@article {pmid32991226,
year = {2020},
author = {Kumar, S and Paul, D and Bhushan, B and Wakchaure, GC and Meena, KK and Shouche, Y},
title = {Traversing the "Omic" landscape of microbial halotolerance for key molecular processes and new insights.},
journal = {Critical reviews in microbiology},
volume = {46},
number = {6},
pages = {631-653},
doi = {10.1080/1040841X.2020.1819770},
pmid = {32991226},
issn = {1549-7828},
mesh = {Bacteria/classification/*genetics/isolation & purification/*metabolism ; Ecosystem ; Metagenome ; Metagenomics ; Microbiota ; Phylogeny ; Sodium Chloride/*metabolism ; },
abstract = {Post-2005, the biology of the salt afflicted habitats is predominantly studied employing high throughput "Omic" approaches comprising metagenomics, transcriptomics, metatranscriptomics, metabolomics, and proteomics. Such "Omic-based" studies have deciphered the unfamiliar details about microbial salt-stress biology. The MAGs (Metagenome-assembled genomes) of uncultured halophilic microbial lineages such as Nanohaloarchaea and haloalkaliphilic members within CPR (Candidate Phyla Radiation) have been reconstructed from diverse hypersaline habitats. The study of MAGs of such uncultured halophilic microbial lineages has unveiled the genomic basis of salt stress tolerance in "yet to culture" microbial lineages. Furthermore, functional metagenomic approaches have been used to decipher the novel genes from uncultured microbes and their possible role in microbial salt-stress tolerance. The present review focuses on the new insights into microbial salt-stress biology gained through different "Omic" approaches. This review also summarizes the key molecular processes that underlie microbial salt-stress response, and their role in microbial salt-stress tolerance has been confirmed at more than one "Omic" levels.},
}

Bacteria/classification/*genetics/isolation & purification/*metabolism
Ecosystem
Metagenome
Metagenomics
Microbiota
Phylogeny
Sodium Chloride/*metabolism

@article {pmid32650814,
year = {2020},
author = {Wu, J and Dai, Y and Lo, ECM and Qi, Y and Zhang, Y and Li, QL and Dai, R},
title = {Using metagenomic analysis to assess the effectiveness of oral health promotion interventions in reducing risk for pneumonia among patients with stroke in acute phase: study protocol for a randomized controlled trial.},
journal = {Trials},
volume = {21},
number = {1},
pages = {634},
pmid = {32650814},
issn = {1745-6215},
support = {8170041044//Young Scientists Fund/ ; 1808085QH247//Natural Science Foundation of Anhui Province/ ; },
mesh = {China ; *Health Promotion ; Humans ; *Metagenomics ; Microbiota ; Mouth/microbiology ; *Oral Health ; Oral Hygiene ; Pneumonia/*prevention & control ; RNA, Ribosomal, 16S ; Randomized Controlled Trials as Topic ; Single-Blind Method ; Stroke/*complications ; },
abstract = {BACKGROUND: The prevalence of pneumonia complicating stroke in acute phase has a poor prognosis and higher risk for death. Oral opportunistic pathogens have been reported to be associated with pneumonia among people with compromised health. Oral health promotion is effective in reducing dental plaque among patients with stroke, which is considered as reservoirs for oral opportunistic pathogens. This study evaluates the effectiveness of oral health promotions in reducing the prevalence of pneumonia via its effects on composition and relative abundance of oral opportunistic pathogens.

METHODS/DESIGN: This study is a randomized, single-blind, parallel trial of 6 months duration. The study is being conducted at one of the largest medical teaching hospitals in Hefei, China. A total of 166 patients with stroke and free from any post-stroke complication will be recruited. After enrollment, patients will be randomized to one of the following groups: (1) oral hygiene instruction (OHI) or (2) OHI, 6-month use of powered tooth brushing, and 0.2% chlorhexidine gluconate mouth rinse (10 ml twice daily). The primary outcome is the prevalence of pneumonia complicating stroke. Patients will be monitored closely for any occurrence of pneumonia over the entire period of this trial. Oral rinse samples will be collected at baseline and multiple follow-up reviews (3, 5, 7 days, and 1, 3, 6 months after baseline). Next-generation sequencing will be employed to detect composition and relative abundances of the microorganism in the oral rinse samples. Questionnaire interviews and clinical oral examinations will be conducted at baseline and 1, 3, and 6 months after baseline.

DISCUSSION: The findings of this trial will provide evidence whether oral health promotion intervention is effective in reducing the prevalence of pneumonia complicating stroke via its effect on the oral microbiome. The analysis of the outcomes of this trial is empowered by metagenomic analysis at 16S rRNA level, which is more sensitive and comprehensive to help us detect how oral health promotion inventions affect the oral microbiome in terms of its composition, relative abundance, and interactions between species, which all may contribute to the occurrence of pneumonia complicating stroke.

TRIAL REGISTRATION: ClinicalTrials.gov NCT04095780 . Registered on 19 September 2019.},
}

China
*Health Promotion
Humans
*Metagenomics
Microbiota
Mouth/microbiology
*Oral Health
Oral Hygiene
Pneumonia/*prevention & control
RNA, Ribosomal, 16S
Randomized Controlled Trials as Topic
Single-Blind Method
Stroke/*complications

@article {pmid32471482,
year = {2020},
author = {Zlitni, S and Bishara, A and Moss, EL and Tkachenko, E and Kang, JB and Culver, RN and Andermann, TM and Weng, Z and Wood, C and Handy, C and Ji, HP and Batzoglou, S and Bhatt, AS},
title = {Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale.},
journal = {Genome medicine},
volume = {12},
number = {1},
pages = {50},
pmid = {32471482},
issn = {1756-994X},
support = {R01 HG006137/HG/NHGRI NIH HHS/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; P01 HG000205/HG/NHGRI NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; K08 CA184420/CA/NCI NIH HHS/United States ; },
mesh = {Anti-Infective Agents/pharmacology ; Azacitidine/pharmacology ; Azithromycin/pharmacology ; Bacteria/classification/drug effects/*genetics/isolation & purification ; Ciprofloxacin/pharmacology ; DNA, Bacterial ; Diet ; Feces/microbiology ; Gastrointestinal Microbiome/drug effects/*genetics ; Genome, Bacterial ; Hematopoietic Stem Cell Transplantation ; Humans ; Immunosuppressive Agents/pharmacology ; Male ; Metagenome ; Middle Aged ; Myelodysplastic Syndromes/microbiology/therapy ; Primary Myelofibrosis/microbiology/therapy ; RNA-Seq ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Populations of closely related microbial strains can be simultaneously present in bacterial communities such as the human gut microbiome. We recently developed a de novo genome assembly approach that uses read cloud sequencing to provide more complete microbial genome drafts, enabling precise differentiation and tracking of strain-level dynamics across metagenomic samples. In this case study, we present a proof-of-concept using read cloud sequencing to describe bacterial strain diversity in the gut microbiome of one hematopoietic cell transplantation patient over a 2-month time course and highlight temporal strain variation of gut microbes during therapy. The treatment was accompanied by diet changes and administration of multiple immunosuppressants and antimicrobials.

METHODS: We conducted short-read and read cloud metagenomic sequencing of DNA extracted from four longitudinal stool samples collected during the course of treatment of one hematopoietic cell transplantation (HCT) patient. After applying read cloud metagenomic assembly to discover strain-level sequence variants in these complex microbiome samples, we performed metatranscriptomic analysis to investigate differential expression of antibiotic resistance genes. Finally, we validated predictions from the genomic and metatranscriptomic findings through in vitro antibiotic susceptibility testing and whole genome sequencing of isolates derived from the patient stool samples.

RESULTS: During the 56-day longitudinal time course that was studied, the patient's microbiome was profoundly disrupted and eventually dominated by Bacteroides caccae. Comparative analysis of B. caccae genomes obtained using read cloud sequencing together with metagenomic RNA sequencing allowed us to identify differences in substrain populations over time. Based on this, we predicted that particular mobile element integrations likely resulted in increased antibiotic resistance, which we further supported using in vitro antibiotic susceptibility testing.

CONCLUSIONS: We find read cloud assembly to be useful in identifying key structural genomic strain variants within a metagenomic sample. These strains have fluctuating relative abundance over relatively short time periods in human microbiomes. We also find specific structural genomic variations that are associated with increased antibiotic resistance over the course of clinical treatment.},
}

Anti-Infective Agents/pharmacology
Azacitidine/pharmacology
Azithromycin/pharmacology
Bacteria/classification/drug effects/*genetics/isolation & purification
Ciprofloxacin/pharmacology
DNA, Bacterial
Diet
Feces/microbiology
Gastrointestinal Microbiome/drug effects/*genetics
Genome, Bacterial
Hematopoietic Stem Cell Transplantation
Humans
Immunosuppressive Agents/pharmacology
Male
Metagenome
Middle Aged
Myelodysplastic Syndromes/microbiology/therapy
Primary Myelofibrosis/microbiology/therapy
RNA-Seq
Sequence Analysis, DNA

@article {pmid31644955,
year = {2020},
author = {Trujillo-Vargas, CM and Schaefer, L and Alam, J and Pflugfelder, SC and Britton, RA and de Paiva, CS},
title = {The gut-eye-lacrimal gland-microbiome axis in Sjögren Syndrome.},
journal = {The ocular surface},
volume = {18},
number = {2},
pages = {335-344},
pmid = {31644955},
issn = {1937-5913},
support = {P30 CA125123/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; R01 EY026893/EY/NEI NIH HHS/United States ; S10 OD025251/OD/NIH HHS/United States ; P30 EY002520/EY/NEI NIH HHS/United States ; },
mesh = {Animals ; Dry Eye Syndromes ; *Gastrointestinal Microbiome ; *Lacrimal Apparatus ; *Microbiota ; *Sjogren's Syndrome ; },
abstract = {The bacterial communities that collectively inhabit our body are called the microbiome. Virtually all body surface harbors bacteria. Recent advances in next-generation sequencing that have provided insight into the diversity, composition of bacterial communities, and their interaction are discussed in this review, as well as the current knowledge of how the microbiome promotes ocular health. The ocular surface is a site of low bacterial load. Sjögren Syndrome is an autoimmune disease that affects the exocrine glands, causing dry mouth and dry eye. Systemic antibiotic treatment and germ-free mice have demonstrated that commensal bacteria have a protective role for the ocular surface and lacrimal gland. The existence of a gut-eye-lacrimal gland axis-microbiome is discussed.},
}

Animals
Dry Eye Syndromes
*Gastrointestinal Microbiome
*Lacrimal Apparatus
*Microbiota
*Sjogren's Syndrome

@article {pmid33923593,
year = {2021},
author = {Fulci, V and Stronati, L and Cucchiara, S and Laudadio, I and Carissimi, C},
title = {Emerging Roles of Gut Virome in Pediatric Diseases.},
journal = {International journal of molecular sciences},
volume = {22},
number = {8},
pages = {},
pmid = {33923593},
issn = {1422-0067},
mesh = {Celiac Disease/microbiology/*virology ; Child ; Diabetes Mellitus, Type 1/microbiology/*virology ; Diarrhea/microbiology/*virology ; Humans ; Inflammatory Bowel Diseases/microbiology/*virology ; Intestinal Mucosa/microbiology/*virology ; Metagenome ; *Virome ; },
abstract = {In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial "dark matter" of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.},
}

Celiac Disease/microbiology/*virology
Child
Diabetes Mellitus, Type 1/microbiology/*virology
Diarrhea/microbiology/*virology
Humans
Inflammatory Bowel Diseases/microbiology/*virology
Intestinal Mucosa/microbiology/*virology
Metagenome
*Virome

@article {pmid33495623,
year = {2021},
author = {He, C and Keren, R and Whittaker, ML and Farag, IF and Doudna, JA and Cate, JHD and Banfield, JF},
title = {Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems.},
journal = {Nature microbiology},
volume = {6},
number = {3},
pages = {354-365},
pmid = {33495623},
issn = {2058-5276},
support = {/HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Agriculture ; Archaea/classification/*physiology/ultrastructure ; Bacteria/classification/ultrastructure ; *Bacterial Physiological Phenomena ; Cell Adhesion ; Cell Proliferation ; *Ecosystem ; Groundwater/chemistry/*microbiology ; Humans ; Metagenome ; Metagenomics/*methods ; Microbiota ; Phylogeny ; Symbiosis ; },
abstract = {Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that are often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity and host association of CPR bacteria and DPANN archaea has not been studied. Here, we performed genome-resolved metagenomic analysis of one agricultural and seven pristine groundwater microbial communities and recovered 746 CPR and DPANN genomes in total. The pristine sites, which serve as local sources of drinking water, contained up to 31% CPR bacteria and 4% DPANN archaea. We observed little species-level overlap of metagenome-assembled genomes (MAGs) across the groundwater sites, indicating that CPR and DPANN communities may be differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy imaging and genomic analyses enabled us to identify CPR and DPANN lineages that reproducibly attach to host cells and showed that the growth of CPR bacteria seems to be stimulated by attachment to host-cell surfaces. Our analysis reveals site-specific diversity of CPR bacteria and DPANN archaea that coexist with diverse hosts in groundwater aquifers. Given that CPR and DPANN organisms have been identified in human microbiomes and their presence is correlated with diseases such as periodontitis, our findings are relevant to considerations of drinking water quality and human health.},
}

Agriculture
Archaea/classification/*physiology/ultrastructure
Bacteria/classification/ultrastructure
*Bacterial Physiological Phenomena
Cell Adhesion
Cell Proliferation
*Ecosystem
Groundwater/chemistry/*microbiology
Humans
Metagenome
Metagenomics/*methods
Microbiota
Phylogeny
Symbiosis

@article {pmid33484150,
year = {2021},
author = {Raffner Basson, A and Gomez-Nguyen, A and LaSalla, A and Buttó, L and Kulpins, D and Warner, A and Di Martino, L and Ponzani, G and Osme, A and Rodriguez-Palacios, A and Cominelli, F},
title = {Replacing Animal Protein with Soy-Pea Protein in an "American Diet" Controls Murine Crohn Disease-Like Ileitis Regardless of Firmicutes: Bacteroidetes Ratio.},
journal = {The Journal of nutrition},
volume = {151},
number = {3},
pages = {579-590},
pmid = {33484150},
issn = {1541-6100},
support = {P01 DK091222/DK/NIDDK NIH HHS/United States ; P30 DK097948/DK/NIDDK NIH HHS/United States ; R01 DK055812/DK/NIDDK NIH HHS/United States ; F32 DK117585/DK/NIDDK NIH HHS/United States ; R21 DK118373/DK/NIDDK NIH HHS/United States ; T32 DK083251/DK/NIDDK NIH HHS/United States ; },
mesh = {Amino Acids/chemistry/metabolism ; Animal Feed ; Animals ; Bacteroidetes ; Colitis/chemically induced/prevention & control ; Dextran Sulfate ; Diet/veterinary ; Dietary Carbohydrates ; Dietary Fats ; Dietary Proteins/*administration & dosage ; Feces/chemistry ; Female ; Firmicutes ; Gastrointestinal Microbiome/*physiology ; Humans ; Ileitis/*prevention & control ; Male ; Mice ; Mice, Inbred C57BL ; *Peas ; *Soybeans ; Specific Pathogen-Free Organisms ; },
abstract = {BACKGROUND: The current nutritional composition of the "American diet" (AD; also known as Western diet) has been linked to the increasing incidence of chronic diseases, including inflammatory bowel disease (IBD), namely Crohn disease (CD).

OBJECTIVES: This study investigated which of the 3 major macronutrients (protein, fat, carbohydrates) in the AD has the greatest impact on preventing chronic inflammation in experimental IBD mouse models.

METHODS: We compared 5 rodent diets designed to mirror the 2011-2012 "What We Eat in America" NHANES. Each diet had 1 macronutrient dietary source replaced. The formulated diets were AD, AD-soy-pea (animal protein replaced by soy + pea protein), AD-CHO ("refined carbohydrate" by polysaccharides), AD-fat [redistribution of the ω-6:ω-3 (n-6:n-3) PUFA ratio; ∼10:1 to 1:1], and AD-mix (all 3 "healthier" macronutrients combined). In 3 separate experiments, 8-wk-old germ-free SAMP1/YitFC mice (SAMP) colonized with human gut microbiota ("hGF-SAMP") from CD or healthy donors were fed an AD, an AD-"modified," or laboratory rodent diet for 24 wk. Two subsequent dextran sodium sulfate-colitis experiments in hGF-SAMP (12-wk-old) and specific-pathogen-free (SPF) C57BL/6 (20-wk-old) mice, and a 6-wk feeding trial in 24-wk-old SPF SAMP were performed. Intestinal inflammation, gut metagenomics, and MS profiles were assessed.

RESULTS: The AD-soy-pea diet resulted in lower histology scores [mean ± SD (56.1% ± 20.7% reduction)] in all feeding trials and IBD mouse models than did other diets (P < 0.05). Compared with the AD, the AD-soy-pea correlated with increased abundance in Lactobacillaceae and Leuconostraceae (1.5-4.7 log2 and 3.0-5.1 log2 difference, respectively), glutamine (6.5 ± 0.8 compared with 3.9 ± 0.3 ng/μg stool, P = 0.0005) and butyric acid (4:0; 3.3 ± 0.5 compared with 2.54 ± 0.4 ng/μg stool, P = 0.006) concentrations, and decreased linoleic acid (18:2n-6; 5.4 ± 0.4 compared with 8.6 ± 0.3 ng/μL plasma, P = 0.01).

CONCLUSIONS: Replacement of animal protein in an AD by plant-based sources reduced the severity of experimental IBD in all mouse models studied, suggesting that similar, feasible adjustments to the daily human diet could help control/prevent IBD in humans.},
}

Amino Acids/chemistry/metabolism
Animal Feed
Animals
Bacteroidetes
Colitis/chemically induced/prevention & control
Dextran Sulfate
Diet/veterinary
Dietary Carbohydrates
Dietary Fats
Dietary Proteins/*administration & dosage
Feces/chemistry
Female
Firmicutes
Gastrointestinal Microbiome/*physiology
Humans
Ileitis/*prevention & control
Male
Mice
Mice, Inbred C57BL
*Peas
*Soybeans
Specific Pathogen-Free Organisms

@article {pmid33432149,
year = {2021},
author = {Lee, SH and Cho, SY and Yoon, Y and Park, C and Sohn, J and Jeong, JJ and Jeon, BN and Jang, M and An, C and Lee, S and Kim, YY and Kim, G and Kim, S and Kim, Y and Lee, GB and Lee, EJ and Kim, SG and Kim, HS and Kim, Y and Kim, H and Yang, HS and Kim, S and Kim, S and Chung, H and Moon, MH and Nam, MH and Kwon, JY and Won, S and Park, JS and Weinstock, GM and Lee, C and Yoon, KW and Park, H},
title = {Bifidobacterium bifidum strains synergize with immune checkpoint inhibitors to reduce tumour burden in mice.},
journal = {Nature microbiology},
volume = {6},
number = {3},
pages = {277-288},
pmid = {33432149},
issn = {2058-5276},
mesh = {Animals ; Bifidobacterium bifidum/classification/genetics/*physiology ; Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology ; Drug Therapy, Combination ; Gastrointestinal Microbiome ; Humans ; Immune Checkpoint Inhibitors/*therapeutic use ; Interferon-gamma/genetics/metabolism ; Lung Neoplasms/drug therapy/microbiology/pathology ; Metabolome/drug effects ; Mice ; Neoplasms, Experimental/drug therapy/pathology ; Probiotics/administration & dosage/*therapeutic use ; Species Specificity ; Transcriptome/drug effects ; Tryptophan/metabolism ; Tumor Burden/*drug effects ; },
abstract = {The gut microbiome can influence the development of tumours and the efficacy of cancer therapeutics1-5; however, the multi-omics characteristics of antitumour bacterial strains have not been fully elucidated. In this study, we integrated metagenomics, genomics and transcriptomics of bacteria, and analyses of mouse intestinal transcriptome and serum metabolome data to reveal an additional mechanism by which bacteria determine the efficacy of cancer therapeutics. In gut microbiome analyses of 96 samples from patients with non-small-cell lung cancer, Bifidobacterium bifidum was abundant in patients responsive to therapy. However, when we treated syngeneic mouse tumours with commercial strains of B. bifidum to establish relevance for potential therapeutic uses, only specific B. bifidum strains reduced tumour burden synergistically with PD-1 blockade or oxaliplatin treatment by eliciting an antitumour host immune response. In mice, these strains induced tuning of the immunological background by potentiating the production of interferon-γ, probably through the enhanced biosynthesis of immune-stimulating molecules and metabolites.},
}

Animals
Bifidobacterium bifidum/classification/genetics/*physiology
Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology
Drug Therapy, Combination
Gastrointestinal Microbiome
Humans
Immune Checkpoint Inhibitors/*therapeutic use
Interferon-gamma/genetics/metabolism
Lung Neoplasms/drug therapy/microbiology/pathology
Metabolome/drug effects
Mice
Neoplasms, Experimental/drug therapy/pathology
Probiotics/administration & dosage/*therapeutic use
Species Specificity
Transcriptome/drug effects
Tryptophan/metabolism
Tumor Burden/*drug effects

@article {pmid32791115,
year = {2020},
author = {Lang, S and Schnabl, B},
title = {Microbiota and Fatty Liver Disease-the Known, the Unknown, and the Future.},
journal = {Cell host & microbe},
volume = {28},
number = {2},
pages = {233-244},
pmid = {32791115},
issn = {1934-6069},
support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; },
mesh = {Animals ; Dysbiosis/microbiology ; Fatty Liver, Alcoholic/*microbiology/*pathology/therapy ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/physiology ; Humans ; Intestines/microbiology/pathology ; Liver/pathology ; Mice ; Non-alcoholic Fatty Liver Disease/*microbiology/*pathology/therapy ; Probiotics/therapeutic use ; },
abstract = {The liver communicates with the intestine via the portal vein, biliary system, and mediators in the circulation. Microbes in the intestine maintain liver homeostasis but can also serve as a source of pathogens and molecules that contribute to fatty liver diseases. We review changes in the gut microbiota that can promote development or progression of alcohol-associated and non-alcoholic fatty liver disease-the most common chronic liver diseases in Western countries. We discuss how microbes and their products contribute to liver disease pathogenesis, putative microbial biomarkers of disease, and potential treatment approaches based on manipulation of the gut microbiota. Increasing our understanding of interactions between the intestinal microbiome and liver might help us identify patients with specific disease subtypes and select specific microbiota-based therapies.},
}

Animals
Dysbiosis/microbiology
Fatty Liver, Alcoholic/*microbiology/*pathology/therapy
Gastrointestinal Microbiome/*physiology
Host Microbial Interactions/physiology
Humans
Intestines/microbiology/pathology
Liver/pathology
Mice
Non-alcoholic Fatty Liver Disease/*microbiology/*pathology/therapy
Probiotics/therapeutic use

@article {pmid32619440,
year = {2020},
author = {Reitmeier, S and Kiessling, S and Clavel, T and List, M and Almeida, EL and Ghosh, TS and Neuhaus, K and Grallert, H and Linseisen, J and Skurk, T and Brandl, B and Breuninger, TA and Troll, M and Rathmann, W and Linkohr, B and Hauner, H and Laudes, M and Franke, A and Le Roy, CI and Bell, JT and Spector, T and Baumbach, J and O'Toole, PW and Peters, A and Haller, D},
title = {Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes.},
journal = {Cell host & microbe},
volume = {28},
number = {2},
pages = {258-272.e6},
doi = {10.1016/j.chom.2020.06.004},
pmid = {32619440},
issn = {1934-6069},
support = {MR/N030125/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Bacteria/classification/genetics/isolation & purification/*metabolism ; Circadian Clocks/physiology ; Circadian Rhythm/*physiology ; Diabetes Mellitus, Type 2/epidemiology/microbiology/*pathology ; Feces/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Germany/epidemiology ; Humans ; Metagenome/genetics ; Metagenomics/methods ; Obesity/microbiology/*pathology ; },
abstract = {Lifestyle, obesity, and the gut microbiome are important risk factors for metabolic disorders. We demonstrate in 1,976 subjects of a German population cohort (KORA) that specific microbiota members show 24-h oscillations in their relative abundance and identified 13 taxa with disrupted rhythmicity in type 2 diabetes (T2D). Cross-validated prediction models based on this signature similarly classified T2D. In an independent cohort (FoCus), disruption of microbial oscillation and the model for T2D classification was confirmed in 1,363 subjects. This arrhythmic risk signature was able to predict T2D in 699 KORA subjects 5 years after initial sampling, being most effective in combination with BMI. Shotgun metagenomic analysis functionally linked 26 metabolic pathways to the diurnal oscillation of gut bacteria. Thus, a cohort-specific risk pattern of arrhythmic taxa enables classification and prediction of T2D, suggesting a functional link between circadian rhythms and the microbiome in metabolic diseases.},
}

Bacteria/classification/genetics/isolation & purification/*metabolism
Circadian Clocks/physiology
Circadian Rhythm/*physiology
Diabetes Mellitus, Type 2/epidemiology/microbiology/*pathology
Feces/microbiology
Gastrointestinal Microbiome/genetics/*physiology
Germany/epidemiology
Humans
Metagenome/genetics
Metagenomics/methods
Obesity/microbiology/*pathology

