Tag Archives: microbiome

August 28, 2023

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Human and General Microbiome

The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia – Ana Elena Pérez-Cobas – Cell Reports. Medicine

A phenome-wide association study (PheWAS) to identify the health impacts of 4-cresol sulfate in the Nagahama Study – Huiting Ou – Scientific Reports

A meta-analysis of tissue microbial biomarkers for recurrence and metastasis in multiple cancer types – Xuebo Li – Journal of Medical Microbiology 

Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts – Nathalie Juge – Microbiology

Oral Porphyromonas gingivalis infection affects intestinal microbiota and promotes atherosclerosis – Sowon Park – Journal of Clinical Periodontology

Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study – Gertrude Ecklu-Mensah – Nature Communications

Very early life microbiome and metabolome correlates with primary vaccination variability in children – Michael Shaffer – mSystems

Carbohydrate quality, fecal microbiota and cardiometabolic health in older adults: a cohort study – Alessandro Atzeni – Gut Microbes

Multi-omics analysis revealing the interplay between gut microbiome and the host following opioid use – Udhghatri Kolli – Gut Microbes

The gut microbiota reprograms intestinal lipid metabolism through long noncoding RNA Snhg9 – Yuhao Wang – Science

Staphylococcus epidermidis activates keratinocyte cytokine expression and promotes skin inflammation through the production of phenol-soluble modulins – Michael R Williams – Cell Reports

Review: Targeting nonalcoholic fatty liver disease via gut microbiome-centered therapies – Mijra Koning – Gut Microbes

Review: Intracellular Fusobacterium nucleatum infection increases METTL3-mediated m6A methylation to promote the metastasis of esophageal squamous cell carcinoma – Songhe Guo – Journal of Advanced Research

Beneficial Microbes and Compounds

Characteristics of gut microbiota determine effects of specific probiotics strains in patients with functional constipation – Haohao Zhang – Chinese Medical Journal

Lacticaseibacillus rhamnosus TF318 prevents depressive behavior in rats by inhibiting HPA-axis hyperactivity and upregulating BDNF expression – Yujuan Zhao – Neuroscience Letters

Animal Model Microbiome

Role of mucin glycosylation in the gut microbiota-brain axis of core 3 O-glycan deficient mice – Erika Coletto – Scientific Reports

Non-Model Animal Microbiome

Outer membrane vesicles from a mosquito commensal mediate targeted killing of Plasmodium parasites via the phosphatidylcholine scavenging pathway – Han Gao – Nature Communications

Whole genome analyses of toxicants tolerance genes of Apis mellifera gut-derived Enterococcus faecium strains – Heba A H Zaghloul – BMC Genomics

Fungal Microbiome

The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research – Julia M Kelliher – Microbiome

Plant Microbiome

Microbiome dataset of bacterial and fungal communities in anthosphere of twelve different wild plants in South Korea – Jihoon Kim – Data in Brief 

Environmental and Soil Microbiome

Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments – Xiaotian Zhou – Microbiome

Long-term agro-management strategies shape soil bacterial community structure in dryland wheat systems – Shikha Singh – Scientific Reports

Microbial community structure and functional prediction in five full-scale industrial park wastewater treatment plants – Tujun Tong – The Science of the Total Environment

Deterministic Development of Soil Microbial Communities in Disturbed Soils Depends on Microbial Biomass of the Bioinoculum – Yuri Pinheiro Alves de Souza – Microbial Ecology

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole – Kai Sun – Microbiology Spectrum

A study of microbial diversity in a biofertilizer consortium – Cristóbal Hernández-Álvarez – PloS One

Microbiome Research: Resources, Tools and Techniques

Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data – Aubrey R Odom – Scientific Reports

Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution – Elisabetta Notario – Genes

A flexible quasi-likelihood model for microbiome abundance count data – Yiming Shi – Statistics in Medicine

Identification of multivariable Boolean patterns in microbiome and microbial gene composition data – George Golovko – Bio Systems

Machine learning classification by fitting amplicon sequences to existing OTUs – Courtney R Armour – mSphere

Review: Statistical normalization methods in microbiome data with application to microbiome cancer research – Yinglin Xia – Gut Microbes

Book Chapter: Elucidating the role of microbes in celiac disease through gnotobiotic modeling – Alberto Caminero – Methods in Cell Biology

August 20, 2023

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Highlights!

