January 25, 2023

Human oral microbiome

Microbiological profile of peri-implantitis: Analyses of microbiome within dental implants – Kensara et al. – Journal of Prosthodontics

Human gut microbiome

Integrated Multi-Cohort Analysis of the Parkinson’s Disease Gut Metagenome – Boktor et al. – Movement Disorders

Gut microbiota and microbiota-derived metabolites promotes endometriosis – Chadchan et al. – Cell Death Discovery

Immune communication between the intestinal microbiota and the cardiovascular system – Ren et al. – Immunology Letters

Animal microbiome

The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome – Chamanakar et al. – Microbiome

The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet – Lin et al. – Microbiome

Fecal Microbiota Was Reshaped in UCP1 Knock-In Pigs via the Adipose-Liver-Gut Axis and Contributed to Less Fat Deposition – Pan et al. – Microbiology Spectrum

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health – Lan et al. – American Journal of Primatology

Housing temperature plays a critical role in determining gut microbiome composition in research mice: Implications for experimental reproducibility – Hylander et al. – Biochimie

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters – Wu et al. – Marine Environmental Research

Bioinformatics

[PREPRINT]Capturing the dynamics of microbiomes using individual-specific networks – Yousefi et al. – bioRxiv

PhaTYP: predicting the lifestyle for bacteriophages using BERT – Shang, Tang & Sun – Briefings in Bioinformatics

November 30, 2022

Human respiratory microbiome

Airway microecology in rifampicin-resistant and rifampicin-sensitive pulmonary tuberculosis patients – Cai et al. – BMC Microbiology

Human oral microbiome

Oral Bacteriome and Mycobiome across Stages of Oral Carcinogenesis – Heng et al. – Microbiology Spectrum

Human gut microbiome

[REVIEW]Double-edged sword: impact of fecal microbiome transplants on the gut resistome – Hallowell, Gao & Suez – Current Opinion in Gastroenterology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Gut microbiome alterations in preclinical Alzheimer’s disease – Jung et al. – PLOS One

[REVIEW]Sex, puberty, and the gut microbiome – Sisk-Hackworth, Kelley & Thackray

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Lactobacillus reuteri tryptophan metabolism promotes host susceptibility to CNS autoimmunity – Montgomery et al. – Microbiome

Animal microbiome (for animals in the wild)

Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont – Sylvain et al. – Microbiology Spectrum

Lack of host phylogenetic structure in the gut bacterial communities of New Zealand cicadas and their interspecific hybrids – Haji et al. – Scientific Reports

Plant, root, and soil microbiome

Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions – Jaiswal et al. – Microbiology Spectrum

Changes of the microbial community in kiwifruit during storage after postharvest application of Wickerhamomyces anomalus – Zhao et al. – Food Chemistry

Food microbiology

[PREPRINT]A dark matter in sake brewing: Origin of microbes producing a Kimoto-style fermentation starter – Ito et al. – bioRxiv

November 23, 2022

General microbiome

[PREPRINT]Patterns and determinants of the global herbivorous mycobiome – Meili et al. – bioRxiv

[EDITORIAL]Helicobacter pylori: Have potential benefits been overlooked? – Schubert et al. – JGH Open

Pregnancy and early life

Mechanisms affecting the gut of preterm infants in enteral feeding trials: a nested cohort within a randomised controlled trial of lactoferrin – Young et al. – Arch Dis Child Fetal Neonatal Ed

Human oral microbiome

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture – Quagliariello et al. – Nature Communications

Human vaginal microbiome

[PREPRINT]Longitudinal dynamics of the human vaginal ecosystem across the reproductive cycle – Costello et al. – bioRxiv

Human gut microbiome

[REVIEW]Maternal obesity and resistance to breast cancer treatments among offspring: Link to gut dysbiosis – Andrade, Verma & Hilakivi-Clark

Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis – Baumgartner et al. – Gut Microbes