@article {pmid32544460,
year = {2020},
author = {Kenny, DJ and Plichta, DR and Shungin, D and Koppel, N and Hall, AB and Fu, B and Vasan, RS and Shaw, SY and Vlamakis, H and Balskus, EP and Xavier, RJ},
title = {Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level.},
journal = {Cell host & microbe},
volume = {28},
number = {2},
pages = {245-257.e6},
pmid = {32544460},
issn = {1934-6069},
support = {R01 HL131015/HL/NHLBI NIH HHS/United States ; R01 HL092577/HL/NHLBI NIH HHS/United States ; P30 DK034854/DK/NIDDK NIH HHS/United States ; HHSN268201500001I/HL/NHLBI NIH HHS/United States ; T32 GM095450/GM/NIGMS NIH HHS/United States ; N01HC25195/HL/NHLBI NIH HHS/United States ; F32 MH095450/MH/NIMH NIH HHS/United States ; 75N92019D00031/HL/NHLBI NIH HHS/United States ; HHSN268201500001C/HL/NHLBI NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; },
mesh = {Bacteria/enzymology/genetics/*metabolism ; Cholestanol/*biosynthesis ; Cholesterol/*blood/*metabolism ; Feces/chemistry/microbiology ; Gastrointestinal Microbiome/genetics/*physiology ; Humans ; Lipid Metabolism/physiology ; Metabolomics ; Metagenomics ; Oxidoreductases/genetics/*metabolism ; },
abstract = {The human microbiome encodes extensive metabolic capabilities, but our understanding of the mechanisms linking gut microbes to human metabolism remains limited. Here, we focus on the conversion of cholesterol to the poorly absorbed sterol coprostanol by the gut microbiota to develop a framework for the identification of functional enzymes and microbes. By integrating paired metagenomics and metabolomics data from existing cohorts with biochemical knowledge and experimentation, we predict and validate a group of microbial cholesterol dehydrogenases that contribute to coprostanol formation. These enzymes are encoded by ismA genes in a clade of uncultured microorganisms, which are prevalent in geographically diverse human cohorts. Individuals harboring coprostanol-forming microbes have significantly lower fecal cholesterol levels and lower serum total cholesterol with effects comparable to those attributed to variations in lipid homeostasis genes. Thus, cholesterol metabolism by these microbes may play important roles in reducing intestinal and serum cholesterol concentrations, directly impacting human health.},
}

Bacteria/enzymology/genetics/*metabolism
Cholestanol/*biosynthesis
Cholesterol/*blood/*metabolism
Feces/chemistry/microbiology
Gastrointestinal Microbiome/genetics/*physiology
Humans
Lipid Metabolism/physiology
Metabolomics
Metagenomics
Oxidoreductases/genetics/*metabolism

@article {pmid33820995,
year = {2021},
author = {Mac Aogáin, M and Narayana, JK and Tiew, PY and Ali, NABM and Yong, VFL and Jaggi, TK and Lim, AYH and Keir, HR and Dicker, AJ and Thng, KX and Tsang, A and Ivan, FX and Poh, ME and Oriano, M and Aliberti, S and Blasi, F and Low, TB and Ong, TH and Oliver, B and Giam, YH and Tee, A and Koh, MS and Abisheganaden, JA and Tsaneva-Atanasova, K and Chalmers, JD and Chotirmall, SH},
title = {Integrative microbiomics in bronchiectasis exacerbations.},
journal = {Nature medicine},
volume = {27},
number = {4},
pages = {688-699},
pmid = {33820995},
issn = {1546-170X},
support = {SCAF/17/03/CSO_/Chief Scientist Office/United Kingdom ; },
mesh = {Bronchiectasis/*microbiology/virology ; Disease Progression ; Humans ; Metagenomics ; Microbial Interactions/genetics ; *Microbiota/genetics ; Phylogeny ; },
abstract = {Bronchiectasis, a progressive chronic airway disease, is characterized by microbial colonization and infection. We present an approach to the multi-biome that integrates bacterial, viral and fungal communities in bronchiectasis through weighted similarity network fusion (https://integrative-microbiomics.ntu.edu.sg). Patients at greatest risk of exacerbation have less complex microbial co-occurrence networks, reduced diversity and a higher degree of antagonistic interactions in their airway microbiome. Furthermore, longitudinal interactome dynamics reveals microbial antagonism during exacerbation, which resolves following treatment in an otherwise stable multi-biome. Assessment of the Pseudomonas interactome shows that interaction networks, rather than abundance alone, are associated with exacerbation risk, and that incorporation of microbial interaction data improves clinical prediction models. Shotgun metagenomic sequencing of an independent cohort validated the multi-biome interactions detected in targeted analysis and confirmed the association with exacerbation. Integrative microbiomics captures microbial interactions to determine exacerbation risk, which cannot be appreciated by the study of a single microbial group. Antibiotic strategies probably target the interaction networks rather than individual microbes, providing a fresh approach to the understanding of respiratory infection.},
}

Bronchiectasis/*microbiology/virology
Disease Progression
Humans
Metagenomics
Microbial Interactions/genetics
*Microbiota/genetics
Phylogeny

@article {pmid32572536,
year = {2020},
author = {Díaz-García, L and Bugg, TDH and Jiménez, DJ},
title = {Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach.},
journal = {Microbial ecology},
volume = {80},
number = {4},
pages = {885-896},
doi = {10.1007/s00248-020-01546-1},
pmid = {32572536},
issn = {1432-184X},
support = {PR.3.2018.5287//Universidad de Los Andes/ ; BB/P01738X/1//BBSRC/ ; },
mesh = {Bacteria/*enzymology/genetics ; Biomass ; Lignin/*metabolism ; *Metagenome ; Metagenomics ; *Microbial Consortia ; Panicum/microbiology ; *Soil Microbiology ; Triticum/microbiology ; Zea mays/microbiology ; },
abstract = {An exploration of the ligninolytic potential of lignocellulolytic microbial consortia can improve our understanding of the eco-enzymology of lignin conversion in nature. In this study, we aimed to detect enriched lignin-transforming enzymes on metagenomes from three soil-derived microbial consortia that were cultivated on "pre-digested" plant biomass (wheat straw, WS1-M; switchgrass, SG-M; and corn stover, CS-M). Of 60 selected enzyme-encoding genes putatively involved in lignin catabolism, 20 genes were significantly abundant in WS1-M, CS-M, and/or SG-M consortia compared with the initial forest soil inoculum metagenome (FS1). These genes could be involved in lignin oxidation (e.g., superoxide dismutases), oxidative stress responses (e.g., catalase/peroxidases), generation of protocatechuate (e.g., vanAB genes), catabolism of gentisate, catechol and 3-phenylpropionic acid (e.g., gentisate 1,2-dioxygenases, muconate cycloisomerases, and hcaAB genes), the beta-ketoadipate pathway (e.g., pcaIJ genes), and tolerance to lignocellulose-derived inhibitors (e.g., thymidylate synthases). The taxonomic affiliation of 22 selected lignin-transforming enzymes from WS1-M and CS-M consortia metagenomes revealed that Pseudomonadaceae, Alcaligenaceae, Sphingomonadaceae, Caulobacteraceae, Comamonadaceae, and Xanthomonadaceae are the key bacterial families in the catabolism of lignin. A predictive "model" was sketched out, where each microbial population has the potential to metabolize an array of aromatic compounds through different pathways, suggesting that lignin catabolism can follow a "task division" strategy. Here, we have established an association between functions and taxonomy, allowing a better understanding of lignin transformations in soil-derived lignocellulolytic microbial consortia, and pinpointing some bacterial taxa and catabolic genes as ligninolytic trait-markers.},
}

Bacteria/*enzymology/genetics
Biomass
Lignin/*metabolism
*Metagenome
Metagenomics
*Microbial Consortia
Panicum/microbiology
*Soil Microbiology
Triticum/microbiology
Zea mays/microbiology

@article {pmid32052588,
year = {2020},
author = {Li, X and Xu, M and Li, X and Christie, P and Wagg, C and Zhang, J},
title = {Linkages between changes in plant and mycorrhizal fungal community composition at high versus low elevation in alpine ecosystems.},
journal = {Environmental microbiology reports},
volume = {12},
number = {2},
pages = {229-240},
doi = {10.1111/1758-2229.12827},
pmid = {32052588},
issn = {1758-2229},
support = {31272251//National Natural Science Foundation of China/International ; 31872182//National Natural Science Foundation of China/International ; 31702002//National Natural Science Foundation of China/International ; },
mesh = {*Altitude ; Biodiversity ; Biomass ; Ecosystem ; Genes, Fungal ; Metagenome ; Metagenomics/methods ; Mycobiome ; *Mycorrhizae/classification/genetics ; Phylogeny ; Plants/*microbiology ; Soil/chemistry ; Soil Microbiology ; Tibet ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) play an important role in maintaining plant diversity and productivity in grassland ecosystems. However, very few studies have investigated how AMF and plant communities co-vary between contrasting environments in natural ecosystems. Intensive sampling (50 soil samples) was conducted in natural open grasslands at both 3570 and 4556 m on Mount Segrila on the Southeast Tibetan Plateau. We used 454-pyrosequencing to investigate soil AMF communities and to explore relationships between AMF diversity and plant richness, productivity and community composition. AMF diversity was negatively correlated with plant richness at 3570 m but positively at 4556 m. Differences in AMF community composition between elevations were attributable to plant community composition, soil pH and available phosphorus concentration. The AMF community was more phylogenetically clustered at the higher elevation than the lower elevation. However, greater phylogenetic clustering (under dispersion) of AMF communities at the two elevations was positively correlated with above-ground biomass. Our results indicate that plant community composition and environmental filtering are the primary drivers structuring the AMF community. Phylogenetic relatedness may be important in explaining the function of AMF communities in alpine ecosystems.},
}

*Altitude
Biodiversity
Biomass
Ecosystem
Genes, Fungal
Metagenome
Metagenomics/methods
Mycobiome
*Mycorrhizae/classification/genetics
Phylogeny
Plants/*microbiology
Soil/chemistry
Soil Microbiology
Tibet

@article {pmid31997562,
year = {2020},
author = {Martinez-Hernandez, F and Luo, E and Tominaga, K and Ogata, H and Yoshida, T and DeLong, EF and Martinez-Garcia, M},
title = {Diel cycling of the cosmopolitan abundant Pelagibacter virus 37-F6: one of the most abundant viruses on earth.},
journal = {Environmental microbiology reports},
volume = {12},
number = {2},
pages = {214-219},
doi = {10.1111/1758-2229.12825},
pmid = {31997562},
issn = {1758-2229},
support = {5334//Gordon and Betty Moore Foundation/International ; RTI2018-094248-B-I00//Secretaría de Estado de Investigación, Desarrollo e Innovación/International ; 329108//Simons Foundation/International ; ACIF/2015/332//Generalitat Valenciana/International ; },
mesh = {Alphaproteobacteria/physiology/*virology ; *Bacteriophages/genetics/physiology ; Circadian Rhythm/*physiology ; Gene Expression Profiling/methods ; Genome, Bacterial ; Genome, Viral ; Metagenomics/methods ; Oceans and Seas ; *Seawater/microbiology/virology ; Transcriptome ; Virome ; },
abstract = {The spatiotemporal dynamics for marine viral populations has only recently been explored. However, nothing is known about temporal activities of the uncultured Pelagibacter virus vSAG 37-F6, which was discovered by single-virus genomics as potentially the most abundant marine virus. Here, we investigate the diel cycling of 37-F6 virus and the putative SAR11 host using coastal and oceanic transcriptomic and viromic time-series data from Osaka Bay and North Pacific Subtropical Gyre. Virus 37-F6 and relatives displayed diel cycling of transcriptional activities synchronized with its putative host. In both virus and host, the lowest transcription rates were observed at 14:00-15:00, coinciding roughly with maximum solar irradiance, while higher transcriptional rates were detected during the night/early morning and afternoon. Diel abundance of free viruses of 37-F6 in seawater roughly mirrored the transcriptional activities of both virus and host. In Osaka Bay, among viral relatives (genus level), virus 37-F6 specifically showed the highest ratio of transcriptional activity to virome abundance, a proxy for viral transcriptional activity relative to free viral particle abundance. This high ratio suggests high infection rate efficiencies in vSAG 37-F6 virus compared to viral relatives. Thus, time-series data revealed temporal transcript activities in one of the most abundant viruses in Earth.},
}

Alphaproteobacteria/physiology/*virology
*Bacteriophages/genetics/physiology
Circadian Rhythm/*physiology
Gene Expression Profiling/methods
Genome, Bacterial
Genome, Viral
Metagenomics/methods
Oceans and Seas
*Seawater/microbiology/virology
Transcriptome
Virome

@article {pmid31773890,
year = {2020},
author = {McDermott, TR and Stolz, JF and Oremland, RS},
title = {Arsenic and the gastrointestinal tract microbiome.},
journal = {Environmental microbiology reports},
volume = {12},
number = {2},
pages = {136-159},
doi = {10.1111/1758-2229.12814},
pmid = {31773890},
issn = {1758-2229},
support = {911310//Montana Agricultural Experiment Station/International ; NNX09AW41G/NASA/NASA/United States ; R01 CA215784/CA/NCI NIH HHS/United States ; MCB-1714556//National Science Foundation/International ; /CA/NCI NIH HHS/United States ; NNX09AW41G/NASA/NASA/United States ; /CA/NCI NIH HHS/United States ; },
mesh = {Arsenates/metabolism ; Arsenic/metabolism/*toxicity ; Arsenite Transporting ATPases/*genetics ; Bacteria/classification/genetics/isolation & purification ; Bacteroidetes/classification/genetics/isolation & purification ; Bioaccumulation/physiology ; Drug Resistance/genetics ; Escherichia coli Proteins/genetics ; Firmicutes/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; Gastrointestinal Tract/anatomy & histology/microbiology ; Genes, Bacterial/drug effects ; Humans ; Ion Pumps/genetics ; Metagenomics ; Molecular Chaperones/genetics ; Multienzyme Complexes/genetics ; Proteobacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S ; },
abstract = {Arsenic is a toxin, ranking first on the Agency for Toxic Substances and Disease Registry and the Environmental Protection Agency Priority List of Hazardous Substances. Chronic exposure increases the risk of a broad range of human illnesses, most notably cancer; however, there is significant variability in arsenic-induced disease among exposed individuals. Human genetics is a known component, but it alone cannot account for the large inter-individual variability in the presentation of arsenicosis symptoms. Each part of the gastrointestinal tract (GIT) may be considered as a unique environment with characteristic pH, oxygen concentration, and microbiome. Given the well-established arsenic redox transformation activities of microorganisms, it is reasonable to imagine how the GIT microbiome composition variability among individuals could play a significant role in determining the fate, mobility and toxicity of arsenic, whether inhaled or ingested. This is a relatively new field of research that would benefit from early dialogue aimed at summarizing what is known and identifying reasonable research targets and concepts. Herein, we strive to initiate this dialogue by reviewing known aspects of microbe-arsenic interactions and placing it in the context of potential for influencing host exposure and health risks. We finish by considering future experimental approaches that might be of value.},
}

Arsenates/metabolism
Arsenic/metabolism/*toxicity
Arsenite Transporting ATPases/*genetics
Bacteria/classification/genetics/isolation & purification
Bacteroidetes/classification/genetics/isolation & purification
Bioaccumulation/physiology
Drug Resistance/genetics
Escherichia coli Proteins/genetics
Firmicutes/classification/genetics/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
Gastrointestinal Tract/anatomy & histology/microbiology
Genes, Bacterial/drug effects
Humans
Ion Pumps/genetics
Metagenomics
Molecular Chaperones/genetics
Multienzyme Complexes/genetics
Proteobacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S

@article {pmid33968595,
year = {2021},
author = {Shet, SA and Garg, S},
title = {Prokaryotic diversity of tropical coastal sand dunes ecosystem using metagenomics.},
journal = {3 Biotech},
volume = {11},
number = {5},
pages = {252},
doi = {10.1007/s13205-021-02809-5},
pmid = {33968595},
issn = {2190-572X},
abstract = {Coastal sand dunes (CSDs), unique, stressed and hostile habitats act as a barrier between marine and terrestrial ecosystems. CSDs are stressed in terms of nutrition and fluctuating physio-chemical conditions. CSD is classified into several types, each of which presents different challenges for life forms. This study focuses on exploring bacterial and archaeal diversity and community structure in four CSD namely, Embryo, Fore, Gray, and Mature dunes of Keri beach, Goa along the west coast of India. The study was carried out using Next Generation Sequencing of hypervariable V3-V4 regions of the 16S rRNA gene using Illumina HiSeq platform. The present study hypothesizes that the prokaryotic communities at each dune may be different and could have different role in the ecosystem. The NGS for Embryo, Fore, Gray, and Mature dunes gave 1,045,447, 1,451,753, 1,321,867, and 1,537,758 paired-end reads, respectively, out of which 54,500, 50,032, 37,819, and 111,186 were retained through various quality filtrations. A total of 74, 63, 65, and 65% of OTUs, respectively, remained unknown at the species level. The highest bacterial and archaeal abundance was reported from Mature and Embryo dunes, respectively. Phylum Actinobacteria dominated the Embryo, Fore, and Mature dunes, whereas phylum Proteobacteria was the dominant in the Gray dune. Streptomyces was predominant in overall CSD followed by Bacillus, Acidobacterium, and Kouleothrix. The commonly and exclusively found members in each dune are cataloged. The highest species dominance, diversity, species richness, and abundance were observed in Embryo, Fore, Gray, and Mature dunes, respectively. The present study clearly elucidates that each dune has a distinct microbial community structure.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-021-02809-5.},
}

@article {pmid33805379,
year = {2021},
author = {Su, H and Xiao, Z and Yu, K and Zhang, Q and Lu, C and Wang, G and Wang, Y and Liang, J and Huang, W and Huang, X and Wei, F},
title = {High Diversity of β-Glucosidase-Producing Bacteria and Their Genes Associated with Scleractinian Corals.},
journal = {International journal of molecular sciences},
volume = {22},
number = {7},
pages = {},
pmid = {33805379},
issn = {1422-0067},
support = {42030502//National Natural Science Foundation of China/ ; 42090041//National Natural Science Foundation of China/ ; 41706158//National Natural Science Foundation of China/ ; AD19245121//Science and Technology Project of Guangxi/ ; AD17129019//Science and Technology Project of Guangxi/ ; AD17129063//Science and Technology Project of Guangxi/ ; AA17204074//Science and Technology Project of Guangxi/ ; AA18242026//Major Research Project of Guangxi for Science and Technology/ ; 2018GXNSFBA281101//Natural Science Foundation of Guangxi Province/ ; },
mesh = {Animals ; Anthozoa/*microbiology ; Bacteria/*enzymology/genetics ; Metagenomics ; Microbiota/*genetics ; Phylogeny ; beta-Glucosidase/*genetics/metabolism ; },
abstract = {β-Glucosidase is a microbial cellulose multienzyme that plays an important role in the regulation of the entire cellulose hydrolysis process, which is the rate-limiting step in bacterial carbon cycling in marine environments. Despite its importance in coral reefs, the diversity of β-glucosidase-producing bacteria, their genes, and enzymatic characteristics are poorly understood. In this study, 87 β-glucosidase-producing cultivable bacteria were screened from 6 genera of corals. The isolates were assigned to 21 genera, distributed among three groups: Proteobacteria, Firmicutes, and Actinobacteria. In addition, metagenomics was used to explore the genetic diversity of bacterial β-glucosidase enzymes associated with scleractinian corals, which revealed that these enzymes mainly belong to the glycosidase hydrolase family 3 (GH3). Finally, a novel recombinant β-glucosidase, referred to as Mg9373, encompassing 670 amino acids and a molecular mass of 75.2 kDa, was classified as a member of the GH3 family and successfully expressed and characterized. Mg9373 exhibited excellent tolerance to ethanol, NaCl, and glucose. Collectively, these results suggest that the diversity of β-glucosidase-producing bacteria and genes associated with scleractinian corals is high and novel, indicating great potential for applications in the food industry and agriculture.},
}

Animals
Anthozoa/*microbiology
Bacteria/*enzymology/genetics
Metagenomics
Microbiota/*genetics
Phylogeny
beta-Glucosidase/*genetics/metabolism

@article {pmid33439103,
year = {2021},
author = {Cuna, A and Morowitz, MJ and Ahmed, I and Umar, S and Sampath, V},
title = {Dynamics of the preterm gut microbiome in health and disease.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {320},
number = {4},
pages = {G411-G419},
doi = {10.1152/ajpgi.00399.2020},
pmid = {33439103},
issn = {1522-1547},
support = {R01 DK117296/DK/NIDDK NIH HHS/United States ; K08DK125735//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
mesh = {Animals ; Bacteria/*growth & development ; Dysbiosis ; Enterocolitis, Necrotizing/*microbiology/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Gestational Age ; Host-Pathogen Interactions ; Humans ; Infant, Newborn ; *Infant, Premature ; Intestines/*microbiology ; Neonatal Sepsis/*microbiology/therapy ; Prebiotics ; Probiotics/therapeutic use ; Prognosis ; Risk Factors ; },
abstract = {Advances in metagenomics have allowed a detailed study of the gut microbiome, and its role in human health and disease. Infants born prematurely possess a fragile gut microbial ecosystem that is vulnerable to perturbation. Alterations in the developing gut microbiome in preterm infants are linked to life-threatening diseases such as necrotizing enterocolitis (NEC) and late-onset sepsis; and may impact future risk of asthma, atopy, obesity, and psychosocial disease. In this mini-review, we summarize recent literature on the origins and patterns of development of the preterm gut microbiome in the perinatal period. The host-microbiome-environmental factors that portend development of dysbiotic intestinal microbial patterns associated with NEC and sepsis are reviewed. Strategies to manipulate the microbiome and mitigate dysbiosis, including the use of probiotics and prebiotics will also be discussed. Finally, we explore the challenges and future directions of gut microbiome research in preterm infants.},
}

Animals
Bacteria/*growth & development
Dysbiosis
Enterocolitis, Necrotizing/*microbiology/therapy
Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
Gestational Age
Host-Pathogen Interactions
Humans
Infant, Newborn
*Infant, Premature
Intestines/*microbiology
Neonatal Sepsis/*microbiology/therapy
Prebiotics
Probiotics/therapeutic use
Prognosis
Risk Factors

@article {pmid33411719,
year = {2021},
author = {Elmassry, MM and Kim, S and Busby, B},
title = {Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244876},
pmid = {33411719},
issn = {1932-6203},
mesh = {Adult ; Bacteria/genetics ; Computational Biology/methods ; Data Management ; Female ; Forecasting/*methods ; Gastrointestinal Microbiome/*drug effects/genetics ; Glucuronidase/genetics/metabolism ; Humans ; Infant, Newborn ; Male ; Metagenome/drug effects/genetics ; Metagenomics/*methods ; Microbiota/drug effects/genetics ; Mothers ; },
abstract = {Characterizing the gut microbiota in terms of their capacity to interfere with drug metabolism is necessary to achieve drug efficacy and safety. Although examples of drug-microbiome interactions are well-documented, little has been reported about a computational pipeline for systematically identifying and characterizing bacterial enzymes that process particular classes of drugs. The goal of our study is to develop a computational approach that compiles drugs whose metabolism may be influenced by a particular class of microbial enzymes and that quantifies the variability in the collective level of those enzymes among individuals. The present paper describes this approach, with microbial β-glucuronidases as an example, which break down drug-glucuronide conjugates and reactivate the drugs or their metabolites. We identified 100 medications that may be metabolized by β-glucuronidases from the gut microbiome. These medications included morphine, estrogen, ibuprofen, midazolam, and their structural analogues. The analysis of metagenomic data available through the Sequence Read Archive (SRA) showed that the level of β-glucuronidase in the gut metagenomes was higher in males than in females, which provides a potential explanation for the sex-based differences in efficacy and toxicity for several drugs, reported in previous studies. Our analysis also showed that infant gut metagenomes at birth and 12 months of age have higher levels of β-glucuronidase than the metagenomes of their mothers and the implication of this observed variability was discussed in the context of breastfeeding as well as infant hyperbilirubinemia. Overall, despite important limitations discussed in this paper, our analysis provided useful insights on the role of the human gut metagenome in the variability in drug response among individuals. Importantly, this approach exploits drug and metagenome data available in public databases as well as open-source cheminformatics and bioinformatics tools to predict drug-metagenome interactions.},
}

Adult
Bacteria/genetics
Computational Biology/methods
Data Management
Female
Forecasting/*methods
Gastrointestinal Microbiome/*drug effects/genetics
Glucuronidase/genetics/metabolism
Humans
Infant, Newborn
Male
Metagenome/drug effects/genetics
Metagenomics/*methods
Microbiota/drug effects/genetics
Mothers

@article {pmid33395690,
year = {2021},
author = {Muturi, SM and Muthui, LW and Njogu, PM and Onguso, JM and Wachira, FN and Opiyo, SO and Pelle, R},
title = {Metagenomics survey unravels diversity of biogas microbiomes with potential to enhance productivity in Kenya.},
journal = {PloS one},
volume = {16},
number = {1},
pages = {e0244755},
pmid = {33395690},
issn = {1932-6203},
mesh = {Archaea/genetics ; Bacteria/genetics ; Bacteria, Anaerobic/genetics/metabolism ; Biodiversity ; Biofuels/*microbiology ; Bioreactors/microbiology ; Euryarchaeota/metabolism ; Fermentation ; Fungi/genetics ; Kenya ; Metagenomics/*methods ; Methane/metabolism ; Methanomicrobiales/metabolism ; Microbiota/*genetics/physiology ; Phylogeny ; RNA, Ribosomal, 16S ; },
abstract = {The obstacle to optimal utilization of biogas technology is poor understanding of biogas microbiomes diversities over a wide geographical coverage. We performed random shotgun sequencing on twelve environmental samples. Randomized complete block design was utilized to assign the twelve treatments to four blocks, within eastern and central regions of Kenya. We obtained 42 million paired-end reads that were annotated against sixteen reference databases using two ENVO ontologies, prior to β-diversity studies. We identified 37 phyla, 65 classes and 132 orders. Bacteria dominated and comprised 28 phyla, 42 classes and 92 orders, conveying substrate's versatility in the treatments. Though, Fungi and Archaea comprised 5 phyla, the Fungi were richer; suggesting the importance of hydrolysis and fermentation in biogas production. High β-diversity within the taxa was largely linked to communities' metabolic capabilities. Clostridiales and Bacteroidales, the most prevalent guilds, metabolize organic macromolecules. The identified Cytophagales, Alteromonadales, Flavobacteriales, Fusobacteriales, Deferribacterales, Elusimicrobiales, Chlamydiales, Synergistales to mention but few, also catabolize macromolecules into smaller substrates to conserve energy. Furthermore, δ-Proteobacteria, Gloeobacteria and Clostridia affiliates syntrophically regulate PH2 and reduce metal to provide reducing equivalents. Methanomicrobiales and other Methanomicrobia species were the most prevalence Archaea, converting formate, CO2(g), acetate and methylated substrates into CH4(g). Thermococci, Thermoplasmata and Thermoprotei were among the sulfur and other metal reducing Archaea that contributed to redox balancing and other metabolism within treatments. Eukaryotes, mainly fungi were the least abundant guild, comprising largely Ascomycota and Basidiomycota species. Chytridiomycetes, Blastocladiomycetes and Mortierellomycetes were among the rare species, suggesting their metabolic and substrates limitations. Generally, we observed that environmental and treatment perturbations influenced communities' abundance, β-diversity and reactor performance largely through stochastic effect. Understanding diversity of biogas microbiomes over wide environmental variables and its' productivity provided insights into better management strategies that ameliorate biochemical limitations to effective biogas production.},
}

