh = {Animals ; *Composting ; Crop Production/methods ; Ecosystem ; *Fertilizers ; Food Chain ; Metagenomics ; *Nematoda/anatomy & histology/classification/genetics/growth & development ; Nitrogen Compounds ; Soil/chemistry ; *Soil Microbiology ; },
abstract = {Soil biodiversity plays a key regulation role in the ecosystem services that underpin regenerative sustainable agriculture. It can be impacted by agricultural management techniques, both positively (through measures such as compost application) and negatively (through, for example, application of synthetic nitrogen). As one of the most numerous members of the soil biota, nematodes are well established as indicators for the soil food web. However, compost application also includes the addition of nematodes present in compost and their subsequent survival in soil is unknown. Nematode communities within the compost applied to soil, and nematode communities in the soil of a multi-year rotational cropping field trial in Melle (Belgium) were studied using morphological and metabarcoding techniques. Compost (C) and nitrogen fertilizer (NF) treated plots were compared. Three replicate plots were investigated for each of the following treatments: C application only; C and NF application; NF only; no C and no NF (control). Plots were sampled six times between 2015-2017, before and after C or NF were added each spring and after crop harvest (except for 2017). NF treatment resulted in a significant decrease of fungal feeding and predatory nematodes, while herbivorous nematodes were positively affected. Remarkably, we did not find compost addition to exert any noticeable effects on the soil nematode community. The morphological and metabarcoding data resulted in different results of the nematode community composition. However, trends and patterns in the two data sets were congruent when observed with NMDS plots and using the nematode maturity index. Metabarcoding of individual compost nematode taxa demonstrated that nematodes originating from compost did not persist in soil.},
}

Animals
*Composting
Crop Production/methods
Ecosystem
*Fertilizers
Food Chain
Metagenomics
*Nematoda/anatomy & histology/classification/genetics/growth & development
Nitrogen Compounds
Soil/chemistry
*Soil Microbiology

@article {pmid31452349,
year = {2019},
author = {Xing, R and Gao, QB and Zhang, FQ and Wang, JL and Chen, SL},
title = {Large-scale distribution of bacterial communities in the Qaidam Basin of the Qinghai-Tibet Plateau.},
journal = {MicrobiologyOpen},
volume = {8},
number = {10},
pages = {e909},
pmid = {31452349},
issn = {2045-8827},
mesh = {Bacteria/*classification/*genetics ; Hydrogen-Ion Concentration ; Magnesium/analysis ; Metagenomics ; *Microbiota ; Phylogeny ; Soil/chemistry ; *Soil Microbiology ; Spatial Analysis ; Tibet ; },
abstract = {Many studies have investigated patterns of soil microbial communities over large spatial scales. However, these studies mainly focused on a few sites. Here, we studied the near-surface (0-30 cm) soil microbial communities of 35 soil samples collected from most of the areas of the Qaidam Basin, which is the largest basin on the Qinghai-Tibet Plateau. A total of 32 phyla and 838 genera were detected from all the samples, in which Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were the most dominant and cosmopolitan phyla. The most abundant phyla (relative abundance > 5%) detected in all 35 soil samples were also the most dominant, which could be explained by their great dispersal ability. The microbial community structures correlated strongly with variations in pH and Mg2+ and were distinct between the high Mg2+ content (>20 g/kg) samples and other samples (Acidobacteria, Actinobacteria, and Chloroflexi were significantly less abundant in the high Mg2+ content group, but the abundance of Firmicutes was significantly greater). Finally, the microbial spatial pattern was influenced by both the local environment and spatial distance, but environmental factors were the primary drivers of microbial spatial patterns in the Qaidam Basin.},
}

Bacteria/*classification/*genetics
Hydrogen-Ion Concentration
Magnesium/analysis
Metagenomics
*Microbiota
Phylogeny
Soil/chemistry
*Soil Microbiology
Spatial Analysis
Tibet

@article {pmid31432609,
year = {2019},
author = {Gao, T and Cui, B and Kong, X and Bai, Z and Zhuang, X and Qian, Z},
title = {Investigation of bacterial diversity and pathogen abundances in gibel carp (Carassius auratus gibelio) ponds during a cyprinid herpesvirus 2 outbreak.},
journal = {MicrobiologyOpen},
volume = {8},
number = {10},
pages = {e907},
pmid = {31432609},
issn = {2045-8827},
mesh = {Animals ; Aquaculture ; Bacteria/*classification/*isolation & purification ; Biological Oxygen Demand Analysis ; *Biota ; China ; Disease Outbreaks ; Fish Diseases/virology ; Goldfish/growth & development/virology ; Herpesviridae/isolation & purification ; Herpesviridae Infections/*veterinary/virology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Nitrogen/analysis ; Ponds/*microbiology ; Real-Time Polymerase Chain Reaction ; Temperature ; Water/analysis ; },
abstract = {Cyprinid herpesvirus 2 (CyHV-2) infection is detrimental to gibel carp health and may result in severe economic loss in freshwater aquaculture. However, information regarding the interaction of this pathogen with the aquatic environment is scarce. In this study, quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to determine the abundances of pathogens and bacterial community compositions in two aquaculture ponds in Jiangsu Province, China. The results indicate that the concentrations of six selected pathogens were higher in the water than in the sediment and that these concentrations peaked during disease outbreak. In total, 8,326 and 18,244 operational taxonomic units were identified from water and sediment samples, respectively. The dominant phyla were Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Chlorobi in water samples and Proteobacteria, Firmicutes, Actinobacteria, Chloroflexi, and Bacteroidetes in sediment samples. Bacterial communities were similar at the phylum level in different ponds, although significant differences were observed at the genus level. In addition, bacterial diversity was associated with environmental factors (temperature, chemical oxygen demand, NO2- -N, NO3- -N, and NH4+ -N) in the pond where the outbreak occurred. Additionally, CyHV-2 abundance was positively correlated with dissolved oxygen levels and Aeromonas spp. abundance in pond water (p < .01). This study provides comprehensive insight into the mechanisms of interaction between potential pathogens and the freshwater environment of aquaculture ponds during CyHV-2 disease outbreaks. Furthermore, the results from this study can contribute to improvement of the aquatic environment and establishment of disease prevention and control measures.},
}

Animals
Aquaculture
Bacteria/*classification/*isolation & purification
Biological Oxygen Demand Analysis
*Biota
China
Disease Outbreaks
Fish Diseases/virology
Goldfish/growth & development/virology
Herpesviridae/isolation & purification
Herpesviridae Infections/*veterinary/virology
High-Throughput Nucleotide Sequencing
Metagenomics
Nitrogen/analysis
Ponds/*microbiology
Real-Time Polymerase Chain Reaction
Temperature
Water/analysis

@article {pmid31271530,
year = {2019},
author = {Huang, Q and Lopez, D and Evans, JD},
title = {Shared and unique microbes between Small hive beetles (Aethina tumida) and their honey bee hosts.},
journal = {MicrobiologyOpen},
volume = {8},
number = {10},
pages = {e899},
pmid = {31271530},
issn = {2045-8827},
mesh = {Animals ; Bacteria/classification/genetics ; Bees/*microbiology/*parasitology ; Coleoptera/growth & development/*microbiology ; Insect Vectors/growth & development/*microbiology/*virology ; Metagenomics ; *Microbiota ; RNA Viruses/genetics ; },
abstract = {The small hive beetle (SHB) is an opportunistic parasite that feeds on bee larvae, honey, and pollen. While SHBs can also feed on fruit and other plant products, like its plant-feeding relatives, SHBs prefer to feed on hive resources and only reproduce inside bee colonies. As parasites, SHBs are inevitably exposed to bee-associated microbes, either directly from the bees or from the hive environment. These microbes have unknown impacts on beetles, nor is it known how extensively beetles transfer microbes among their bee hosts. To identify sets of beetle microbes and the transmission of microbes from bees to beetles, a metagenomic analysis was performed. We identified sets of herbivore-associated bacteria, as well as typical bee symbiotic bacteria for pollen digestion, in SHB larvae and adults. Deformed wing virus was highly abundant in beetles, which colonize SHBs as suggested by a controlled feeding trial. Our data suggest SHBs are vectors for pathogen transmission among bees and between colonies. The dispersal of host pathogens by social parasites via floral resources and the hive environment increases the threats of these parasites to honey bees.},
}

Animals
Bacteria/classification/genetics
Bees/*microbiology/*parasitology
Coleoptera/growth & development/*microbiology
Insect Vectors/growth & development/*microbiology/*virology
Metagenomics
*Microbiota
RNA Viruses/genetics

@article {pmid31271529,
year = {2019},
author = {Klemetsen, T and Willassen, NP and Karlsen, CR},
title = {Full-length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis.},
journal = {MicrobiologyOpen},
volume = {8},
number = {10},
pages = {e898},
pmid = {31271529},
issn = {2045-8827},
mesh = {Animals ; Bacteria/*classification/*genetics ; *Biota ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Genes, rRNA ; Intestines/microbiology ; Metagenomics/*methods ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; Salmo salar/*microbiology ; Sequence Analysis, DNA ; Skin/microbiology ; },
abstract = {Understanding fish-microbial relationships may be of great value for fish producers as fish growth, development and welfare are influenced by the microbial community associated with the rearing systems and fish surfaces. Accurate methods to generate and analyze these microbial communities would be an important tool to help improve understanding of microbial effects in the industry. In this study, we performed taxonomic classification and determination of operational taxonomic units on Atlantic salmon microbiota by taking advantage of full-length 16S rRNA gene sequences. Skin mucus was dominated by the genera Flavobacterium and Psychrobacter. Intestinal samples were dominated by the genera Carnobacterium, Aeromonas, Mycoplasma and by sequences assigned to the order Clostridiales. Applying Sanger sequencing on the full-length bacterial 16S rRNA gene from the pool of 46 isolates obtained in this study showed a clear assignment of the PacBio full-length bacterial 16S rRNA gene sequences down to the genus level. One of the bottlenecks in comparing microbial profiles is that different studies use different 16S rRNA gene regions. Comparisons of sequence assignments between full-length and in silico derived variable 16S rRNA gene regions showed different microbial profiles with variable effects between phylogenetic groups and taxonomic ranks.},
}

Animals
Bacteria/*classification/*genetics
*Biota
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Genes, rRNA
Intestines/microbiology
Metagenomics/*methods
Phylogeny
RNA, Ribosomal, 16S/*genetics
Salmo salar/*microbiology
Sequence Analysis, DNA
Skin/microbiology

@article {pmid31250991,
year = {2019},
author = {Kandasamy, S and Liu, EYR and Patterson, G and Saldias, S and Ali, S and Lazarovits, G},
title = {Introducing key microbes from high productive soil transforms native soil microbial community of low productive soil.},
journal = {MicrobiologyOpen},
volume = {8},
number = {10},
pages = {e895},
pmid = {31250991},
issn = {2045-8827},
mesh = {Agriculture/*methods ; Bacteria/*classification/genetics/*growth & development ; Metagenomics ; *Microbiota ; Ontario ; *Soil Microbiology ; Triticum/*growth & development ; Zea mays/*growth & development ; },
abstract = {This study aimed to understand the changes in rhizosphere microbial structure and diversity of an average corn yielding field site soil with the introduced microbial candidates from a high-yielding site. Soils used in this study were from two growers' fields located in Dunnville, Ontario, Canada, where one of the farms has an exceptional high corn yield (G-site soil; ca 20 tons/acre) and the other yields an average crop (H-site soil; 12 tons/acre) (8 years of unpublished A & L data). In growth room experiments using wheat as the indicator crop, calcium alginate beads with microbes composed of Azospirillum lipoferum, Rhizobium leguminosarum, Burkholderia ambifaria, Burkholderia graminis, Burkholderia vietnamiensis, Pseudomonas lurida, Exiguobacterium acetylicum, Kosakonia cowanii, and Paenibacillus polymyxa was introduced into the soil at planting to the average-yielding soil. These bacteria had been isolated from the high-yielding farm soil. Among the nine microbial candidates tested, three (P. polymyxa, E. acetylicum and K. cowanii) significantly impacted the plant health and biometrics in addition to microbial richness and diversity, where the microbial profile became very similar to the high productive G-site soil. One hundred and forty-two bacterial terminal restriction fragments (TRFs) were involved in the community shift and 48 of them showed significant correlation to several interacting soil factors. This study indicates the potential of shifting microbial profiles of average-yielding soils by introducing key candidates from highly productive soils to increase biological soil health.},
}

Agriculture/*methods
Bacteria/*classification/genetics/*growth & development
Metagenomics
*Microbiota
Ontario
*Soil Microbiology
Triticum/*growth & development
Zea mays/*growth & development

@article {pmid31215766,
year = {2019},
author = {Sheng, Y and Cong, J and Lu, H and Yang, L and Liu, Q and Li, D and Zhang, Y},
title = {Broad-leaved forest types affect soil fungal community structure and soil organic carbon contents.},
journal = {MicrobiologyOpen},
volume = {8},
number = {10},
pages = {e874},
pmid = {31215766},
issn = {2045-8827},
mesh = {China ; Forests ; Fungi/classification/genetics ; Metabolic Networks and Pathways/genetics ; Metagenomics ; *Mycobiome ; Organic Chemicals/*analysis ; Plants/*classification ; Soil/*chemistry ; *Soil Microbiology ; },
abstract = {Evergreen broad-leaved (EBF) and deciduous broad-leaved (DBF) forests are two important vegetation types in terrestrial ecosystems that play key roles in sustainable biodiversity and global carbon (C) cycling. However, little is known about their associated soil fungal community and the potential metabolic activities involved in biogeochemical processes. In this study, soil samples were collected from EBF and DBF in Shennongjia Mountain, China, and soil fungal community structure and functional gene diversity analyzed based on combined Illumina MiSeq sequencing with GeoChip technologies. The results showed that soil fungal species richness (p = 0.079) and fungal functional gene diversity (p < 0.01) were higher in DBF than EBF. Zygomycota was the most dominant phylum in both broad-leaved forests, and the most dominant genera found in each forest varied (Umbelopsis dominated in DBF, whereas Mortierella dominated in EBF). A total of 4, 439 soil fungi associated functional gene probes involved in C and nitrogen (N) cycling were detected. Interestingly, the relative abundance of functional genes related to labile C degradation (e.g., starch, pectin, hemicellulose, and cellulose) was significantly higher (p < 0.05) in DBF than EBF, and the functional gene relative abundance involved in C cycling was significantly negatively correlated with soil labile organic C (r = -0.720, p = 0.002). In conclusion, the soil fungal community structure and potential metabolic activity showed marked divergence in different broad-leaved forest types, and the higher relative abundance of functional genes involved in C cycling in DBF may be caused by release of loss of organic C in the soil.},
}

China
Forests
Fungi/classification/genetics
Metabolic Networks and Pathways/genetics
Metagenomics
*Mycobiome
Organic Chemicals/*analysis
Plants/*classification
Soil/*chemistry
*Soil Microbiology