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Impact of antibiotic perturbation on fecal viral communities in mice – Anderson et al. – G3

Animal microbiome (for animals in the wild)

Assessing Fungal Diversity and Abundance in the Black Soldier Fly and its Environment – Vitenberg & Opatovsky – Journal of Insect Science

Plant, root, and soil microbiome

Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front – Scherer, Mason & Rast – FEMS Microbiology Ecology

Bioinformatics

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes – Fullam et al. – NAR

[PREPRINT]Sparsification of Large Ultrametric Matrices: Insights into the Microbial Tree of Life – Gorman & Lladser

Techniques

[PREPRINT]Soil metatranscriptomics: An improved RNA extraction method toward functional analysis using nanopore direct RNA sequencing – Poursalavati et al. – bioRxix

November 16, 2022

General microbiome

Enhancing nutritional niche and host defenses by modifying the gut microbiome – Sun et al. – Molecular Systems Biology

Evolution of immune genes is associated with the Black Death – Klunk et al. – Nature

Pregnancy and early life

Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report – Wei et al. – Microbiome

Multi-site human microbiome

Age-Related Changes, Influencing Factors, and Crosstalk Between Vaginal and Gut Microbiota: A Cross-Sectional Comparative Study of Pre- and Postmenopausal Women – Yoshikata et al. – Journal of Women’s Health

Human oral microbiome

Characterization of oral microbiota in HPV and non-HPV head and neck squamous cell carcinoma and its association with patient outcomes – Chan et al. – Oral Oncology

Human gut microbiome

[REVIEW]Making gut microbiomes from scratch – Tiang & Bisanz – Cell Host &Microbe

Impairments of intestinal arginine and NO metabolisms trigger aging-associated intestinal barrier dysfunction and ‘inflammaging’ – Brandt et al. – Redox Biology

Dietary fiber ameliorates sleep disturbance connected to the gut–brain axis – Tang et al. – Food & Function

Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases – Cheng et al. – BMC Microbiology

Relationships between dietary diversity and gut microbial diversity in the elderly – Amamoto et al. – Beneficial Microbes

Alteration of the faecal microbiota composition in patients with constipation: evidence of American Gut Project – Xu et al. – Beneficial Microbes

Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis – Liang et al. – Translational Neurodegeneration

Microbiome insights into pediatric familial adenomatous polyposis – Attard et al. – Orphanet Journal of Rare Diseases

[REVIEW]The crosstalk between intestinal bacterial microbiota and immune cells in colorectal cancer progression – Wen et al. – Clinical and Translational Oncology

[REVIEW]Epigenetic regulation by metabolites from the gut microbiome – Marin-Tello et al. – Benefical Microbes

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

A tetrapeptide from maize combined with probiotics exerted strong anti-inflammatory effects and modulated gut microbiota in DSS-induced colitis mice – Li et al. – Food & Function

IGF1R is a mediator of sex-specific metabolism in mice: Effects of age and high-fat diet – Perez-Matute et al. – Front. Endocrinol.

Animal microbiome (for animals in the wild)

Nutrient dynamics in coral symbiosis depend on both the relative and absolute abundance of Symbiodiniaceae species – McIlroy et al. – Microbiome

Plant, root, and soil microbiome

Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea – Wicaksono et al. – mSystems

Bioinformatics

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments – Hempel et al. – NAR

Metagenome-assembled genome extraction and analysis from microbiomes using KBase – Chivian et al. – Nature Protocols

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies – Aytan-Aktug et al. – Microbiology Spectrum

TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes – Gupta et al. – mSystems

Techniques

Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution – Clokie et al. – Microbiology Spectrum

November 14, 2022

Human and General Microbiome

Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits – Lili Liu – Nature Communications

Kidney microbiota dysbiosis contributes to the development of hypertension – Xin-Yu Liu – Gut Microbes

Gut mycobiota dysbiosis in drug-naïve, first-episode schizophrenia – Xiuxia Yuan – Schizophrenia Research