Archaea/genetics
Bacteria/genetics
Bacteria, Anaerobic/genetics/metabolism
Biodiversity
Biofuels/*microbiology
Bioreactors/microbiology
Euryarchaeota/metabolism
Fermentation
Fungi/genetics
Kenya
Metagenomics/*methods
Methane/metabolism
Methanomicrobiales/metabolism
Microbiota/*genetics/physiology
Phylogeny
RNA, Ribosomal, 16S

@article {pmid33172257,
year = {2020},
author = {Li, M and Rong, L and Zhou, S and Xiao, X and Wu, L and Fan, Y and Lu, C and Zou, X},
title = {Dissipation of Sulfonamides in Soil Emphasizing Taxonomy and Function of Microbiomes by Metagenomic Analysis.},
journal = {Journal of agricultural and food chemistry},
volume = {68},
number = {47},
pages = {13594-13607},
doi = {10.1021/acs.jafc.0c04496},
pmid = {33172257},
issn = {1520-5118},
mesh = {Kinetics ; Metagenomics ; *Microbiota ; Soil ; *Soil Pollutants/analysis ; Sulfonamides ; },
abstract = {Sulfonamides (SAs) are widespread in soils, and their dissipation behavior is important for their fate, risk assessment, and pollution control. In this work, we investigated the dissipation behavior of different SAs in a soil under aerobic condition, focusing on revealing the relationship between overall dissipation (without sterilization and in dark) and individual abiotic (sorption, hydrolysis)/biotic (with sterilization and in dark) factors and taxonomy/function of microbiomes. The results showed that dissipation of all SAs in the soil followed the pseudo-first-order kinetic model with dissipation time at 50% removal (DT50) of 2.16-15.27 days. Based on, experimentally, abiotic/biotic processes and, theoretically, partial least-squares modeling, a relationship between overall dissipation and individual abiotic/biotic factors was developed with microbial degradation as the dominant contributor. Metagenomic analysis showed that taxonomic genera like Bradyrhizobium/Sphingomonas/Methyloferula and functions like CAZy family GT51/GH23/GT2, eggNOG category S, KEGG pathway ko02024/ko02010, and KEGG ortholog K01999/K03088 are putatively involved in SA microbial degradation in soil. Spearman correlation suggests abundant genera being multifunctional. This study provides some new insights into SA dissipation and can be applied to other antibiotics/soils in the future.},
}

Kinetics
Metagenomics
*Microbiota
Soil
*Soil Pollutants/analysis
Sulfonamides

@article {pmid32858186,
year = {2020},
author = {Tepaamorndech, S and Nookaew, I and Higdon, SM and Santiyanont, P and Phromson, M and Chantarasakha, K and Mhuantong, W and Plengvidhya, V and Visessanguan, W},
title = {Metagenomics in bioflocs and their effects on gut microbiome and immune responses in Pacific white shrimp.},
journal = {Fish & shellfish immunology},
volume = {106},
number = {},
pages = {733-741},
doi = {10.1016/j.fsi.2020.08.042},
pmid = {32858186},
issn = {1095-9947},
mesh = {Animals ; *Aquaculture ; Bacterial Physiological Phenomena ; *Gastrointestinal Microbiome ; Immunity, Innate ; Metagenomics ; *Penaeidae/genetics/immunology/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {Biofloc systems generate and accumulate microbial aggregates known as bioflocs. The presence of bioflocs has been shown to change gut bacterial diversity and stimulate innate immunity in shrimp. The microbial niche of bioflocs may therefore have the potential to drive shifts in the shrimp gut microbiota associated with stimulation of innate immunity. We performed shotgun metagenomic analysis and 16S rRNA-based amplicon sequencing to characterize complex bacterial members in bioflocs and the shrimp digestive tract, respectively. Moreover, we determined whether biofloc-grown shrimp with discrete gut microbiomes had an elevation in local immune-related gene expression and systemic immune activities. Our findings demonstrated that the bacterial community in bioflocs changed dynamically during Pacific white shrimp cultivation. Metagenomic analysis revealed that Vibrio comprised 90% of the biofloc population, while Pseualteromonas, Photobacterium, Shewanella, Alteromonas, Bacillus, Lactobacillus, Acinetobacter, Clostridium, Marinifilum, and Pseudomonas were also detected. In the digestive tract, biofloc-grown shrimp maintained the presence of commensal bacteria including Vibrio, Photobacterium, Shewanella, Granulosicoccus, and Ruegeria similar to control shrimp. However, Vibrio and Photobacterium were significantly enriched and declined, respectively, in biofloc-grown shrimp. The presence of bioflocs upregulated immune-related genes encoding serine proteinase and prophenoloxidase in digestive organs which are routinely exposed to gut microbiota. Biofloc-grown shrimp also demonstrated a significant increase in systemic immune status. As a result, the survival rate of biofloc-grown shrimp was substantially higher than that of the control shrimp. Our findings suggested that the high relative abundance of vibrios in bioflocs enriched the number of vibrios in the digestive tract of biofloc-grown shrimp. This shift in gut microbiota composition may be partially responsible for local upregulation of immune-related gene expression in digestive organs and systemic promotion of immune status in circulating hemolymph.},
}

Animals
*Aquaculture
Bacterial Physiological Phenomena
*Gastrointestinal Microbiome
Immunity, Innate
Metagenomics
*Penaeidae/genetics/immunology/microbiology
RNA, Ribosomal, 16S

@article {pmid32949277,
year = {2020},
author = {Ding, X and Lan, W and Wu, J and Hong, Y and Li, Y and Ge, Q and Urzì, C and Katayama, Y and Gu, JD},
title = {Microbiome and nitrate removal processes by microorganisms on the ancient Preah Vihear temple of Cambodia revealed by metagenomics and N-15 isotope analyses.},
journal = {Applied microbiology and biotechnology},
volume = {104},
number = {22},
pages = {9823-9837},
doi = {10.1007/s00253-020-10886-4},
pmid = {32949277},
issn = {1432-0614},
support = {31870100, 91851111//National Natural Science Foundation of China/ ; JCYJ20170410103015603//Shenzhen Scientific Project Fund/ ; 17302119//Research Grants Council, University Grants Committee/ ; },
mesh = {Cambodia ; Denitrification ; Metagenomics ; *Microbiota ; *Nitrates/analysis ; Nitrogen ; Nitrogen Isotopes ; Oxidation-Reduction ; Phylogeny ; },
abstract = {Preah Vihear temple is one of the most significant representatives of the ancient Angkorian temples listed as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The surfaces of this Angkor sandstone monument are covered with deteriorated materials, broadly called "sediments" here, resulting from a long time of weathering of the sandstone. The sediments might adversely affect the ancient sandstone substratum of this cultural heritage, and the potential risk from them is essential information for current strategies and on-going protection and management. The extracted DNA from the sediment samples of this temple was used for Illumina high-throughput sequencing analysis, resulting in approximately 12 Gb of metagenomic dataset. The results of this shotgun metagenomic analysis provided a thorough information of the phylogenetic groups presented in the microbiome of the sediment samples, indicating that potential metabolic activities, involving different geomicrobiological cycles, may occur in this microbiome. The phylogenetic result revealed that the majority of metagenomic reads were affiliated with Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes at the phylum level. The metabolic reconstruction results indicated that the important geomicrobiological cycling processes include carbon sequestration, and nitrogen and sulfur transformation as the potentially active ones in the sediments of the sampling sites. Specifically, the dissimilatory nitrate reduction to ammonium (DNRA) and the newly discovered complete ammonia oxidation (comammox) were retrieved from this metagenomic dataset. Furthermore, the genetic information on the presence of acid-producing processes by sulfur- and ammonia-oxidizing bacteria and archaea in this metagenomic dataset suggested that the microbial flora in these samples has the potential to participate in the degradation of sandstone cultural heritage by producing acids. N-15 isotope amendment and incubation analysis results confirmed the presence of active denitrification, but not anammox activity at this temple. These results are important for our knowledge on the microbial community composition and microbial biodeterioration processes affecting this sandstone cultural heritage and will aid in the protection and management of the ancient Preah Vihear temple.Key Points• Microbiota on Preah Viher temple was analyzed using NGS.• Nitrate-N transformation by DNRA, comammox, and denitrifcation was detected.• N-15 isotope analysis confirmed the active denitrifcation, but not Anammox.• Accumulation of nitrate is a result of less active removal by denitrification.},
}

Cambodia
Denitrification
Metagenomics
*Microbiota
*Nitrates/analysis
Nitrogen
Nitrogen Isotopes
Oxidation-Reduction
Phylogeny

@article {pmid32396115,
year = {2020},
author = {Reiman, D and Metwally, AA and Sun, J and Dai, Y},
title = {PopPhy-CNN: A Phylogenetic Tree Embedded Architecture for Convolutional Neural Networks to Predict Host Phenotype From Metagenomic Data.},
journal = {IEEE journal of biomedical and health informatics},
volume = {24},
number = {10},
pages = {2993-3001},
doi = {10.1109/JBHI.2020.2993761},
pmid = {32396115},
issn = {2168-2208},
support = {UL1 TR002003/TR/NCATS NIH HHS/United States ; },
mesh = {Algorithms ; Databases, Genetic ; Deep Learning ; Gastrointestinal Microbiome/*genetics ; Genetic Predisposition to Disease/classification/*genetics ; Metagenomics/*methods ; *Neural Networks, Computer ; Phenotype ; Phylogeny ; },
abstract = {Accurate prediction of the host phenotype from a metagenomic sample and identification of the associated microbial markers are important in understanding potential host-microbiome interactions related to disease initiation and progression. We introduce PopPhy-CNN, a novel convolutional neural network (CNN) learning framework that effectively exploits phylogenetic structure in microbial taxa for host phenotype prediction. Our approach takes an input format of a 2D matrix representing the phylogenetic tree populated with the relative abundance of microbial taxa in a metagenomic sample. This conversion empowers CNNs to explore the spatial relationship of the taxonomic annotations on the tree and their quantitative characteristics in metagenomic data. We show the competitiveness of our model compared to other available methods using nine metagenomic datasets of moderate size for binary classification. With synthetic and biological datasets, we show the superior and robust performance of our model for multi-class classification. Furthermore, we design a novel scheme for feature extraction from the learned CNN models and demonstrate improved performance when the extracted features. PopPhy-CNN is a practical deep learning framework for the prediction of host phenotype with the ability of facilitating the retrieval of predictive microbial taxa.},
}

Algorithms
Databases, Genetic
Deep Learning
Gastrointestinal Microbiome/*genetics
Genetic Predisposition to Disease/classification/*genetics
Metagenomics/*methods
*Neural Networks, Computer
Phenotype
Phylogeny

@article {pmid33953314,
year = {2021},
author = {Melkonian, C and Fillinger, L and Atashgahi, S and da Rocha, UN and Kuiper, E and Olivier, B and Braster, M and Gottstein, W and Helmus, R and Parsons, JR and Smidt, H and van der Waals, M and Gerritse, J and Brandt, BW and Röling, WFM and Molenaar, D and van Spanning, RJM},
title = {High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers.},
journal = {Communications biology},
volume = {4},
number = {1},
pages = {530},
pmid = {33953314},
issn = {2399-3642},
abstract = {A key question in microbial ecology is what the driving forces behind the persistence of large biodiversity in natural environments are. We studied a microbial community with more than 100 different types of species which evolved in a 15-years old bioreactor with benzene as the main carbon and energy source and nitrate as the electron acceptor. Using genome-centric metagenomics plus metatranscriptomics, we demonstrate that most of the community members likely feed on metabolic left-overs or on necromass while only a few of them, from families Rhodocyclaceae and Peptococcaceae, are candidates to degrade benzene. We verify with an additional succession experiment using metabolomics and metabarcoding that these few community members are the actual drivers of benzene degradation. As such, we hypothesize that high species richness is maintained and the complexity of a natural community is stabilized in a controlled environment by the interdependencies between the few benzene degraders and the rest of the community members, ultimately resulting in a food web with different trophic levels.},
}

@article {pmid33941275,
year = {2021},
author = {Altabtbaei, K and Maney, P and Ganesan, SM and Dabdoub, SM and Nagaraja, HN and Kumar, PS},
title = {Anna Karenina and the subgingival microbiome associated with periodontitis.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {97},
doi = {10.1186/s40168-021-01056-3},
pmid = {33941275},
issn = {2049-2618},
support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; },
mesh = {*Aggressive Periodontitis ; Cross-Sectional Studies ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Although localized aggressive periodontitis (LAP), generalized aggressive periodontitis (GAP), and chronic periodontitis (CP) are microbially driven diseases, our inability to separate disease-specific associations from those common to all three forms of periodontitis has hampered biomarker discovery. Therefore, we aimed to map the genomic content of, and the biological pathways encoded by, the microbiomes associated with these clinical phenotypes. We also estimated the extent to which these biomes are governed by the Anna Karenina principle (AKP), which states that eubiotic communities are similar between individuals while disease-associated communities are highly individualized.

METHODS: We collected subgingival plaque from 25 periodontally healthy individuals and diseased sites of 59 subjects with stage 3 periodontitis and used shotgun metagenomics to characterize the aggregate of bacterial genes.

RESULTS: Beta-dispersion metrics demonstrated that AKP was most evident in CP, followed by GAP and LAP. We discovered broad dysbiotic signatures spanning the three phenotypes, with over-representation of pathways that facilitate life in an oxygen-poor, protein- and heme-rich, pro-oxidant environment and enhance capacity for attachment and biofilm formation. Phenotype-specific indicators were more readily evident in LAP microbiome than GAP or CP. Genes that enable acetate-scavenging lifestyle, utilization of alternative nutritional sources, oxidative and nitrosative stress responses, and siderophore production were unique to LAP. An attenuation of virulence-related functionalities and stress response from LAP to GAP to CP was apparent. We also discovered that clinical phenotypes of disease resolved variance in the microbiome with greater clarity than the newly established grading system. Importantly, we observed that one third of the metagenome of LAP is unique to this phenotype while GAP shares significant functional and taxonomic features with both LAP and CP, suggesting either attenuation of an aggressive disease or an early-onset chronic disease.

CONCLUSION: Within the limitations of a small sample size and a cross-sectional study design, the distinctive features of the microbiomes associated with LAP and CP strongly persuade us that these are discrete disease entities, while calling into question whether GAP is a separate disease, or an artifact induced by cross-sectional study designs. Further studies on phenotype-specific microbial genes are warranted to explicate their role in disease etiology. Video Abstract.},
}

*Aggressive Periodontitis
Cross-Sectional Studies
Humans
Metagenome
Metagenomics
*Microbiota/genetics

@article {pmid33910647,
year = {2021},
author = {Tourlousse, DM and Narita, K and Miura, T and Sakamoto, M and Ohashi, A and Shiina, K and Matsuda, M and Miura, D and Shimamura, M and Ohyama, Y and Yamazoe, A and Uchino, Y and Kameyama, K and Arioka, S and Kataoka, J and Hisada, T and Fujii, K and Takahashi, S and Kuroiwa, M and Rokushima, M and Nishiyama, M and Tanaka, Y and Fuchikami, T and Aoki, H and Kira, S and Koyanagi, R and Naito, T and Nishiwaki, M and Kumagai, H and Konda, M and Kasahara, K and Ohkuma, M and Kawasaki, H and Sekiguchi, Y and Terauchi, J},
title = {Validation and standardization of DNA extraction and library construction methods for metagenomics-based human fecal microbiome measurements.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {95},
pmid = {33910647},
issn = {2049-2618},
mesh = {DNA ; Humans ; *Metagenomics ; *Microbiota/genetics ; Reference Standards ; Reproducibility of Results ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Validation and standardization of methodologies for microbial community measurements by high-throughput sequencing are needed to support human microbiome research and its industrialization. This study set out to establish standards-based solutions to improve the accuracy and reproducibility of metagenomics-based microbiome profiling of human fecal samples.

RESULTS: In the first phase, we performed a head-to-head comparison of a wide range of protocols for DNA extraction and sequencing library construction using defined mock communities, to identify performant protocols and pinpoint sources of inaccuracy in quantification. In the second phase, we validated performant protocols with respect to their variability of measurement results within a single laboratory (that is, intermediate precision) as well as interlaboratory transferability and reproducibility through an industry-based collaborative study. We further ascertained the performance of our recommended protocols in the context of a community-wide interlaboratory study (that is, the MOSAIC Standards Challenge). Finally, we defined performance metrics to provide best practice guidance for improving measurement consistency across methods and laboratories.

CONCLUSIONS: The validated protocols and methodological guidance for DNA extraction and library construction provided in this study expand current best practices for metagenomic analyses of human fecal microbiota. Uptake of our protocols and guidelines will improve the accuracy and comparability of metagenomics-based studies of the human microbiome, thereby facilitating development and commercialization of human microbiome-based products. Video Abstract.},
}

DNA
Humans
*Metagenomics
*Microbiota/genetics
Reference Standards
Reproducibility of Results
Sequence Analysis, DNA

@article {pmid33845910,
year = {2021},
author = {Restrepo, L and Domínguez-Borbor, C and Bajaña, L and Betancourt, I and Rodríguez, J and Bayot, B and Reyes, A},
title = {Microbial community characterization of shrimp survivors to AHPND challenge test treated with an effective shrimp probiotic (Vibrio diabolicus).},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {88},
pmid = {33845910},
issn = {2049-2618},
mesh = {Animals ; Humans ; *Microbiota ; Necrosis ; *Penaeidae ; Phylogeny ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; Survivors ; Vibrio ; *Vibrio parahaemolyticus/genetics ; },
abstract = {BACKGROUND: Acute hepatopancreatic necrosis disease (AHPND) is an important shrimp bacterial disease caused by some Vibrio species. The severity of the impact of this disease on aquaculture worldwide has made it necessary to develop alternatives to prophylactic antibiotics use, such as the application of probiotics. To assess the potential to use probiotics in order to limit the detrimental effects of AHNPD, we evaluated the effect of the ILI strain, a Vibrio sp. bacterium and efficient shrimp probiotic, using metabarcoding (16S rRNA gene) on the gastrointestinal microbiota of shrimp after being challenged with AHPND-causing V. parahaemolyticus.

RESULTS: We showed how the gastrointestinal microbiome of shrimp varied between healthy and infected organisms. Nevertheless, a challenge of working with AHPND-causing Vibrio pathogens and Vibrio-related bacteria as probiotics is the potential risk of the probiotic strain becoming pathogenic. Consequently, we evaluated whether ILI strain can acquire the plasmid pV-AHPND via horizontal transfer and further cause the disease in shrimp. Conjugation assays were performed resulting in a high frequency (70%) of colonies harboring the pv-AHPND. However, no shrimp mortality was observed when transconjugant colonies of the ILI strain were used in a challenge test using healthy shrimp. We sequenced the genome of the ILI strain and performed comparative genomics analyses using AHPND and non-AHPND Vibrio isolates. Using available phylogenetic and phylogenomics analyses, we reclassified the ILI strain as Vibrio diabolicus. In summary, this work represents an effort to study the role that probiotics play in the normal gastrointestinal shrimp microbiome and in AHPND-infected shrimp, showing that the ILI probiotic was able to control pathogenic bacterial populations in the host's gastrointestinal tract and stimulate the shrimp's survival. The identification of probiotic bacterial species that are effective in the host's colonization is important to promote animal health and prevent disease.

CONCLUSIONS: This study describes probiotic bacteria capable of controlling pathogenic populations of bacteria in the shrimp gastrointestinal tract. Our work provides new insights into the complex dynamics between shrimp and the changes in the microbiota. It also addresses the practical application of probiotics to solve problems with pathogens that cause high mortality-rate in shrimp farming around the world. Video Abstract.},
}

Animals
Humans
*Microbiota
Necrosis
*Penaeidae
Phylogeny
*Probiotics
RNA, Ribosomal, 16S/genetics
Survivors
Vibrio
*Vibrio parahaemolyticus/genetics

@article {pmid33494335,
year = {2021},
author = {Baragetti, A and Severgnini, M and Olmastroni, E and Dioguardi, CC and Mattavelli, E and Angius, A and Rotta, L and Cibella, J and Caredda, G and Consolandi, C and Grigore, L and Pellegatta, F and Giavarini, F and Caruso, D and Norata, GD and Catapano, AL and Peano, C},
title = {Gut Microbiota Functional Dysbiosis Relates to Individual Diet in Subclinical Carotid Atherosclerosis.},
journal = {Nutrients},
volume = {13},
number = {2},
pages = {},
pmid = {33494335},
issn = {2072-6643},
support = {AL_RIC19ABARA_01//Vini di Batasiolo S.p.A/ ; 2020-3318//Fondazione Umberto Veronesi/ ; 2016-0852//Fondazione Cariplo/ ; GGP19146//Fondazione Telethon/ ; PRIN 2017K55HLC//Italian Ministry of Health/ ; H2020 REPROGRAM PHC-03-2015/667837-2//European Union Commission/ ; 2015-0524//Fondazione Cariplo/ ; 2015-0564//Fondazione Cariplo/ ; ERANET ER-2017-2364981//European Union Commission/ ; PRIN 2017 - LS 4 2017HTKLRF_003//Italian Ministry of Health/ ; PRIN 2017H5F943//Italian Ministry of Health/ ; GR-2011-02346974//Italian Ministry of Health-IRCCS MultiMedica/ ; },
mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/drug effects ; Carnitine/therapeutic use ; Carotid Artery Diseases/*complications/microbiology ; Choline/therapeutic use ; *Diet ; Dysbiosis/*complications/drug therapy/microbiology ; Escherichia coli ; Faecalibacterium prausnitzii ; Feces/microbiology ; Feeding Behavior ; Female ; Gastrointestinal Microbiome/genetics/*physiology ; High-Throughput Nucleotide Sequencing ; Humans ; Life Style ; Male ; Metagenomics ; Methylamines ; Middle Aged ; Palmitates/therapeutic use ; },
abstract = {Gut Microbiota (GM) dysbiosis associates with Atherosclerotic Cardiovascular Diseases (ACVD), but whether this also holds true in subjects without clinically manifest ACVD represents a challenge of personalized prevention. We connected exposure to diet (self-reported by food diaries) and markers of Subclinical Carotid Atherosclerosis (SCA) with individual taxonomic and functional GM profiles (from fecal metagenomic DNA) of 345 subjects without previous clinically manifest ACVD. Subjects without SCA reported consuming higher amounts of cereals, starchy vegetables, milky products, yoghurts and bakery products versus those with SCA (who reported to consume more mechanically separated meats). The variety of dietary sources significantly overlapped with the separations in GM composition between subjects without SCA and those with SCA (RV coefficient between nutrients quantities and microbial relative abundances at genus level = 0.65, p-value = 0.047). Additionally, specific bacterial species (Faecalibacterium prausnitzii in the absence of SCA and Escherichia coli in the presence of SCA) are directly related to over-representation of metagenomic pathways linked to different dietary sources (sulfur oxidation and starch degradation in absence of SCA, and metabolism of amino acids, syntheses of palmitate, choline, carnitines and Trimethylamine n-oxide in presence of SCA). These findings might contribute to hypothesize future strategies of personalized dietary intervention for primary CVD prevention setting.},
}

Adult
Aged
Aged, 80 and over
Bacteria/classification/drug effects
Carnitine/therapeutic use
Carotid Artery Diseases/*complications/microbiology
Choline/therapeutic use
*Diet
Dysbiosis/*complications/drug therapy/microbiology
Escherichia coli
Faecalibacterium prausnitzii
Feces/microbiology
Feeding Behavior
Female
Gastrointestinal Microbiome/genetics/*physiology
High-Throughput Nucleotide Sequencing
Humans
Life Style
Male
Metagenomics
Methylamines
Middle Aged
Palmitates/therapeutic use

@article {pmid32747678,
year = {2020},
author = {Zeng, Q and Shen, J and Chen, K and Zhou, J and Liao, Q and Lu, K and Yuan, J and Bi, F},
title = {The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients.},
journal = {Scientific reports},
volume = {10},
number = {1},
pages = {12998},
pmid = {32747678},
issn = {2045-2322},
mesh = {Adult ; Amyotrophic Lateral Sclerosis/*metabolism/*microbiology ; Bacteroidetes/genetics ; Case-Control Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease accompanied with severe paralysis or even death, while the pathogenesis of ALS is still unclear and no effective therapy exists. The accumulating evidence has indicated the association between gut microbiota and various neurological diseases. Thus, to explore the potential role of gut microbiome in ALS, 20 patients diagnosed with probable or definite ALS and 20 healthy controls were enrolled and their fecal excrements were collected. The analysis of fecal community diversity with 16S rDNA sequencing showed an obvious change in microbial structure of ALS patients, where Bacteroidetes at the phylum level and several microbes at the genus level were up-regulated, while Firmicutes at the phylum level and Megamonas at the genus level were down-regulated compared to healthy controls. Additionally, decreased gene function associated with metabolic pathways was observed in ALS patients. The metagenomics further demonstrated the discrepancies in microflora at the species level and relevant metabolites thereof were also revealed when combined with metabolomics. In conclusion, the altered composition of the gut microbiota and metabolic products in ALS patients provided deeper insights into the pathogenesis of ALS, and these biomarkers might be established as potential therapeutic targets which deserve further exploration.},
}

Adult
Amyotrophic Lateral Sclerosis/*metabolism/*microbiology
Bacteroidetes/genetics
Case-Control Studies
Female
*Gastrointestinal Microbiome
Humans
Male
Metabolomics
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid32056227,
year = {2020},
author = {Smirnova, E and Puri, P and Muthiah, MD and Daitya, K and Brown, R and Chalasani, N and Liangpunsakul, S and Shah, VH and Gelow, K and Siddiqui, MS and Boyett, S and Mirshahi, F and Sikaroodi, M and Gillevet, P and Sanyal, AJ},
title = {Fecal Microbiome Distinguishes Alcohol Consumption From Alcoholic Hepatitis But Does Not Discriminate Disease Severity.},
journal = {Hepatology (Baltimore, Md.)},
volume = {72},
number = {1},
pages = {271-286},
pmid = {32056227},
issn = {1527-3350},
support = {UL1 TR002649/TR/NCATS NIH HHS/United States ; UO1 AA021891-01/NH/NIH HHS/United States ; U01 AA021891/AA/NIAAA NIH HHS/United States ; T32 DK07150-40/NH/NIH HHS/United States ; CTSA UL1TR002649/NH/NIH HHS/United States ; KL2 TR002648/TR/NCATS NIH HHS/United States ; T32 DK007150/DK/NIDDK NIH HHS/United States ; K23 AA021179/AA/NIAAA NIH HHS/United States ; },
mesh = {Adult ; *Alcohol Drinking ; Diagnosis, Differential ; Feces/*microbiology ; Female ; *Gastrointestinal Microbiome ; Hepatitis, Alcoholic/*diagnosis/*microbiology ; Humans ; Male ; Middle Aged ; Severity of Illness Index ; },
abstract = {BACKGROUND AND AIMS: The role of the intestinal microbiome in alcoholic hepatitis is not established. The aims of this study were to (1) characterize the fecal microbial ecology associated with alcoholic hepatitis, (2) relate microbiome changes to disease severity, and (3) infer the functional relevance of shifts in microbial ecology.