@article {pmid31168933,
year = {2019},
author = {Mizutani, Y and Iehata, S and Mori, T and Oh, R and Fukuzaki, S and Tanaka, R},
title = {Diversity, enumeration, and isolation of Arcobacter spp. in the giant abalone, Haliotis gigantea.},
journal = {MicrobiologyOpen},
volume = {8},
number = {10},
pages = {e890},
pmid = {31168933},
issn = {2045-8827},
mesh = {Animals ; Arcobacter/*classification/genetics/*isolation & purification ; *Biodiversity ; Cluster Analysis ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Gastropoda/*microbiology ; Genotype ; In Situ Hybridization, Fluorescence ; Metagenomics ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Arcobacter have been frequently detected in and isolated from bivalves, but there is very little information on the genus Arcobacter in the abalone, an important fishery resource. This study aimed to investigate the genetic diversity and abundance of bacteria from the genus Arcobacter in the Japanese giant abalone, Haliotis gigantea, using molecular methods such as Arcobacter-specific clone libraries and fluorescence in situ hybridization (FISH). Furthermore, we attempted to isolate the Arcobacter species detected. Twelve genotypes of clones were obtained from Arcobacter-specific clone libraries. These sequences are not classified with any other known Arcobacter species including pathogenic Arcobacter spp., A. butzleri, A. skirrowii, and A. cryaerophilus, commonly isolated or detected from bivalves. From the FISH analysis, we observed that ARC94F-positive cells, presumed to be Arcobacter, accounted for 6.96 ± 0.72% of all EUB338-positive cells. In the culture method, three genotypes of Arcobacter were isolated from abalones. One genotype had a similarity of 99.2%-100.0% to the 16S rRNA gene of Arcobacter marinus, while the others showed only 93.3%-94.3% similarity to other Arcobacter species. These data indicate that abalones carry Arcobacter as a common bacterial genus which includes uncultured species.},
}

Animals
Arcobacter/*classification/genetics/*isolation & purification
*Biodiversity
Cluster Analysis
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Gastropoda/*microbiology
Genotype
In Situ Hybridization, Fluorescence
Metagenomics
*Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid31163139,
year = {2019},
author = {Mariani, S and Baillie, C and Colosimo, G and Riesgo, A},
title = {Sponges as natural environmental DNA samplers.},
journal = {Current biology : CB},
volume = {29},
number = {11},
pages = {R401-R402},
doi = {10.1016/j.cub.2019.04.031},
pmid = {31163139},
issn = {1879-0445},
mesh = {Animals ; Antarctic Regions ; *Aquatic Organisms/genetics ; *Biodiversity ; DNA Barcoding, Taxonomic/instrumentation/*methods ; Environmental DNA/*analysis ; Mediterranean Sea ; Metagenomics/instrumentation ; Oceans and Seas ; *Porifera ; },
abstract = {At a time of unprecedented impacts on marine biodiversity, scientists are rapidly becoming persuaded by the potential of screening large swathes of the oceans through the retrieval, amplification and sequencing of trace DNA fragments left behind by marine organisms; an approach known as 'environmental DNA' (eDNA) [1]. In trying to circumvent the many challenges associated with water filtration and DNA isolation from environmental samples, significant investment is being made in high-tech solutions, such as automated underwater vehicles and robots [2]. Here, instead, we explored a simpler, alternative option, based on the recovery of eDNA from sponges (phylum Porifera), the planet's most effective water-filterers. We obtained sponge samples from Mediterranean and Antarctic surveys, extracted total DNA from their tissues, and obtained tens of thousands of fish DNA reads via metabarcoding, which were able to clearly distinguish samples from the two regions. One Antarctic sample yielded hundreds of reads from chinstrap penguin (Pygoscelis antarcticus) and Weddell seal (Leptonychotes weddellii). We argue that this 'natural sampler DNA' (nsDNA) approach is poised to become a powerful, affordable, universal tool for aquatic biodiversity monitoring globally.},
}

Animals
Antarctic Regions
*Aquatic Organisms/genetics
*Biodiversity
DNA Barcoding, Taxonomic/instrumentation/*methods
Environmental DNA/*analysis
Mediterranean Sea
Metagenomics/instrumentation
Oceans and Seas
*Porifera

@article {pmid31005411,
year = {2019},
author = {Hollister, EB and Oezguen, N and Chumpitazi, BP and Luna, RA and Weidler, EM and Rubio-Gonzales, M and Dahdouli, M and Cope, JL and Mistretta, TA and Raza, S and Metcalf, GA and Muzny, DM and Gibbs, RA and Petrosino, JF and Heitkemper, M and Savidge, TC and Shulman, RJ and Versalovic, J},
title = {Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {21},
number = {3},
pages = {449-461},
pmid = {31005411},
issn = {1943-7811},
support = {U01 AI124290/AI/NIAID NIH HHS/United States ; K23 DK101688/DK/NIDDK NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; R03 DK117219/DK/NIDDK NIH HHS/United States ; R01 NR005337/NR/NINR NIH HHS/United States ; },
mesh = {Abdominal Pain/etiology/microbiology ; Bacteria/genetics ; Case-Control Studies ; Child ; Feces/microbiology ; Female ; Gastrointestinal Tract/microbiology ; Genomics ; Humans ; Irritable Bowel Syndrome/complications/*microbiology ; Male ; Metabolome ; *Microbiota ; Multivariate Analysis ; Principal Component Analysis ; Statistics, Nonparametric ; },
abstract = {Accurate diagnosis and stratification of children with irritable bowel syndrome (IBS) remain challenging. Given the central role of recurrent abdominal pain in IBS, we evaluated the relationships of pediatric IBS and abdominal pain with intestinal microbes and fecal metabolites using a comprehensive clinical characterization and multiomics strategy. Using rigorous clinical phenotyping, we identified preadolescent children (aged 7 to 12 years) with Rome III IBS (n = 23) and healthy controls (n = 22) and characterized their fecal microbial communities using whole-genome shotgun metagenomics and global unbiased fecal metabolomic profiling. Correlation-based approaches and machine learning algorithms identified associations between microbes, metabolites, and abdominal pain. IBS cases differed from controls with respect to key bacterial taxa (eg, Flavonifractor plautii and Lachnospiraceae bacterium 7_1_58FAA), metagenomic functions (eg, carbohydrate metabolism and amino acid metabolism), and higher-order metabolites (eg, secondary bile acids, sterols, and steroid-like compounds). Significant associations between abdominal pain frequency and severity and intestinal microbial features were identified. A random forest classifier built on metagenomic and metabolic markers successfully distinguished IBS cases from controls (area under the curve, 0.93). Leveraging multiple lines of evidence, intestinal microbes, genes/pathways, and metabolites were associated with IBS, and these features were capable of distinguishing children with IBS from healthy children. These multi-omics features, and their links to childhood IBS coupled with nutritional interventions, may lead to new microbiome-guided diagnostic and therapeutic strategies.},
}

Abdominal Pain/etiology/microbiology
Bacteria/genetics
Case-Control Studies
Child
Feces/microbiology
Female
Gastrointestinal Tract/microbiology
Genomics
Humans
Irritable Bowel Syndrome/complications/*microbiology
Male
Metabolome
*Microbiota
Multivariate Analysis
Principal Component Analysis
Statistics, Nonparametric

@article {pmid30640553,
year = {2019},
author = {Ozkan, J and Willcox, MD},
title = {The Ocular Microbiome: Molecular Characterisation of a Unique and Low Microbial Environment.},
journal = {Current eye research},
volume = {44},
number = {7},
pages = {685-694},
doi = {10.1080/02713683.2019.1570526},
pmid = {30640553},
issn = {1460-2202},
mesh = {Bacteria/*isolation & purification ; Conjunctiva/*microbiology ; Eyelids/*microbiology ; Genome, Bacterial/*genetics ; Humans ; Metagenomics ; Microbiota/*genetics ; RNA, Ribosomal, 16S/*genetics ; },
abstract = {Aim: The ocular surface is continually exposed to bacteria from the environment and traditional culture-based microbiological studies have isolated a low diversity of microorganisms from this region. The use of culture-independent methods to define the ocular microbiome, primarily involving 16S ribosomal RNA gene sequencing studies, have shown that the microbial communities present on the ocular surface have a greater diversity than previously reported. Method: A review of the literature on ocular microbiome research in health and disease. Results: Molecular techniques have been used to investigate the effect of contact lens wear and disease on the microbiota of the ocular surface and eyelids and the immunoregulatory role of the ocular surface microbiota. Studies have shown that compositional changes in the microbiota occur in ocular surface disorders such as blepharitis, trachoma and dry eye and also suggest a role of the ocular and non-ocular microbiome in retinal disease including age-related macular degeneration, glaucoma, uveitis and diabetic retinopathy. However, ocular microbiome studies need to recognise the potential for contamination to impact findings and carefully control each stage of the experimental procedure and to utilise statistical methods to identify contamination signals. Conclusion: The healthy ocular surface is characterised by a relatively stable, comparatively low diversity microbiome with recent findings that the bacteria of the ocular surface appear to have a role in maintaining homeostasis by modulating immune function.},
}

Bacteria/*isolation & purification
Conjunctiva/*microbiology
Eyelids/*microbiology
Genome, Bacterial/*genetics
Humans
Metagenomics
Microbiota/*genetics
RNA, Ribosomal, 16S/*genetics

@article {pmid30885720,
year = {2019},
author = {LaPierre, N and Ju, CJ and Zhou, G and Wang, W},
title = {MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction.},
journal = {Methods (San Diego, Calif.)},
volume = {166},
number = {},
pages = {74-82},
pmid = {30885720},
issn = {1095-9130},
support = {R01 GM115833/GM/NIGMS NIH HHS/United States ; T32 EB016640/EB/NIBIB NIH HHS/United States ; },
mesh = {Algorithms ; *Deep Learning ; Diabetes Mellitus, Type 2/*genetics/microbiology ; Humans ; Machine Learning/statistics & numerical data ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/genetics ; Obesity/*genetics/microbiology ; },
abstract = {The human microbiome plays a number of critical roles, impacting almost every aspect of human health and well-being. Conditions in the microbiome have been linked to a number of significant diseases. Additionally, revolutions in sequencing technology have led to a rapid increase in publicly-available sequencing data. Consequently, there have been growing efforts to predict disease status from metagenomic sequencing data, with a proliferation of new approaches in the last few years. Some of these efforts have explored utilizing a powerful form of machine learning called deep learning, which has been applied successfully in several biological domains. Here, we review some of these methods and the algorithms that they are based on, with a particular focus on deep learning methods. We also perform a deeper analysis of Type 2 Diabetes and obesity datasets that have eluded improved results, using a variety of machine learning and feature extraction methods. We conclude by offering perspectives on study design considerations that may impact results and future directions the field can take to improve results and offer more valuable conclusions. The scripts and extracted features for the analyses conducted in this paper are available via GitHub:https://github.com/nlapier2/metapheno.},
}

Algorithms
*Deep Learning
Diabetes Mellitus, Type 2/*genetics/microbiology
Humans
Machine Learning/statistics & numerical data
Metagenome/*genetics
Metagenomics/methods
Microbiota/genetics
Obesity/*genetics/microbiology

@article {pmid32417556,
year = {2020},
author = {Gallego, S and Barkay, T and Fahrenfeld, NL},
title = {Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells.},
journal = {The Science of the total environment},
volume = {732},
number = {},
pages = {138865},
doi = {10.1016/j.scitotenv.2020.138865},
pmid = {32417556},
issn = {1879-1026},
mesh = {Anti-Bacterial Agents ; Bacterial Proteins ; Carbon-Oxygen Ligases ; In Situ Hybridization, Fluorescence ; Microbial Sensitivity Tests ; *Microbiota ; Phylogeny ; Waste Water ; },
abstract = {Failure to understand the microbial ecology driving the proliferation of antibiotic resistance in the environment prevents us from developing strategies to limit the spread of antibiotic resistant infectious disease. In this study, we developed for the first time a tyramide signal amplification-fluorescence in situ hybridization-fluorescence-activated cell sorting protocol (TSA-FISH-FACS) for the characterization of all vanA carrying bacteria in wastewater samples. Firstly, we validated the TSA-FISH protocol through microscopy in pure cultures and wastewater influent. Then, samples were sorted and quantified by FACS and qPCR. Significantly higher percentage tagging of cells was detected in vanA carrying pure cultures and wastewater samples spiked with vanA carrying cells as compared to vanA negative Gram positive strains and non-spiked wastewater samples respectively. qPCR analysis targeting vanZ, a regulating gene in the vanA cluster, showed its relative abundance was significantly greater in Enterococcus faecium ATCC 700221-spiked and positively sorted samples compared to the E. faecium spiked and negatively sorted samples. Phylogenetic analysis was then performed. Although further efforts are needed to overcome technical problems, we have, for the first time, demonstrated sorting bacterial-cells carrying antibiotic resistance genes from wastewater samples through a TSA-FISH-FACS protocol and provided insight into the microbial ecology of vancomycin resistant bacteria. Future potential applications using this approach will include the separation of members of an environmental microbial community (cultured and hard-to-culture) to allow for metagenomics on single cells or, in the case of clumping, targeting a smaller portion of the community with a priori knowledge that the target gene is present.},
}

Anti-Bacterial Agents
Bacterial Proteins
Carbon-Oxygen Ligases
In Situ Hybridization, Fluorescence
Microbial Sensitivity Tests
*Microbiota
Phylogeny
Waste Water

@article {pmid31750259,
year = {2019},
author = {Lin, DM and Koskella, B and Ritz, NL and Lin, D and Carroll-Portillo, A and Lin, HC},
title = {Transplanting Fecal Virus-Like Particles Reduces High-Fat Diet-Induced Small Intestinal Bacterial Overgrowth in Mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {348},
pmid = {31750259},
issn = {2235-2988},
mesh = {Animals ; Bacterial Load ; Bacteriophages/isolation & purification/ultrastructure ; Clostridium difficile ; Diet, High-Fat/*adverse effects ; Disease Models, Animal ; Dysbiosis/*therapy ; Enterocolitis, Pseudomembranous/microbiology/therapy ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Intestine, Small/*microbiology ; Metagenomics/methods ; Mice ; RNA, Ribosomal, 16S ; Treatment Outcome ; },
abstract = {Fecal microbiota transplantation (FMT) is an effective tool for treating Clostridium difficile infection in the setting of dysbiosis of the intestinal microbiome. FMT for other forms of human disorders linked to dysbiosis have been less effective. The fecal microbiota contains a high density of virus-like particles (VLP), up to 90% of which are bacteriophages, thought to have a role in regulating gut bacterial populations. We hypothesized that transplantation of the phage-containing fecal VLP fraction may reduce bacterial density in the dysbiotic setting of small intestinal bacterial overgrowth (SIBO). In an experiment using fecal transplantation, we compared the effect of the fecal VLP fraction (bacteria removed) against "Whole" FMT (bacteria intact) on the ileal microbiome. Recipients were either treated with a 30-day high-fat diet (HFD) as a model of dysbiosis to induce SIBO or were on a standard diet (SD). We observed that transplantation of fecal VLPs from donors on a HFD was sufficient to alter the ileal microbiota, but the effect was dependent on diet of the recipient. In recipients on a HFD, ileal bacterial density was reduced. In recipients on a SD, the ileal microbiome transitioned toward the composition associated with a HFD. In both recipient groups, transplantation of fecal VLP fraction alone produced the same outcome as whole FMT. Neither treatment altered expression of antimicrobial peptides. These findings demonstrated a potential role of VLPs, likely phages, for modifying the gut microbiome during dysbiosis.},
}

Animals
Bacterial Load
Bacteriophages/isolation & purification/ultrastructure
Clostridium difficile
Diet, High-Fat/*adverse effects
Disease Models, Animal
Dysbiosis/*therapy
Enterocolitis, Pseudomembranous/microbiology/therapy
*Fecal Microbiota Transplantation/methods
*Gastrointestinal Microbiome
Intestine, Small/*microbiology
Metagenomics/methods
Mice
RNA, Ribosomal, 16S
Treatment Outcome