Transcriptomic analysis reveals an association of FCGBP with Parkinson’s disease – Pilar Gómez-Garre – NPJ Parkinson’s Disease

Integration of stool microbiota, proteome and amino acid profiles to discriminate patients with adenomas and colorectal cancer – Sofie Bosch – Gut Microbes

Human gut homeostasis and regeneration: the role of the gut microbiota and its metabolites – Claudia Marcela Arenas-Gómez – Critical Reviews in Microbiology

Colibactin possessing E. coli isolates in association with colorectal cancer and their genetic diversity among Pakistani population – Habiba Tariq – PloS one

Intestinal toxicity to CTLA-4 blockade driven by IL-6 and myeloid infiltration – Yifan Zhou – The Journal of Experimental Medicine

Genome-microbiome interplay provides insight into the determinants of the human blood metabolome – Christian Diener – Nature Metabolism

Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study – Edgar Gulavi – BMC Microbiology

Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis – Zhixia Zhang – BMC Oral Health

Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome – Qin Liu – Nature Communications

Characterization of antibiotic-resistance traits in Akkermansia muciniphila strains of human origin – Rossella Filardi – Scientific Reports

Food Microbiome

Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses – Ryosuke Unno – Microbiology Spectrum

Animal Microbiome

Microbiota of healthy and bleached corals of the species Siderastrea stellata in response to river influx and seasonality in Brazilian northeast – Gustavo Vasconcelos Bastos Paulino – Environmental Science and Pollution Research International

Environmental Microbiome

Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches – Beatrice Farda – Scientific Reports

Plant Microbiome

High throughput method of 16S rRNA gene sequencing library preparation for plant root microbial community profiling – Kie Kumaishi – Scientific Reports

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure – Ana Paula Corrêa Moneda – Scientific Reports

Effects of Two Bacillus velezensis Microbial Inoculants on the Growth and Rhizosphere Soil Environment of Prunus davidiana – Huimin Shi – International Journal of Molecular Sciences

Review: Climate change and plant pathogens – Muhammad M Raza – Current Opinion in Microbiology

Bioinformatics and Microbiome Analysis

Faecal microbiome-based machine learning for multi-class disease diagnosis – Qi Su – Nature Communications

Wochenende – modular and flexible alignment-based shotgun metagenome analysis – Ilona Rosenboom – BMC Genomics

De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee – Yunxi Liu – Nature Communications

November 7, 2022

Human and General Microbiome

Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure – Matthew R Stutz – Nature Communications

Taxonomic Abundance in Primary and Secondary Root Canal Infections – Ronald Ordinola-Zapata – International Endodontic Journal

Review: The intestinal barrier in disorders of the central nervous system – Carolina Pellegrini – The Lancet. Gastroenterology & Hepatology

Review: Resistance is futile? Mucosal immune mechanisms in the context of microbial ecology and evolution – Emma Slack – Mucosal Immunology

Correspondence: A critical analysis of eating disorders and the gut microbiome – Sydney M Terry – Journal of Eating Disorders

Beneficial Microbes and Compounds

Bifidobacterial carbohydrate/nucleoside metabolism enhances oxidative phosphorylation in white adipose tissue to protect against diet-induced obesity – Gihyeon Kim – Microbiome

Lactobacillus rhamnosus GG supernatant promotes intestinal mucin production through regulating 5-HT4R and gut microbiota – Yu Gu – Food & Function

Animal Model Microbiome

Genetic and environmental circadian disruption induce weight gain through changes in the gut microbiome – Baraa Altaha – Molecular Metabolism

Strains producing different short-chain fatty acids alleviate DSS-induced ulcerative colitis by regulating intestinal microecology – Shuo Yang – Food & Function

Non-Model Animal Microbiome

Microbiome assembly and maintenance across the lifespan of bumble bee workers – Tobin J Hammer – Molecular Ecology