APPROACH AND RESULTS: The fecal microbiome in patients with moderate alcoholic hepatitis (MAH) or severe alcoholic hepatitis (SAH) was compared with healthy controls (HCs) and heavy drinking controls (HDCs). Microbial taxa were identified by 16S pyrosequencing. Functional metagenomics was performed using PICRUSt. Fecal short chain fatty acids (SCFAs) were measured using a liquid chromatography-mass spectrometry platform. A total of 78 participants (HC, n = 24; HDC, n = 20; MAH, n = 10; SAH, n = 24) were studied. HDC had a distinct signature compared with HC with depletion of Bacteroidetes (46% vs. 26%; P = 0.01). Alcoholic hepatitis was associated with a distinct microbiome signature compared with HDC (area under the curve = 0.826); differential abundance of Ruminococcaceae, Veillonellaceae, Lachnospiraceae, Porphyromonadaceae, and Rikenellaceae families were the key contributors to these differences. The beta diversity was significantly different among the groups (permutational multivariate analysis of variance [PERMANOVA] P < 0.001). SAH was associated with increased Proteobacteria (SAH 14% vs. HDC 7% and SAH vs. HC 2%, P = 0.20 and 0.01, respectively). Firmicutes abundance declined from HDC to MAH to SAH (63% vs. 53% vs. 48%, respectively; P = 0.09, HDC vs. SAH). Microbial taxa did not distinguish between MAH and SAH (PERMANOVA P = 0.785). SCFAs producing bacteria (Lachnospiraceae and Ruminococcaceae) were decreased in alcoholic hepatitis, and a similar decrease was observed in fecal SCFAs among alcoholic hepatitis patients.

CONCLUSIONS: There are distinct changes in fecal microbiome associated with the development, but not severity, of alcoholic hepatitis.},
}

Adult
*Alcohol Drinking
Diagnosis, Differential
Feces/*microbiology
Female
*Gastrointestinal Microbiome
Hepatitis, Alcoholic/*diagnosis/*microbiology
Humans
Male
Middle Aged
Severity of Illness Index

@article {pmid33182758,
year = {2020},
author = {Moon, J and Yoon, CH and Choi, SH and Kim, MK},
title = {Can Gut Microbiota Affect Dry Eye Syndrome?.},
journal = {International journal of molecular sciences},
volume = {21},
number = {22},
pages = {},
pmid = {33182758},
issn = {1422-0067},
mesh = {Adaptive Immunity ; Animals ; Autoimmune Diseases/etiology/immunology/microbiology ; Autoimmunity ; Disease Models, Animal ; Dry Eye Syndromes/*etiology/immunology/microbiology ; Dysbiosis/complications/immunology/microbiology ; Gastrointestinal Microbiome/genetics/*immunology ; Homeostasis/immunology ; Host Microbial Interactions/immunology ; Humans ; Immunity, Innate ; Metagenomics ; Models, Biological ; Prebiotics ; Probiotics/therapeutic use ; Sjogren's Syndrome/etiology/immunology/microbiology ; },
abstract = {Using metagenomics, continuing evidence has elicited how intestinal microbiota trigger distant autoimmunity. Sjögren's syndrome (SS) is an autoimmune disease that affects the ocular surface, with frequently unmet therapeutic needs requiring new interventions for dry eye management. Current studies also suggest the possible relation of autoimmune dry eye with gut microbiota. Herein, we review the current knowledge of how the gut microbiota interact with the immune system in homeostasis as well as its influence on rheumatic and ocular autoimmune diseases, and compare their characteristics with SS. Both rodent and human studies regarding gut microbiota in SS and environmental dry eye are explored, and the effects of prebiotics and probiotics on dry eye are discussed. Recent clinical studies have commonly observed a correlation between gut dysbiosis and clinical manifestations of SS, while environmental dry eye portrays characteristics in between normal and autoimmune. Moreover, a decrease in both the Firmicutes/Bacteroidetes ratio and genus Faecalibacterium have most commonly been observed in SS subjects. The presumable pathways forming the "gut dysbiosis-ocular surface-lacrimal gland axis" are introduced. This review may provide perspectives into the link between the gut microbiome and dry eye, enhance our understanding of the pathogenesis in autoimmune dry eye, and be useful in the development of future interventions.},
}

Adaptive Immunity
Animals
Autoimmune Diseases/etiology/immunology/microbiology
Autoimmunity
Disease Models, Animal
Dry Eye Syndromes/*etiology/immunology/microbiology
Dysbiosis/complications/immunology/microbiology
Gastrointestinal Microbiome/genetics/*immunology
Homeostasis/immunology
Host Microbial Interactions/immunology
Humans
Immunity, Innate
Metagenomics
Models, Biological
Prebiotics
Probiotics/therapeutic use
Sjogren's Syndrome/etiology/immunology/microbiology

@article {pmid33831764,
year = {2021},
author = {Pandit, PR and Kumar, R and Kumar, D and Patel, Z and Pandya, L and Kumar, M and Joshi, C},
title = {Deciphering the black box of microbial community of common effluent treatment plant through integrated metagenomics: Tackling industrial effluent.},
journal = {Journal of environmental management},
volume = {289},
number = {},
pages = {112448},
doi = {10.1016/j.jenvman.2021.112448},
pmid = {33831764},
issn = {1095-8630},
mesh = {Bacteria/genetics ; Metagenome ; *Metagenomics ; *Microbiota ; Waste Water ; },
abstract = {Identifying the microbial community and their functional potential from different stages of common effluent treatment plants (CETP) can enhance the efficiency of wastewater treatment systems. In this study, wastewater metagenomes from 8 stages of CETP were screened for microbial diversity and gene profiling along with their corresponding degradation activities. The microbial community displayed 98.46% of bacterial species, followed by Eukarya (0.10%) and Archaea 0.02%. At the Phylum level, Proteobacteria (28.8%) was dominant, followed by Bacteroidetes (16.1%), Firmicutes (11.7%), and Fusobacteria (6.9%) which are mainly capable of degrading the aromatic compounds. Klebsiella pneumoniae, Wolinella succinogenes, Pseudomonas stutzeri, Desulfovibrio vulgaris, and Clostridium sticklandii were the most prevalent species. The functional analysis further demonstrated the presence of enzymes linked with genes/pathways known to be involved in the degradation/metabolization of aromatic compounds like benzoate, bisphenol, 1,2-dichloroethane phenylalanine. This information was further validated with the whole genome analysis of the bacteria isolated from the CETP. We anticipate that integrating both shotgun and whole-genome analyses can reveal the rich reservoir for novel enzymes and genes present in CETP effluent that can contribute to designing efficient bioremediation strategies for the environment in general CETP system, in particular.},
}

Bacteria/genetics
Metagenome
*Metagenomics
*Microbiota
Waste Water

@article {pmid33819653,
year = {2021},
author = {Zhang, Z and Wan, J and Liu, L and Ye, M and Jiang, X},
title = {Metagenomics reveals functional profiling of microbial communities in OCP contaminated sites with rapeseed oil and tartaric acid biostimulation.},
journal = {Journal of environmental management},
volume = {289},
number = {},
pages = {112515},
doi = {10.1016/j.jenvman.2021.112515},
pmid = {33819653},
issn = {1095-8630},
mesh = {Biodegradation, Environmental ; Humans ; Metagenomics ; *Microbiota ; Rapeseed Oil ; Soil Microbiology ; *Soil Pollutants/analysis ; Tartrates ; },
abstract = {Organochlorine pesticides (OCPs) contaminated sites pose great threats to both human health and environmental safety. Targeted bioremediation in these regions largely depends on microbial diversity and activity. This study applied metagenomics to characterize the microbial communities and functional groups composition features during independent or simultaneous rapeseed oil and tartaric acid applications, as well as the degradation kinetics of OCPs. Results showed that: the degradation rates of α-chlordane, β-chlordane and mirex were better when (0.50% w/w) rapeseed oil and (0.05 mol L-1) tartaric acid were applied simultaneously than singular use, yielding removal rates of 56.4%, 53.9%, and 49.4%, respectively. Meanwhile, bio-stimulation facilitated microbial enzyme (catalase/superoxide dismutase/peroxidase) activity in soils significantly, promoting the growth of dominant bacterial communities. Classification at phylum level showed that the relative abundance of Proteobacteria was significantly increased (p < 0.05). Network analysis showed that bio-stimulation substantially increased the dominant bacterial community's proportion, especially Proteobacteria. The functional gene results illustrated that bio-stimulation facilitated total relative abundance of degradation genes, phosphorus, carbon, nitrogen, sulfur metabolic genes, and iron transporting genes (p < 0.05). In metabolic pathways, functional genes related to methanogenesis and ammonia generation were markedly upregulated, indicating that bio-stimulation promoted the transformation of metabolic genes, such as carbon and nitrogen. This research is conducive to exploring the microbiological response mechanisms of bio-stimulation in indigenous flora, which may provide technical support for assessing the microbial ecological remediation outcomes of bio-stimulation in OCP contaminated sites.},
}

Biodegradation, Environmental
Humans
Metagenomics
*Microbiota
Rapeseed Oil
Soil Microbiology
*Soil Pollutants/analysis
Tartrates

@article {pmid33775067,
year = {2021},
author = {Dunaj, J and Drewnowska, J and Moniuszko-Malinowska, A and Swiecicka, I and Pancewicz, S},
title = {First metagenomic report of Borrelia americana and Borrelia carolinensis in Poland - a preliminary study.},
journal = {Annals of agricultural and environmental medicine : AAEM},
volume = {28},
number = {1},
pages = {49-55},
doi = {10.26444/aaem/118134},
pmid = {33775067},
issn = {1898-2263},
mesh = {Animals ; Dermacentor/*microbiology ; Francisella/classification/genetics/isolation & purification ; Genome, Bacterial ; Ixodes/*microbiology ; Metagenomics ; *Microbiota ; Poland ; Pseudomonas/classification/isolation & purification ; Sphingomonas/classification/genetics/isolation & purification ; Spirochaetales/classification/*genetics/isolation & purification ; },
abstract = {INTRODUCTION AND OBJECTIVE: Ixodes ricinus (I. ricinus) and Dermacentor reticulatus (D. reticulatus) are the most common ticks in Poland. These ticks contain many bacteria, which compose a microbiome with potential impact on humans. The aim of the study was to discover the microbiome of ticks in Poland.

MATERIAL AND METHODS: Ticks were collected in The Protected Landscape Area of the Bug and Nurzec Valley, Poland, in 2016-2018 by flagging. They were cleaned in 70% ethanol and damaged in mortar with PBS (without Ca2+ and Mg2+ ions). DNA was extracted from the homogenates with spin columns kits, and used as a matrix in end-point PCR for bacterial 16S rRNA fragments amplifications, and further for next generation sequencing (NGS) by ILLUMINA.

RESULTS: In 22 ticks (3 I. ricinus and 19 D. reticulatus) 38 microorganisms were detected. The most common were Francisella hispaniensis and Francisella novicida. In 17 ticks, Sphingomonas oligophenolica, and in 12 Rickettsia aeshlimanii were found. In 2, I. ricinus specific DNA of Borrelia americana and Borrelia carolinensis were found. In one female, D. reticulatus Anaplasma phagocytophilum and Anaplasma centrale were found. Pseudomonas lutea and Ps. moraviensis were detected in 9 and 8 ticks, respectively.

CONCLUSIONS: Polish ticks microbiome contains not only well-known tick-borne pathogens, but also other pathogenic microorganisms. For the first time in Poland, Borrelia americana and Borrelia carolinensis in I. ricinus collected from the environment were detected. The dominant pathogenic microorganisms for humans were Francisella spp. and Rickettsia spp., and non-pathogenic - Sphingomonas oligophenolica. Knowledge of a tick microbiome might be useful in tick-borne biocontrol and tick-borne diseases prevention.},
}

Animals
Dermacentor/*microbiology
Francisella/classification/genetics/isolation & purification
Genome, Bacterial
Ixodes/*microbiology
Metagenomics
*Microbiota
Poland
Pseudomonas/classification/isolation & purification
Sphingomonas/classification/genetics/isolation & purification
Spirochaetales/classification/*genetics/isolation & purification

@article {pmid33649565,
year = {2021},
author = {Meyer, F and Lesker, TR and Koslicki, D and Fritz, A and Gurevich, A and Darling, AE and Sczyrba, A and Bremges, A and McHardy, AC},
title = {Tutorial: assessing metagenomics software with the CAMI benchmarking toolkit.},
journal = {Nature protocols},
volume = {16},
number = {4},
pages = {1785-1801},
pmid = {33649565},
issn = {1750-2799},
mesh = {Animals ; *Benchmarking ; Computer Simulation ; Databases, Genetic ; Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics/*methods ; Mice ; Phylogeny ; Reference Standards ; Reproducibility of Results ; *Software ; },
abstract = {Computational methods are key in microbiome research, and obtaining a quantitative and unbiased performance estimate is important for method developers and applied researchers. For meaningful comparisons between methods, to identify best practices and common use cases, and to reduce overhead in benchmarking, it is necessary to have standardized datasets, procedures and metrics for evaluation. In this tutorial, we describe emerging standards in computational meta-omics benchmarking derived and agreed upon by a larger community of researchers. Specifically, we outline recent efforts by the Critical Assessment of Metagenome Interpretation (CAMI) initiative, which supplies method developers and applied researchers with exhaustive quantitative data about software performance in realistic scenarios and organizes community-driven benchmarking challenges. We explain the most relevant evaluation metrics for assessing metagenome assembly, binning and profiling results, and provide step-by-step instructions on how to generate them. The instructions use simulated mouse gut metagenome data released in preparation for the second round of CAMI challenges and showcase the use of a repository of tool results for CAMI datasets. This tutorial will serve as a reference for the community and facilitate informative and reproducible benchmarking in microbiome research.},
}

Animals
*Benchmarking
Computer Simulation
Databases, Genetic
Gastrointestinal Microbiome/genetics
Metagenome
Metagenomics/*methods
Mice
Phylogeny
Reference Standards
Reproducibility of Results
*Software

@article {pmid33372654,
year = {2020},
author = {Belcour, A and Frioux, C and Aite, M and Bretaudeau, A and Hildebrand, F and Siegel, A},
title = {Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species.},
journal = {eLife},
volume = {9},
number = {},
pages = {},
pmid = {33372654},
issn = {2050-084X},
support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; ANR-10-BTBR-04//ANR/ ; BBS/E/F/000PR1035/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Bacteria/genetics/*metabolism ; Cattle ; Databases, Factual ; *Gastrointestinal Microbiome ; Genome, Bacterial ; Metagenomics ; *Software ; Species Specificity ; },
abstract = {To capture the functional diversity of microbiota, one must identify metabolic functions and species of interest within hundreds or thousands of microorganisms. We present Metage2Metabo (M2M) a resource that meets the need for de novo functional screening of genome-scale metabolic networks (GSMNs) at the scale of a metagenome, and the identification of critical species with respect to metabolic cooperation. M2M comprises a flexible pipeline for the characterisation of individual metabolisms and collective metabolic complementarity. In addition, M2M identifies key species, that are meaningful members of the community for functions of interest. We demonstrate that M2M is applicable to collections of genomes as well as metagenome-assembled genomes, permits an efficient GSMN reconstruction with Pathway Tools, and assesses the cooperation potential between species. M2M identifies key organisms by reducing the complexity of a large-scale microbiota into minimal communities with equivalent properties, suitable for further analyses.},
}

Animals
Bacteria/genetics/*metabolism
Cattle
Databases, Factual
*Gastrointestinal Microbiome
Genome, Bacterial
Metagenomics
*Software
Species Specificity

@article {pmid32654263,
year = {2020},
author = {Jiang, L and Lang, S and Duan, Y and Zhang, X and Gao, B and Chopyk, J and Schwanemann, LK and Ventura-Cots, M and Bataller, R and Bosques-Padilla, F and Verna, EC and Abraldes, JG and Brown, RS and Vargas, V and Altamirano, J and Caballería, J and Shawcross, DL and Ho, SB and Louvet, A and Lucey, MR and Mathurin, P and Garcia-Tsao, G and Kisseleva, T and Brenner, DA and Tu, XM and Stärkel, P and Pride, D and Fouts, DE and Schnabl, B},
title = {Intestinal Virome in Patients With Alcoholic Hepatitis.},
journal = {Hepatology (Baltimore, Md.)},
volume = {72},
number = {6},
pages = {2182-2196},
doi = {10.1002/hep.31459},
pmid = {32654263},
issn = {1527-3350},
support = {R01 AA24726/AA/NIAAA NIH HHS/United States ; R01AA020703/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; BX004594/BX/BLRD VA/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; },
mesh = {Adult ; Aged ; Animals ; Bacteriophages/genetics/isolation & purification ; Case-Control Studies ; DNA, Viral/isolation & purification ; End Stage Liver Disease/diagnosis/mortality/therapy/*virology ; Feces/virology ; Female ; Hepatitis, Alcoholic/diagnosis/mortality/therapy/*virology ; Herpesviridae/genetics/isolation & purification ; Humans ; Intestinal Mucosa/*virology ; Liver/pathology ; Liver Cirrhosis/diagnosis/mortality/therapy/*virology ; Male ; Metagenomics ; Middle Aged ; Parvoviridae/genetics/isolation & purification ; RNA, Viral/isolation & purification ; Severity of Illness Index ; Survival Rate ; Virome/*genetics ; },
abstract = {BACKGROUND AND AIMS: Alcoholic hepatitis (AH) is a severe manifestation of alcohol-associated liver disease (ALD) with high mortality. Although gut bacteria and fungi modulate disease severity, little is known about the effects of the viral microbiome (virome) in patients with ALD.

APPROACH AND RESULTS: We extracted virus-like particles from 89 patients with AH who were enrolled in a multicenter observational study, 36 with alcohol use disorder (AUD), and 17 persons without AUD (controls). Virus-like particles from fecal samples were fractionated using differential filtration techniques, and metagenomic sequencing was performed to characterize intestinal viromes. We observed an increased viral diversity in fecal samples from patients with ALD, with the most significant changes in samples from patients with AH. Escherichia-, Enterobacteria-, and Enterococcus phages were over-represented in fecal samples from patients with AH, along with significant increases in mammalian viruses such as Parvoviridae and Herpesviridae. Antibiotic treatment was associated with higher viral diversity. Specific viral taxa, such as Staphylococcus phages and Herpesviridae, were associated with increased disease severity, indicated by a higher median Model for End-Stage Liver Disease score, and associated with increased 90-day mortality.

CONCLUSIONS: In conclusion, intestinal viral taxa are altered in fecal samples from patients with AH and associated with disease severity and mortality. Our study describes an intestinal virome signature associated with AH.},
}

Adult
Aged
Animals
Bacteriophages/genetics/isolation & purification
Case-Control Studies
DNA, Viral/isolation & purification
End Stage Liver Disease/diagnosis/mortality/therapy/*virology
Feces/virology
Female
Hepatitis, Alcoholic/diagnosis/mortality/therapy/*virology
Herpesviridae/genetics/isolation & purification
Humans
Intestinal Mucosa/*virology
Liver/pathology
Liver Cirrhosis/diagnosis/mortality/therapy/*virology
Male
Metagenomics
Middle Aged
Parvoviridae/genetics/isolation & purification
RNA, Viral/isolation & purification
Severity of Illness Index
Survival Rate
Virome/*genetics

@article {pmid33859184,
year = {2021},
author = {Couch, CE and Stagaman, K and Spaan, RS and Combrink, HJ and Sharpton, TJ and Beechler, BR and Jolles, AE},
title = {Diet and gut microbiome enterotype are associated at the population level in African buffalo.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2267},
pmid = {33859184},
issn = {2041-1723},
support = {BB/L011085/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Buffaloes/*microbiology/physiology ; Communicable Diseases/epidemiology/microbiology/*veterinary ; DNA, Bacterial/isolation & purification ; Feces/microbiology ; Feeding Behavior/*physiology ; Firmicutes/genetics/isolation & purification ; Gastrointestinal Microbiome/*immunology ; Incidence ; Metagenomics ; Phylogeny ; Planococcaceae/genetics/isolation & purification ; Prevalence ; RNA, Ribosomal, 16S/genetics ; South Africa/epidemiology ; Symbiosis/immunology ; },
abstract = {Studies in humans and laboratory animals link stable gut microbiome "enterotypes" with long-term diet and host health. Understanding how this paradigm manifests in wild herbivores could provide a mechanistic explanation of the relationships between microbiome dynamics, changes in dietary resources, and outcomes for host health. We identify two putative enterotypes in the African buffalo gut microbiome. The enterotype prevalent under resource-abundant dietary regimes, regardless of environmental conditions, has high richness, low between- and within-host beta diversity, and enrichment of genus Ruminococcaceae-UCG-005. The second enterotype, prevalent under restricted dietary conditions, has reduced richness, elevated beta diversity, and enrichment of genus Solibacillus. Population-level gamma diversity is maintained during resource restriction by increased beta diversity between individuals, suggesting a mechanism for population-level microbiome resilience. We identify three pathogens associated with microbiome variation depending on host diet, indicating that nutritional background may impact microbiome-pathogen dynamics. Overall, this study reveals diet-driven enterotype plasticity, illustrates ecological processes that maintain microbiome diversity, and identifies potential associations between diet, enterotype, and disease.},
}

Animals
Buffaloes/*microbiology/physiology
Communicable Diseases/epidemiology/microbiology/*veterinary
DNA, Bacterial/isolation & purification
Feces/microbiology
Feeding Behavior/*physiology
Firmicutes/genetics/isolation & purification
Gastrointestinal Microbiome/*immunology
Incidence
Metagenomics
Phylogeny
Planococcaceae/genetics/isolation & purification
Prevalence
RNA, Ribosomal, 16S/genetics
South Africa/epidemiology
Symbiosis/immunology

@article {pmid33837203,
year = {2021},
author = {Das, S and Bernasconi, E and Koutsokera, A and Wurlod, DA and Tripathi, V and Bonilla-Rosso, G and Aubert, JD and Derkenne, MF and Mercier, L and Pattaroni, C and Rapin, A and von Garnier, C and Marsland, BJ and Engel, P and Nicod, LP},
title = {A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2126},
pmid = {33837203},
issn = {2041-1723},
mesh = {Adult ; Allografts/immunology/microbiology ; Bacteria/genetics/immunology/isolation & purification/pathogenicity ; Bacterial Load/immunology ; Bacteriological Techniques ; Bronchoalveolar Lavage Fluid/microbiology ; Bronchoscopy ; DNA, Bacterial/isolation & purification ; Female ; Graft Rejection/diagnosis/immunology/*microbiology ; Humans ; Immune Tolerance ; Longitudinal Studies ; Lung/immunology/*microbiology ; Lung Transplantation/*adverse effects ; Male ; Metagenomics ; Microbiota/genetics/*immunology ; Middle Aged ; Pneumonia, Bacterial/diagnosis/immunology/*microbiology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; },
abstract = {There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, 'pneumotypes'. The predominant 'balanced' pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant.},
}

Adult
Allografts/immunology/microbiology
Bacteria/genetics/immunology/isolation & purification/pathogenicity
Bacterial Load/immunology
Bacteriological Techniques
Bronchoalveolar Lavage Fluid/microbiology
Bronchoscopy
DNA, Bacterial/isolation & purification
Female
Graft Rejection/diagnosis/immunology/*microbiology
Humans
Immune Tolerance
Longitudinal Studies
Lung/immunology/*microbiology
Lung Transplantation/*adverse effects
Male
Metagenomics
Microbiota/genetics/*immunology
Middle Aged
Pneumonia, Bacterial/diagnosis/immunology/*microbiology
Prospective Studies
RNA, Ribosomal, 16S/genetics

@article {pmid33927711,
year = {2021},
author = {Griggs, RG and Steenwerth, KL and Mills, DA and Cantu, D and Bokulich, NA},
title = {Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing.},
journal = {Frontiers in microbiology},
volume = {12},
number = {},
pages = {673810},
doi = {10.3389/fmicb.2021.673810},
pmid = {33927711},
issn = {1664-302X},
abstract = {Microbiomes are integral to viticulture and winemaking - collectively termed winegrowing - where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.},
}

@article {pmid33927454,
year = {2021},
author = {Bae, J and Cho, HW and Jung, H and Park, J and Yun, S and Ha, S and Lee, Y and Kim, TJ},
title = {Changes in Intestinal Microbiota Due to the Expanded Polystyrene Diet of Mealworms (Tenebrio molitor).},
journal = {Indian journal of microbiology},
volume = {61},
number = {2},
pages = {130-136},
doi = {10.1007/s12088-021-00922-w},
pmid = {33927454},
issn = {0046-8991},
abstract = {Expanded polystyrene (EPS), which is difficult to decompose, is usually buried or incinerated, causing the natural environment to be contaminated with microplastics and environmental hormones. Digestion of EPS by mealworms has been identified as a possible biological solution to the problem of pollution, but the complete degradation mechanism of EPS is not yet known. Intestinal microorganisms play a significant role in the degradation of EPS by mealworms, and relatively few other EPS degradation microorganisms are currently known. This study observed significant differences in the intestinal microbiota of mealworms according to the dietary results of metagenomics analysis and biodiversity indices. We have proposed two new candidates of EPS-degrading bacteria, Cronobacter sakazakii and Lactococcus garvieae, which increased significantly in the EPS feeding group population. The population change and the new two bacteria will help us understand the biological mechanism of EPS degradation and develop practical EPS degradation methods.},
}