@article {pmid31737256,
year = {2019},
author = {Thang, MWC and Chua, XY and Price, G and Gorse, D and Field, MA},
title = {MetaDEGalaxy: Galaxy workflow for differential abundance analysis of 16s metagenomic data.},
journal = {F1000Research},
volume = {8},
number = {},
pages = {726},
pmid = {31737256},
issn = {2046-1402},
mesh = {Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; *Software ; *Workflow ; },
abstract = {Metagenomic sequencing is an increasingly common tool in environmental and biomedical sciences. While software for detailing the composition of microbial communities using 16S rRNA marker genes is relatively mature, increasingly researchers are interested in identifying changes exhibited within microbial communities under differing environmental conditions. In order to gain maximum value from metagenomic sequence data we must improve the existing analysis environment by providing accessible and scalable computational workflows able to generate reproducible results. Here we describe a complete end-to-end open-source metagenomics workflow running within Galaxy for 16S differential abundance analysis. The workflow accepts 454 or Illumina sequence data (either overlapping or non-overlapping paired end reads) and outputs lists of the operational taxonomic unit (OTUs) exhibiting the greatest change under differing conditions. A range of analysis steps and graphing options are available giving users a high-level of control over their data and analyses. Additionally, users are able to input complex sample-specific metadata information which can be incorporated into differential analysis and used for grouping / colouring within graphs. Detailed tutorials containing sample data and existing workflows are available for three different input types: overlapping and non-overlapping read pairs as well as for pre-generated Biological Observation Matrix (BIOM) files. Using the Galaxy platform we developed MetaDEGalaxy, a complete metagenomics differential abundance analysis workflow. MetaDEGalaxy is designed for bench scientists working with 16S data who are interested in comparative metagenomics. MetaDEGalaxy builds on momentum within the wider Galaxy metagenomics community with the hope that more tools will be added as existing methods mature.},
}

Metagenomics
*Microbiota
RNA, Ribosomal, 16S
*Software
*Workflow

@article {pmid31681625,
year = {2019},
author = {Acharya, A and Chen, T and Chan, Y and Watt, RM and Jin, L and Mattheos, N},
title = {Species-Level Salivary Microbial Indicators of Well-Resolved Periodontitis: A Preliminary Investigation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {347},
pmid = {31681625},
issn = {2235-2988},
mesh = {Adult ; Aged ; Biodiversity ; Case-Control Studies ; Computational Biology ; DNA, Bacterial ; Female ; High-Throughput Nucleotide Sequencing ; Hong Kong/epidemiology ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota ; Middle Aged ; Periodontitis/epidemiology/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/*microbiology ; },
abstract = {Objective: To profile the salivary microbiomes of a Hong Kong Chinese cohort at a species-level resolution and determine species that discriminated clinically resolved periodontitis from periodontally healthy cases. Methods: Salivary microbiomes of 35 Hong Kong Chinese subjects' under routine supportive dental care were analyzed. All subjects had been treated for any dental caries or periodontal disease with all restorative treatment completed at least 1 year ago and had ≤3 residual pockets. They were categorized based on a past diagnosis of chronic periodontitis into "healthy" (H) or "periodontitis" (P) categories. Unstimulated whole saliva was collected, genomic DNA was isolated, and high throughput Illumina MiSeq sequencing of 16S rRNA (V3-V4) gene amplicons was performed. The sequences were assigned taxonomy at the species level by using a BLASTN based algorithm that used a combined reference database of HOMD RefSeqV14.51, HOMD RefSeqExtended V1.1 and GreenGeneGold. Species-level OTUs were subjected to downstream analysis in QIIME and R. For P and H group comparisons, community diversity measures were compared, differentially abundant species were determined using DESeq2, and disease indicator species were determined using multi-level pattern analysis within the R package "indicspecies." Results: P subjects were significantly older than H subjects (p = 0.003) but not significantly different in their BOP scores (p = 0.82). No significant differences were noted in alpha diversity measures after adjusting for age, gender, and BOP or in the beta diversity estimates. Four species; Treponema sp. oral taxon 237, TM7 sp. Oral Taxon A56, Prevotella sp. oral taxon 314, Prevotella sp. oral taxon 304, and Capnocytophaga leadbetteri were significantly more abundant in P than in the H group. Indicator species analysis showed 7 significant indicators species of P group. Fusobacterium sp oral taxon 370 was the sole positive indicator of P group (positive predictive value = 0.9, p = 0.04). Significant indicators of the H category were Leptotrichia buccalis, Corynebacterium matruchotii, Leptotrichia hofstadii, and Streptococcus intermedius. Conclusion: This exploratory study showed salivary microbial species could discriminate treated, well-maintained chronic periodontitis from healthy controls with similar gingival inflammation levels. The findings suggest that certain salivary microbiome features may identify periodontitis-susceptible individuals despite clinical disease resolution.},
}

Adult
Aged
Biodiversity
Case-Control Studies
Computational Biology
DNA, Bacterial
Female
High-Throughput Nucleotide Sequencing
Hong Kong/epidemiology
Humans
Male
Metagenome
Metagenomics/methods
*Microbiota
Middle Aged
Periodontitis/epidemiology/*microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Saliva/*microbiology

@article {pmid31681624,
year = {2019},
author = {Zhu, S and Liu, S and Li, H and Zhang, Z and Zhang, Q and Chen, L and Zhao, Y and Chen, Y and Gu, J and Min, L and Zhang, S},
title = {Identification of Gut Microbiota and Metabolites Signature in Patients With Irritable Bowel Syndrome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {346},
pmid = {31681624},
issn = {2235-2988},
mesh = {Case-Control Studies ; Computational Biology/methods ; Disease Susceptibility ; Energy Metabolism ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Irritable Bowel Syndrome/diagnosis/*etiology/*metabolism ; Male ; *Metabolome ; *Metabolomics/methods ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; },
abstract = {Background and Aims: Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder. However, the underlying mechanism of IBS is not fully understood. The aim of this study was to investigate potential mechanism and novel biomarkers of IBS through evaluation of the metabolomic and microbiologic profile. Methods: Fecal samples were collected from 15 irritable bowel syndrome patients and 15 healthy controls. By using gas chromatography coupled to time-of-flight mass spectrometry (GC-TOFMS) and 16S rDNA amplicon sequencing, fecal metabolites and microbiota of healthy controls and the IBS patients were measured. Results: IBS patients had a significantly differential metabolite profile as compared to healthy controls, and 4 clusters with 31 metabolites, including a group of amino acids and fatty acids, were significantly up-regulated as compared to the healthy controls. In addition, 19 microbes were significantly up-regulated, and 12 microbes were down-regulated in the IBS group, when compared with the healthy controls. Some clusters of fecal metabolites or microorganisms were significantly correlated with the severity of IBS symptoms, such as the frequency of abdominal pain/discomfort and the number of bowel movements. Correlation of the metabolite levels with abundances of microbial genera showed some statistically significant metabolite-microbe associations. Four differentially abundant amino acids clustered together were positively correlated with some microbes, including Lachnospira, Clostridium, and so on. Conclusion: The finding of this study puts a global perspective on metabolomics and microbiota profiling in IBS patients and provides a theoretical basis for future research on pathophysiology of IBS.},
}

Case-Control Studies
Computational Biology/methods
Disease Susceptibility
Energy Metabolism
Feces/microbiology
Female
*Gastrointestinal Microbiome
Humans
Irritable Bowel Syndrome/diagnosis/*etiology/*metabolism
Male
*Metabolome
*Metabolomics/methods
Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Severity of Illness Index
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

@article {pmid31637220,
year = {2019},
author = {Kolbe, AR and Castro-Nallar, E and Preciado, D and Pérez-Losada, M},
title = {Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {339},
pmid = {31637220},
issn = {2235-2988},
mesh = {Biodiversity ; Child ; Child, Preschool ; Chronic Disease ; Ear, Middle/*microbiology ; Female ; Humans ; Infant ; Male ; Metagenomics ; *Microbiota ; Otitis Media with Effusion/metabolism/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S ; Respiratory Tract Diseases/*etiology/metabolism ; },
abstract = {Chronic otitis media with effusion (COME) is a common childhood disease characterized by an accumulation of fluid behind the eardrum. COME often requires surgical intervention and can also lead to significant hearing loss and subsequent learning disabilities. Recent characterization of the middle ear fluid (MEF) microbiome in pediatric patients has led to an improved understanding of the microbiota present in the middle ear during COME. However, it is not currently known how the MEF microbiome might vary due to other conditions, particularly respiratory disorders. Here, we apply an amplicon sequence variant (ASV) pipeline to MEF 16S rRNA high-throughput sequencing data from 50 children with COME (ages 3-176 months) undergoing tube placement. We achieve a more detailed taxonomic resolution than previously reported, including species and genus level resolution. Additionally, we provide the first report of the functional roles of the MEF microbiome and demonstrate that despite high taxonomic diversity, the functional capacity of the MEF microbiome remains uniform between patients. Furthermore, we analyze microbiome differences between children with COME with and without a history of lower airway disease (i.e., asthma or bronchiolitis). The MEF microbiome was less diverse in participants with lower airway disease than in patients without, and phylogenetic β-diversity (weighted UniFrac) was significantly different based on lower airway disease status. Differential abundance between patients with lower airway disease and those without was observed for the genera Haemophilus, Moraxella, Staphylococcus, Alloiococcus, and Turicella. These findings support previous suggestions of a link between COME and respiratory illnesses and emphasize the need for future study of the middle ear and respiratory tract microbiomes in diseases such as asthma and bronchiolitis.},
}

Biodiversity
Child
Child, Preschool
Chronic Disease
Ear, Middle/*microbiology
Female
Humans
Infant
Male
Metagenomics
*Microbiota
Otitis Media with Effusion/metabolism/*microbiology
Phylogeny
RNA, Ribosomal, 16S
Respiratory Tract Diseases/*etiology/metabolism

@article {pmid31601676,
year = {2019},
author = {Moeller, JB and Leonardi, I and Schlosser, A and Flamar, AL and Bessman, NJ and Putzel, GG and Thomsen, T and Hammond, M and Jepsen, CS and Skjødt, K and Füchtbauer, EM and Farber, DL and Sorensen, GL and Iliev, ID and Holmskov, U and Artis, D},
title = {Modulation of the fungal mycobiome is regulated by the chitin-binding receptor FIBCD1.},
journal = {The Journal of experimental medicine},
volume = {216},
number = {12},
pages = {2689-2700},
pmid = {31601676},
issn = {1540-9538},
support = {R01 AI074878/AI/NIAID NIH HHS/United States ; R01 AI095466/AI/NIAID NIH HHS/United States ; U01 AI095608/AI/NIAID NIH HHS/United States ; R56 AI137157/AI/NIAID NIH HHS/United States ; R01 DK113136/DK/NIDDK NIH HHS/United States ; F32 AI124517/AI/NIAID NIH HHS/United States ; R01 AI102942/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Chitin/metabolism ; DNA, Ribosomal Spacer ; Disease Models, Animal ; Enteritis/etiology/metabolism/pathology ; Fungi/*physiology ; Gastrointestinal Microbiome ; Gene Expression ; Humans ; Intestinal Mucosa/metabolism/microbiology/pathology ; Metagenomics ; Mice ; Mice, Transgenic ; *Microbial Interactions ; *Mycobiome ; Protein Binding ; RNA, Ribosomal, 16S ; Receptors, Cell Surface/*metabolism ; },
abstract = {Host-microbiota interactions are critical in regulating mammalian health and disease. In addition to bacteria, parasites, and viruses, beneficial communities of fungi (the mycobiome) are important modulators of immune- and tissue-homeostasis. Chitin is a major component of the fungal cell wall, and fibrinogen C containing domain 1 (FIBCD1) is a chitin-binding protein; however, the role of this molecule in influencing host-mycobiome interactions in vivo has never been examined. Here, we identify direct binding of FIBCD1 to intestinal-derived fungi and demonstrate that epithelial-specific expression of FIBCD1 results in significantly reduced fungal colonization and amelioration of fungal-driven intestinal inflammation. Collectively, these results identify FIBCD1 as a previously unrecognized microbial pattern recognition receptor through which intestinal epithelial cells can recognize and control fungal colonization, limit fungal dysbiosis, and dampen intestinal inflammation.},
}

Animals
Chitin/metabolism
DNA, Ribosomal Spacer
Disease Models, Animal
Enteritis/etiology/metabolism/pathology
Fungi/*physiology
Gastrointestinal Microbiome
Gene Expression
Humans
Intestinal Mucosa/metabolism/microbiology/pathology
Metagenomics
Mice
Mice, Transgenic
*Microbial Interactions
*Mycobiome
Protein Binding
RNA, Ribosomal, 16S
Receptors, Cell Surface/*metabolism

@article {pmid31510682,
year = {2019},
author = {Valdes, C and Stebliankin, V and Narasimhan, G},
title = {Large scale microbiome profiling in the cloud.},
journal = {Bioinformatics (Oxford, England)},
volume = {35},
number = {14},
pages = {i13-i22},
pmid = {31510682},
issn = {1367-4811},
support = {R15 AI128714/AI/NIAID NIH HHS/United States ; },
mesh = {Algorithms ; *Cloud Computing ; *High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; Sequence Analysis, DNA ; Software ; },
abstract = {MOTIVATION: Bacterial metagenomics profiling for metagenomic whole sequencing (mWGS) usually starts by aligning sequencing reads to a collection of reference genomes. Current profiling tools are designed to work against a small representative collection of genomes, and do not scale very well to larger reference genome collections. However, large reference genome collections are capable of providing a more complete and accurate profile of the bacterial population in a metagenomics dataset. In this paper, we discuss a scalable, efficient and affordable approach to this problem, bringing big data solutions within the reach of laboratories with modest resources.

RESULTS: We developed Flint, a metagenomics profiling pipeline that is built on top of the Apache Spark framework, and is designed for fast real-time profiling of metagenomic samples against a large collection of reference genomes. Flint takes advantage of Spark's built-in parallelism and streaming engine architecture to quickly map reads against a large (170 GB) reference collection of 43 552 bacterial genomes from Ensembl. Flint runs on Amazon's Elastic MapReduce service, and is able to profile 1 million Illumina paired-end reads against over 40 K genomes on 64 machines in 67 s-an order of magnitude faster than the state of the art, while using a much larger reference collection. Streaming the sequencing reads allows this approach to sustain mapping rates of 55 million reads per hour, at an hourly cluster cost of $8.00 USD, while avoiding the necessity of storing large quantities of intermediate alignments.