The gut microbiome reflects ancestry despite dietary shifts across a hybrid zone – Danny P Nielsen – Ecology Letters

Characterization of the core gut microbiota of Nile tilapia (Oreochromis niloticus): indication of a putative novel Cetobacterium species and analysis of its potential function on nutrition – Ziyue Zhang – Archives of Microbiology

Forensic Microbiome

Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes – Thomas Clarke – Scientific Reports

Plant Microbiome

Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation – Hetty KleinJan – Molecular Ecology

Built Environment Microbiome

Review: Microplastics in urban waters and its effects on microbial communities: a critical review – Saber Entezari – Environmental Science and Pollution Research International

Microbiome Analysis and Techniques

Assessing the Dark Field of Metaproteome – Haonan Duan – Analytical Chemistry

October 05, 2022

Pregnancy and early life

Multi-omic factors associated with future wheezing in infants – Beheshti et al. – Pediatric Research

Multi-site human microbiome

Race is a key determinant of the human intratumor microbiome – Lua et al. – Cancer Cell

Human respiratory microbiome

Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance – Merenstein, Bushman & Collman – Microbiome

Human milk microbiome

Maternal weight status and the composition of the human milk microbiome: A scoping review – Daiy et al. – PLOS One

Human oral microbiome

Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study – Carda-Dieguez, Mazzez & Mira – Microbiome

Remembering St. Louis individual—structural violence and acute bacterial infections in a historical anatomical collection – Austin et al. – Communications Biology

Human gut microbiome

[REVIEW]SARS-CoV-2-associated gut microbiome alteration; A new contributor to colorectal cancer pathogenesis – Mozaffari et al. – Pathology – Research and Practice

Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin – Ma et al. – Genome Biology

Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome – Kawano et al. – Cell

Rural environment reduces allergic inflammation by modulating the gut microbiota – Yang et al. – Gut Microbes

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Six types of tea extracts attenuated high-fat diet-induced metabolic syndrome via modulating gut microbiota in rats – Zhou et al. – Food Research International

Adaptation of the gut holobiont to malnutrition during mouse pregnancy depends on the type of nutritional adversity – Connor et al. – The Journal of Nutritional Biochemistry

Animal microbiome (for animals in the wild)

A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle – Teseo et al. – Microbiome

Comparative multiomics study of the effects of Ellagic acid on the gut environment in young and adult mice – Duan et al. – Food Research International

[REVIEW]Crosstalk between the microbiota and insect postembryonic development – Girard et al. – Trends in Microbiology

Culturomic, metagenomic, and transcriptomic-based characterization of commensal lactic acid bacteria isolated from domestic dogs using Caenorhabditis elegans as a model for aging – Kang et al. – Journal of Animal Science

Plant, root, sponge and soil microbiome

Recruitment of specific microbes through exudates affects cadmium activation and accumulation in Brassica napus – Wu et al. – Journal of Hazardous Materials

Novel trends of genome evolution in highly complex tropical sponge microbiomes – Kelly et al. – Microbiome

[Petroleum pollution affects soil chemistry and reshapes the diversity and networks of microbial communities](Ecotoxicology and Environmental Safety) – Li et al. –

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics – Seong et al. – Microbiome

Untangling microbial diversity and assembly patterns in rare earth element mine drainage in South China – Chen et al. – Water Research

Bioinformatics/Software

Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics – Weissman et al. – mSystems

[SOFTWARE]PhyloDM is a high-performance library that converts a phylogenetic tree into a pairwise distance matrix. – Aaron Mussig – github

October 3, 2022

Human and General Microbiome

Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease – Eiko Hayase – Cell

Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions – Lian Narunsky-Haziza – Cell

A pan-cancer mycobiome analysis reveals fungal involvement in gastrointestinal and lung tumors – Anders B Dohlman – Cell