@article {pmid33766942,
year = {2021},
author = {Levin, D and Raab, N and Pinto, Y and Rothschild, D and Zanir, G and Godneva, A and Mellul, N and Futorian, D and Gal, D and Leviatan, S and Zeevi, D and Bachelet, I and Segal, E},
title = {Diversity and functional landscapes in the microbiota of animals in the wild.},
journal = {Science (New York, N.Y.)},
volume = {372},
number = {6539},
pages = {},
doi = {10.1126/science.abb5352},
pmid = {33766942},
issn = {1095-9203},
mesh = {Animals ; Animals, Wild/classification/*microbiology/physiology ; *Bacteria/classification/genetics/isolation & purification ; Bacterial Toxins/metabolism ; Behavior, Animal ; Biodiversity ; Databases, Nucleic Acid ; Diet ; Ecosystem ; Falkland Islands ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Genome, Bacterial ; Host Microbial Interactions ; Israel ; Madagascar ; *Metagenome ; Metagenomics ; Peptide Hydrolases/genetics/metabolism ; Phylogeny ; Queensland ; Uganda ; },
abstract = {Animals in the wild are able to subsist on pathogen-infected and poisonous food and show immunity to various diseases. These may be due to their microbiota, yet we have a poor understanding of animal microbial diversity and function. We used metagenomics to analyze the gut microbiota of more than 180 species in the wild, covering diverse classes, feeding behaviors, geographies, and traits. Using de novo metagenome assembly, we constructed and functionally annotated a database of more than 5000 genomes, comprising 1209 bacterial species of which 75% are unknown. The microbial composition, diversity, and functional content exhibit associations with animal taxonomy, diet, activity, social structure, and life span. We identify the gut microbiota of wild animals as a largely untapped resource for the discovery of therapeutics and biotechnology applications.},
}

Animals
Animals, Wild/classification/*microbiology/physiology
*Bacteria/classification/genetics/isolation & purification
Bacterial Toxins/metabolism
Behavior, Animal
Biodiversity
Databases, Nucleic Acid
Diet
Ecosystem
Falkland Islands
Feces/microbiology
*Gastrointestinal Microbiome
*Genome, Bacterial
Host Microbial Interactions
Israel
Madagascar
*Metagenome
Metagenomics
Peptide Hydrolases/genetics/metabolism
Phylogeny
Queensland
Uganda

@article {pmid33608294,
year = {2021},
author = {Fortunato, CS and Butterfield, DA and Larson, B and Lawrence-Slavas, N and Algar, CK and Zeigler Allen, L and Holden, JF and Proskurowski, G and Reddington, E and Stewart, LC and Topçuoğlu, BD and Vallino, JJ and Huber, JA},
title = {Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities.},
journal = {Applied and environmental microbiology},
volume = {87},
number = {9},
pages = {},
pmid = {33608294},
issn = {1098-5336},
mesh = {Autotrophic Processes ; Bacteria/genetics ; Bacteriological Techniques/*methods ; Base Sequence ; Hydrothermal Vents/*microbiology ; Metagenome ; Microbiota/*genetics ; Pressure ; RNA, Ribosomal, 16S/genetics ; Seawater ; Ships ; Time Factors ; },
abstract = {Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean.IMPORTANCE Diverse microbial communities drive biogeochemical cycles in Earth's ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delays, with shipboard microbial communities being more stressed than seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean.},
}

Autotrophic Processes
Bacteria/genetics
Bacteriological Techniques/*methods
Base Sequence
Hydrothermal Vents/*microbiology
Metagenome
Microbiota/*genetics
Pressure
RNA, Ribosomal, 16S/genetics
Seawater
Ships
Time Factors

@article {pmid33202274,
year = {2021},
author = {Ferreira-Lazarte, A and Fernández, J and Gallego-Lobillo, P and Villar, CJ and Lombó, F and Moreno, FJ and Villamiel, M},
title = {Behaviour of citrus pectin and modified citrus pectin in an azoxymethane/dextran sodium sulfate (AOM/DSS)-induced rat colorectal carcinogenesis model.},
journal = {International journal of biological macromolecules},
volume = {167},
number = {},
pages = {1349-1360},
doi = {10.1016/j.ijbiomac.2020.11.089},
pmid = {33202274},
issn = {1879-0003},
mesh = {Acetates/metabolism ; Animals ; Azoxymethane/pharmacology/*toxicity ; Bifidobacterium/isolation & purification ; Blood Glucose/drug effects ; Body Weight/drug effects ; Butyrates/metabolism ; Carcinogenesis/*drug effects/metabolism/pathology ; Chromatography, High Pressure Liquid ; Citrus/chemistry ; Colorectal Neoplasms/chemically induced/*diet therapy/metabolism/mortality ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; Gastrointestinal Microbiome/*drug effects ; Hydrogen-Ion Concentration ; Lactic Acid/metabolism ; Lactobacillaceae/isolation & purification ; Male ; Metagenomics ; Pectins/analysis/*therapeutic use ; Phylogeny ; Propionates/metabolism ; Proteobacteria/isolation & purification ; Rats ; Rats, Inbred F344 ; Triglycerides/blood ; },
abstract = {Large intestine cancer is one of the most relevant chronic diseases taking place at present. Despite therapies have evolved very positively, this pathology is still under deep investigation. One of the recent approaches is the prevention by natural compounds such as pectin. In this paper, we have assessed the impact of citrus pectin and modified citrus pectin on colorectal cancer in rats (Rattus norvegicus F344) to which azoxymethane and DSS were supplied. The lowest intake of food and body weight were detected in animals fed with citrus pectin, together with an increase in the caecum weight, probably due to the viscosity, water retention capacity and bulking properties of pectin. The most striking feature was that, neither citrus pectin nor modified citrus pectin gave rise to a tumorigenesis prevention. Moreover, in both, more than 50% of rats with cancer died, probably ascribed to a severe dysbiosis state in the gut, as shown by the metabolism and metagenomics studies carried out. This was related to a decrease of pH in caecum lumen and increase in acetate and lactic acid levels together with the absence of propionic and butyric acids. A relevant increase in Proteobacteria (Enterobacteriaceae) were thought to be one of the reasons for enteric infection that could have provoked the death of rats and the lack of cancer prevention. However, a reduction of blood glucose and triacylglycerides level and an increase of Bifidobacterium and Lactobacillaceae were found in animals that intake pectin, as compared to universal and modified citrus pectin feeding.},
}

Acetates/metabolism
Animals
Azoxymethane/pharmacology/*toxicity
Bifidobacterium/isolation & purification
Blood Glucose/drug effects
Body Weight/drug effects
Butyrates/metabolism
Carcinogenesis/*drug effects/metabolism/pathology
Chromatography, High Pressure Liquid
Citrus/chemistry
Colorectal Neoplasms/chemically induced/*diet therapy/metabolism/mortality
Dextran Sulfate/pharmacology
Disease Models, Animal
Gastrointestinal Microbiome/*drug effects
Hydrogen-Ion Concentration
Lactic Acid/metabolism
Lactobacillaceae/isolation & purification
Male
Metagenomics
Pectins/analysis/*therapeutic use
Phylogeny
Propionates/metabolism
Proteobacteria/isolation & purification
Rats
Rats, Inbred F344
Triglycerides/blood

@article {pmid32973805,
year = {2020},
author = {Xu, R and Tan, C and He, Y and Wu, Q and Wang, H and Yin, J},
title = {Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Encephalitis: A Chinese Pilot Study.},
journal = {Frontiers in immunology},
volume = {11},
number = {},
pages = {1994},
pmid = {32973805},
issn = {1664-3224},
mesh = {Adult ; Aged ; Biomarkers ; Blood-Brain Barrier/metabolism ; China ; *Disease Susceptibility ; *Dysbiosis ; Encephalitis/diagnosis/*etiology/*metabolism/mortality ; Fatty Acids, Volatile/*metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metagenome ; Metagenomics/methods ; Middle Aged ; Permeability ; Pilot Projects ; Prognosis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: Encephalitis, the inflammation of the brain, may be caused by an infection or an autoimmune reaction. However, few researches were focused on the gut microbiome characteristics in encephalitis patients.

Methods: A prospective observational study was conducted in an academic hospital in Guangzhou from February 2017 to February 2018. Patients with encephalitis were recruited. Fecal and serum samples were collected at admission. Healthy volunteers were enrolled from a community. Disease severity scores were recorded by specialized physicians, including Glasgow Coma Scale (GCS), Sequential Organ Failure Assessment (SOFA), and Acute Physiology and Chronic Health Evaluation-II (APACHE-II). 16S rRNA sequence was performed to analyze the gut microbiome, then the α-diversities and β-diversities were estimated. Short-chain fatty acids (SCFAs) were extracted from fecal samples and determined by gas chromatography-mass spectrometry. Serum D-lactate (D-LA), intestinal fatty acid-binding protein (iFABP), lipopolysaccharide (LPS), and lipopolysaccharide-binding protein (LBP) were measured by enzyme-linked immunosorbent assay (ELISA). The associations among microbial indexes and clinical parameters were evaluated by Spearman correlation analysis.

Results: In total, twenty-eight patients were recruited for analysis (median age 46 years; 82.1% male; median GCS 6.5; median SOFA 6.5; median APACHE-II 14.5). Twenty-eight age- and sex-matched healthy subjects were selected as controls. The β-diversities between patients and healthy subjects were significantly different. The α-diversities did not show significant differences between these two groups. In the patient group, the abundances of Bacteroidetes, Proteobacteria, and Bacilli were significantly enriched. Accordingly, fecal SCFA levels were decreased in the patient group, whereas serum D-LA, iFABP, LPS, and LBP levels were increased compared with those in healthy subjects. Correlation analyses showed that disease severity had positive correlations with Proteobacteria and Akkermansia but negative correlations with Firmicutes, Clostridia, and Ruminococcaceae abundances. The cerebrospinal fluid albumin-to-serum albumin ratio (CSAR) was positively related to the α-diversity but negatively correlated with the fecal butyrate concentration.

Conclusion: Gut microbiota disruption was observed in encephalitis patients, which manifested as pathogen dominance and health-promoting commensal depletion. Disease severity and brain damage may have associations with the gut microbiota or its metabolites. The causal relationship should be further explored in future studies.},
}

Adult
Aged
Biomarkers
Blood-Brain Barrier/metabolism
China
*Disease Susceptibility
*Dysbiosis
Encephalitis/diagnosis/*etiology/*metabolism/mortality
Fatty Acids, Volatile/*metabolism
Female
*Gastrointestinal Microbiome
Humans
Male
Metagenome
Metagenomics/methods
Middle Aged
Permeability
Pilot Projects
Prognosis
RNA, Ribosomal, 16S/genetics

@article {pmid32627750,
year = {2020},
author = {Yang, J and Howe, A and Lee, J and Yoo, K and Park, J},
title = {An Improved Approach to Identify Bacterial Pathogens to Human in Environmental Metagenome.},
journal = {Journal of microbiology and biotechnology},
volume = {30},
number = {9},
pages = {1335-1342},
doi = {10.4014/jmb.2005.05033},
pmid = {32627750},
issn = {1738-8872},
mesh = {Bacteria/classification/genetics/isolation & purification/pathogenicity ; Databases, Genetic ; *Environmental Microbiology ; Humans ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Systems Integration ; },
abstract = {The identification of bacterial pathogens to humans is critical for environmental microbial risk assessment. However, current methods for identifying pathogens in environmental samples are limited in their ability to detect highly diverse bacterial communities and accurately differentiate pathogens from commensal bacteria. In the present study, we suggest an improved approach using a combination of identification results obtained from multiple databases, including the multilocus sequence typing (MLST) database, virulence factor database (VFDB), and pathosystems resource integration center (PATRIC) databases to resolve current challenges. By integrating the identification results from multiple databases, potential bacterial pathogens in metagenomes were identified and classified into eight different groups. Based on the distribution of genes in each group, we proposed an equation to calculate the metagenomic pathogen identification index (MPII) of each metagenome based on the weighted abundance of identified sequences in each database. We found that the accuracy of pathogen identification was improved by using combinations of multiple databases compared to that of individual databases. When the approach was applied to environmental metagenomes, metagenomes associated with activated sludge were estimated with higher MPII than other environments (i.e., drinking water, ocean water, ocean sediment, and freshwater sediment). The calculated MPII values were statistically distinguishable among different environments (p<0.05). These results demonstrate that the suggested approach allows more for more accurate identification of the pathogens associated with metagenomes.},
}

Bacteria/classification/genetics/isolation & purification/pathogenicity
Databases, Genetic
*Environmental Microbiology
Humans
Metagenome/*genetics
Metagenomics/*methods
Microbiota/genetics
Systems Integration

@article {pmid32557173,
year = {2020},
author = {Hinsu, AT and Patel, AB and Pandit, RJ and Thakkar, JR and Shah, RK and Jakhesara, SJ and Koringa, PG and Joshi, CG},
title = {MetaRNAseq analysis of surti buffalo rumen content reveals that transcriptionally active microorganisms need not be abundant.},
journal = {Molecular biology reports},
volume = {47},
number = {7},
pages = {5101-5114},
doi = {10.1007/s11033-020-05581-6},
pmid = {32557173},
issn = {1573-4978},
support = {AAU/GVC/CPCSEA-IAEC/108/2013 dated 05/10/2013//Indian Council of Agricultural Research/ ; },
mesh = {Animals ; Buffaloes/genetics/*microbiology ; Carbohydrate Metabolism ; *Gastrointestinal Microbiome ; *Metagenome ; RNA-Seq ; Rumen/metabolism/*microbiology ; *Transcriptome ; },
abstract = {The present study describes rumen microbiota composition and their functional profiles in Indian Surti buffaloes by metagenomic (MG) and metatranscriptomic (MT) approaches. The study compares samples from buffaloes fed three different proportion of roughages; green and dry type of roughage; and different rumen liquor fractions. Irrespective of sample, Bacteroidetes and Firmicutes were the most predominant bacterial phyla, followed by Proteobacteria, Fibrobacteres and Actinobacteria while, Prevotella, Bacteroides, Ruminococcus and Clostridium were the most abundant genera. Different proportions of taxa were observed in both MG and MT approaches indicating the differences in organisms present and organisms active in the rumen. Higher proportions of fungal taxa were observed in MT while important organisms like Fibrobacter and Butyrivibrio and abundant organisms like Bacteroides and Prevotella were underrepresented in MT data. Functionally, higher proportions of genes involved in Carbohydrate metabolism, Amino acid metabolism and Translation were observed in both data. Genes involved in Metabolism were observed to be underrepresented in MT data while, those involved in Genetic information processing were overrepresented in MT data. Further, genes involved in Carbohydrate metabolism were overexpressed compared to genes involved in Amino acid metabolism in MT data compared to MG data which had higher proportion of genes involved in Amino acid metabolism than Carbohydrate metabolism. In all significant differences were observed between both approaches, different fractions of rumen liquor (liquid and solid) and different proportions of roughage in diet.},
}

Animals
Buffaloes/genetics/*microbiology
Carbohydrate Metabolism
*Gastrointestinal Microbiome
*Metagenome
RNA-Seq
Rumen/metabolism/*microbiology
*Transcriptome

@article {pmid32221908,
year = {2020},
author = {Caraballo Guzmán, A and González Hurtado, MI and Cuesta-Astroz, Y and Torres, G},
title = {Metagenomic characterization of bacterial biofilm in four food processing plants in Colombia.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {51},
number = {3},
pages = {1259-1267},
pmid = {32221908},
issn = {1678-4405},
support = {55965//Colciencias/ ; },
mesh = {Bacteria/classification/*genetics/isolation & purification ; *Biofilms ; Colombia ; Disinfection ; Equipment Contamination/*statistics & numerical data ; Food Handling/*instrumentation ; Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {Bacteria inside biofilms are more persistent and resistant to stress conditions found in the production environment of food processing plants, thus representing a constant risk for product safety and quality. Therefore, the aim of this study was to characterize, using 16S rRNA sequencing, the bacterial communities from biofilms found in four food processing plants (P1, P2, P3, and P4). In total, 50 samples from these four processing plants were taken after cleaning and disinfection processes. Four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroides represented over 94% of the operational taxonomic units found across these four plants. A total of 102 families and 189 genera were identified. Two genera, Pseudomonas spp. and Acinetobacter spp., were the most frequently found (93.47%) across the four plants. In P1, Pseudomonas spp. and Lactobacillus spp. were the dominant genera, whereas Lactobacillus spp. and Streptococcus spp. were identified in P2. On the other hand, biofilms found in P3 and P4 mainly consisted of Pseudomonas spp. and Acinetobacter spp. Our results indicate that different bacterial genera of interest to the food industry due to their ability to form biofilm and affect food quality can coexist inside biofilms, and as such, persist in production environments, representing a constant risk for manufactured foods. In addition, the core microbiota identified across processing plants evaluated was probably influenced by type of food produced and cleaning and disinfection processes performed in each one of these.},
}

Bacteria/classification/*genetics/isolation & purification
*Biofilms
Colombia
Disinfection
Equipment Contamination/*statistics & numerical data
Food Handling/*instrumentation
Metagenome
Metagenomics
*Microbiota

@article {pmid32073995,
year = {2020},
author = {Laudadio, I and Cesi, V and Carissimi, C},
title = {Metagenomics in Italy and Europe: Three Actionable Challenges/Prospects in 2020.},
journal = {Omics : a journal of integrative biology},
volume = {24},
number = {3},
pages = {122-123},
doi = {10.1089/omi.2020.0006},
pmid = {32073995},
issn = {1557-8100},
mesh = {Anti-Bacterial Agents/*therapeutic use ; Bacteriocins/*therapeutic use ; Drug Resistance, Multiple, Bacterial/*drug effects/genetics ; Europe ; Humans ; Metagenomics/*trends ; Microbiota/genetics ; Probiotics/administration & dosage ; },
}

Anti-Bacterial Agents/*therapeutic use
Bacteriocins/*therapeutic use
Drug Resistance, Multiple, Bacterial/*drug effects/genetics
Europe
Humans
Metagenomics/*trends
Microbiota/genetics
Probiotics/administration & dosage

@article {pmid32912581,
year = {2021},
author = {de C Lima, CO and Vaz, ABM and De Castro, GM and Lobo, F and Solar, R and Rodrigues, C and Martins Pinto, LR and Vandenberghe, L and Pereira, G and Miúra da Costa, A and Benevides, RG and Azevedo, V and Trovatti Uetanabaro, AP and Soccol, CR and Góes-Neto, A},
title = {Integrating microbial metagenomics and physicochemical parameters and a new perspective on starter culture for fine cocoa fermentation.},
journal = {Food microbiology},
volume = {93},
number = {},
pages = {103608},
doi = {10.1016/j.fm.2020.103608},
pmid = {32912581},
issn = {1095-9998},
mesh = {Acetic Acid/metabolism ; Acetobacter/metabolism ; Bacteria/metabolism ; Brazil ; Cacao/*microbiology ; Chocolate ; *Fermentation ; *Fermented Foods and Beverages ; Flavoring Agents ; *Food Microbiology ; Hanseniaspora/genetics/metabolism ; Metagenomics/*methods ; Microbiota/genetics ; Seeds/microbiology ; },
abstract = {Cocoa beans used for chocolate production are fermented seeds of Theobroma cacao obtained by a natural fermentation process. The flavors and chemical compounds produced during the fermentation process make this step one of the most important in fine chocolate production. Herein, an integrative analysis of the variation of microbial community structure, using a shotgun metagenomics approach and associated physicochemical features, was performed during fermentation of fine cocoa beans. Samples of Forastero variety (FOR) and a mixture of two hybrids (PS1319 and CCN51) (MIX) from Bahia, Brazil, were analyzed at 7 different times. In the beginning (0 h), the structures of microbial communities were very different between FOR and MIX, reflecting the original plant-associated microbiomes. The highest change in microbial community structures occurred at the first 24 h of fermentation, with a marked increase in temperature and acetic acid concentration, and pH decrease. At 24-48 h both microbial community structures were quite homogenous regarding temperature, acetic acid, succinic acid, pH, soluble proteins and total phenols. During 72-96 h, the community structure resembles an acidic and warmer environment, prevailing few acetic acid bacteria. Taxonomic richness and abundance at 72-144 h exhibited significant correlation with temperature, reducing sugars, succinic, and acetic acids. Finally, we recommend that dominant microbial species of spontaneous fine cocoa fermentations should be considered as inoculum in accordance with the farm/region and GMP to maintain a differential organoleptic feature for production of fine chocolate. In our study, a starter inoculum composed of Acetobacter pausterianus and Hanseniaspora opuntiae strains is indicated.},
}

Acetic Acid/metabolism
Acetobacter/metabolism
Bacteria/metabolism
Brazil
Cacao/*microbiology
Chocolate
*Fermentation
*Fermented Foods and Beverages
Flavoring Agents
*Food Microbiology
Hanseniaspora/genetics/metabolism
Metagenomics/*methods
Microbiota/genetics
Seeds/microbiology

@article {pmid31962124,
year = {2020},
author = {Niu, J and Li, XL and Wu, YL and Sun, QZ and Zhang, W and Cao, M and Wang, JJ},
title = {RNA virome screening in diverse but ecologically related citrus pests reveals potential virus-host interactions.},
journal = {Journal of invertebrate pathology},
volume = {170},
number = {},
pages = {107329},
doi = {10.1016/j.jip.2020.107329},
pmid = {31962124},
issn = {1096-0805},
mesh = {Animals ; Gene Library ; *Host-Pathogen Interactions ; Insecta/*virology ; Mites/*virology ; RNA, Viral/*analysis ; Snails/*virology ; *Virome ; },
abstract = {As an evergreen ecosystem, citrus orchards have specialized pest species and stable ecological homeostasis; thus, they provide an ideal model for investigating RNA viromes in diverse but ecologically related species. For this purpose, we collected specialized citrus pests from three classes of invertebrates, Insecta, Arachnida, and Gastropoda and we constructed two kinds of libraries (RNA and small RNA) for the pests by deep sequencing. In total, six virus-derived sequences were identified, including four Picornavirales, one Jingchuvirales and one Nidovirales. The picornavirus-derived small RNAs showed significant small RNA peaks and symmetric distribution patterns along the genome, which suggests these viruses infected the hosts and triggered host antiviral immunity RNA interference. Screening of virus-derived sequences in multiple species of citrus pests (n = 10 per species) showed that Eotetranychus kankitus picorna-like virus and Tetranychus urticae mivirus may be present in multiple pests. Our investigation in citrus pests confirmed that RNA viruses revealed by metagenomics could impact host immunity (e.g. RNAi). An approach with parallel deep sequencing of RNAs and small RNAs is useful not only for viral discoveries but also for understanding virus-host interactions of ecologically related but divergent pest species.},
}

Animals
Gene Library
*Host-Pathogen Interactions
Insecta/*virology
Mites/*virology
RNA, Viral/*analysis
Snails/*virology
*Virome

@article {pmid33850115,
year = {2021},
author = {Raes, EJ and Karsh, K and Sow, SLS and Ostrowski, M and Brown, MV and van de Kamp, J and Franco-Santos, RM and Bodrossy, L and Waite, AM},
title = {Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2213},
pmid = {33850115},
issn = {2041-1723},
mesh = {Bacteria/classification/*genetics ; Bacterial Physiological Phenomena ; Biodiversity ; Ecology ; Genes, Bacterial/*genetics ; Metabolic Networks and Pathways/*genetics ; Metagenome ; Metagenomics/*methods ; Pacific Ocean ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Thermodynamics ; },
abstract = {Global oceanographic monitoring initiatives originally measured abiotic essential ocean variables but are currently incorporating biological and metagenomic sampling programs. There is, however, a large knowledge gap on how to infer bacterial functions, the information sought by biogeochemists, ecologists, and modelers, from the bacterial taxonomic information (produced by bacterial marker gene surveys). Here, we provide a correlative understanding of how a bacterial marker gene (16S rRNA) can be used to infer latitudinal trends for metabolic pathways in global monitoring campaigns. From a transect spanning 7000 km in the South Pacific Ocean we infer ten metabolic pathways from 16S rRNA gene sequences and 11 corresponding metagenome samples, which relate to metabolic processes of primary productivity, temperature-regulated thermodynamic effects, coping strategies for nutrient limitation, energy metabolism, and organic matter degradation. This study demonstrates that low-cost, high-throughput bacterial marker gene data, can be used to infer shifts in the metabolic strategies at the community scale.},
}

Bacteria/classification/*genetics
Bacterial Physiological Phenomena
Biodiversity
Ecology
Genes, Bacterial/*genetics
Metabolic Networks and Pathways/*genetics
Metagenome
Metagenomics/*methods
Pacific Ocean
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Thermodynamics

@article {pmid32951639,
year = {2020},
author = {Zhang, X and Das, S and Dunbar, S and Tang, YW},
title = {Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis.},
journal = {Advances in clinical chemistry},
volume = {99},
number = {},
pages = {49-85},
doi = {10.1016/bs.acc.2020.02.007},
pmid = {32951639},
issn = {2162-9471},
mesh = {Animals ; Feces/microbiology ; Gastroenteritis/*diagnosis/etiology/microbiology ; Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Microscopy/methods ; },
abstract = {Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.},
}

Animals
Feces/microbiology
Gastroenteritis/*diagnosis/etiology/microbiology
Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing/methods
Humans
Metagenomics/methods
Microscopy/methods

@article {pmid32891158,
year = {2020},
author = {Ortiz-Baez, AS and Cousins, K and Eden, JS and Chang, WS and Harvey, E and Pettersson, JH and Carver, S and Polkinghorne, A and Šlapeta, J and Rose, K and Holmes, EC},
title = {Meta-transcriptomic identification of Trypanosoma spp. in native wildlife species from Australia.},
journal = {Parasites & vectors},
volume = {13},
number = {1},
pages = {447},
pmid = {32891158},
issn = {1756-3305},
support = {FL170100022//Australian Research Council (AU)/ ; },
mesh = {Animals ; Animals, Wild/*parasitology ; Australia ; Biodiversity ; Biological Evolution ; DNA, Protozoan/genetics ; Host-Parasite Interactions ; Marsupialia/parasitology ; Metagenomics ; Passeriformes/parasitology ; Phylogeny ; RNA, Ribosomal, 18S/genetics ; Ranidae/parasitology ; Transcriptome ; *Trypanosoma/classification/genetics/isolation & purification ; Vertebrates/parasitology ; },
abstract = {BACKGROUND: Wildlife species carry a remarkable diversity of trypanosomes. The detection of trypanosome infection in native Australian fauna is central to understanding their diversity and host-parasite associations. The implementation of total RNA sequencing (meta-transcriptomics) in trypanosome surveillance and diagnosis provides a powerful methodological approach to better understand the host species distribution of this important group of parasites.