Flint is open source software, available under the MIT License (MIT). Source code is available at https://github.com/camilo-v/flint.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

Algorithms
*Cloud Computing
*High-Throughput Nucleotide Sequencing
Metagenomics
*Microbiota
Sequence Analysis, DNA
Software

@article {pmid31484218,
year = {2019},
author = {Goodman, KR and Prost, S and Bi, K and Brewer, MS and Gillespie, RG},
title = {Host and geography together drive early adaptive radiation of Hawaiian planthoppers.},
journal = {Molecular ecology},
volume = {28},
number = {19},
pages = {4513-4528},
pmid = {31484218},
issn = {1365-294X},
support = {S10 OD018174/OD/NIH HHS/United States ; },
mesh = {*Adaptation, Physiological ; Animals ; *Computational Biology ; Ecology ; Exons/genetics ; Genetics, Population ; Geography ; Hawaii ; Hemiptera/genetics/*physiology ; Host Specificity ; Islands ; Male ; *Metagenomics ; Phylogeny ; Plants/*parasitology ; Species Specificity ; *Transcriptome ; },
abstract = {The interactions between insects and their plant host have been implicated in driving diversification of both players. Early arguments highlighted the role of ecological opportunity, with the idea that insects "escape and radiate" on new hosts, with subsequent hypotheses focusing on the interplay between host shifting and host tracking, coupled with isolation and fusion, in generating diversity. Because it is rarely possible to capture the initial stages of diversification, it is particularly difficult to ascertain the relative roles of geographic isolation versus host shifts in initiating the process. The current study examines genetic diversity between populations and hosts within a single species of endemic Hawaiian planthopper, Nesosydne umbratica (Hemiptera, Delphacidae). Given that the species was known as a host generalist occupying unrelated hosts, Clermontia (Campanulaceae) and Pipturus (Urticaceae), we set out to determine the relative importance of geography and host in structuring populations in the early stages of differentiation on the youngest islands of the Hawaiian chain. Results from extensive exon capture data showed that N. umbratica is highly structured, both by geography, with discrete populations on each volcano, and by host plant, with parallel radiations on Clermontia and Pipturus leading to extensive co-occurrence. The marked genetic structure suggests that populations can readily become established on novel hosts provided opportunity; subsequent adaptation allows monopolization of the new host. The results support the role of geographic isolation in structuring populations and with host shifts occurring as discrete events that facilitate subsequent parallel geographic range expansion.},
}

*Adaptation, Physiological
Animals
*Computational Biology
Ecology
Exons/genetics
Genetics, Population
Geography
Hawaii
Hemiptera/genetics/*physiology
Host Specificity
Islands
Male
*Metagenomics
Phylogeny
Plants/*parasitology
Species Specificity
*Transcriptome

@article {pmid31344223,
year = {2019},
author = {Willis, C and Desai, D and LaRoche, J},
title = {Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic.},
journal = {FEMS microbiology letters},
volume = {366},
number = {13},
pages = {},
pmid = {31344223},
issn = {1574-6968},
mesh = {Aquatic Organisms/*classification/*genetics ; Archaea/classification/genetics ; Atlantic Ocean ; Bacteria/classification/genetics ; Biodiversity ; Metagenomics/methods ; *Microbiota ; Phylogeny ; *RNA, Ribosomal, 16S ; },
abstract = {Marine microbes play essential roles in global energy and nutrient cycles. A primary method of determining their diversity and distribution is through sequencing of 16S ribosomal RNA genes from environmental samples. However, the perceived community composition may vary significantly based on differences in methodology, including choice of 16S variable region(s). This study investigated the influence of 16S variable region selection (V4-V5 or V6-V8) on perceived community composition and diversity for bacteria, Archaea and chloroplasts by tag-Illumina sequencing. We used 24 samples from the photic zone of the Scotian Shelf, northwest Atlantic, collected during a spring phytoplankton bloom. Taxonomic assignment and community composition varied greatly depending on the choice of variable regions while observed patterns of beta diversity were reproducible between variable regions. V4-V5 was considered the preferred variable region for future studies based on its superior recognition of Archaea, which has received little attention in bloom dynamics. The V6-V8 region captured more of the bacterial diversity, including the abundant SAR11 clades and, to a lesser extent, that of chloroplasts. However, the magnitude of difference between variable regions for bacteria and chloroplast was less than for Archaea.},
}

Aquatic Organisms/*classification/*genetics
Archaea/classification/genetics
Atlantic Ocean
Bacteria/classification/genetics
Biodiversity
Metagenomics/methods
*Microbiota
Phylogeny
*RNA, Ribosomal, 16S

@article {pmid31310663,
year = {2019},
author = {Feng, S and Liu, Y and Huang, Y and Zhao, J and Zhang, H and Zhai, Q and Chen, W},
title = {Influence of oral administration of Akkermansia muciniphila on the tissue distribution and gut microbiota composition of acute and chronic cadmium exposure mice.},
journal = {FEMS microbiology letters},
volume = {366},
number = {13},
pages = {},
doi = {10.1093/femsle/fnz160},
pmid = {31310663},
issn = {1574-6968},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Administration, Oral ; Animals ; Biodiversity ; Cadmium/*administration & dosage/adverse effects ; Dietary Exposure/*adverse effects ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Male ; Metagenomics ; Mice ; *Probiotics/administration & dosage ; RNA, Ribosomal, 16S ; Tissue Distribution ; *Verrucomicrobia ; },
abstract = {Cadmium (Cd) contamination is a serious food safety problem. Acute and chronic Cd exposure changes the gut microbiota composition and damages the gut barrier function. Akkermansia muciniphila (AKK), a promising candidate for the next-generation probiotics, has been reported to protect the mucus layer in the colon and significantly decrease the effects of Cd exposure in mice. Thus, the mice model was adopted to investigate the influence of oral administration of AKK on the toxic distribution and changes of gut microbiota composition caused by acute and chronic Cd exposure. In both acute and chronic Cd exposure experiments, 40 mice were divided into four groups (normal group, AKK group, Cd group and Cd plus AKK group). The Cd contents in feces and tissues were measured by a flame or graphite furnace atomic absorption spectrophotometer and gut microbiota composition was determined through 16S rRNA gene sequencing. The results showed that the gavage of AKK could not reduce the accumulation of Cd in the liver and kidney. The oral administration of AKK showed a certain influence on the gut microbiota composition of acute Cd exposure mice and limited influence on that of chronic Cd exposure mice. These results indicate the failure of AKK, as a potential protective probiotic, to reduce Cd toxicity. However, the gavage of AKK did have an influence on the gut microbiota composition of normal mice, especially on some genera in the Clostridiales order. Besides, when considering AKK's probiotic potential and its effects on host health and disease, we should take into consideration its influence on the gut microbiota composition and micro-environment.},
}

Administration, Oral
Animals
Biodiversity
Cadmium/*administration & dosage/adverse effects
Dietary Exposure/*adverse effects
Disease Models, Animal
*Gastrointestinal Microbiome
Male
Metagenomics
Mice
*Probiotics/administration & dosage
RNA, Ribosomal, 16S
Tissue Distribution
*Verrucomicrobia

@article {pmid30877015,
year = {2019},
author = {Gómez-Acata, ES and Centeno, CM and Falcón, LI},
title = {Methods for extracting 'omes from microbialites.},
journal = {Journal of microbiological methods},
volume = {160},
number = {},
pages = {1-10},
doi = {10.1016/j.mimet.2019.02.014},
pmid = {30877015},
issn = {1872-8359},
mesh = {DNA, Bacterial/*isolation & purification ; Geologic Sediments/*microbiology ; Metagenome ; *Microbiota/genetics/physiology ; RNA, Bacterial/*isolation & purification ; Viruses/*isolation & purification ; },
abstract = {Microbialites are organo-sedimentary structures formed by complex microbial communities that interact with abiotic factors to form carbonate rich fabrics. Extraction of DNA or total RNA from microbialites can be difficult because of the high carbonate mineral concentration and exopolymeric substances. The methods employed until now include substances such as cetyltrimethylammonium bromide, sodium dodecyl sulfate, xanthogenate, lysozyme and proteinase K, as well as mechanical disruption. Additionally, several commercial kits have been used to improve DNA and total RNA extraction. This minireview presents different methods applied for DNA and RNA extraction from microbialites and discusses their advantages and disadvantages. Moreover, extraction of all 'omes (DNA, RNA, Protein, Lipids, polar metabolites) using multiomic extraction methods (MPlex), as well as the state of art for extraction of viruses from microbialites, are also discussed.},
}

DNA, Bacterial/*isolation & purification
Geologic Sediments/*microbiology
Metagenome
*Microbiota/genetics/physiology
RNA, Bacterial/*isolation & purification
Viruses/*isolation & purification

@article {pmid32534383,
year = {2020},
author = {Muccee, F and Ejaz, S},
title = {Whole genome shotgun sequencing of POPs degrading bacterial community dwelling tannery effluents and petrol contaminated soil.},
journal = {Microbiological research},
volume = {238},
number = {},
pages = {126504},
doi = {10.1016/j.micres.2020.126504},
pmid = {32534383},
issn = {1618-0623},
abstract = {The present study involved identification of genes which are present in the genome of native bacteria to make them effective tools for bioremediation of persistent organic pollutants (POPs). During this study, forty-one POPs (naphthalene, toluene and petrol) metabolizing bacteria were isolated from tannery effluents and petrol contaminated soil samples by successive enrichment culturing. The taxonomic diversity and gene repertoire conferring POPs degradation ability to the isolated bacterial community were studied through whole genome shotgun sequencing of DNA consortium. The DNA consortium contained equimolar concentration of DNA extracted from each bacterial isolate using organic method. To add a double layer of confirmation the established DNA consortium was subjected to 16S rRNA metagenome sequencing and whole genome shotgun sequencing analysis. Biodiversity analysis revealed that the consortium was composed of phyla Firmicutes (80 %), Proteobacteria (12 %) and Actinobacteria (5%). Genera found included Bacillus (45 %), Burkholderia (25 %), Brevibacillus (9%) and Geobacillus (4%). Functional profiling of consortium helped us to identify genes associated with degradation pathways of a variety of organic compounds including toluene, naphthalene, caprolactam, benzoate, aminobenzoate, xylene, 4-hydroxyphenyl acetic acid, biphenyl, anthracene, aminobenzoate, chlorocyclohexane, chlorobenzene, n-phenylalkanoic acid, phenylpropanoid, salicylate, gentisate, central meta cleavage of aromatic compounds, cinnamic acid, catechol and procatechuate branch of β-ketoadipate pathway, phenyl-acetyl CoA and homogentisate catabolic pathway. The information thus generated has ensured not only biodegradation potential but also revealed many possible future applications of the isolated bacteria.},
}

@article {pmid32369006,
year = {2020},
author = {Shah, S and Donze-Reiner, T and Shah, V},
title = {Diversity of navel microbiome in young adults.},
journal = {Journal of medical microbiology},
volume = {69},
number = {5},
pages = {721-727},
doi = {10.1099/jmm.0.001192},
pmid = {32369006},
issn = {1473-5644},
mesh = {Adolescent ; Adult ; Body Piercing ; Cluster Analysis ; DNA Barcoding, Taxonomic ; Female ; Humans ; Male ; Metagenomics/methods ; *Microbiota ; Opportunistic Infections/microbiology ; RNA, Ribosomal, 16S/genetics ; Sex Factors ; Skin/*microbiology ; Young Adult ; },
abstract = {Introduction. Human skin microbial communities represent a tremendous source of genetic diversity that evolves as a function of human age. Microbiota differs between regions of oily and moist skin, and appears to stabilize with age.Aim. We have a minimal understanding of the time frame required for the stabilization of skin microbiota, and the role played by gender. In the current study, we examined the microbiota present in the navel region of college-attending young adults in the age group of 18-25 years and investigated if diversity is associated with gender (male and female).Method. The study involved 16 female and six male subjects. Isolated DNA samples from navel swabs were processed using the Nextera XT library preparation kit and sequenced using the MiSeq platform. Data were analysed using QIIME and statistical analysis performed in R.Results. Microbiota of navel skin is dominated by Corynebacterium and Staphylococcus and includes opportunistic pathogens like Clostridium and Pseudomonas. Also present as the major component of the flora were the organisms normally associated with the gastrointestinal tract such as Acinetobacter, Campylobacter, Klebsiella and organisms from the Enterobacteriaceae and Moraxellaceae families. Comparison of alpha and beta diversity of the microbiota in the male and female navel regions suggests that the flora is not statistically different (P>0.05). However, pairwise comparison suggests that the abundance of 12 specific genera varied with gender, including higher abundance of Klebsiella and Enterobacter in females.Conclusion. Our findings indicate that the navel skin microbiota of young adults has a core microbiota of Corynebacterium and Staphylococcus. We also noted the presence of a significant number of opportunistic pathogens. A minor gender difference in the abundance of individual organisms was also observed.},
}

Adolescent
Adult
Body Piercing
Cluster Analysis
DNA Barcoding, Taxonomic
Female
Humans
Male
Metagenomics/methods
*Microbiota
Opportunistic Infections/microbiology
RNA, Ribosomal, 16S/genetics
Sex Factors
Skin/*microbiology
Young Adult

@article {pmid31229040,
year = {2019},
author = {Ticinesi, A and Nouvenne, A and Meschi, T},
title = {Gut microbiome and kidney stone disease: not just an Oxalobacter story.},
journal = {Kidney international},
volume = {96},
number = {1},
pages = {25-27},
doi = {10.1016/j.kint.2019.03.020},
pmid = {31229040},
issn = {1523-1755},
mesh = {*Gastrointestinal Microbiome ; Homeostasis ; Humans ; *Kidney Calculi ; Oxalates ; Oxalobacter formigenes ; *Urinary Calculi ; },
abstract = {Intestinal regulation of oxalate absorption is a complex mechanism, not exclusively reliant on the oxalate-degrading anaerobe Oxalobacter formigenes. Using metagenomics, Miller et al. were able to describe a network of bacterial taxa co-occurring with Oxalobacter formigenes in fecal samples from non-stone forming controls and less represented in stone formers. These findings may help to illuminate why previous intervention studies with probiotics have failed to reduce the risk of hyperoxaluria, opening new possibilities for future research.},
}

*Gastrointestinal Microbiome
Homeostasis
Humans
*Kidney Calculi
Oxalates
Oxalobacter formigenes
*Urinary Calculi

@article {pmid31848793,
year = {2020},
author = {Firmino, FC and Porcellato, D and Cox, M and Suen, G and Broadbent, JR and Steele, JL},
title = {Characterization of microbial communities in ethanol biorefineries.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {47},
number = {2},
pages = {183-195},
pmid = {31848793},
issn = {1476-5535},
mesh = {Bioreactors ; Ethanol/*metabolism ; Fermentation ; Firmicutes/genetics/metabolism ; Lactobacillus/genetics/metabolism ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Bacterial contamination of corn-based ethanol biorefineries can reduce their efficiency and hence increase their carbon footprint. To enhance our understanding of these bacterial contaminants, we temporally sampled four biorefineries in the Midwestern USA that suffered from chronic contamination and characterized their microbiomes using both 16S rRNA sequencing and shotgun metagenomics. These microbiotas were determined to be relatively simple, with 13 operational taxonomic units (OTUs) accounting for 90% of the bacterial population. They were dominated by Firmicutes (89%), with Lactobacillus comprising 80% of the OTUs from this phylum. Shotgun metagenomics confirmed our 16S rRNA data and allowed us to characterize bacterial succession at the species level, with the results of this analysis being that Lb. helveticus was the dominant contaminant in this fermentation. Taken together, these results provide insights into the microbiome of ethanol biorefineries and identifies a species likely to be commonly responsible for chronic contamination of these facilities.},
}

Bioreactors
Ethanol/*metabolism
Fermentation
Firmicutes/genetics/metabolism
Lactobacillus/genetics/metabolism
Metagenomics
*Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid31553956,
year = {2019},
author = {Ye, W and Zhang, Y and He, M and Zhu, C and Feng, XP},
title = {Relationship of tongue coating microbiome on volatile sulfur compounds in healthy and halitosis adults.},
journal = {Journal of breath research},
volume = {14},
number = {1},
pages = {016005},
doi = {10.1088/1752-7163/ab47b4},
pmid = {31553956},
issn = {1752-7163},
mesh = {Adult ; Biodiversity ; Breath Tests ; Case-Control Studies ; Female ; Halitosis/*microbiology ; *Healthy Volunteers ; Humans ; Male ; *Microbiota ; Sulfur Compounds/*analysis ; Tongue/*microbiology ; Volatile Organic Compounds/*analysis ; },
abstract = {AIM: This study aims to assess the microbiome variations related to intraoral halitosis and its relationship with volatile sulfur compounds (VSCs) among periodontally healthy Chinese adults.