Gut microbiota of hepatitis B virus-infected patients in the immune-tolerant and immune-active phases and their implications in metabolite changes – Ya-Nan Li – World Journal of Gastroenterology

Streptococcus mutans promotes tumor progression in oral squamous cell carcinoma – Ming-Shao Tsai – Journal of Cancer

Short-chain fatty acid concentrations in the incidence and risk-stratification of colorectal cancer: a systematic review and meta-analysis – Ehsan Alvandi – BMC Medicine

Mycobacterium potentiates protection from colorectal cancer by gut microbial alterations – Yu-Mi Kim – Immunology

Nutrition, Immunosenescence, and Infectious Disease: An Overview of the Scientific Evidence on Micronutrients and on Modulation of the Gut Microbiota – Philip C Calder – Advances in Nutrition 

Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients – Heather K Armstrong – Gastroenterology

Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects – Andrea McDowell – Experimental & Molecular Medicine

Microbiome ethics, guiding principles for microbiome research, use and knowledge management – Lene Lange – Environmental Microbiome

Review: The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly – Fen Zhang – The Lancet. Microbe

Beneficial Microbes and Compounds

Review: Tailoring gut microbiota with a combination of Vitamin K and probiotics as a possible adjuvant in the treatment of rheumatic arthritis: a systematic review – Luciana Pereira – Clinical Nutrition ESPEN

Dietary Isoflavones Alter Gut Microbiota and Lipopolysaccharide Biosynthesis to Reduce Inflammation – Sudeep Ghimire – Gut Microbes

Bacteroides thetaiotaomicron rough-type lipopolysaccharide: The chemical structure and the immunological activity – Molly Dorothy Pither – Carbohydrate Polymers

Animal Microbiome

Study of cattle microbiota in different regions of Kazakhstan using 16S metabarcoding analysis – Aida Daugaliyeva – Scientific Reports

Microscopic marine invertebrates are reservoirs for cryptic and diverse protists and fungi – Corey C Holt – Microbiome

Plant Microbiome

Review: Microbiomes in agroecosystem: Diversity, function and assembly mechanisms – Chao Xiong – Environmental Microbiology Reports

Bioinformatics and Microbiome Analysis

Integrating Phylogenetic and Functional Data in Microbiome Studies – Gavin M Douglas – Bioinformatics 

Higher off-target amplicon detection rate in MiSeq v3 compared to v2 reagent kits in the context of 16S-rRNA-sequencing – Mari-Lee Odendaal – Scientific Reports

September 21, 2022

Human respiratory microbiome

The Microbiota of Human Lung of Pulmonary Tuberculosis and the Alteration Caused by Anti-tuberculosis Drugs – Zhang et al. – Current Microbiology

Human urinary microbiome

Mechanisms of the intestinal and urinary microbiome in kidney stone disease – Miller et al. – Nature Reviews Urology

Human oral microbiome

Comparison of tumor-associated and nontumor-associated esophageal mucosa microbiota in patients with esophageal squamous cell carcinoma – Zhang et al. – Medicine

Human gut microbiome

Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients – Thompson et al. – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Early fecal microbiome transfer after donor defecation determines response in patients with moderate to severe ulcerative colitis – Singh et al. – Indian Journal of Gastroenterology

[REVIEW]Modulatory role of gut microbiota in cholesterol and glucose metabolism: Potential implications for atherosclerotic cardiovascular disease Atherosclerosis – Roessler et al. – Atherosclerosis

Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population – Bai et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle – Hoces et al. – PLOS Biology

Inhibitory effects of antibiotic-induced gut microbiota depletion on acute itch behavior in mice – Zhang et al. – Brain Research Bulletin

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Yang et al. – Microbiome

Animal microbiome (for animals in the wild)

Community and shotgun metagenomic analysis of Alligator mississippiensis oral cavity and GI tracts reveal complex ecosystems and potential reservoirs of antibiotic resistance – Perez-Marron et al. – Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology

Microbiome composition is shaped by geography and population structure in the parasitic wasp Asobara japonica, but not in the presence of the endosymbiont Wolbachia – Brinker et al. – Molecular Ecology

Plant, root, and soil microbiome

Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds – Loiola et al. – Science of The Total Environment

[REVIEW]Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture – Diwan, Rashid & Vaishnav – Microbiological Research

Mitigating abiotic stress: microbiome engineering for improving agricultural production and environmental sustainability – Phour & Sindhu – Planta

[OPINION]Plant microbiota dysbiosis and the Anna Karenina Principle – Arnault, Money & Vandenkoornhuyse

Food microbiology

Anthocyanin Addition to Kefir: Metagenomic Analysis of Microbial Community Structure – Aydin et al. – Current Microbiology

Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance – Calabrese et al. – Microbiome

September 18, 2022

Human and General Microbiome

Neisseria species as pathobionts in bronchiectasis – Liang Li – Cell Host & Microbe

The gut microbiome molecular complex in human health and disease – Paul Wilmes – Cell Host & Microbe

Codiversification of gut microbiota with humans – Taichi A Suzuki – Science

Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course – The iMSMS Consortium – Cell

Composition and diverse differences of intestinal microbiota in ulcerative colitis patients – Siying Zhu – Frontiers in Cellular and Infection Microbiology

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease – Paola Di Carlo – Frontiers in Physiology

Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases – Gianluca Ianiro – Nature Medicine

Drivers and determinants of strain dynamics following fecal microbiota transplantation – Thomas S B Schmidt – Nature Medicine

Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects – Jonathan T L Kang – Nature Microbiology

Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease – Qi Cheng – Genomics

Growth of succinate consumer Dialister hominis is supported by Bacteroides thetaiotaomicron – Mitsuo Sakamoto – Anaerobe

RhoB affects colitis through modulating cell signaling and intestinal microbiome – Jianming Yang – Microbiome

Review: Diet fuelling inflammatory bowel diseases: preclinical and clinical concepts – Timon E Adolph – Gut

Review: Recent findings in Akkermansia muciniphila-regulated metabolism and its role in intestinal diseases – Meng-Jie Liu – Clinical Nutrition

Beneficial Microbes and Compounds

Comprehensive analysis of microbiome, metabolome and transcriptome revealed the mechanisms of Moringa oleifera polysaccharide on preventing ulcerative colitis – Hanchen Tian – International Journal of Biological Macromolecules

Probiotics ameliorates pulmonary inflammation via modulating gut microbiota and rectifying Th17/Treg imbalance in a rat model of PM2.5 induced lung injury – Yongcan Wu – Ecotoxicology and Environmental Safety

Short-term supplementation with ω-3 polyunsaturated fatty acids modulates primarily mucolytic species from the gut luminal mucin niche in a human fermentation system – Charlène Roussel – Gut Microbes

Model Animal Microbiome

Interactive Effect of Combined Intermittent and Sustained Hypoxia and High-Fat Diet on the Colonic Mucosal Microbiome and Host Gene Expression in Mice – Saif Mashaqi – Nature and Science of Sleep

Non-Model Animal Microbiome

Fungi are more transient than bacteria in caterpillar gut microbiomes – Martin Šigut – Scientific Reports

Adapting to climate with limited genetic diversity: Nucleotide, DNA methylation and microbiome variation among populations of the social spider Stegodyphus dumicola – Anne Aagaard – Molecular Ecology

Bioinformatics and Microbiome Analysis

Filtering ASVs/OTUs via mutual information-based microbiome network analysis – Elham Bayat Mokhtari – BMC Bioinformatics

Batch effects removal for microbiome data via conditional quantile regression – Wodan Ling – Nature Communications

Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families – Sweta Nidhi – Molecular Biotechnology

Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights – Mason R Stothart – Molecular Ecology Resources

SnapShot: The Expobiome Map – Velma T E Aho – Cell Host & Microbe