METHODS: We implemented a meta-transcriptomic approach to detect trypanosomes in a variety of tissues (brain, liver, lung, skin, gonads) sampled from native Australian wildlife, comprising four marsupials (koala, Phascolarctos cinereus; southern brown bandicoot, Isoodon obesulus; swamp wallaby, Wallabia bicolor; bare-nosed wombat, Vombatus ursinus), one bird (regent honeyeater, Anthochaera phrygia) and one amphibian (eastern dwarf tree frog, Litoria fallax). Samples corresponded to both clinically healthy and diseased individuals. Sequencing reads were de novo assembled into contigs and annotated. The evolutionary relationships among the trypanosomatid sequences identified were determined through phylogenetic analysis of 18S rRNA sequences.

RESULTS: We detected trypanosome sequences in all six species of vertebrates sampled, with positive samples in multiple organs and tissues confirmed by PCR. Phylogenetic analysis indicated that the trypanosomes infecting marsupials were related to those previously detected in placental and marsupial mammals, while the trypanosome in the regent honeyeater grouped with avian trypanosomes. In contrast, we provide the first evidence for a trypanosome in the eastern dwarf tree frog that was phylogenetically distinct from those described in other amphibians.

CONCLUSIONS: To our knowledge, this is the first meta-transcriptomic analysis of trypanosomes in native Australian wildlife, expanding the known genetic diversity of these important parasites. We demonstrated that RNA sequencing is sufficiently sensitive to detect low numbers of Trypanosoma transcripts and from diverse hosts and tissues types, thereby representing an effective means to detect trypanosomes that are divergent in genome sequence.},
}

Animals
Animals, Wild/*parasitology
Australia
Biodiversity
Biological Evolution
DNA, Protozoan/genetics
Host-Parasite Interactions
Marsupialia/parasitology
Metagenomics
Passeriformes/parasitology
Phylogeny
RNA, Ribosomal, 18S/genetics
Ranidae/parasitology
Transcriptome
*Trypanosoma/classification/genetics/isolation & purification
Vertebrates/parasitology

@article {pmid33902743,
year = {2021},
author = {Cabello-Yeves, PJ and Callieri, C and Picazo, A and Mehrshad, M and Haro-Moreno, JM and Roda-Garcia, JJ and Dzhembekova, N and Slabakova, V and Slabakova, N and Moncheva, S and Rodriguez-Valera, F},
title = {The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics.},
journal = {Environmental microbiome},
volume = {16},
number = {1},
pages = {5},
pmid = {33902743},
issn = {2524-6372},
support = {CGL2016-76273-p//Ministerio de Ciencia, Innovación y Universidades/ ; PROMETEO/2019/009//Conselleria d'Educació, Investigació, Cultura i Esport/ ; APOSTD/2019/009//Conselleria d'Educació, Investigació, Cultura i Esport/ ; D01-230/06.12.2018//Bulgarian Academy of Sciences/ ; },
abstract = {BACKGROUND: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former, albeit with lower salinity and temperature. Despite its well-known hydrology and physicochemical features, this enormous water mass remains poorly studied at the microbial genomics level.

RESULTS: We have sampled its different water masses and analyzed the microbiome by shotgun and genome-resolved metagenomics, generating a large number of metagenome-assembled genomes (MAGs) from them. We found various similarities with previously described Black Sea metagenomic datasets, that show remarkable stability in its microbiome. Our datasets are also comparable to other marine anoxic water columns like the Cariaco Basin. The oxic zone resembles to standard marine (e.g. Mediterranean) photic zones, with Cyanobacteria (Synechococcus but a conspicuously absent Prochlorococcus), and photoheterotrophs domination (largely again with marine relatives). The chemocline presents very different characteristics from the oxic surface with many examples of chemolithotrophic metabolism (Thioglobus) and facultatively anaerobic microbes. The euxinic anaerobic zone presents, as expected, features in common with the bottom of meromictic lakes with a massive dominance of sulfate reduction as energy-generating metabolism, a few (but detectable) methanogenesis marker genes, and a large number of "dark matter" streamlined genomes of largely unpredictable ecology.

CONCLUSIONS: The Black Sea oxic zone presents many similarities to the global ocean while the redoxcline and euxinic water masses have similarities to other similar aquatic environments of marine (Cariaco Basin or other Black Sea regions) or freshwater (meromictic monimolimnion strata) origin. The MAG collection represents very well the different types of metabolisms expected in this kind of environment. We are adding critical information about this unique and important ecosystem and its microbiome.},
}

@article {pmid33853691,
year = {2021},
author = {Zuo, T and Liu, Q and Zhang, F and Yeoh, YK and Wan, Y and Zhan, H and Lui, GCY and Chen, Z and Li, AYL and Cheung, CP and Chen, N and Lv, W and Ng, RWY and Tso, EYK and Fung, KSC and Chan, V and Ling, L and Joynt, G and Hui, DSC and Chan, FKL and Chan, PKS and Ng, SC},
title = {Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {91},
pmid = {33853691},
issn = {2049-2618},
mesh = {*COVID-19 ; Child, Preschool ; DNA ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA ; SARS-CoV-2 ; Virome ; },
abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need.

METHODS: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had fecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial fecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the fecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters.

RESULTS: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in fecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Fecal virome in SARS-CoV-2 infection harbored more stress-, inflammation-, and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells, and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects.

CONCLUSIONS: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether, our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19. Video Abstract.},
}

*COVID-19
Child, Preschool
DNA
*Gastrointestinal Microbiome/genetics
Humans
RNA
SARS-CoV-2
Virome

@article {pmid33795009,
year = {2021},
author = {Stamboulian, M and Li, S and Ye, Y},
title = {Using high-abundance proteins as guides for fast and effective peptide/protein identification from human gut metaproteomic data.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {80},
pmid = {33795009},
issn = {2049-2618},
support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Peptides/genetics ; Proteomics ; Tandem Mass Spectrometry ; },
abstract = {BACKGROUND: A few recent large efforts significantly expanded the collection of human-associated bacterial genomes, which now contains thousands of entities including reference complete/draft genomes and metagenome assembled genomes (MAGs). These genomes provide useful resource for studying the functionality of the human-associated microbiome and their relationship with human health and diseases. One application of these genomes is to provide a universal reference for database search in metaproteomic studies, when matched metagenomic/metatranscriptomic data are unavailable. However, a greater collection of reference genomes may not necessarily result in better peptide/protein identification because the increase of search space often leads to fewer spectrum-peptide matches, not to mention the drastic increase of computation time. Video Abstract METHODS: Here, we present a new approach that uses two steps to optimize the use of the reference genomes and MAGs as the universal reference for human gut metaproteomic MS/MS data analysis. The first step is to use only the high-abundance proteins (HAPs) (i.e., ribosomal proteins and elongation factors) for metaproteomic MS/MS database search and, based on the identification results, to derive the taxonomic composition of the underlying microbial community. The second step is to expand the search database by including all proteins from identified abundant species. We call our approach HAPiID (HAPs guided metaproteomics IDentification).

RESULTS: We tested our approach using human gut metaproteomic datasets from a previous study and compared it to the state-of-the-art reference database search method MetaPro-IQ for metaproteomic identification in studying human gut microbiota. Our results show that our two-steps method not only performed significantly faster but also was able to identify more peptides. We further demonstrated the application of HAPiID to revealing protein profiles of individual human-associated bacterial species, one or a few species at a time, using metaproteomic data.

CONCLUSIONS: The HAP guided profiling approach presents a novel effective way for constructing target database for metaproteomic data analysis. The HAPiID pipeline built upon this approach provides a universal tool for analyzing human gut-associated metaproteomic data.},
}

*Gastrointestinal Microbiome/genetics
Humans
Metagenomics
Peptides/genetics
Proteomics
Tandem Mass Spectrometry

@article {pmid33781324,
year = {2021},
author = {Snipen, L and Angell, IL and Rognes, T and Rudi, K},
title = {Reduced metagenome sequencing for strain-resolution taxonomic profiles.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {79},
pmid = {33781324},
issn = {2049-2618},
mesh = {Humans ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data.

RESULTS: We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time.

CONCLUSION: We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS . Video abstract.},
}

Humans
*Metagenome
Metagenomics
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid33775256,
year = {2021},
author = {Zhao, Y and Federico, A and Faits, T and Manimaran, S and Segrè, D and Monti, S and Johnson, WE},
title = {animalcules: interactive microbiome analytics and visualization in R.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {76},
pmid = {33775256},
issn = {2049-2618},
support = {R01 GM127430/GM/NIGMS NIH HHS/United States ; U01 CA220413/CA/NCI NIH HHS/United States ; },
mesh = {Data Interpretation, Statistical ; Humans ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Software ; },
abstract = {BACKGROUND: Microbial communities that live in and on the human body play a vital role in health and disease. Recent advances in sequencing technologies have enabled the study of microbial communities at unprecedented resolution. However, these advances in data generation have presented novel challenges to researchers attempting to analyze and visualize these data.

RESULTS: To address some of these challenges, we have developed animalcules, an easy-to-use interactive microbiome analysis toolkit for 16S rRNA sequencing data, shotgun DNA metagenomics data, and RNA-based metatranscriptomics profiling data. This toolkit combines novel and existing analytics, visualization methods, and machine learning models. For example, the toolkit features traditional microbiome analyses such as alpha/beta diversity and differential abundance analysis, combined with new methods for biomarker identification are. In addition, animalcules provides interactive and dynamic figures that enable users to understand their data and discover new insights. animalcules can be used as a standalone command-line R package or users can explore their data with the accompanying interactive R Shiny interface.

CONCLUSIONS: We present animalcules, an R package for interactive microbiome analysis through either an interactive interface facilitated by R Shiny or various command-line functions. It is the first microbiome analysis toolkit that supports the analysis of all 16S rRNA, DNA-based shotgun metagenomics, and RNA-sequencing based metatranscriptomics datasets. animalcules can be freely downloaded from GitHub at https://github.com/compbiomed/animalcules or installed through Bioconductor at https://www.bioconductor.org/packages/release/bioc/html/animalcules.html . Video abstract.},
}

Data Interpretation, Statistical
Humans
Metagenomics
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
*Software

@article {pmid33508686,
year = {2021},
author = {Dionizio, A and Uyghurturk, DA and Melo, CGS and Sabino-Arias, IT and Araujo, TT and Ventura, TMS and Perles, JVCM and Zanoni, JN and Den Besten, P and Buzalaf, MAR},
title = {Intestinal changes associated with fluoride exposure in rats: Integrative morphological, proteomic and microbiome analyses.},
journal = {Chemosphere},
volume = {273},
number = {},
pages = {129607},
doi = {10.1016/j.chemosphere.2021.129607},
pmid = {33508686},
issn = {1879-1298},
mesh = {Animals ; Firmicutes ; *Fluorides/toxicity ; *Gastrointestinal Microbiome ; Male ; Mice ; Proteome ; Proteomics ; Rats ; },
abstract = {Gastrointestinal signs and symptoms are the first signs of toxicity due to exposure to fluoride (F). This suggests the possibility that lower levels of subchronic F exposure may affect the gut. The aim of this study was to evaluate changes in the morphology, proteome and microbiome of the ileum of rats, after subchronic exposure to F. Male rats ingested water with 0, 10, or 50 mgF/L for thirty days. Treatment with F, regardless of the dose, significantly decreased the density of HuC/D-IR neurons, whereas CGRP-IR and SP-IR varicosities were significantly increased compared to the control group. Increased VIP-IR varicosities were significantly increased only in the group treated with 50 mgF/L. A significant increase in thickness of the tunica muscularis, as well as in the total thickness of the ileum wall was observed at both F doses when compared to controls. In proteomics analysis, myosin isoforms were increased, and Gastrotopin was decreased in F-exposed mice. In the microbiome metagenomics analysis, Class Clostridia was significantly reduced upon exposure to 10 mgF/L. At the higher F dose of 50 mg/L, genus Ureaplasma was significantly reduced in comparison with controls. Morphological and proteomics alterations induced by F were marked by changes associated with inflammation, and alterations in the gut microbiome. Further studies are needed to determine whether F exposure increases inflammation with secondary effects of the gut microbiome, and/or whether primary effects of F on the gut microbiome enhance changes associated with inflammation.},
}

Animals
Firmicutes
*Fluorides/toxicity
*Gastrointestinal Microbiome
Male
Mice
Proteome
Proteomics
Rats

@article {pmid33416984,
year = {2021},
author = {Busch, P and Suleiman, M and Schäfers, C and Antranikian, G},
title = {A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases.},
journal = {Extremophiles : life under extreme conditions},
volume = {25},
number = {2},
pages = {101-114},
pmid = {33416984},
issn = {1433-4909},
mesh = {Bacteria/genetics ; Glycoside Hydrolases/genetics ; Metagenome ; *Metagenomics ; *Microbiota ; },
abstract = {Next-generation sequencing and computational biology have facilitated the implementation of new combinatorial screening approaches to discover novel enzymes of biotechnological interest. In this study, we describe the successful establishment of a multi-omic approach for the identification of thermostable hydrolase-encoding genes by determination of gene expression levels. We applied this combinatorial approach using an anaerobic enrichment culture from an Azorean hot spring sample grown on green coffee beans as recalcitrant substrate. An in-depth analysis of the microbial community resulted in microorganisms capable of metabolizing the selected substrate, such as the genera Caloramator, Dictyoglomus and Thermoanaerobacter as active and abundant microorganisms. To discover glycoside hydrolases, 90,342 annotated genes were screened for specific reaction types. A total number of 106 genes encoding cellulases (EC 3.2.1.4), beta-glucosidases (EC 3.2.1.21) and endo-1,4-beta-mannosidases (EC 3.2.1.78) were selected. Mapping of RNA-Seq reads to the related metagenome led to expression levels for each gene. Amongst those, 14 genes, encoding glycoside hydrolases, showed highest expression values, and were used for further cloning. Four proteins were biochemically characterized and were identified as thermoactive glycoside hydrolases with a broad substrate range. This work demonstrated that a combinatory omic approach is a suitable strategy identifying unique thermoactive enzymes from environmental samples.},
}

Bacteria/genetics
Glycoside Hydrolases/genetics
Metagenome
*Metagenomics
*Microbiota

@article {pmid32747219,
year = {2020},
author = {Yu, D and Shu, XO and Howard, EF and Long, J and English, WJ and Flynn, CR},
title = {Fecal metagenomics and metabolomics reveal gut microbial changes after bariatric surgery.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {16},
number = {11},
pages = {1772-1782},
doi = {10.1016/j.soard.2020.06.032},
pmid = {32747219},
issn = {1878-7533},
support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK105847/DK/NIDDK NIH HHS/United States ; },
mesh = {*Bariatric Surgery ; Female ; *Gastric Bypass ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; Metagenomics ; Middle Aged ; Pilot Projects ; },
abstract = {BACKGROUND: Evidence from longitudinal patient studies regarding gut microbial changes after bariatric surgery is limited.

OBJECTIVE: To examine intraindividual changes in fecal microbiome and metabolites among patients undergoing Roux-en-Y gastric bypass or vertical sleeve gastrectomy.

SETTING: Observational study.

METHODS: Twenty patients were enrolled and provided stool samples before and 1 week, 1 month, and/or 3 months after surgery. Shallow shotgun metagenomics and untargeted fecal metabolomics were performed. Zero-inflated generalized additive models and linear mixed models were applied to identify fecal microbiome and metabolites changes, with adjustment for potential confounders and correction for multiple testing.

RESULTS: We enrolled 16 women and 4 men, including 16 white and 4 black participants (median age = 45 years; presurgery body mass index = 47.7 kg/m2). Ten patients had Roux-en-Y gastric bypass, 10 had vertical sleeve gastrectomy, and 14 patients provided postsurgery stool samples. Of 47 samples, median sequencing depth was 6.3 million reads and 1073 metabolites were identified. Microbiome alpha-diversity increased after surgery, especially at 3 months. Significant genus-level changes included increases in Odoribacter, Streptococcus, Anaerotruncus, Alistipes, Klebsiella, and Bifidobacterium, while decreases in Bacteroides, Coprocosccus, Dorea, and Faecalibacterium. Large increases in Streptococcus, Akkermansia, and Prevotella were observed at 3 months. Beta-diversity and fecal metabolites were also changed, including reduced caffeine metabolites, indoles, and butyrate.

CONCLUSIONS: Despite small sample size and missing repeated samples in some participants, our pilot study showed significant postsurgery changes in fecal microbiome and metabolites among bariatric surgery patients. Future large-scale, longitudinal studies are warranted to investigate gut microbial changes and their associations with metabolic outcomes after bariatric surgery.},
}

*Bariatric Surgery
Female
*Gastric Bypass
*Gastrointestinal Microbiome
Humans
Male
Metabolomics
Metagenomics
Middle Aged
Pilot Projects

@article {pmid32360114,
year = {2020},
author = {Farin, W and Oñate, FP and Plassais, J and Bonny, C and Beglinger, C and Woelnerhanssen, B and Nocca, D and Magoules, F and Le Chatelier, E and Pons, N and Cervino, ACL and Ehrlich, SD},
title = {Impact of laparoscopic Roux-en-Y gastric bypass and sleeve gastrectomy on gut microbiota: a metagenomic comparative analysis.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {16},
number = {7},
pages = {852-862},
doi = {10.1016/j.soard.2020.03.014},
pmid = {32360114},
issn = {1878-7533},
mesh = {France ; Gastrectomy ; *Gastric Bypass ; *Gastrointestinal Microbiome ; Humans ; *Laparoscopy ; *Obesity, Morbid/surgery ; Switzerland ; },
abstract = {BACKGROUND: Bariatric surgery is an effective therapeutic procedure for morbidly obese patients. The 2 most common interventions are sleeve gastrectomy (SG) and laparoscopic Roux-en-Y gastric bypass (LRYGB).

OBJECTIVES: The aim of this study was to compare microbiome long-term microbiome after SG and LRYGB surgery in obese patients.

SETTING: University Hospital, France; University Hospital, United States; and University Hospital, Switzerland.

METHODS: Eighty-nine and 108 patients who underwent SG and LRYGB, respectively, were recruited. Stools were collected before and 6 months after surgery. Microbial DNA was analyzed with shotgun metagenomic sequencing (SOLiD 5500 xl Wildfire). MSPminer, a novel innovative tool to characterize new in silico biological entities, was used to identify 715 Metagenomic Species Pan-genome. One hundred forty-eight functional modules were analyzed using GOmixer and KEGG database.

RESULTS: Both interventions resulted in a similar increase of Shannon's diversity index and gene richness of gut microbiota, in parallel with weight loss, but the changes of microbial composition were different. LRYGB led to higher relative abundance of aero-tolerant bacteria, such as Escherichia coli and buccal species, such as Streptococcus and Veillonella spp. In contrast, anaerobes, such as Clostridium, were more abundant after SG, suggesting better conservation of anaerobic conditions in the gut. Enrichment of Akkermansia muciniphila was also observed after both surgeries. Function-level changes included higher potential for bacterial use of supplements, such as vitamin B12, B1, and iron upon LRYGB.

CONCLUSION: Microbiota changes after bariatric surgery depend on the nature of the intervention. LRYGB induces greater taxonomic and functional changes in gut microbiota than SG. Possible long-term health consequences of these alterations remain to be established.},
}

France
Gastrectomy
*Gastric Bypass
*Gastrointestinal Microbiome
Humans
*Laparoscopy
*Obesity, Morbid/surgery
Switzerland

@article {pmid33810609,
year = {2021},
author = {Uchida, F and Oh, S and Shida, T and Suzuki, H and Yamagata, K and Mizokami, Y and Bukawa, H and Tanaka, K and Shoda, J},
title = {Effects of Exercise on the Oral Microbiota and Saliva of Patients with Non-Alcoholic Fatty Liver Disease.},
journal = {International journal of environmental research and public health},
volume = {18},
number = {7},
pages = {},
pmid = {33810609},
issn = {1660-4601},
mesh = {Bacteria/genetics ; Humans ; Male ; Metagenomics ; *Microbiota ; Middle Aged ; *Non-alcoholic Fatty Liver Disease ; Saliva ; },
abstract = {Exercise can be hypothesized to play an important role in non-alcoholic fatty liver disease (NAFLD) treatment by changing the oral bacterial flora and in the mechanism underlying periodontal disease. We performed salivary component analysis before and after an exercise regimen, and genome analysis of the oral bacterial flora to elucidate the underlying mechanism. Obese middle-aged men with NAFLD and periodontal disease were allocated to 12-week exercise (n = 49) or dietary restriction (n = 21) groups. We collected saliva to compare the oral microflora; performed predictive analysis of metagenomic functions; and, measured the salivary immunoglobulin A, cytokine, bacterial lipopolysaccharide (LPS), and lactoferrin concentrations. The exercise group showed improvements in the clinical indices of oral environment. Salivary component analysis revealed significant reductions in LPS, and lactoferrin during the exercise regimen. Diversity analysis of oral bacterial flora revealed higher alpha- and beta-diversity after the exercise regimen. Analysis of the microbial composition revealed that the numbers of Campylobacter (+83.9%), Corynebacterium (+142.3%), Actinomyces (+75.9%), and Lautropia (+172.9%) were significantly higher, and that of Prevotella (-28.3%) was significantly lower. The findings suggest that an exercise regimen improves the oral environment of NAFLD patients by increasing the diversity of the oral microflora and reducing the number of periodontal bacteria that produce LPS and its capability.},
}

Bacteria/genetics
Humans
Male
Metagenomics
*Microbiota
Middle Aged
*Non-alcoholic Fatty Liver Disease
Saliva

@article {pmid33685682,
year = {2021},
author = {Choi, Y and Park, E and Kim, S and Ha, J and Oh, H and Kim, Y and Lee, Y and Seo, Y and Kang, J and Lee, S and Lee, H and Yoon, Y and Choi, KH},
title = {Fermented milk with Lactobacillus curvatus SMFM2016-NK alleviates periodontal and gut inflammation, and alters oral and gut microbiota.},
journal = {Journal of dairy science},
volume = {104},
number = {5},
pages = {5197-5207},
doi = {10.3168/jds.2020-19625},
pmid = {33685682},
issn = {1525-3198},
mesh = {Animals ; *Gastrointestinal Microbiome ; Inflammation/veterinary ; Lactobacillus ; Milk ; *Probiotics ; Rats ; *Rodent Diseases ; },
abstract = {This study aimed to analyze the effect of milk fermented with Lactobacillus curvatus SMFM2016-NK on periodontal diseases and gut health in a rat model. To improve the effect of Lb. curvatus SMFM2016-NK-fermented milk administration for relieving periodontitis, the periodontitis rat models were treated with the following for 4 wk: 10% skim milk (normal), periodontitis + 10% skim milk (negative control), periodontitis + Lactobacillus rhamnosus GG-fermented milk (positive control), and periodontitis + Lb. curvatus SMFM2016-NK-fermented milk (PD+LCFM). Transcriptional analysis of inflammatory cytokines [tumor necrosis factor α (TNF-α), IL-1β, IL-6, and IL-10] was performed via quantitative reverse-transcription PCR. The changes in the oral and gut microbiomes after administering Lb. curvatus SMFM2016-NK-fermented milk were analyzed with metagenomics sequencing using DNA extracted from the oral gingival tissues and feces from the cecum of the rat models. After treatment with Lb. curvatus SMFM2016-NK-fermented milk, the relative gene expression levels of TNFA and IL1B in the gingiva decreased in the PD+LCFM group compared with those in the negative control group. In the oral microbiome, the proportion of the phylum Proteobacteria in the PD+LCFM group was lower than that in the negative control after treatment with Lb. curvatus SMFM2016-NK-fermented milk. For the effect in the gut, the relative gene expression levels of inflammatory cytokines in the colon between the normal and negative control groups were not different; however, the expression levels of TNFA and IL1B in the PD+LCFM and positive control groups, respectively, were lower than those in the negative control group. The composition and diversity of the gut microbiome differed among normal, periodontitis, and Lb. curvatus SMFM2016-NK-fermented milk treatment groups. These results indicate that Lb. curvatus SMFM2016-NK-fermented milk could alleviate periodontal and gut inflammation and change oral and gut microbiota.},
}

Animals
*Gastrointestinal Microbiome
Inflammation/veterinary
Lactobacillus
Milk
*Probiotics
Rats
*Rodent Diseases

@article {pmid33596519,
year = {2021},
author = {Kleerebezem, R and Stouten, G and Koehorst, J and Langenhoff, A and Schaap, P and Smidt, H},
title = {Experimental infrastructure requirements for quantitative research on microbial communities.},
journal = {Current opinion in biotechnology},
volume = {67},
number = {},
pages = {158-165},
doi = {10.1016/j.copbio.2021.01.017},
pmid = {33596519},
issn = {1879-0429},
mesh = {Bacteria/genetics ; *Ecosystem ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {Natural microbial communities are composed of a large diversity of interacting microorganisms, each with a specific role in the functional properties of the ecosystem. The objectives in microbial ecology research are related to identifying, understanding and exploring the role of these different microorganisms. Because of the rapidly increasing power of DNA sequencing and the rapid increase of genomic data, main attention of microbial ecology research shifted from cultivation-oriented studies towards metagenomic studies. Despite these efforts, the direct link between the molecular properties and the measurable changes in the functional performance of the ecosystem is often poorly documented. A quantitative understanding of functional properties in relation to the molecular changes requires effective integration, standardization, and parallelization of experiments. High-resolution functional characterization is a prerequisite for interpretation of changes in metagenomic properties, and will improve our understanding of microbial communities and facilitate their exploration for health and circular economy related objectives.},
}