MATERIAL AND METHODS: Tongue coating samples were collected from 28 periodontally healthy subjects (16 subjects with halitosis and 12 subjects without halitosis) who fulfilled the selection criteria. The organoleptic score (OS) was used to evaluate the halitosis status. The characterization of associated microbial communities was performed using 16S rRNA gene pyrosequencing and metagenomics methods.

RESULTS: A wide range of microbial communities, including 13 phyla, 23 classes, 37 orders, 134 genera, 266 species and 349 operational taxonomic units (OTUs), were detected. The Shannon index values were significantly higher in the halitosis group. Genera, such as Prevotella, Alloprevotella, Leptotrichia, Peptostreptococcus and Stomatobaculum, exhibited significantly higher relative percentages in halitosis samples, when compared to healthy samples. Peptostreptococcus, Alloprevotella, Eubacterium nodatum and Stomatobaculum exhibited significantly positive correlations with the total number of VSCs. Prevotella, Peptostreptococcus, Eubacterium nodatum and Alloprevotella were correlated with increased H2S and CH3SH concentration values. Bergeyella was correlated with decreased total VSC, H2S and CH3SH concentration values.

CONCLUSION: Microbial diversity was higher in the halitosis group than in the control group, and several bacteria were significantly correlated to halitosis. Furthermore, there were correlations between tongue bacterial composition structure and VSC gases. Tongue coating microbiota can offer important clues in the investigation of the pathogenesis and treatment of halitosis.},
}

Adult
Biodiversity
Breath Tests
Case-Control Studies
Female
Halitosis/*microbiology
*Healthy Volunteers
Humans
Male
*Microbiota
Sulfur Compounds/*analysis
Tongue/*microbiology
Volatile Organic Compounds/*analysis

@article {pmid32200181,
year = {2020},
author = {Samson, R and Rajput, V and Shah, M and Yadav, R and Sarode, P and Dastager, SG and Dharne, MS and Khairnar, K},
title = {Deciphering taxonomic and functional diversity of fungi as potential bioindicators within confluence stretch of Ganges and Yamuna Rivers, impacted by anthropogenic activities.},
journal = {Chemosphere},
volume = {252},
number = {},
pages = {126507},
doi = {10.1016/j.chemosphere.2020.126507},
pmid = {32200181},
issn = {1879-1298},
mesh = {*Environmental Biomarkers ; Environmental Monitoring/*methods ; Fungi ; Metagenomics ; *Microbiota ; Rivers/chemistry/microbiology ; *Water Microbiology ; },
abstract = {River confluences are interesting ecological niche with limited information in respect of the structure and the functions of diverse microbial communities. Fungi are gaining global attention as promising biological spectacles for defining the trophic status of riverine systems. We condense existing knowledge in confluence diversity in two Indian rivers (i.e. Ganges and Yamuna), by combining sediment metagenomics using long read aided MinION nanopore sequencing. A total of 63 OTU's were observed, of which top 20 OTU's were considered based on relative abundance of each OTU at a particular location. Fungal genera such as Aspergillus, Penicillium, Kluveromyces, Lodderomyces, and Nakaseomyces were deciphered as potential bio indicators of river pollution and eutrophication in the confluent zone. In silico functional gene analysis uncovered hits for neurodegenerative diseases and xenobiotic degradation potential, supporting bioindication of river pollution in wake of anthropogenic intervention.},
}

*Environmental Biomarkers
Environmental Monitoring/*methods
Fungi
Metagenomics
*Microbiota
Rivers/chemistry/microbiology
*Water Microbiology

@article {pmid31828159,
year = {2019},
author = {Nuli, R and Azhati, J and Cai, J and Kadeer, A and Zhang, B and Mohemaiti, P},
title = {Metagenomics and Faecal Metabolomics Integrative Analysis towards the Impaired Glucose Regulation and Type 2 Diabetes in Uyghur-Related Omics.},
journal = {Journal of diabetes research},
volume = {2019},
number = {},
pages = {2893041},
pmid = {31828159},
issn = {2314-6753},
mesh = {Actinobacteria ; Adult ; Bacteroides ; Case-Control Studies ; China/epidemiology ; Diabetes Mellitus, Type 2/epidemiology/metabolism/*microbiology ; Dysbiosis/epidemiology/metabolism/*microbiology ; Feces/chemistry/microbiology ; Female ; Firmicutes ; Gastrointestinal Microbiome/*genetics ; Glucose Intolerance/epidemiology/metabolism/*microbiology ; Humans ; Male ; *Metabolomics ; *Metagenomics ; Middle Aged ; },
abstract = {Objective: Gut microbiota and their metabolites play an important role in the development of type 2 diabetes mellitus (T2DM). This research was designed to study the relationship between gut microbiota and faecal metabolites of Uyghur newly onset T2DM and impaired glucose regulation (IGR) patients.

Materials and Methods: A total of 60 different glycemic Uyghur subjects were enrolled and divided into T2DM, IGR, and normal glucose tolerance (NGT) groups. Metagenomics and LC-MS-based untargeted faecal metabolomics were employed. Correlations between bacterial composition and faecal metabolomics were evaluated.

Results: We discovered that the composition and diversity of gut microbiota in newly onset T2DM and IGR were different from those in NGT. The α-diversity was higher in NGT than in T2DM and IGR; β-diversity analysis revealed apparent differences in the bacterial community structures between patients with T2DM, IGR, and NGT. LC-MS faecal metabolomics analysis discovered different metabolomics features in the three groups. Alchornoic acid, PE (14 : 0/20 : 3), PI, L-tyrosine, LysoPC (15 : 0), protorifamycin I, pimelic acid, epothilone A, 7-dehydro-desmosterol, L-lysine, LysoPC (14 : 1), and teasterone are the most significant differential enriched metabolites. Most of the differential enriched metabolites were involved in metabolic processes, including carbohydrate metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, and biosynthesis of amino acids. Procrustes analysis and correlation analysis identified correlations between gut microbiota and faecal metabolites. Matricin was positively correlated with Bacteroides and negatively correlated with Actinobacteria; protorifamycin I was negatively correlated with Actinobacteria; epothilone A was negatively correlated with Actinobacteria and positively correlated with Firmicutes; PA was positively correlated with Bacteroides and negatively correlated with Firmicutes; and cristacarpin was positively correlated with Actinobacteria; however, this correlation relationship does not imply causality.

Conclusions: This study used joint metagenomics and metabolomics analyses to elucidate the relationship between gut microbiota and faecal metabolites in different glycemic groups, and the result suggested that metabolic disorders and gut microbiota dysbiosis occurred in Uyghur T2DM and IGR. The results provide a theoretical basis for studying the pathological mechanism for further research.},
}

Actinobacteria
Adult
Bacteroides
Case-Control Studies
China/epidemiology
Diabetes Mellitus, Type 2/epidemiology/metabolism/*microbiology
Dysbiosis/epidemiology/metabolism/*microbiology
Feces/chemistry/microbiology
Female
Firmicutes
Gastrointestinal Microbiome/*genetics
Glucose Intolerance/epidemiology/metabolism/*microbiology
Humans
Male
*Metabolomics
*Metagenomics
Middle Aged

@article {pmid31572693,
year = {2019},
author = {Reid, G},
title = {The Need to Focus on Therapy Instead of Associations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {9},
number = {},
pages = {327},
pmid = {31572693},
issn = {2235-2988},
mesh = {Dysbiosis/microbiology/*therapy ; Female ; Humans ; Metagenomics ; *Microbial Interactions ; *Microbiota ; Probiotics/*administration & dosage ; Sequence Analysis, DNA ; Vagina/*microbiology ; Vaginosis, Bacterial/microbiology/*therapy ; },
abstract = {Molecular analyses of the vaginal microbiota have uncovered a vast array of organisms in this niche, but not so far changed what has been known for a long time: lactobacilli are dominant in health, and the diagnosis and treatment of symptomatic bacterial vaginosis is sub-optimal, and has not changed for over 40 years. While the lowering cost of DNA sequencing has attracted more researchers to the field, and bioinformatics, and statistical tools have made it possible to produce large datasets, it is functional and actionable studies that are more urgently needed, not more microbial abundance, and health or disease-associative data. The triggers of dysbiosis remain to be identified, but ultimately treatment will require disrupting biofilms of primarily anaerobic bacteria and replacing them with the host's own lactobacilli, or health-promoting organisms. The options of using probiotic strains to displace the biofilms and for prebiotics to encourage resurgence of the indigenous lactobacilli hold great promise, but more researchers need to develop, and test these concepts in humans. The enormity of the problem of vaginal dysbiosis cannot be understated. It should not take another 40 years to offer better management options.},
}

Dysbiosis/microbiology/*therapy
Female
Humans
Metagenomics
*Microbial Interactions
*Microbiota
Probiotics/*administration & dosage
Sequence Analysis, DNA
Vagina/*microbiology
Vaginosis, Bacterial/microbiology/*therapy

@article {pmid30951391,
year = {2020},
author = {Suez, J and Zmora, N and Elinav, E},
title = {Probiotics in the next-generation sequencing era.},
journal = {Gut microbes},
volume = {11},
number = {1},
pages = {77-93},
pmid = {30951391},
issn = {1949-0984},
mesh = {Anti-Bacterial Agents/*adverse effects ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Humans ; Metagenomics ; Probiotics/*therapeutic use ; },
abstract = {Technological developments, including massively parallel DNA sequencing, gnotobiotics, metabolomics, RNA sequencing and culturomics, have markedly propelled the field of microbiome research in recent years. These methodologies can be harnessed to improve our in-depth mechanistic understanding of basic concepts related to consumption of probiotics, including their rules of engagement with the indigenous microbiome and impacts on the human host. We have recently demonstrated that even during probiotic supplementation, resident gut bacteria in a subset of individuals resist the mucosal presence of probiotic strains, limiting their modulatory effect on the microbiome and on the host gut transcriptional landscape. Resistance is partly alleviated by antibiotics treatment, which enables probiotics to interact with the host at the gut mucosal interface, although rather than promoting reconstitution of the indigenous microbiome and of the host transcriptional profile, they inhibit these components from returning to their naïve pre-antibiotic configurations. In this commentary, we discuss our findings in the context of previous and recent works, and suggest that incorporating the state-of-the-art methods currently utilized in microbiome research into the field of probiotics may lead to improved understanding of their mechanisms of activity, as well as their efficacy and long-term safety.},
}

Anti-Bacterial Agents/*adverse effects
*Gastrointestinal Microbiome/drug effects/genetics/physiology
Humans
Metagenomics
Probiotics/*therapeutic use

@article {pmid30885689,
year = {2019},
author = {Hildonen, M and Kodama, M and Puetz, LC and Gilbert, MTP and Limborg, MT},
title = {A comparison of storage methods for gut microbiome studies in teleosts: Insights from rainbow trout (Oncorhynchus mykiss).},
journal = {Journal of microbiological methods},
volume = {160},
number = {},
pages = {42-48},
doi = {10.1016/j.mimet.2019.03.010},
pmid = {30885689},
issn = {1872-8359},
mesh = {Animals ; Freezing ; Gastrointestinal Microbiome/*genetics ; Oncorhynchus mykiss/*microbiology ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Specimen Handling/*methods ; },
abstract = {Immediate freezing is perhaps the most preferred method used for preserving gut microbial samples, but research on sample preservation has been principally based around samples from mammalian species, and little is known about the advantages or disadvantages relating to different storage methods for fish guts. Fish gut samples may pose additional challenges due to the different chemical and enzymatic profile, as well as the higher water content, which might affect the yield and purity of DNA recovered. To explore this, we took gut content and mucosal scrape samples from 10 rainbow trout (Oncorhynchus mykiss), and tested whether different preservation methods have any effect on the ability to construct high quality genomic libraries for shotgun and 16S rRNA gene sequencing. Four different storage methods were compared for the gut content samples (immediate freezing on dry ice, 96% ethanol, RNAlater and DNA/RNA shield), while two different methods were compared for mucosal scrape samples (96% ethanol and RNAlater). The samples were thereafter stored at -80 °C. Our findings concluded that 96% ethanol outperforms the other storage methods when considering DNA quantity, quality, cost and labor. Ethanol works consistently well for both gut content and mucosal scrape samples, and enables construction of DNA sequencing libraries of sufficient quantity and with a fragment length distribution suitable for shotgun sequencing. Two main conclusions from our study are i) sample storage optimisation is an important part of establishing a microbiome research program in a new species or sample type system, and ii) 96% ethanol is the preferred method for storing rainbow trout gut content and mucosal scrape samples.},
}

Animals
Freezing
Gastrointestinal Microbiome/*genetics
Oncorhynchus mykiss/*microbiology
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/methods
Specimen Handling/*methods

@article {pmid31778179,
year = {2019},
author = {Megaw, J and Kelly, SA and Thompson, TP and Skvortsov, T and Gilmore, BF},
title = {Profiling the microbial community of a Triassic halite deposit in Northern Ireland: an environment with significant potential for biodiscovery.},
journal = {FEMS microbiology letters},
volume = {366},
number = {22},
pages = {},
doi = {10.1093/femsle/fnz242},
pmid = {31778179},
issn = {1574-6968},
support = {BB/L017083/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Archaea/*classification/genetics/*isolation & purification ; Bacteria/*classification/genetics/*isolation & purification ; Cluster Analysis ; DNA, Archaeal/chemistry/genetics ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; Geologic Sediments/*microbiology ; Metagenomics ; Microbiological Techniques ; *Microbiota ; Northern Ireland ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {Kilroot salt mine, a Triassic halite deposit located in County Antrim, Northern Ireland, is the only permanent hypersaline environment on the island of Ireland. In this study, the microbiome of this unstudied environment was profiled for the first time using conventional and enhanced culturing techniques, and culture independent metagenomic approaches. Using both conventional isolation plates and iChip devices, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained, based on 16S rRNA gene sequencing. The archaeal isolates were similar to those previously isolated from other ancient halite deposits, and as expected, numerous genera were identified in the metagenome which were not represented among the culturable isolates. Preliminary screening of a selection of isolates from this environment identified antimicrobial activities against a panel of clinically important bacterial pathogens from 15 of the bacterial isolates and one of the archaea. This, alongside previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be a new, untapped source of of chemical diversity with high biodiscovery potential.},
}

Archaea/*classification/genetics/*isolation & purification
Bacteria/*classification/genetics/*isolation & purification
Cluster Analysis
DNA, Archaeal/chemistry/genetics
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
Geologic Sediments/*microbiology
Metagenomics
Microbiological Techniques
*Microbiota
Northern Ireland
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid31589310,
year = {2019},
author = {Ye, L and Das, P and Li, P and Ji, B and Nielsen, J},
title = {Carbohydrate active enzymes are affected by diet transition from milk to solid food in infant gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {11},
pages = {},
doi = {10.1093/femsec/fiz159},
pmid = {31589310},
issn = {1574-6941},
mesh = {Adult ; Animals ; *Carbohydrate Metabolism ; *Diet ; Enzymes/*metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; *Infant Food ; Male ; Metagenomics ; Milk, Human ; Polysaccharides/metabolism ; },
abstract = {Infants experience a dramatic change in their food in the first year after birth when they shift from breast milk to solid food. This results in a large change in presence of indigestible polysaccharides, a primary energy resource of gut microbes. How the gut microbiota adapts to this dietary shift has not been well examined. Here, by using metagenomics data, we studied carbohydrate-active enzymes (CAZymes) of gut microbiota, which are essential enzymes catalyzing the breakdown of polysaccharides, during this dietary shift. We developed a new approach to categorize CAZyme families by food intake and found CAZyme families associated with milk or solid food. We also found CAZymes with most abundance in 12 months infants that are not associated with solid food or milk but may be related to modulating carbohydrates in the mucus. Additionally, the abundance of gut CAZymes were found to be affected by many other factors, including delivery modes and life style in adults. Taken together, our findings provide novel insights into the dynamic change of gut CAZymes in early human life and provide potential markers for food interference or gut microbiota restoration.},
}

Adult
Animals
*Carbohydrate Metabolism
*Diet
Enzymes/*metabolism
Female
*Gastrointestinal Microbiome
Humans
Infant
*Infant Food
Male
Metagenomics
Milk, Human
Polysaccharides/metabolism

@article {pmid31504457,
year = {2019},
author = {Hoyos-Hernandez, C and Courbert, C and Simonucci, C and David, S and Vogel, TM and Larose, C},
title = {Community structure and functional genes in radionuclide contaminated soils in Chernobyl and Fukushima.},
journal = {FEMS microbiology letters},
volume = {366},
number = {21},
pages = {},
doi = {10.1093/femsle/fnz180},
pmid = {31504457},
issn = {1574-6968},
mesh = {*Biota ; Cesium Radioisotopes/*analysis ; Cluster Analysis ; DNA, Ribosomal/chemistry/genetics ; Japan ; Metabolic Networks and Pathways/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil/*chemistry ; *Soil Microbiology ; Soil Pollutants, Radioactive/*analysis ; Strontium Radioisotopes/*analysis ; Ukraine ; },
abstract = {Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680-0.4 and 90Sr 209.1-1.9 kBq kg-1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8-0.4 kBq kg-1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.},
}

*Biota
Cesium Radioisotopes/*analysis
Cluster Analysis
DNA, Ribosomal/chemistry/genetics
Japan
Metabolic Networks and Pathways/genetics
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Soil/*chemistry
*Soil Microbiology
Soil Pollutants, Radioactive/*analysis
Strontium Radioisotopes/*analysis
Ukraine

@article {pmid31397876,
year = {2019},
author = {Happel, EM and Markussen, T and Teikari, JE and Huchaiah, V and Alneberg, J and Andersson, AF and Sivonen, K and Middelboe, M and Kisand, V and Riemann, L},
title = {Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {9},
pages = {},
doi = {10.1093/femsec/fiz123},
pmid = {31397876},
issn = {1574-6941},
mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Bacterial Proteins/*genetics/metabolism ; Baltic States ; Estuaries ; Heterotrophic Processes ; *Microbiota ; Nitrification ; Nitrogen/analysis/*metabolism ; Rivers/chemistry/*microbiology ; Seawater/chemistry/*microbiology ; },
abstract = {Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing of dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads of riverine DOM to the Baltic Sea and likely affect the composition and function of bacterioplankton communities. To investigate this, the effects of riverine DOM from two different catchment areas (agricultural and forest) on natural bacterioplankton assemblages from two contrasting sites in the Baltic Sea were examined. Two microcosm experiments were carried out, where the community composition (16S rRNA gene sequencing), the composition of a suite of N-cycling genes (metagenomics) and the abundance and transcription of ammonia monooxygenase (amoA) genes involved in nitrification (quantitative PCR) were investigated. The river water treatments evoked a significant response in bacterial growth, but the effects on overall community composition and the representation of N-cycling genes were limited. Instead, treatment effects were reflected in the prevalence of specific taxonomic families, specific N-related functions and in the transcription of amoA genes. The study suggests that bacterioplankton responses to changes in the DOM pool are constrained to part of the bacterial community, whereas most taxa remain relatively unaffected.},
}

Bacteria/classification/genetics/isolation & purification/*metabolism
Bacterial Proteins/*genetics/metabolism
Baltic States
Estuaries
Heterotrophic Processes
*Microbiota
Nitrification
Nitrogen/analysis/*metabolism
Rivers/chemistry/*microbiology
Seawater/chemistry/*microbiology

@article {pmid31344227,
year = {2019},
author = {Alessandri, G and Milani, C and Mancabelli, L and Mangifesta, M and Lugli, GA and Viappiani, A and Duranti, S and Turroni, F and Ossiprandi, MC and van Sinderen, D and Ventura, M},
title = {The impact of human-facilitated selection on the gut microbiota of domesticated mammals.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {9},
pages = {},
doi = {10.1093/femsec/fiz121},
pmid = {31344227},
issn = {1574-6941},
mesh = {Animal Feed/analysis ; Animals ; Bacteria/classification/genetics/*isolation & purification ; Domestication ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Mammals/growth & development/*microbiology ; Metagenomics ; Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Domestication is the process by which anthropogenic forces shape lifestyle and behavior of wild species to accommodate human needs. The impact of domestication on animal physiology and behavior has been extensively studied, whereas its effect on the gut microbiota is still largely unexplored. For this reason, 16S rRNA gene-based and internal transcribed spacer-mediated bifidobacterial profiling, together with shotgun metagenomics, was employed to investigate the taxonomic composition and metabolic repertoire of 146 mammalian fecal samples, corresponding to 12 domesticated-feral dyads. Our results revealed that changes induced by domestication have extensively shaped the taxonomic composition of the mammalian gut microbiota. In this context, the selection of microbial taxa linked to a more efficient feed conversion into body mass and putative horizontal transmission of certain bacterial genera from humans were observed in the fecal microbiota of domesticated animals when compared to their feral relatives and to humans. In addition, profiling of the metabolic arsenal through metagenomics highlighted extensive functional adaptation of the fecal microbial community of domesticated mammals to changes induced by domestication. Remarkably, domesticated animals showed, when compared to their feral relatives, increased abundance of specific glycosyl hydrolases, possibly due to the higher intake of complex plant carbohydrates typical of commercial animal feeds.},
}

Animal Feed/analysis
Animals
Bacteria/classification/genetics/*isolation & purification
Domestication
Feces/microbiology
*Gastrointestinal Microbiome
Humans
Mammals/growth & development/*microbiology
Metagenomics
Microbiota
RNA, Ribosomal, 16S/genetics

@article {pmid31988585,
year = {2020},
author = {Lv, XY and Ding, HG and Zheng, JF and Fan, CL and Li, L},
title = {Rifaximin improves survival in cirrhotic patients with refractory ascites: A real-world study.},
journal = {World journal of gastroenterology},
volume = {26},
number = {2},
pages = {199-218},
pmid = {31988585},
issn = {2219-2840},
mesh = {Aged ; Anti-Bacterial Agents/pharmacology/*therapeutic use ; Ascites/*drug therapy/immunology/microbiology/mortality ; Bacterial Infections/*drug therapy/immunology/microbiology/mortality ; Drug Resistance ; Female ; Gastrointestinal Microbiome/drug effects/immunology ; Humans ; Liver Cirrhosis/complications/*drug therapy/microbiology/mortality ; Male ; Middle Aged ; Peritonitis/*drug therapy/immunology/microbiology/mortality ; Rifaximin/pharmacology/*therapeutic use ; Treatment Outcome ; },
abstract = {BACKGROUND: Rifaximin has been shown to reduce the incidence of hepatic encephalopathy and other complications in patients with cirrhosis. However, few studies have investigated the effect of rifaximin in cirrhotic patients with refractory ascites.

AIM: To evaluate the effects of rifaximin in the treatment of refractory ascites and to preliminarily explore its possible mechanism.

METHODS: A total of 75 cirrhotic patients with refractory ascites were enrolled in the study (50 in a rifaximin and 25 in a control group). Patients in the rifaximin group were divided into two subgroups according to the presence of spontaneous bacterial peritonitis and treatment with or without other antibiotics (19 patients treated with rifaximin and 31 patients treated with rifaximin plus intravenous antibiotics). All patients received conventional treatment for refractory ascites, while patients in the rifaximin group received oral rifaximin-α 200 mg four times daily for at least 2 wk. The ascites grade, fasting weight, liver and kidney function, and inflammatory factors in the plasma were evaluated before and after treatment. In addition, the gut microbiota was determined by metagenomics sequencing to analyse the changes in the characteristics of the gut microbiota before and after rifaximin treatment. The patients were followed for 6 mo.

RESULTS: Compared with the control group, the fasting weight of patients significantly decreased and the ascites significantly subsided after treatment with rifaximin (P = 0.011 and 0.009, respectively). The 6-mo survival rate of patients in the rifaximin group was significantly higher than that in the control group (P = 0.048). The concentration of interferon-inducible protein 10 decreased significantly in the rifaximin group compared with that in the control group (P = 0.024). The abundance of Roseburia, Haemophilus, and Prevotella was significantly reduced after rifaximin treatment, while the abundance of Lachnospiraceae_noname, Subdoligranulum, and Dorea decreased and the abundance of Coprobacillus increased after treatment with rifaximin plus intravenous antibiotics. The gene expression of virulence factors was significantly reduced after treatment in both subgroups treated with rifaximin or rifaximin plus intravenous antibiotics.

CONCLUSION: Rifaximin mitigates ascites and improves survival of cirrhotic patients with refractory ascites. A possible mechanism is that rifaximin regulates the structure and function of intestinal bacteria, thus improving the systemic inflammatory state.},
}

Aged
Anti-Bacterial Agents/pharmacology/*therapeutic use
Ascites/*drug therapy/immunology/microbiology/mortality
Bacterial Infections/*drug therapy/immunology/microbiology/mortality
Drug Resistance
Female
Gastrointestinal Microbiome/drug effects/immunology
Humans
Liver Cirrhosis/complications/*drug therapy/microbiology/mortality
Male
Middle Aged
Peritonitis/*drug therapy/immunology/microbiology/mortality
Rifaximin/pharmacology/*therapeutic use
Treatment Outcome

@article {pmid31730200,
year = {2019},
author = {Esposito, A and Borruso, L and Rattray, JE and Brusetti, L and Ahmed, E},
title = {Taxonomic and functional insights into rock varnish microbiome using shotgun metagenomics.},
journal = {FEMS microbiology ecology},
volume = {95},
number = {12},
pages = {},
doi = {10.1093/femsec/fiz180},
pmid = {31730200},
issn = {1574-6941},
mesh = {Acidobacteria/*genetics ; Actinobacteria/*genetics ; Chloroflexi/*genetics ; Genome, Bacterial/genetics ; Iron ; Manganese Compounds ; Metagenome/*genetics ; Metagenomics/methods ; Microbiota/physiology ; Oxides ; Paint ; *Soil Microbiology ; },
abstract = {Rock varnish is a microbial habitat, characterised by thin (5-500 μm) and shiny coatings of iron (Fe) and manganese (Mn) oxides associated with clay minerals. This structure is well studied by geologists, and recently there have been reports about the taxonomical composition of its microbiome. In this study, we investigated the rock varnish microbiome using shotgun metagenomics together with analyses of elemental composition, lipid and small molecule biomarkers, and rock surface analyses to explore the biogeography of microbial communities and their functional features. We report taxa and encoded functions represented in metagenomes retrieved from varnish or non-varnish samples, additionally, eight nearly complete genomes have been reconstructed spanning four phyla (Acidobacteria, Actinobacteria, Chloroflexi and TM7). The functional and taxonomic analyses presented in this study provide new insights into the ecosystem dynamics and survival strategies of microbial communities inhabiting varnish and non-varnish rock surfaces.},
}

Acidobacteria/*genetics
Actinobacteria/*genetics
Chloroflexi/*genetics
Genome, Bacterial/genetics
Iron
Manganese Compounds
Metagenome/*genetics
Metagenomics/methods
Microbiota/physiology
Oxides
Paint
*Soil Microbiology

@article {pmid31722729,
year = {2019},
author = {Kawulok, J and Kawulok, M and Deorowicz, S},
title = {Environmental metagenome classification for constructing a microbiome fingerprint.},
journal = {Biology direct},
volume = {14},
number = {1},
pages = {20},
pmid = {31722729},
issn = {1745-6150},
mesh = {*DNA Fingerprinting ; *Metagenome ; Metagenomics/*methods ; *Microbiota ; },
abstract = {BACKGROUND: Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.

RESULTS: We report the results of our extensive experimental study to investigate the behavior of our method and its sensitivity to different parameters. In our tests, we have followed the protocol of the MetaSUB Challenge, which allowed us to compare the obtained results with the solutions based on taxonomic and functional classification.

CONCLUSIONS: The results reported in the paper indicate that our method is competitive with those based on taxonomic classification. Importantly, by measuring the similarity at the reads level, we avoid the necessity of using large databases with annotated gene sequences. Hence our main finding is that environmental classification of metagenomic data can be proceeded without using large databases required for taxonomic or functional classification.

REVIEWERS: This article was reviewed by Eran Elhaik, Alexandra Bettina Graf, Chengsheng Zhu, and Andre Kahles.},
}

*DNA Fingerprinting
*Metagenome
Metagenomics/*methods
*Microbiota

@article {pmid31166185,
year = {2019},
author = {Smith, GJ and Wrighton, KC},
title = {Metagenomic Approaches Unearth Methanotroph Phylogenetic and Metabolic Diversity.},
journal = {Current issues in molecular biology},
volume = {33},
number = {},
pages = {57-84},
doi = {10.21775/cimb.033.057},
pmid = {31166185},
issn = {1467-3045},
mesh = {Archaea/classification/genetics/metabolism ; *Biodiversity ; Energy Metabolism/*genetics ; *Metagenome/genetics ; Metagenomics/methods ; Methane/*metabolism ; Methanobacteriales/classification/genetics/metabolism ; Microbiota/*genetics ; Phylogeny ; *Soil Microbiology ; },
abstract = {Methanotrophic microorganisms utilize methane as an electron donor and a carbon source. To date, the capacity to oxidize methane is restricted to microorganisms from three bacterial and one archaeal phyla. Most of our knowledge of methanotrophic metabolism has been obtained using highly enriched or pure cultures grown in the laboratory. However, many methanotrophs currently evade cultivation, thus metagenomics provides a complementary approach for gaining insight into currently unisolated microorganisms. Here we synthesize the studies using metagenomics to glean information about methanotrophs. We complement this summary with an analysis of methanotroph marker genes from 235 publically available metagenomic datasets. We analyze the phylogenetic and environmental distribution of methanotrophs sampled by metagenomics. We also highlight metabolic insights that methanotroph genomes assembled from metagenomes are illuminating. In summary, metagenomics has increased methanotrophic foliage within the tree of life, as well as provided new insights into methanotroph metabolism, which collectively can guide new cultivation efforts. Lastly, given the importance of methanotrophs for biotechnological applications and their capacity to filter greenhouse gases from a variety of ecosystems, metagenomics will continue to be an important component in the arsenal of tools needed for understanding methanotroph diversity and metabolism in both engineered and natural systems.},
}

Archaea/classification/genetics/metabolism
*Biodiversity
Energy Metabolism/*genetics
*Metagenome/genetics
Metagenomics/methods
Methane/*metabolism
Methanobacteriales/classification/genetics/metabolism
Microbiota/*genetics
Phylogeny
*Soil Microbiology

@article {pmid32306993,
year = {2020},
author = {Mejia, R and Damania, A and Jeun, R and Bryan, PE and Vargas, P and Juarez, M and Cajal, PS and Nasser, J and Krolewiecki, A and Lefoulon, E and Long, C and Drake, E and Cimino, RO and Slatko, B},
title = {Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study.},
journal = {Parasites & vectors},
volume = {13},
number = {1},
pages = {200},
pmid = {32306993},
issn = {1756-3305},
support = {D34HP31024/HRSA/HRSA HHS/United States ; },
mesh = {Animals ; Child ; Child, Preschool ; *Coinfection/microbiology/parasitology ; Cross-Sectional Studies ; DNA, Helminth ; DNA, Protozoan ; Female ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial ; Giardia lamblia/classification/genetics/isolation & purification ; Helminths/classification/genetics/isolation & purification ; Humans ; *Intestines/microbiology/parasitology ; Male ; Metagenomics ; Parasites/classification/*genetics/isolation & purification ; Pilot Projects ; Real-Time Polymerase Chain Reaction ; Vitamin B 12/*genetics/metabolism ; Whole Genome Sequencing ; },
abstract = {BACKGROUND: Approximately 30% of children worldwide are infected with gastrointestinal parasites. Depending on the species, parasites can disrupt intestinal bacterial microbiota affecting essential vitamin biosynthesis.