Bacteria/genetics
*Ecosystem
Metagenome
Metagenomics
*Microbiota/genetics
Sequence Analysis, DNA

@article {pmid33592536,
year = {2021},
author = {Taş, N and de Jong, AE and Li, Y and Trubl, G and Xue, Y and Dove, NC},
title = {Metagenomic tools in microbial ecology research.},
journal = {Current opinion in biotechnology},
volume = {67},
number = {},
pages = {184-191},
doi = {10.1016/j.copbio.2021.01.019},
pmid = {33592536},
issn = {1879-0429},
mesh = {Ecology ; High-Throughput Nucleotide Sequencing ; Metagenome/genetics ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {Ability to directly sequence DNA from the environment permanently changed microbial ecology. Here, we review the new insights to microbial life gleaned from the applications of metagenomics, as well as the extensive set of analytical tools that facilitate exploration of diversity and function of complex microbial communities. While metagenomics is shaping our understanding of microbial functions in ecosystems via gene-centric and genome-centric methods, annotating functions, metagenome assembly and binning in heterogeneous samples remains challenging. Development of new analysis and sequencing platforms generating high-throughput long-read sequences and functional screening opportunities will aid in harnessing metagenomes to increase our understanding of microbial taxonomy, function, ecology, and evolution in the environment.},
}

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

@article {pmid33578068,
year = {2021},
author = {Núñez, A and García, AM and Moreno, DA and Guantes, R},
title = {Seasonal changes dominate long-term variability of the urban air microbiome across space and time.},
journal = {Environment international},
volume = {150},
number = {},
pages = {106423},
doi = {10.1016/j.envint.2021.106423},
pmid = {33578068},
issn = {1873-6750},
mesh = {*Air Microbiology ; Cities ; Fungi ; Humans ; *Microbiota ; Seasons ; Spain ; },
abstract = {Compared to soil or aquatic ecosystems, the atmosphere is still an underexplored environment for microbial diversity. In this study, we surveyed the composition, variability and sources of microbes (bacteria and fungi) in the near surface atmosphere of a highly populated area, spanning ~ 4,000 Km2 around the city center of Madrid (Spain), in different seasonal periods along two years. We found a core of abundant bacterial genera robust across space and time, most of soil origin, while fungi were more sensitive to environmental conditions. Microbial communities showed clear seasonal patterns driven by variability of environmental factors, mainly temperature and accumulated rain, while local sources played a minor role. We also identified taxa in both groups characteristic of seasonal periods, but not of specific sampling sites or plant coverage. The present study suggests that the near surface atmosphere of urban environments contains an ecosystem stable across relatively large spatial and temporal scales, with a rather homogenous composition, modulated by climatic variations. As such, it contributes to our understanding of the long-term changes associated to the human exposome in the air of highly populated areas.},
}

*Air Microbiology
Cities
Fungi
Humans
*Microbiota
Seasons
Spain

@article {pmid33486296,
year = {2021},
author = {Zhou, Z and Xu, L and Zhu, L and Liu, Y and Shuai, X and Lin, Z and Chen, H},
title = {Metagenomic analysis of microbiota and antibiotic resistome in household activated carbon drinking water purifiers.},
journal = {Environment international},
volume = {148},
number = {},
pages = {106394},
doi = {10.1016/j.envint.2021.106394},
pmid = {33486296},
issn = {1873-6750},
mesh = {Anti-Bacterial Agents/pharmacology ; Charcoal ; *Drinking Water/analysis ; Genes, Bacterial ; Metagenomics ; *Microbiota/genetics ; },
abstract = {Existing drinking water treatment systems have limited ability to control emerging contaminants such as antibiotic resistance genes (ARGs). Household activated carbon water purifiers (HWPs) are convenient measures to assure drinking water quality. However, ARGs distribution in HWPs has not been reported. Here, ARGs, mobile genetic elements (MGEs) and bacteria communities were profiled in tap water (TW), filter water (FW) and activated carbon (AC) biofilm from six kinds of HWPs after 80 days operation, using metagenomics. Results showed that the bacteria community diversities in FW and AC were higher than those in TW. A total of 88, 116 and 80 ARG subtypes were detected in TW, AC and FW, respectively. The AC structure was an important factor influencing the bacterial communities and ARG profiles in FW. The network analysis revealed the co-occurrence patterns between ARGs and bacteria. SourceTracker analyses showed AC biofilms were important contributors of microbes (29-79%) and ARGs (17-53%) in FW. Moreover, MGEs e.g. pBBta01, pMKMS02 and pMFLV01 plasmids, and ISMysp3 had significant co-occurrence patterns with ARGs in the AC biofilms. This study helps to understand the actual purification effect of HWPs and provides a theoretical reference for the management and control of ARGs pollution in domestic drinking water.},
}

Anti-Bacterial Agents/pharmacology
Charcoal
*Drinking Water/analysis
Genes, Bacterial
Metagenomics
*Microbiota/genetics

@article {pmid33406160,
year = {2021},
author = {Taylor, JC and Gao, X and Xu, J and Holder, M and Petrosino, J and Kumar, R and Liu, W and Höök, M and Mackenzie, C and Hillhouse, A and Brashear, W and Nunez, MP and Xu, Y},
title = {A type VII secretion system of Streptococcus gallolyticus subsp. gallolyticus contributes to gut colonization and the development of colon tumors.},
journal = {PLoS pathogens},
volume = {17},
number = {1},
pages = {e1009182},
pmid = {33406160},
issn = {1553-7374},
mesh = {Animals ; *Cell Proliferation ; Colonic Neoplasms/chemically induced/microbiology/*pathology ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/*microbiology ; Humans ; Mice ; Mice, Inbred A ; Streptococcal Infections/metabolism/*microbiology ; Streptococcus gallolyticus subspecies gallolyticus/*physiology ; Type VII Secretion Systems/*metabolism ; },
abstract = {Streptococcus gallolyticus subspecies gallolyticus (Sgg) has a strong clinical association with colorectal cancer (CRC) and actively promotes the development of colon tumors. However, the molecular determinants involved in Sgg pathogenicity in the gut are unknown. Bacterial type VII secretion systems (T7SS) mediate pathogen interactions with their host and are important for virulence in pathogenic mycobacteria and Staphylococcus aureus. Through genome analysis, we identified a locus in Sgg strain TX20005 that encodes a putative type VII secretion system (designated as SggT7SST05). We showed that core genes within the SggT7SST05 locus are expressed in vitro and in the colon of mice. Western blot analysis showed that SggEsxA, a protein predicted to be a T7SS secretion substrate, is detected in the bacterial culture supernatant, indicating that this SggT7SST05 is functional. Deletion of SggT7SST05 (TX20005Δesx) resulted in impaired bacterial adherence to HT29 cells and abolished the ability of Sgg to stimulate HT29 cell proliferation. Analysis of bacterial culture supernatants suggest that SggT7SST05-secreted factors are responsible for the pro-proliferative activity of Sgg, whereas Sgg adherence to host cells requires both SggT7SST05-secreted and bacterial surface-associated factors. In a murine gut colonization model, TX20005Δesx showed significantly reduced colonization compared to the parent strain. Furthermore, in a mouse model of CRC, mice exposed to TX20005 had a significantly higher tumor burden compared to saline-treated mice, whereas those exposed to TX20005Δesx did not. Examination of the Sgg load in the colon in the CRC model suggests that SggT7SST05-mediated activities are directly involved in the promotion of colon tumors. Taken together, these results reveal SggT7SST05 as a previously unrecognized pathogenicity determinant for Sgg colonization of the colon and promotion of colon tumors.},
}

Animals
*Cell Proliferation
Colonic Neoplasms/chemically induced/microbiology/*pathology
*Gastrointestinal Microbiome
Gastrointestinal Tract/*microbiology
Humans
Mice
Mice, Inbred A
Streptococcal Infections/metabolism/*microbiology
Streptococcus gallolyticus subspecies gallolyticus/*physiology
Type VII Secretion Systems/*metabolism

@article {pmid33308114,
year = {2021},
author = {Wu, X and Chen, X and Lyu, X and Zheng, H},
title = {Advances in Microbiome Detection Technologies and Application in Antirheumatic Drug Design.},
journal = {Current pharmaceutical design},
volume = {27},
number = {7},
pages = {891-899},
doi = {10.2174/1381612826666201211114609},
pmid = {33308114},
issn = {1873-4286},
mesh = {*Antirheumatic Agents/pharmacology/therapeutic use ; Dysbiosis/drug therapy ; Humans ; Metagenomics ; *Microbiota ; Technology ; },
abstract = {Rheumatic diseases are a kind of chronic inflammatory and autoimmune disease affecting the connection or supporting structures of the human body, such as the most common diseases Ankylosing spondylitis (AS), gout and Systemic lupus erythematosus (SLE). Although the precise etiology and pathogenesis of the different types of rheumatic diseases remain mostly unknown, it is now commonly believed that these diseases are attributed to some complex interactions between genetics and environmental factors, especially the gut microbiome. Altered microbiome showed clinical improvement in disease symptoms and partially restored to normality after prescribing disease-modifying antirheumatic drugs (DMARDs) or other treatment strategies. Recent advances in next-generation sequencing-based microbial profiling technology, especially metagenomics, have identified alteration of the composition and function of the gut microbiota in patients. Clinical and experimental data suggest that dysbiosis may play a pivotal role in the pathogenesis of these diseases. In this paper, we provide a brief review of the advances in the microbial profiling technology and up-to-date resources for accurate taxonomic assignment of metagenomic reads, which is a key step for metagenomics studies. In addition, we review the altered gut microbiota signatures that have been reported so far across various studies, upon which diagnostics classification models can be constructed, and the drug-induced regulation of the host microbiota can be used to control disease progression and symptoms.},
}

*Antirheumatic Agents/pharmacology/therapeutic use
Dysbiosis/drug therapy
Humans
Metagenomics
*Microbiota
Technology

@article {pmid30403635,
year = {2020},
author = {Zheng, H and Wang, H and Dewhurst, RJ and Roehe, R},
title = {Improving the Inference of Co-Occurrence Networks in the Bovine Rumen Microbiome.},
journal = {IEEE/ACM transactions on computational biology and bioinformatics},
volume = {17},
number = {3},
pages = {858-867},
doi = {10.1109/TCBB.2018.2879342},
pmid = {30403635},
issn = {1557-9964},
mesh = {Animal Feed ; Animals ; Cattle ; Diet ; *Gastrointestinal Microbiome/genetics/physiology ; Metagenome/genetics ; Metagenomics/*methods ; Methane/metabolism ; Rumen/*microbiology ; },
abstract = {The importance of the composition and signature of rumen microbial communities has gained increasing attention. One of the key techniques was to infer co-abundance networks through correlation analysis based on relative abundances. While substantial insights and progress have been made, it has been found that due to the compositional nature of data, correlation analysis derived from relative abundance could produce misleading results and spurious associations. In this study, we proposed the use of a framework including a compendium of two correlation measures and three dissimilarity metrics in an attempt to mitigate the compositional effect in the inference of significant associations in the bovine rumen microbiome. We tested the framework on rumen microbiome data including both 16S rRNA and KEGG genes associated with methane production in cattle. Based on the identification of significant positive and negative associations supported by multiple metrics, two co-occurrence networks, e.g., co-presence and mutual-exclusion networks, were constructed. Significant modules associated with methane emissions were identified. In comparison to previous studies, our analysis demonstrates that deriving microbial associations based on the correlations between relative abundances may not only lead to missing information but also produce spurious associations. To bridge together different co-presence and mutual-exclusion relations, a multiplex network model has been proposed for integrative analysis of co-occurrence networks which has great potential to support the prediction of animal phytotypes and to provide additional insights into biological mechanisms of the microbiome associated with the traits.},
}

Animal Feed
Animals
Cattle
Diet
*Gastrointestinal Microbiome/genetics/physiology
Metagenome/genetics
Metagenomics/*methods
Methane/metabolism
Rumen/*microbiology

@article {pmid33884825,
year = {2021},
author = {Cheng, S and Lu, P and Feng, QY},
title = {[Distribution of Antibiotic Resistance Genes and Microbial Communities in a Fishery Reclamation Mining Subsidence Area].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {42},
number = {5},
pages = {2541-2549},
doi = {10.13227/j.hjkx.202009166},
pmid = {33884825},
issn = {0250-3301},
mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Fisheries ; Genes, Bacterial/genetics ; *Microbiota/genetics ; },
abstract = {The widespread use of antibiotics in the aquaculture industry has caused antibiotic resistance genes (ARGs) pollution. Metagenomics technology was used to detect and analyze the relative abundance of ARGs and microbial community structure in a fishery reclamation mining subsidence area. A total of 29 ARGs were detected, and bacA had the highest relative abundance in all the samples, reaching 1.96×10-5-1.19×10-4. The relative abundance of sulfonamide and tetracycline ARGs in sediments was relatively high and the relative abundance of multidrug ARGs in well water was relatively high. Proteobacteria was the most dominant bacterial phylum in all the samples, and Chloroflexi and Euryarchaeota were relatively abundant in the sediments. Thiobacillus was the most dominant bacterial genus in the sediments, and Acinetobacter and Pseudomonas were the dominant bacterial genera in the well water. The correlation analysis between the ARGs and microorganisms showed that the genera and ARGs were mainly correlated to a moderate degree, and multiple genera had significant positive correlations with ARGs. The distribution of ARGs was affected by the structure of the microbial community. The sediments and well water in the fishery reclamation mining subsidence area were both contaminated by ARGs, and corresponding control measures should be strengthened to protect the regional environment.},
}

*Anti-Bacterial Agents/pharmacology
Drug Resistance, Microbial/genetics
Fisheries
Genes, Bacterial/genetics
*Microbiota/genetics

@article {pmid33291229,
year = {2020},
author = {Suskind, DL and Lee, D and Kim, YM and Wahbeh, G and Singh, N and Braly, K and Nuding, M and Nicora, CD and Purvine, SO and Lipton, MS and Jansson, JK and Nelson, WC},
title = {The Specific Carbohydrate Diet and Diet Modification as Induction Therapy for Pediatric Crohn's Disease: A Randomized Diet Controlled Trial.},
journal = {Nutrients},
volume = {12},
number = {12},
pages = {},
pmid = {33291229},
issn = {2072-6643},
support = {IBD Nutrition Grant//Kenneth Rainin Foundation/ ; Academic Enrichment Fund//Seattle Children's Center for Clinical and Translational Research/ ; UL1TR000423//National Center for Advancing Translational Sciences of the National Institutes of Health/ ; grid.436923.9//Environmental Molecular Sciences Laboratory (EMSL)/ ; },
mesh = {Adolescent ; C-Reactive Protein ; Carbohydrates ; Child ; Crohn Disease/*diet therapy/therapy ; *Diet ; *Dietary Carbohydrates ; Double-Blind Method ; Dysbiosis/*drug therapy ; Female ; Humans ; *Induction Chemotherapy ; Inflammatory Bowel Diseases ; Male ; Metabolomics ; Metagenomics ; Microbiota ; Proteomics ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory intestinal disorder associated with intestinal dysbiosis. Diet modulates the intestinal microbiome and therefore has a therapeutic potential. The aim of this study is to determine the potential efficacy of three versions of the specific carbohydrate diet (SCD) in active Crohn's Disease.

METHODS: 18 patients with mild/moderate CD (PCDAI 15-45) aged 7 to 18 years were enrolled. Patients were randomized to either SCD, modified SCD(MSCD) or whole foods (WF) diet. Patients were evaluated at baseline, 2, 4, 8 and 12 weeks. PCDAI, inflammatory labs and multi-omics evaluations were assessed.

RESULTS: Mean age was 14.3 ± 2.9 years. At week 12, all participants (n = 10) who completed the study achieved clinical remission. The C-reactive protein decreased from 1.3 ± 0.7 at enrollment to 0.9 ± 0.5 at 12 weeks in the SCD group. In the MSCD group, the CRP decreased from 1.6 ± 1.1 at enrollment to 0.7 ± 0.1 at 12 weeks. In the WF group, the CRP decreased from 3.9 ± 4.3 at enrollment to 1.6 ± 1.3 at 12 weeks. In addition, the microbiome composition shifted in all patients across the study period. While the nature of the changes was largely patient specific, the predicted metabolic mode of the organisms increasing and decreasing in activity was consistent across patients.

CONCLUSIONS: This study emphasizes the impact of diet in CD. Each diet had a positive effect on symptoms and inflammatory burden; the more exclusionary diets were associated with a better resolution of inflammation.},
}

Adolescent
C-Reactive Protein
Carbohydrates
Child
Crohn Disease/*diet therapy/therapy
*Diet
*Dietary Carbohydrates
Double-Blind Method
Dysbiosis/*drug therapy
Female
Humans
*Induction Chemotherapy
Inflammatory Bowel Diseases
Male
Metabolomics
Metagenomics
Microbiota
Proteomics

@article {pmid32975702,
year = {2021},
author = {Omori, M and Kato-Kogoe, N and Sakaguchi, S and Fukui, N and Yamamoto, K and Nakajima, Y and Inoue, K and Nakano, H and Motooka, D and Nakano, T and Nakamura, S and Ueno, T},
title = {Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods.},
journal = {Clinical oral investigations},
volume = {25},
number = {5},
pages = {2779-2789},
pmid = {32975702},
issn = {1436-3771},
mesh = {Humans ; *Microbiota ; Mouthwashes ; RNA, Ribosomal, 16S/genetics ; *Saliva ; Specimen Handling ; },
abstract = {OBJECTIVES: Recently, the oral microbiome has been found to be associated with oral and general health status. Although various oral sample collection protocols are available, the potential differences between the results yielded by these protocols remain unclear. In this study, we aimed to determine the effects of different time points and methods of oral sample collection on the outcomes of microbiome analysis.

MATERIALS AND METHODS: Oral samples were collected from eight healthy individuals at four different time points: 2 h after eating, immediately after teeth brushing, immediately after waking up, and 2 h after eating on the subsequent day. Four methods of saliva collection were evaluated: spitting, gum chewing, cotton swab, and oral rinse. Oral microbiomes of these samples were compared by analyzing the bacterial 16S rRNA gene sequence data.

RESULTS: The oral microbial composition at the genus level was similar among all sample collection time points and methods. Alpha diversity was not significantly different among the groups, whereas beta diversity was different between the spitting and cotton swab methods. Compared with the between-subject variations, the weighted UniFrac distances between the groups were not minor.

CONCLUSIONS: Although the oral microbiome profiles obtained at different collection time points and using different methods were similar, some differences were detected.

CLINICAL RELEVANCE: The results of the present study suggest that although all the described protocols are useful, comparisons among microbiomes of samples collected by different methods are not appropriate. Researchers must be aware of the issues regarding the impact of saliva collection methods.},
}

Humans
*Microbiota
Mouthwashes
RNA, Ribosomal, 16S/genetics
*Saliva
Specimen Handling

@article {pmid33398096,
year = {2021},
author = {Bay, SK and Dong, X and Bradley, JA and Leung, PM and Grinter, R and Jirapanjawat, T and Arndt, SK and Cook, PLM and LaRowe, DE and Nauer, PA and Chiri, E and Greening, C},
title = {Trace gas oxidizers are widespread and active members of soil microbial communities.},
journal = {Nature microbiology},
volume = {6},
number = {2},
pages = {246-256},
pmid = {33398096},
issn = {2058-5276},
mesh = {Bacteria/classification/*enzymology/genetics ; Carbon Monoxide/*metabolism ; Hydrogen/*metabolism ; Metagenomics ; *Microbiota ; Oxidation-Reduction ; Phylogeny ; *Soil ; *Soil Microbiology ; },
abstract = {Soil microorganisms globally are thought to be sustained primarily by organic carbon sources. Certain bacteria also consume inorganic energy sources such as trace gases, but they are presumed to be rare community members, except within some oligotrophic soils. Here we combined metagenomic, biogeochemical and modelling approaches to determine how soil microbial communities meet energy and carbon needs. Analysis of 40 metagenomes and 757 derived genomes indicated that over 70% of soil bacterial taxa encode enzymes to consume inorganic energy sources. Bacteria from 19 phyla encoded enzymes to use the trace gases hydrogen and carbon monoxide as supplemental electron donors for aerobic respiration. In addition, we identified a fourth phylum (Gemmatimonadota) potentially capable of aerobic methanotrophy. Consistent with the metagenomic profiling, communities within soil profiles from diverse habitats rapidly oxidized hydrogen, carbon monoxide and to a lesser extent methane below atmospheric concentrations. Thermodynamic modelling indicated that the power generated by oxidation of these three gases is sufficient to meet the maintenance needs of the bacterial cells capable of consuming them. Diverse bacteria also encode enzymes to use trace gases as electron donors to support carbon fixation. Altogether, these findings indicate that trace gas oxidation confers a major selective advantage in soil ecosystems, where availability of preferred organic substrates limits microbial growth. The observation that inorganic energy sources may sustain most soil bacteria also has broad implications for understanding atmospheric chemistry and microbial biodiversity in a changing world.},
}

Bacteria/classification/*enzymology/genetics
Carbon Monoxide/*metabolism
Hydrogen/*metabolism
Metagenomics
*Microbiota
Oxidation-Reduction
Phylogeny
*Soil
*Soil Microbiology

@article {pmid32928304,
year = {2020},
author = {Korte, SW and Dorfmeyer, RA and Franklin, CL and Ericsson, AC},
title = {Acute and long-term effects of antibiotics commonly used in laboratory animal medicine on the fecal microbiota.},
journal = {Veterinary research},
volume = {51},
number = {1},
pages = {116},
pmid = {32928304},
issn = {1297-9716},
support = {U42 OD010918/OD/NIH HHS/United States ; K01 OD019924/NH/NIH HHS/United States ; },
mesh = {Administration, Oral ; Administration, Topical ; Animals ; Anti-Bacterial Agents/*administration & dosage ; Bacitracin/*administration & dosage ; Enrofloxacin/*administration & dosage ; Feces/*microbiology ; Female ; Injections, Subcutaneous/veterinary ; Mice ; Mice, Inbred C57BL ; Microbiota/*drug effects ; Neomycin/*administration & dosage ; Ointments/administration & dosage ; Polymyxins/*administration & dosage ; Trimethoprim, Sulfamethoxazole Drug Combination/*administration & dosage ; },
abstract = {Biomedical research relies on the use of animal models, and the animals used in those models receive medical care, including antibiotics for brief periods of time to treat conditions such as dermatitis, fight wounds, and suspected bacterial pathogens of unknown etiology. As many mouse model phenotypes are sensitive to changes in the gut microbiota, our goal was to examine the effect of antibiotics commonly administered to mice. Therefore, four treatment groups (subcutaneous enrofloxacin for 7 days, oral enrofloxacin for 14 days, oral trimethoprim-sulfamethoxazole for 14 days, and topical triple antibiotic ointment for 14 days) alongside a fifth control group receiving no treatment (n = 12/group) were included in our study. Fecal samples were collected prior to treatment, immediately after two weeks of exposure, and four weeks after cessation of treatment, and subjected to 16S rRNA library sequencing. The entire experimental design was replicated in mice from two different suppliers. As expected, several treatments including enrofloxacin and triple antibiotic ointment substantially decreased the amount of DNA recovered from fecal material, as well as the microbial richness. Notably, many of these effects were long-lasting with diminished gut microbiota (GM) richness four weeks following exposure, in both substrains of mice. Trimethoprim-sulfamethoxazole induced minimal to no discernible changes in the taxonomic composition beyond that seen in control mice. Collectively, these data highlight the need to consider the impact on GM of brief and seemingly routine use of antibiotics in the clinical care of research animals.},
}

Administration, Oral
Administration, Topical
Animals
Anti-Bacterial Agents/*administration & dosage
Bacitracin/*administration & dosage
Enrofloxacin/*administration & dosage
Feces/*microbiology
Female
Injections, Subcutaneous/veterinary
Mice
Mice, Inbred C57BL
Microbiota/*drug effects
Neomycin/*administration & dosage
Ointments/administration & dosage
Polymyxins/*administration & dosage
Trimethoprim, Sulfamethoxazole Drug Combination/*administration & dosage

@article {pmid33705534,
year = {2021},
author = {Lim, SJ and Davis, B and Gill, D and Swetenburg, J and Anderson, LC and Engel, AS and Campbell, BJ},
title = {Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {4},
pages = {},
doi = {10.1093/femsec/fiab042},
pmid = {33705534},
issn = {1574-6941},
mesh = {Animals ; Bacteria ; *Bivalvia ; Gills ; *Microbiota ; Phylogeny ; Symbiosis ; },
abstract = {Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes and their environment.},
}

Animals
Bacteria
*Bivalvia
Gills
*Microbiota
Phylogeny
Symbiosis

@article {pmid33681975,
year = {2021},
author = {Keller, AG and Apprill, A and Lebaron, P and Robbins, J and Romano, TA and Overton, E and Rong, Y and Yuan, R and Pollara, S and Whalen, KE},
title = {Characterizing the culturable surface microbiomes of diverse marine animals.},
journal = {FEMS microbiology ecology},
volume = {97},
number = {4},
pages = {},
pmid = {33681975},
issn = {1574-6941},
support = {R21 AI119311/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {Biofilm-forming bacteria have the potential to contribute to the health, physiology, behavior and ecology of the host and serve as its first line of defense against adverse conditions in the environment. While metabarcoding and metagenomic information furthers our understanding of microbiome composition, fewer studies use cultured samples to study the diverse interactions among the host and its microbiome, as cultured representatives are often lacking. This study examines the surface microbiomes cultured from three shallow-water coral species and two whale species. These unique marine animals place strong selective pressures on their microbial symbionts and contain members under similar environmental and anthropogenic stress. We developed an intense cultivation procedure, utilizing a suite of culture conditions targeting a rich assortment of biofilm-forming microorganisms. We identified 592 microbial isolates contained within 15 bacterial orders representing 50 bacterial genera, and two fungal species. Culturable bacteria from coral and whale samples paralleled taxonomic groups identified in culture-independent surveys, including 29% of all bacterial genera identified in the Megaptera novaeangliae skin microbiome through culture-independent methods. This microbial repository provides raw material and biological input for more nuanced studies which can explore how members of the microbiome both shape their micro-niche and impact host fitness.},
}