METHODS: Stool samples were collected from 37 asymptomatic children from a previous cross-sectional Argentinian study. A multi-parallel real-time quantitative PCR was implemented for Ascaris lumbricoides, Ancylostoma duodenale, Necator americanus, Strongyloides stercoralis, Trichuris trichiura, Cryptosporidium spp., Entamoeba histolytica and Giardia duodenalis. In addition, whole-genome sequencing analysis was conducted for bacterial microbiota on all samples and analyzed using Livermore Metagenomic Analysis Toolkit and DIAMOND software. Separate analyses were carried out for uninfected, Giardia-only, Giardia + helminth co-infections, and helminth-only groups.

RESULTS: For Giardia-only infected children compared to uninfected children, DNA sequencing data showed a decrease in microbiota biodiversity that correlated with increasing Giardia burden and was statistically significant using Shannon's alpha diversity (Giardia-only > 1 fg/µl 2.346; non-infected group 3.253, P = 0.0317). An increase in diversity was observed for helminth-only infections with a decrease in diversity for Giardia + helminth co-infections (P = 0.00178). In Giardia-only infections, microbiome taxonomy changed from Firmicutes towards increasing proportions of Prevotella, with the degree of change related to the intensity of infection compared to uninfected (P = 0.0317). The abundance of Prevotella bacteria was decreased in the helminths-only group but increased for Giardia + helminth co-infections (P = 0.0262). Metagenomic analysis determined cobalamin synthesis was decreased in the Giardia > 1 fg/µl group compared to both the Giardia < 1 fg/µl and the uninfected group (P = 0.0369). Giardia + helminth group also had a decrease in cobalamin CbiM genes from helminth-only infections (P = 0.000754).

CONCLUSION: The study results may provide evidence for an effect of parasitic infections enabling the permissive growth of anaerobic bacteria such as Prevotella, suggesting an altered capacity of vitamin B12 (cobalamin) biosynthesis and potential impact on growth and development in children .},
}

Animals
Child
Child, Preschool
*Coinfection/microbiology/parasitology
Cross-Sectional Studies
DNA, Helminth
DNA, Protozoan
Female
Gastrointestinal Microbiome/*genetics
Genes, Bacterial
Giardia lamblia/classification/genetics/isolation & purification
Helminths/classification/genetics/isolation & purification
Humans
*Intestines/microbiology/parasitology
Male
Metagenomics
Parasites/classification/*genetics/isolation & purification
Pilot Projects
Real-Time Polymerase Chain Reaction
Vitamin B 12/*genetics/metabolism
Whole Genome Sequencing

@article {pmid32046772,
year = {2020},
author = {Chen, HL and Zhao, XY and Zhao, GX and Huang, HB and Li, HR and Shi, CW and Yang, WT and Jiang, YL and Wang, JZ and Ye, LP and Zhao, Q and Wang, CF and Yang, GL},
title = {Dissection of the cecal microbial community in chickens after Eimeria tenella infection.},
journal = {Parasites & vectors},
volume = {13},
number = {1},
pages = {56},
pmid = {32046772},
issn = {1756-3305},
support = {2017YFD0500400//The National Key Research and Development Program of China/ ; 2017YFD0501200//The National Key Research and Development Program of China/ ; 31672528//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; Bacteria/classification/isolation & purification ; Cecum/microbiology/parasitology/pathology ; *Chickens/microbiology/parasitology ; Coccidiosis/therapy/*veterinary ; *Eimeria tenella/genetics/parasitology ; Gastrointestinal Microbiome/*genetics ; Metagenomics ; Poultry Diseases/*parasitology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Eimeria spp. are responsible for chicken coccidiosis which is the most important enteric protozoan disease resulting in tremendous economic losses in the poultry industry. Understanding the interaction between the avian cecal microbiota and coccidia is of interest in the development of alternative treatments that do not rely on chemotherapeutics and do not lead to drug resistance.

METHODS: We utilized 16S rRNA gene sequencing to detect the dynamics of the cecal microbial community in AA broilers challenged with Eimeria tenella. Histopathological analysis of the cecum was also conducted.

RESULTS: We found that microbial shifts occur during the infection. Lactobacillus, Faecalibacterium, Ruminococcaceae UCG-013, Romboutsia and Shuttleworthia decreased in abundance. However, the opportunistic pathogens Enterococcus and Streptococcus increased in abundance over time in response to the infection.

CONCLUSIONS: Eimeria tenella disrupts the integrity of the cecal microbiota and could promote the establishment and growth of potentially pathogenic bacteria. Defining bacterial populations affected by coccidial infection might help identify bacterial markers for intestinal disease as well as populations or species that could be beneficial in maintaining and restoring gut homeostasis during and after infection with E. tenella.},
}

Animals
Bacteria/classification/isolation & purification
Cecum/microbiology/parasitology/pathology
*Chickens/microbiology/parasitology
Coccidiosis/therapy/*veterinary
*Eimeria tenella/genetics/parasitology
Gastrointestinal Microbiome/*genetics
Metagenomics
Poultry Diseases/*parasitology
RNA, Ribosomal, 16S/genetics

@article {pmid31852805,
year = {2019},
author = {Engel, K and Ford, SE and Coyotzi, S and McKelvie, J and Diomidis, N and Slater, G and Neufeld, JD},
title = {Stability of Microbial Community Profiles Associated with Compacted Bentonite from the Grimsel Underground Research Laboratory.},
journal = {mSphere},
volume = {4},
number = {6},
pages = {},
pmid = {31852805},
issn = {2379-5042},
mesh = {Bacteria/chemistry/*classification/genetics ; *Bentonite ; Cluster Analysis ; Cytosol/chemistry ; DNA, Bacterial/chemistry/genetics ; DNA, Ribosomal/chemistry/genetics ; *Environmental Microbiology ; Fatty Acids/analysis ; Metagenomics ; *Microbiota ; Phospholipids/analysis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Switzerland ; },
abstract = {To assess the microbiology and corrosion potential of engineered components of a deep geological repository for long-term storage of high-level nuclear waste, the Materials Corrosion Test is being conducted at the Underground Research Laboratory in Grimsel, Switzerland. Modules containing metal coupons surrounded by highly compacted MX-80 bentonite, at two dry densities (1.25 and 1.50 g/cm3), were emplaced within 9-m-deep boreholes, and the first modules were retrieved after 13 months of exposure. Bentonite and associated module materials were sampled, and microbial communities and their distributions were assessed using 16S rRNA gene sequencing and phospholipid fatty acid (PLFA) analysis. Borehole fluid was dominated by amplicon sequence variants (ASVs) affiliated with Desulfosporosinus and Desulfovibrio, which are putatively involved in sulfate reduction. The relative abundance of these ASVs was lower for samples from inside the borehole module, and they were almost undetectable in samples of the inner bentonite layer. The dominant ASV in case and filter sample sequence data was affiliated with Pseudomonas stutzeri, yet its relative abundance decreased in the inner layer samples. Streptomyces sp. ASVs were relatively abundant in all bentonite core sample data both prior to emplacement and after 13 months of exposure, presumably as metabolically inactive spores or extracellular "relic" DNA. PLFA concentrations in outer and inner layer bentonite samples suggested cellular abundances of 1 × 106 to 3 × 106 cells/g, with similar PLFA distributions within all bentonite samples. Our results demonstrate consistent microbial communities inside the saturated borehole module, providing the first evidence for microbial stability under conditions that mimic a deep geological repository.IMPORTANCE The Materials Corrosion Test in Grimsel Underground Research Laboratory, Switzerland, enables an evaluation of microbiological implications of bentonite clay at densities relevant for a deep geological repository. Our research demonstrates that after 13 months of exposure within a granitic host rock, the microbial 16S rRNA gene signatures of saturated bentonite clay within the modules were consistent with the profiles in the original clay used to pack the modules. Such results provide evidence that densities chosen for this emplacement test are refractory to microbial activity, at least on the relatively short time frame leading to the first time point sampling event, which will help inform in situ engineered barrier system science. This study has important implications for the design of deep geological repository sites under consideration for the Canadian Shield.},
}

Bacteria/chemistry/*classification/genetics
*Bentonite
Cluster Analysis
Cytosol/chemistry
DNA, Bacterial/chemistry/genetics
DNA, Ribosomal/chemistry/genetics
*Environmental Microbiology
Fatty Acids/analysis
Metagenomics
*Microbiota
Phospholipids/analysis
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Switzerland

@article {pmid31835036,
year = {2019},
author = {Pachiadaki, MG and Brown, JM and Brown, J and Bezuidt, O and Berube, PM and Biller, SJ and Poulton, NJ and Burkart, MD and La Clair, JJ and Chisholm, SW and Stepanauskas, R},
title = {Charting the Complexity of the Marine Microbiome through Single-Cell Genomics.},
journal = {Cell},
volume = {179},
number = {7},
pages = {1623-1635.e11},
doi = {10.1016/j.cell.2019.11.017},
pmid = {31835036},
issn = {1097-4172},
support = {R21 AI134037/AI/NIAID NIH HHS/United States ; },
mesh = {Archaea/classification/genetics ; Bacteria/classification/genetics ; Energy Metabolism ; *Metagenome ; Metagenomics/methods ; *Microbiota ; Phylogeography ; Plankton ; Seawater/*microbiology ; Single-Cell Analysis/methods ; Transcriptome ; },
abstract = {Marine bacteria and archaea play key roles in global biogeochemistry. To improve our understanding of this complex microbiome, we employed single-cell genomics and a randomized, hypothesis-agnostic cell selection strategy to recover 12,715 partial genomes from the tropical and subtropical euphotic ocean. A substantial fraction of known prokaryoplankton coding potential was recovered from a single, 0.4 mL ocean sample, which indicates that genomic information disperses effectively across the globe. Yet, we found each genome to be unique, implying limited clonality within prokaryoplankton populations. Light harvesting and secondary metabolite biosynthetic pathways were numerous across lineages, highlighting the value of single-cell genomics to advance the identification of ecological roles and biotechnology potential of uncultured microbial groups. This genome collection enabled functional annotation and genus-level taxonomic assignments for >80% of individual metagenome reads from the tropical and subtropical surface ocean, thus offering a model to improve reference genome databases for complex microbiomes.},
}

Archaea/classification/genetics
Bacteria/classification/genetics
Energy Metabolism
*Metagenome
Metagenomics/methods
*Microbiota
Phylogeography
Plankton
Seawater/*microbiology
Single-Cell Analysis/methods
Transcriptome

@article {pmid31826972,
year = {2019},
author = {Pierce, ML and Ward, JE},
title = {Gut Microbiomes of the Eastern Oyster (Crassostrea virginica) and the Blue Mussel (Mytilus edulis): Temporal Variation and the Influence of Marine Aggregate-Associated Microbial Communities.},
journal = {mSphere},
volume = {4},
number = {6},
pages = {},
pmid = {31826972},
issn = {2379-5042},
mesh = {Animals ; Bacteria/*classification/genetics ; Cluster Analysis ; Connecticut ; Crassostrea/*microbiology ; DNA, Ribosomal/chemistry/genetics ; *Gastrointestinal Microbiome ; Metagenomics ; Mytilus edulis/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; Seawater/*microbiology ; Sequence Analysis, DNA ; },
abstract = {Gut microbial community structure was evaluated for two species of bivalve molluscs, the eastern oyster (Crassostrea virginica) and the blue mussel (Mytilus edulis) collected from Long Island Sound, Connecticut, over the course of a year. These bivalves utilize a shared feeding mechanism, which may result in similar gut microbial communities. Their particle diet, marine aggregates, and surrounding environment, aggregate-free seawater (AFSW), were also collected for comparison. Due to the suspension-feeding activities of bivalves, the potential for aggregate- and AFSW-associated microbiota to influence their microbial communities may be significant. Both taxonomic and functional diversity of the samples were assessed. 16S rRNA gene amplicon sequencing indicated that oysters and mussels maintained similar, but not identical, gut microbiomes, with some temporal variation. Throughout the year, bivalve species had gut microbial community compositions that were more similar to one another than to aggregates. Within a month, bivalves shared on average a quarter of their total operational taxonomic units (OTUs) with each other and a 10th of their total OTUs with aggregates. During months with warm water temperatures, individuals within each of the four sample types had similar alpha diversity, but again, temporal variation was observed. On a functional level, bivalve gut microbial communities exhibited variation attributed to host species and season. Unlike oysters, mussel gut bacterial communities maintained high richness and evenness values throughout the year, even when values for the particle diet and AFSW were reduced. Overall, a core gut bivalve microbiome was present, and it was partially influenced by the marine aggregate microbial community.IMPORTANCE This work investigates the influence that extrinsic factors, diet, and the environment can have on the microbiomes of shellfish. Over the course of a year, the gut microbial communities of two species of bivalves, oysters and mussels, held under identical conditions in coastal marine waters were compared. While the mussels and oysters harbored gut microbial communities with similar composition, on a functional level, they exhibited species and temporal variation. These results indicate that intrinsic factors influence the bivalve microbiome, resulting in species variability, even when environmental conditions, feeding mechanism, and particle diet are constant. Seasonal and multispecies comparisons for bivalve-associated microbial communities are rare, and we believe this research represents an important contribution. The results presented here advance our understanding of the symbiotic interactions between marine invertebrates, the microbial communities they harbor, and the environment.},
}

Animals
Bacteria/*classification/genetics
Cluster Analysis
Connecticut
Crassostrea/*microbiology
DNA, Ribosomal/chemistry/genetics
*Gastrointestinal Microbiome
Metagenomics
Mytilus edulis/*microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Seasons
Seawater/*microbiology
Sequence Analysis, DNA

@article {pmid31759944,
year = {2020},
author = {Rapin, A and Chuat, A and Lebon, L and Zaiss, MM and Marsland, BJ and Harris, NL},
title = {Infection with a small intestinal helminth, Heligmosomoides polygyrus bakeri, consistently alters microbial communities throughout the murine small and large intestine.},
journal = {International journal for parasitology},
volume = {50},
number = {1},
pages = {35-46},
doi = {10.1016/j.ijpara.2019.09.005},
pmid = {31759944},
issn = {1879-0135},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Helminthiasis ; Host Microbial Interactions ; Host-Parasite Interactions ; *Intestinal Diseases, Parasitic ; Intestinal Mucosa/microbiology/parasitology ; Intestine, Large/microbiology/parasitology ; Intestines/*microbiology/*parasitology ; Metagenomics ; Mice ; *Nematospiroides dubius/microbiology/parasitology ; Peptostreptococcus/growth & development ; },
abstract = {Increasing evidence suggests that intestinal helminth infection can alter intestinal microbial communities with important impacts on the mammalian host. However, all of the studies to date utilize different techniques to study the microbiome and access different sites of the intestine with little consistency noted between studies. In the present study, we set out to perform a comprehensive analysis of the impact of intestinal helminth infection on the mammalian intestinal bacterial microbiome. For this purpose, we investigated the impact of experimental infection using the natural murine small intestinal helminth, Heligmosomoides polygyrus bakeri and examined possible alterations in both the mucous and luminal bacterial communities along the entire small and large intestine. We also explored the impact of common experimental variables including the parasite batch and pre-infection microbiome, on the outcome of helminth-bacterial interactions. This work provides evidence that helminth infection reproducibly alters intestinal microbial communities, with an impact of infection noted along the entire length of the intestine. Although the exact nature of helminth-induced alterations to the intestinal microbiome differed depending on the microbiome community structure present prior to infection, changes extended well beyond the introduction of new bacterial species by the infecting larvae. Moreover, striking similarities between different experiments were noted, including the consistent outgrowth of a bacterium belonging to the Peptostreptococcaceae family throughout the intestine.},
}

Animals
*Gastrointestinal Microbiome
*Helminthiasis
Host Microbial Interactions
Host-Parasite Interactions
*Intestinal Diseases, Parasitic
Intestinal Mucosa/microbiology/parasitology
Intestine, Large/microbiology/parasitology
Intestines/*microbiology/*parasitology
Metagenomics
Mice
*Nematospiroides dubius/microbiology/parasitology
Peptostreptococcus/growth & development

@article {pmid31357928,
year = {2019},
author = {Ogier, JC and Pagès, S and Galan, M and Barret, M and Gaudriault, S},
title = {rpoB, a promising marker for analyzing the diversity of bacterial communities by amplicon sequencing.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {171},
pmid = {31357928},
issn = {1471-2180},
mesh = {Animals ; Bacteria/classification ; DNA, Bacterial ; DNA-Directed RNA Polymerases/genetics ; Genes, Essential ; *Genetic Markers ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Metagenomics/*methods ; Microbiota/*genetics ; Nematoda/*microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Microbiome composition is frequently studied by the amplification and high-throughput sequencing of specific molecular markers (metabarcoding). Various hypervariable regions of the 16S rRNA gene are classically used to estimate bacterial diversity, but other universal bacterial markers with a finer taxonomic resolution could be employed. We compared specificity and sensitivity between a portion of the rpoB gene and the V3 V4 hypervariable region of the 16S rRNA gene.

RESULTS: We first designed universal primers for rpoB suitable for use with Illumina sequencing-based technology and constructed a reference rpoB database of 45,000 sequences. The rpoB and V3 V4 markers were amplified and sequenced from (i) a mock community of 19 bacterial strains from both Gram-negative and Gram-positive lineages; (ii) bacterial assemblages associated with entomopathogenic nematodes. In metabarcoding analyses of mock communities with two analytical pipelines (FROGS and DADA2), the estimated diversity captured with the rpoB marker resembled the expected composition of these mock communities more closely than that captured with V3 V4. The rpoB marker had a higher level of taxonomic affiliation, a higher sensitivity (detection of all the species present in the mock communities), and a higher specificity (low rates of spurious OTU detection) than V3 V4. We compared the performance of the rpoB and V3 V4 markers in an animal ecosystem model, the infective juveniles of the entomopathogenic nematode Steinernema glaseri carrying the symbiotic bacteria Xenorhabdus poinarii. Both markers showed the bacterial community associated with this nematode to be of low diversity (< 50 OTUs), but only rpoB reliably detected the symbiotic bacterium X. poinarii.

CONCLUSIONS: Our results confirm that different microbiota composition data may be obtained with different markers. We found that rpoB was a highly appropriate marker for assessing the taxonomic structure of mock communities and the nematode microbiota. Further studies on other ecosystems should be considered to evaluate the universal usefulness of the rpoB marker. Our data highlight two crucial elements that should be taken into account to ensure more reliable and accurate descriptions of microbial diversity in high-throughput amplicon sequencing analyses: i) the need to include mock communities as controls; ii) the advantages of using a multigenic approach including at least one housekeeping gene (rpoB is a good candidate) and one variable region of the 16S rRNA gene. This study will be useful to the growing scientific community describing bacterial communities by metabarcoding in diverse ecosystems.},
}

Animals
Bacteria/classification
DNA, Bacterial
DNA-Directed RNA Polymerases/genetics
Genes, Essential
*Genetic Markers
High-Throughput Nucleotide Sequencing/methods
Metagenome
Metagenomics/*methods
Microbiota/*genetics
Nematoda/*microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid31331734,
year = {2019},
author = {Díaz-Sánchez, S and Estrada-Peña, A and Cabezas-Cruz, A and de la Fuente, J},
title = {Evolutionary Insights into the Tick Hologenome.},
journal = {Trends in parasitology},
volume = {35},
number = {9},
pages = {725-737},
doi = {10.1016/j.pt.2019.06.014},
pmid = {31331734},
issn = {1471-5007},
mesh = {Animals ; *Biological Evolution ; Genome/*genetics ; Host Microbial Interactions/physiology ; Microbiota/physiology ; Symbiosis ; Ticks/classification/*genetics/*microbiology ; },
abstract = {Recently, our knowledge of the composition and complexity of tick microbial communities has increased and supports microbial impact on tick biology. Results support a phylogenetic association between ticks and their microbiota across evolution; this is known as phylosymbiosis. Herein, using published datasets, we confirm the existence of phylosymbiosis between Ixodes ticks and their microbial communities. The strong phylosymbiotic signal and the phylogenetic structure of microbial communities associated with Ixodid ticks revealed that phylosymbiosis may be a widespread phenomenon in tick-microbiota evolution. This finding supports the existence of a species-specific tick hologenome with a largely unexplored influence on tick biology and pathogen transmission. These results may provide potential targets for the construction of paratransgenic ticks to control tick infestations and tick-borne diseases.},
}

Animals
*Biological Evolution
Genome/*genetics
Host Microbial Interactions/physiology
Microbiota/physiology
Symbiosis
Ticks/classification/*genetics/*microbiology

@article {pmid31291888,
year = {2019},
author = {Chen, L and Wang, YC and Qin, LY and He, HY and Yu, XL and Yang, MZ and Zhang, HB},
title = {Dynamics of fungal communities during Gastrodia elata growth.},
journal = {BMC microbiology},
volume = {19},
number = {1},
pages = {158},
pmid = {31291888},
issn = {1471-2180},
mesh = {Agaricales/genetics/isolation & purification ; Basidiomycota/genetics/isolation & purification ; DNA, Ribosomal Spacer/genetics ; *Gastrodia/growth & development/microbiology ; High-Throughput Nucleotide Sequencing ; *Host Microbial Interactions ; Metagenomics ; Mycobiome/*genetics ; Phylogeny ; Soil Microbiology ; Symbiosis ; },
abstract = {BACKGROUND: Gastrodia elata is a widely distributed achlorophyllous orchid and is highly valued as both medicine and food. Gastrodia elata produces dust-like seeds and relies on mycorrhizal fungi for its germination and growth. In its life cycle, G. elata is considered to switch from a specific single-fungus relationship (Mycena) to another single-fungus relationship (Armillaria). However, no studies have investigated the changes in the plant-fungus relationship during the growth of G. elata in the wild. In this study, high-throughput sequencing was used to characterize the fungal community of tubers in different growth phases as well as the soils surrounding G. elata.

RESULTS: The predominant fungi were Basidiomycota (60.44%) and Ascomycota (26.40%), which exhibited changes in abundance and diversity with the growth phases of G. elata. Diverse basidiomycetes in protocorms (phase P) were Hyphodontia, Sistotrema, Tricholoma, Mingxiaea, Russula, and Mycena, but the community changed from a large proportion of Resinicium bicolor (40%) in rice-like tubers (phase M) to an unidentified Agaricales operational taxonomic unit 1(OTU1,98.45%) in propagation vegetation tubers (phase B). The soil fungi primarily included Simocybe, Psathyrella, Conocybe, and Subulicystidium. Three Mycena OTUs obtained in this study were differentially distributed among the growth phases of G. elata, accounting for less than 1.0% of the total reads, and were phylogenetically close to Mycena epipterygia and M. alexandri.

CONCLUSIONS: Our data indicated that G. elata interacts with a broad range of fungi beyond the Mycena genus. These fungi changed with the growth phases of G. elata. In addition, these data suggested that the development of the fungal community during the growth of G. elata was more complex than previously assumed and that at least two different fungi could be involved in development before the arrival of Armillaria.},
}

Agaricales/genetics/isolation & purification
Basidiomycota/genetics/isolation & purification
DNA, Ribosomal Spacer/genetics
*Gastrodia/growth & development/microbiology
High-Throughput Nucleotide Sequencing
*Host Microbial Interactions
Metagenomics
Mycobiome/*genetics
Phylogeny
Soil Microbiology
Symbiosis

@article {pmid31240754,
year = {2019},
author = {Firrman, J and Liu, L and Tanes, C and Bittinger, K and Mahalak, K and Rinaldi, W},
title = {Metagenomic assessment of the Cebus apella gut microbiota.},
journal = {American journal of primatology},
volume = {81},
number = {10-11},
pages = {e23023},
doi = {10.1002/ajp.23023},
pmid = {31240754},
issn = {1098-2345},
support = {//Agricultural Research Service/International ; //US Congress/International ; //US Department of Agriculture and Agricultural Research Service. Project number 8072-41000-102-00-D, In Vitro Human Intestinal Microbial Ecosystem: Effects of Diet/International ; },
mesh = {Animals ; Bacteria/classification/metabolism ; Fatty Acids, Volatile/*metabolism ; Gastrointestinal Microbiome/*genetics/physiology ; Intestines/microbiology ; Male ; *Metagenome ; Phylogeny ; Sapajus apella/*microbiology ; },
abstract = {Cebus Apella (C. apella) is a species of Nonhuman Primate (NHP) used for biomedical research because it is phylogenetically similar and shares anatomical commonalities with humans. Here, the gut microbiota of three C. apella were examined in the different regions of the intestinal tract. Using metagenomics, the gut microbiota associated with the luminal content and mucus layer for each intestinal region was identified, and functionality was investigated by quantifying the levels of short chain fatty acids (SCFAs) produced. The results of this study show a high degree of similarity in the intestinal communities among C. apella subjects, with multiple shared characteristics. First, the communities in the lumen were more phylogenetically diverse and rich compared to the mucus layer communities throughout the entire intestinal tract. The small intestine communities in the lumen displayed a higher Shannon diversity index compared to the colon communities. Second, all the communities were dominated by aero-tolerant taxa such as Streptococcus, Enterococcus, Abiotrophia, and Lactobacillus, although there was preferential colonization of specific taxa observed. Finally, the primary SCFA produced throughout the intestinal tract was acetic acid, with some propionic acid and butyric acid detected in the colon regions. The small intestine microbiota produced significantly less SCFAs compared to the communities in the colon. Collectively, these data provide an in-depth report on the composition, distribution, and SCFA production of the gut microbiota along the intestinal tract of the C. apella NHP animal model.},
}

Animals
Bacteria/classification/metabolism
Fatty Acids, Volatile/*metabolism
Gastrointestinal Microbiome/*genetics/physiology
Intestines/microbiology
Male
*Metagenome
Phylogeny
Sapajus apella/*microbiology

@article {pmid31021335,
year = {2019},
author = {Zhang, Y and Ying, H and Xu, Y},
title = {Comparative genomics and metagenomics of the metallomes.},
journal = {Metallomics : integrated biometal science},
volume = {11},
number = {6},
pages = {1026-1043},
doi = {10.1039/c9mt00023b},
pmid = {31021335},
issn = {1756-591X},
mesh = {Animals ; Biological Evolution ; Genomics/*methods ; Humans ; Metagenomics/methods ; Metalloproteins/genetics/metabolism ; Metals/*metabolism ; Microbiota ; Trace Elements/metabolism ; },
abstract = {Biological trace metals are needed by all living organisms in very small quantities. They play important roles in a variety of key cellular processes, resulting in a varying degree of dependence on metals for different organisms. While most effort has been placed on identifying metal metabolic pathways and characterizing metalloproteins and their functions, computational and systematical analyses of the metallomes (or metalloproteomes) have been limited. In the past several years, comparative genomics of the metallomes has arisen, which provides significant insights into the metabolism and function of metals as well as their evolution. This review focuses on recent progress in comparative genomic analysis of trace metals (such as copper, molybdenum, nickel, cobalt, selenium, iron and zinc) in both prokaryotes and eukaryotes. These studies reveal distinct and dynamic evolutionary patterns of the utilization of different metals and metalloproteins. We also discuss advances in comparative metagenomic analysis of metals in microbial communities in diverse environments such as the global marine ecosystem, which offer new clues to the relationship between metal utilization and different types of environmental factors. Overall, comparative genomic and metagenomic analyses of the metallomes provide a foundation for systematic understanding of metal utilization, function and related evolutionary trends in the three domains of life.},
}

Animals
Biological Evolution
Genomics/*methods
Humans
Metagenomics/methods
Metalloproteins/genetics/metabolism
Metals/*metabolism
Microbiota
Trace Elements/metabolism

@article {pmid31844663,
year = {2019},
author = {Olm, MR and Bhattacharya, N and Crits-Christoph, A and Firek, BA and Baker, R and Song, YS and Morowitz, MJ and Banfield, JF},
title = {Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria.},
journal = {Science advances},
volume = {5},
number = {12},
pages = {eaax5727},
pmid = {31844663},
issn = {2375-2548},
support = {R01 AI092531/AI/NIAID NIH HHS/United States ; R01 GM109454/GM/NIGMS NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; },
mesh = {Enterobacteriaceae/genetics ; Enterocolitis, Necrotizing/*genetics/microbiology ; Feces/microbiology ; Fimbriae, Bacterial/*genetics/microbiology ; Gastrointestinal Microbiome/*genetics ; Humans ; Infant, Newborn ; Infant, Premature ; Infant, Premature, Diseases/genetics/microbiology ; Klebsiella/genetics ; *Metagenomics ; Multigene Family/genetics ; },
abstract = {Necrotizing enterocolitis (NEC) is a devastating intestinal disease that occurs primarily in premature infants. We performed genome-resolved metagenomic analysis of 1163 fecal samples from premature infants to identify microbial features predictive of NEC. Features considered include genes, bacterial strain types, eukaryotes, bacteriophages, plasmids, and growth rates. A machine learning classifier found that samples collected before NEC diagnosis harbored significantly more Klebsiella, bacteria encoding fimbriae, and bacteria encoding secondary metabolite gene clusters related to quorum sensing and bacteriocin production. Notably, replication rates of all bacteria, especially Enterobacteriaceae, were significantly higher 2 days before NEC diagnosis. The findings uncover biomarkers that could lead to early detection of NEC and targets for microbiome-based therapeutics.},
}

Enterobacteriaceae/genetics
Enterocolitis, Necrotizing/*genetics/microbiology
Feces/microbiology
Fimbriae, Bacterial/*genetics/microbiology
Gastrointestinal Microbiome/*genetics
Humans
Infant, Newborn
Infant, Premature
Infant, Premature, Diseases/genetics/microbiology
Klebsiella/genetics
*Metagenomics
Multigene Family/genetics