Animals
*Anthozoa
Bacteria/genetics
Metagenome
Metagenomics
*Microbiota

@article {pmid33233570,
year = {2020},
author = {Horne, RG and Yu, Y and Zhang, R and Abdalqadir, N and Rossi, L and Surette, M and Sherman, PM and Adeli, K},
title = {High Fat-High Fructose Diet-Induced Changes in the Gut Microbiota Associated with Dyslipidemia in Syrian Hamsters.},
journal = {Nutrients},
volume = {12},
number = {11},
pages = {},
pmid = {33233570},
issn = {2072-6643},
support = {KA:CIHR 201508FDN-353989-FDN PMS: CIHR MOP-89894 and IOP-92890/CAPMC/CIHR/Canada ; },
mesh = {Animals ; Bacteria/classification/genetics ; Cholesterol/blood ; Diet, Carbohydrate Loading/*adverse effects ; Diet, High-Fat/*adverse effects ; *Dyslipidemias ; Feces/microbiology ; Fructose/*pharmacology ; Gastrointestinal Microbiome/*drug effects ; Lipid Metabolism ; Male ; Mesocricetus ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Triglycerides/blood ; },
abstract = {Aim: The objective of this study was to characterize the early effects of high fructose diets (with and without high fat) on both the composition of the gut microbiota and lipid metabolism in Syrian hamsters, a reproducible preclinical model of diet-induced dyslipidemia. Methods: Eight-week-old male hamsters were fed diets consisting of high-fat/high-fructose, low-fat/high-fructose or a standard chow diet for 14 days. Stool was collected at baseline (day 0), day 7 and day 14. Fasting levels of plasma triglycerides and cholesterol were monitored on day 0, day 7 and day 14, and nonfasting levels were also assayed on day 15. Then, 16S rRNA sequencing of stool samples was used to determine gut microbial composition, and predictive metagenomics was performed to evaluate dietary-induced shifts in deduced microbial functions. Results: Both high-fructose diets resulted in divergent gut microbiota composition. A high-fat/high-fructose diet induced the largest shift in overall gut microbial composition, with dramatic shifts in the Firmicute/Bacteroidetes ratio, and changes in beta diversity after just seven days of dietary intervention. Significant associations between genus level taxa and dietary intervention were identified, including an association with Ruminococceace NK4A214 group in high-fat/high-fructose fed animals and an association with Butryimonas with the low-fat/high-fructose diet. High-fat/high-fructose feeding induced dyslipidemia with increases in plasma triglycerides and cholesterol, and hepatomegaly. Dietary-induced changes in several genus level taxa significantly correlated with lipid levels over the two-week period. Differences in microbial metabolic pathways between high-fat/high-fructose and low-fat/high-fructose diet fed hamsters were identified, and several of these pathways also correlated with lipid profiles in hamsters. Conclusions: The high-fat/high-fructose diet caused shifts in the host gut microbiota. These dietary-induced alterations in gut microbial composition were linked to changes in the production of secondary metabolites, which contributed to the development of metabolic syndrome in the host.},
}

Animals
Bacteria/classification/genetics
Cholesterol/blood
Diet, Carbohydrate Loading/*adverse effects
Diet, High-Fat/*adverse effects
*Dyslipidemias
Feces/microbiology
Fructose/*pharmacology
Gastrointestinal Microbiome/*drug effects
Lipid Metabolism
Male
Mesocricetus
Metagenomics
RNA, Ribosomal, 16S/genetics
Triglycerides/blood

@article {pmid33226714,
year = {2021},
author = {Kumar, PS and Dabdoub, SM and Ganesan, SM},
title = {Probing periodontal microbial dark matter using metataxonomics and metagenomics.},
journal = {Periodontology 2000},
volume = {85},
number = {1},
pages = {12-27},
doi = {10.1111/prd.12349},
pmid = {33226714},
issn = {1600-0757},
mesh = {Bacteria ; Humans ; *Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; },
abstract = {Our view of the periodontal microbial community has been shaped by a century or more of cultivation-based and microscopic investigations. While these studies firmly established the infection-mediated etiology of periodontal diseases, it was apparent from the very early days that periodontal microbiology suffered from what Staley and Konopka described as the "great plate count anomaly", in that these culturable bacteria were only a minor part of what was visible under the microscope. For nearly a century, much effort has been devoted to finding the right tools to investigate this uncultivated majority, also known as "microbial dark matter". The discovery that DNA was an effective tool to "see" microbial dark matter was a significant breakthrough in environmental microbiology, and oral microbiologists were among the earliest to capitalize on these advances. By identifying the order in which nucleotides are arranged in a stretch of DNA (DNA sequencing) and creating a repository of these sequences, sequence databases were created. Computational tools that used probability-driven analysis of these sequences enabled the discovery of new and unsuspected species and ascribed novel functions to these species. This review will trace the development of DNA sequencing as a quantitative, open-ended, comprehensive approach to characterize microbial communities in their native environments, and explore how this technology has shifted traditional dogmas on how the oral microbiome promotes health and its role in disease causation and perpetuation.},
}

Bacteria
Humans
*Metagenomics
*Microbiota/genetics
Sequence Analysis, DNA

@article {pmid33226693,
year = {2021},
author = {Teles, F and Wang, Y and Hajishengallis, G and Hasturk, H and Marchesan, JT},
title = {Impact of systemic factors in shaping the periodontal microbiome.},
journal = {Periodontology 2000},
volume = {85},
number = {1},
pages = {126-160},
doi = {10.1111/prd.12356},
pmid = {33226693},
issn = {1600-0757},
support = {R01 DE024767/DE/NIDCR NIH HHS/United States ; },
mesh = {*Arthritis, Rheumatoid ; Female ; Humans ; Metagenomics ; *Microbiota ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Since 2010, next-generation sequencing platforms have laid the foundation to an exciting phase of discovery in oral microbiology as it relates to oral and systemic health and disease. Next-generation sequencing has allowed large-scale oral microbial surveys, based on informative marker genes, such as 16S ribosomal RNA, community gene inventories (metagenomics), and functional analyses (metatranscriptomics), to be undertaken. More specifically, the availability of next-generation sequencing has also paved the way for studying, in greater depth and breadth, the effect of systemic factors on the periodontal microbiome. It was natural to investigate systemic diseases, such as diabetes, in such studies, along with systemic conditions or states, , pregnancy, menopause, stress, rheumatoid arthritis, and systemic lupus erythematosus. In addition, in recent years, the relevance of systemic "variables" (ie, factors that are not necessarily diseases or conditions, but may modulate the periodontal microbiome) has been explored in detail. These include ethnicity and genetics. In the present manuscript, we describe and elaborate on the new and confirmatory findings unveiled by next-generation sequencing as it pertains to systemic factors that may shape the periodontal microbiome. We also explore the systemic and mechanistic basis for such modulation and highlight the importance of those relationships in the management and treatment of patients.},
}

*Arthritis, Rheumatoid
Female
Humans
Metagenomics
*Microbiota
Pregnancy
RNA, Ribosomal, 16S/genetics

@article {pmid33226670,
year = {2021},
author = {Kumar, PS},
title = {Microbiomics: Were we all wrong before?.},
journal = {Periodontology 2000},
volume = {85},
number = {1},
pages = {8-11},
doi = {10.1111/prd.12373},
pmid = {33226670},
issn = {1600-0757},
mesh = {Bacteria/genetics ; Female ; Humans ; *Metagenomics ; *Microbiota ; Proteomics ; },
abstract = {Periodontal microbiology has historically been based on an "us against them" paradigm, one that focuses mainly on identifying microbes and viruses that cause disease. However, such a bottom-up approach limits our appreciation of the incredible diversity of this ecosystem and the essential ways in which microbial interactions contribute to health and homeostasis of the subgingival niche. Microbiomics-the science of collectively characterizing and quantifying molecules responsible for the structure, function, and dynamics of a microbial community-has enabled us to study these communities in their natural habitat, thereby revolutionizing our knowledge of host-associated microbes and reconceptualizing our definition of "human." When this systems-biology approach is combined with ecologic principles, it explicates the complex relationship that exist between microbiota and between them and us, the human. In this volume of Periodontology 2000, a group of 12 female scientists take the lead in investigating how metagenomics, genomics, metatranscriptomics, proteomics, metaproteomics, and metabolomics have achieved the following: (a) widened our view of the periodontal microbiome; (b) expanded our understanding of the evolution of the human oral microbiome; (c) shone a light on not just bacteria, but also other prokaryotic and eukaryotic members of the community; (d) elucidated the effects of anthropogenic behavior and systemic diseases on shaping these communities; and (e) influenced traditional patterns of periodontal therapeutics.},
}

Bacteria/genetics
Female
Humans
*Metagenomics
*Microbiota
Proteomics

@article {pmid32687904,
year = {2020},
author = {Bi, Q and Gu, W and Meng, F and Yang, X and Zeng, L and Liang, L and Yang, M and Zhang, T and Yu, J},
title = {Pharmacological and metagenomics evidence of polysaccharide from Polygonum multiflorum in the alleviation of insulin resistance.},
journal = {International journal of biological macromolecules},
volume = {164},
number = {},
pages = {1070-1079},
doi = {10.1016/j.ijbiomac.2020.07.085},
pmid = {32687904},
issn = {1879-0003},
mesh = {AMP-Activated Protein Kinases/metabolism ; Animals ; Fallopia multiflora/*chemistry ; Fatty Acids, Volatile/metabolism ; Feces ; Gastrointestinal Microbiome/*drug effects ; Glucosides/*pharmacology ; Insulin/metabolism ; *Insulin Resistance ; Liver/metabolism ; Male ; Metagenomics ; Polysaccharides/*pharmacology ; RNA, Ribosomal, 16S/metabolism ; Rats ; Rats, Sprague-Dawley ; Receptors, G-Protein-Coupled/*metabolism ; Signal Transduction ; Stilbenes/*pharmacology ; },
abstract = {Total polysaccharide from Polygonum multiflorum (PS) and 2,3,5,4'-tetrahydroxy-stilbene-2-O-β-D-glucoside (TSG) could relieve high-fat and high-sugar diet (HF-HSD) induced rats' insulin resistance (IR) by gut microbiota and host regulation. We found that PS and TSG significantly reversed the increase of fasting blood glucose and the decrease of glucose tolerance in HF-HSD induced IR rats. PS and TSG effectively reversed the imbalance of Firmicutes/Bacteroides caused by an HF-HSD, and significantly reduced the relative abundance of Proteobacteria. It also affected the functional genes of gut microbiota and regulated short-chain fatty acids (SCFAs) and its downstream signal protein molecules. Together, these results indicated that PS and TSG alleviated HF-HSD induced IR by promoting gut microbiota and host function. Thus, PS and TSG may be promising lead substances for developing IR inhibitors that could regulate gut microbiota and its molecular messenger SCFAs to remedy IR.},
}

AMP-Activated Protein Kinases/metabolism
Animals
Fallopia multiflora/*chemistry
Fatty Acids, Volatile/metabolism
Feces
Gastrointestinal Microbiome/*drug effects
Glucosides/*pharmacology
Insulin/metabolism
*Insulin Resistance
Liver/metabolism
Male
Metagenomics
Polysaccharides/*pharmacology
RNA, Ribosomal, 16S/metabolism
Rats
Rats, Sprague-Dawley
Receptors, G-Protein-Coupled/*metabolism
Signal Transduction
Stilbenes/*pharmacology

@article {pmid33706240,
year = {2021},
author = {DeBofsky, A and Xie, Y and Challis, JK and Jain, N and Brinkmann, M and Jones, PD and Giesy, JP},
title = {Responses of juvenile fathead minnow (Pimephales promelas) gut microbiome to a chronic dietary exposure of benzo[a]pyrene.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {278},
number = {},
pages = {116821},
doi = {10.1016/j.envpol.2021.116821},
pmid = {33706240},
issn = {1873-6424},
abstract = {The microbiome has been described as an additional host "organ" with well-established beneficial roles. However, the effects of exposures to chemicals on both structure and function of the gut microbiome of fishes are understudied. To determine effects of benzo[a]pyrene (BaP), a model persistent organic pollutant, on structural shifts of gut microbiome in juvenile fathead minnows (Pimephales promelas), fish were exposed ad libitum in the diet to concentrations of 1, 10, 100, or 1000 μg BaP g-1 food, in addition to a vehicle control, for two weeks. To determine the link between exposure to BaP and changes in the microbial community, concentrations of metabolites of BaP were measured in fish bile and 16S rRNA amplicon sequencing was used to evaluate the microbiome. Exposure to BaP only reduced alpha-diversity at the greatest exposure concentrations. However, it did alter community composition assessed as differential abundance of taxa and reduced network complexity of the microbial community in all exposure groups. Results presented here illustrate that environmentally-relevant concentrations of BaP can alter the diversity of the gut microbiome and community network connectivity.},
}

@article {pmid32388254,
year = {2020},
author = {Zhou, J and Tang, L and Shen, CL and Wang, JS},
title = {Green tea polyphenols boost gut-microbiota-dependent mitochondrial TCA and urea cycles in Sprague-Dawley rats.},
journal = {The Journal of nutritional biochemistry},
volume = {81},
number = {},
pages = {108395},
doi = {10.1016/j.jnutbio.2020.108395},
pmid = {32388254},
issn = {1873-4847},
support = {U01 AT006691/AT/NCCIH NIH HHS/United States ; },
abstract = {Green tea polyphenols (GTPs) were found to boost mammal energy conversion by modulating gut-microbial community structure, gene orthologs and metabolic pathways. Here we examined the metabolites present in the gut-microbiota-dependent mitochondrial tricarboxylic acid (TCA) cycle and urea cycle using hydrophilic interaction liquid chromatography (HILIC)-heated electrospray ionization (HESI)-tandem liquid chromatogram mass spectrometry (LC-MS). Six groups (n=12) of Sprague-Dawley rats (6-mo, ~250 g) were administered with water containing 0%, 0.5%, and 1.5% GTPs (wt/vol or g/dL). Gut-content samples were collected at 3- and 6-mo. Untargeted metabolomics detected 2177 features, with 91 features demonstrating significant dose- and time-dependencies on the GTPs treatment. Targeted metabolomics analysis revealed remarkable changes of 39 metabolites in the mitochondrial TCA cycle and urea cycle, including argininosuccunic acid (0.9-fold vs control), dihydrouracil (1.14-fold vs control), fumaric acid (1.19-fold vs control), malic acid (2.17-fold vs control), citrulline (1.86-fold vs control), and succinic acid (0.4-fold vs control). The untargeted metabolomics data were mined using bioinformatics approaches, such as analysis of variance-simultaneous component analysis (ASCA), enrichment pathway analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping analysis. The results of 16S rRNA survey, metagenomics analysis, and metabolomics analysis were extrapolated and integrated using databases of Integrated Microbial Genomes and Microbiomes (IMG/M) and KEGG. Our analysis demonstrates that GTPs enhance energy conversion by boosting mitochondrial TCA cycle and urea cycle of gut-microbiota in rats. This metabolic modulation is achieved by enriching many gene orthologs, following the increase of beneficial microbials in families C. Ruminococcaceae, C. Lachnospiraceae and B. Bacteroidaceae.},
}

@article {pmid33868800,
year = {2021},
author = {Gilroy, R and Ravi, A and Getino, M and Pursley, I and Horton, DL and Alikhan, NF and Baker, D and Gharbi, K and Hall, N and Watson, M and Adriaenssens, EM and Foster-Nyarko, E and Jarju, S and Secka, A and Antonio, M and Oren, A and Chaudhuri, RR and La Ragione, R and Hildebrand, F and Pallen, MJ},
title = {Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture.},
journal = {PeerJ},
volume = {9},
number = {},
pages = {e10941},
doi = {10.7717/peerj.10941},
pmid = {33868800},
issn = {2167-8359},
abstract = {Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community.

Results: We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii.

Conclusions: Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.},
}

@article {pmid33790294,
year = {2021},
author = {Singleton, CM and Petriglieri, F and Kristensen, JM and Kirkegaard, RH and Michaelsen, TY and Andersen, MH and Kondrotaite, Z and Karst, SM and Dueholm, MS and Nielsen, PH and Albertsen, M},
title = {Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {2009},
pmid = {33790294},
issn = {2041-1723},
mesh = {Bacteria/classification/genetics ; Bioreactors/microbiology ; Denmark ; Genome, Bacterial/*genetics ; High-Throughput Nucleotide Sequencing/*methods ; Metagenome/*genetics ; Metagenomics/*methods ; Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/*genetics ; RNA, Ribosomal, 23S/genetics ; RNA, Ribosomal, 5S/genetics ; Sewage/*microbiology ; Waste Water/microbiology ; Water Purification/methods ; },
abstract = {Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such data cannot be linked to functional potential in the absence of high-quality metagenome-assembled genomes (MAGs) for nearly all species. Here, we use long-read and short-read sequencing to recover 1083 high-quality MAGs, including 57 closed circular genomes, from 23 Danish full-scale wastewater treatment plants. The MAGs account for ~30% of the community based on relative abundance, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We use the information provided by these MAGs in combination with >13 years of 16S rRNA amplicon sequencing data, as well as Raman microspectroscopy and fluorescence in situ hybridisation, to uncover abundant undescribed lineages belonging to important functional groups.},
}

Bacteria/classification/genetics
Bioreactors/microbiology
Denmark
Genome, Bacterial/*genetics
High-Throughput Nucleotide Sequencing/*methods
Metagenome/*genetics
Metagenomics/*methods
Microbiota/genetics
Phylogeny
RNA, Ribosomal, 16S/*genetics
RNA, Ribosomal, 23S/genetics
RNA, Ribosomal, 5S/genetics
Sewage/*microbiology
Waste Water/microbiology
Water Purification/methods

@article {pmid33774727,
year = {2021},
author = {Wani, GA and Khan, MA and Dar, MA and Shah, MA and Reshi, ZA},
title = {Next Generation High Throughput Sequencing to Assess Microbial Communities: An Application Based on Water Quality.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {106},
number = {5},
pages = {727-733},
pmid = {33774727},
issn = {1432-0800},
support = {PDF/20l8/001689//DST-SERB, Govt. of India/ ; },
mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microbiota ; Phylogeny ; *Water Quality ; },
abstract = {Traditional techniques to identify different contaminants (biological or chemical) in the waters are slow, laborious, and can require specialized expertise. Hence, the rapid determination of water quality using more sensitive and reliable metagenomic based approaches attains special importance. Metagenomics deals with the study of genetic material that is recovered from microbial communities present in environmental samples. In traditional techniques cultivation-based methodologies were used to describe the diversity of microorganisms in environmental samples. It has failed to function as a robust marker because of limited taxonomic and phylogenetic implications. In this backdrop, high-throughput DNA sequencing approaches have proven very powerful in microbial source tracking because of investigating the full variety of genome-based analysis such as microbial genetic diversity and population structure played by them. Next generation sequencing technologies can reveal a greater proportion of microbial communities that have not been reported earlier by traditional techniques. The present review highlights the shift from traditional techniques for the basic study of community composition to next-generation sequencing (NGS) platforms and their potential applications to the biomonitoring of water quality in relation to human health.},
}

High-Throughput Nucleotide Sequencing
Humans
Metagenomics
*Microbiota
Phylogeny
*Water Quality

@article {pmid32979562,
year = {2021},
author = {Lai, WT and Zhao, J and Xu, SX and Deng, WF and Xu, D and Wang, MB and He, FS and Liu, YH and Guo, YY and Ye, SW and Yang, QF and Zhang, YL and Wang, S and Li, MZ and Yang, YJ and Liu, TB and Tan, ZM and Xie, XH and Rong, H},
title = {Shotgun metagenomics reveals both taxonomic and tryptophan pathway differences of gut microbiota in bipolar disorder with current major depressive episode patients.},
journal = {Journal of affective disorders},
volume = {278},
number = {},
pages = {311-319},
doi = {10.1016/j.jad.2020.09.010},
pmid = {32979562},
issn = {1573-2517},
mesh = {*Bipolar Disorder/genetics ; Cross-Sectional Studies ; *Depressive Disorder, Major/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; Tryptophan ; },
abstract = {BACKGROUND: The microbiome-gut-brain axis, especially the microbial tryptophan biosynthesis and metabolism pathway (MiTBamp), is closely connected to bipolar disorder with current major depressive episode (BPD).

METHODS: We performed shotgun metagenomics sequencing (SMS) of faecal samples from 25 BPD patients and 28 healthy controls (HCs). Except for the microbiota taxa and MiTBamp analyses, we also built a classification model using the Random Forests (RF) and Boruta algorithm to find the microbial biomarkers for BPD.

RESULTS: Compared to HCs, the phylum Bacteroidetes abundance was significantly reduced, whereas that of the Actinobacteria and Firmicutes were significantly increased in BPD patients. We also identified 38 species increased and 6 species decreased significantly in the BPD group. In the MiTBamp, we identified that two Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologies (KOs) (K00658 and K00837) were significantly lower in the BPD, and five KOs (K01696, K00382, K00626, K01667, and K03781) were significantly higher in the BPD group. We also identified significant genera and species which were closely related to these KOs. Finally, RF classification based on gut microbiota at the genus level can achieve an area under the receiver operating characteristic curve of 0.997.

LIMITATIONS: The features of cross-sectional design, limited sample size, the heterogeneity of bipolar disorders, and a lack of serum/plasma tryptophan concentration measurements.

CONCLUSIONS: The present findings enable a better understanding of changes in gastrointestinal microbiome and MiTBamp in BPD. Alterations of microbes may have potential as biomarkers for distinguishing the BPD patients form HCs.},
}

*Bipolar Disorder/genetics
Cross-Sectional Studies
*Depressive Disorder, Major/genetics
*Gastrointestinal Microbiome/genetics
Humans
Metagenomics
Tryptophan

@article {pmid32027927,
year = {2020},
author = {Fadiji, AE and Babalola, OO},
title = {Metagenomics methods for the study of plant-associated microbial communities: A review.},
journal = {Journal of microbiological methods},
volume = {170},
number = {},
pages = {105860},
doi = {10.1016/j.mimet.2020.105860},
pmid = {32027927},
issn = {1872-8359},
mesh = {Computational Biology/*methods ; Endophytes/*genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome/genetics ; Metagenomics/*methods ; Microbiota/*genetics ; Sequence Analysis, DNA/methods ; Zea mays/growth & development/*microbiology ; },
abstract = {Plant microbiota have different effects on the plant which can be beneficial or pathogenic. In this study, we concentrated on beneficial microbes associated with plants using endophytic microbes as a case study. Detailed knowledge of the microbial diversity, abundance, composition, functional genes patterns, and metabolic pathways at genome level could assist in understanding the contributions of microbial community towards plant growth and health. Recently, the study of microbial community has improved greatly with the discovery of next-generation sequencing and bioinformatics technologies. Analysis of next generation sequencing data and a proper computational method plays a key role in examining microbial metagenome. This review presents the general metagenomics and computational methods used in processing plant associated metagenomes with concentration on endophytes. This includes 1) introduction of plant-associated microbiota and the factors driving their diversity. 2) plant metagenome focusing on DNA extraction, verification and quality control. 3) metagenomics methods used in community analysis of endophytes focusing on maize plant and, 4) computational methods used in the study of endophytic microbiomes. Limitations and future prospects of metagenomics and computational methods for the analysis of plant-associated metagenome (endophytic metagenome) were also discussed with the aim of fostering its development. We conclude that there is need to adopt advanced genomic features such as k-mers of random size, which do not depend on annotation and can represent other sequence alternatives.},
}

Computational Biology/*methods
Endophytes/*genetics
High-Throughput Nucleotide Sequencing/methods
Metagenome/genetics
Metagenomics/*methods
Microbiota/*genetics
Sequence Analysis, DNA/methods
Zea mays/growth & development/*microbiology

@article {pmid32007505,
year = {2020},
author = {Heravi, FS and Zakrzewski, M and Vickery, K and Hu, H},
title = {Host DNA depletion efficiency of microbiome DNA enrichment methods in infected tissue samples.},
journal = {Journal of microbiological methods},
volume = {170},
number = {},
pages = {105856},
doi = {10.1016/j.mimet.2020.105856},
pmid = {32007505},
issn = {1872-8359},
mesh = {Bacteria/classification/*genetics/isolation & purification ; DNA, Bacterial/*genetics ; Diabetic Foot/*microbiology/pathology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Infections/*diagnosis/microbiology ; Metagenomics/methods ; Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/*methods ; },
abstract = {Shotgun metagenomic sequencing or metagenomic whole genome sequencing is a genome-wide sequencing approach to explore bacterial communities directly from their habitat or sites of infection. However, host DNA contamination in metagenomic sequencing overwhelm low biomass of microbial signals and decrease sensitivity for microbial detection. In this study, we evaluated the host DNA depletion efficiency of four different microbiome DNA enrichment methods (NEBNext Microbiome DNA Enrichment kit, Molzym Ultra-Deep Microbiome Prep, QIAamp DNA Microbiome kit and Zymo HostZERO microbial DNA kit) in diabetic foot infection (DFI) tissue samples using quantitative real-time PCR and their effect on bacterial community composition by 16S ribosomal RNA amplicon sequencing. The host DNA depletion ratio (18S/16S rRNA), the percentage of bacterial DNA component and the microbial community profile of DFI were compared before (control) and after each microbiome DNA enrichment method. There was a significant difference in the 18S/16S rRNA ratio among different microbiome DNA enrichment methods (p <.001). QIAamp and HostZERO method reduced 18S/16S rRNA ratio by 32 and 57 fold than control method respectively. The percentage of bacterial DNA component increased more than ten-fold in QiaAmp (71.0 ± 2.7%) and HostZERO (79.9 ± 3.1%) method respectively than those in control method without host DNA depletion (6.7 ± 0.1%). It demonstrated the host DNA contamination was efficiently depleted and bacterial DNA was effectively enriched in HostZERO and QIAamp methods, attesting to the efficacy of these two methods in shotgun metagenomic sequencing studies. Overall, bacterial community composition of DFI samples was similar between control and microbiome enriched DNA samples.},
}

Bacteria/classification/*genetics/isolation & purification
DNA, Bacterial/*genetics
Diabetic Foot/*microbiology/pathology
High-Throughput Nucleotide Sequencing/methods
Humans
Infections/*diagnosis/microbiology
Metagenomics/methods
Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/methods
Whole Genome Sequencing/*methods