Human microbiome variation associated with race and ethnicity emerges as early as 3 months of age – Elizabeth K Mallott – PLoS Biology

Mapping the T cell repertoire to a complex gut bacterial community – Kazuki Nagashima – Nature

Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome – Liam H. Walsh – npj Science of Food 

High-resolution strain-level microbiome composition analysis from short reads – Herui Liao – Microbiome

Preprint: Profiling novel lateral gene transfer events in the human microbiome –  Tiffany Y. Hsu – bioRxiv

Human and General Microbiome

Preprint: Major data analysis errors invalidate cancer microbiome findings –  Abraham Gihawi – bioRxiv

Microdiversity of the vaginal microbiome is associated with preterm birth – Jingqiu Liao – Nature Communications

Dysbiosis of gut microbiota during fecal stream diversion in patients with colorectal cancer – Soo Young Lee – Gut Pathogens

The gut microbiome contributes to somatic morphine withdrawal behavior and implicates a TLR2 mediated mechanism – Bridget Truitt – Gut Microbes

Association of the human gut microbiota with vascular stiffness – Rafael R C Cuadrat – Scientific Reports

Gut microbiota and intervertebral disc degeneration: a bidirectional two-sample Mendelian randomization study – Ziming Geng – Journal of Orthopaedic Surgery and Research

News & Views: Microbiome alterations in autism spectrum disorder – Elena J Coley-O’Rourke – Nature Microbiology

Beneficial Microbes and Compounds

Rosmarinic acid alleviates intestinal inflammatory damage and inhibits endoplasmic reticulum stress and smooth muscle contraction abnormalities in intestinal tissues by regulating gut microbiota – Kan Li – Microbiology Spectrum

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline – Xiaolei Liu – Journal of Cachexia, Sarcopenia and Muscle

The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome – Carolina Baldisserotto Comerlato – Probiotics and Antimicrobial Proteins

Kombucha tea as an anti-hyperglycemic agent in humans with diabetes – a randomized controlled pilot investigation – Chagai Mendelson – Frontiers in Nutrition 

Animal Microbiome

The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host’s dietary adaption to bamboo – Feilong Deng – Microbiome

Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations – M McCauley – Nature Communications

Review: Toward an Integrated Understanding of the Lepidoptera Microbiome – Yongqi Shao – Annual Review of Entomology

Plant Microbiome

Characterization of bacterial community in tobacco leaves at flue-curing and redrying processing stages – Yue Yang – Scientific Reports

Environmental Microbiome

Inter-comparison of marine microbiome sampling protocols – Francisco Pascoal – ISME Communications

Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog – Adrien Vigneron – ISME Communications

Microbiome Research: Resources, Tools and Techniques

MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome assembled genomes – Wanxin Li – PloS one

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J Pavia – Microbiome

Detection of viable commensal bacteria in murine melanoma tumors by culturomics – Catherine M Phelps – STAR Protocols

August 13, 2023

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Highlights!

Enterotypes of the human gut mycobiome – Senying Lai – Microbiome

Effect of butyrate-producing enterobacteria on advanced hepatocellular carcinoma treatment with atezolizumab and bevacizumab – Kazuhiro Nouso – Cancer Medicine

Parvimonas micra can translocate from the subgingival sulcus of the human oral cavity to colorectal adenocarcinoma – Kelly Conde-Pérez – Molecular Oncology

An Oral Microbial Biomarker for Early Detection of Recurrence of Oral Squamous Cell Carcinoma – Wei-Ni Lyu – ACS Infectious Diseases

Human and General Microbiome

Multilocus-sequence typing reveals clonality of Staphylococcus aureus in atopic dermatitis – Leszek Blicharz – Clinical and Experimental Dermatology

Metabarcoding approach to identify bacterial community profiling related to nosocomial infection and bacterial trafficking-routes in hospital environments – Bárbara Gimenes de Castro – Journal of Toxicology and Environmental Health. Part A

Identification of host gene-microbiome associations in colorectal cancer patients using mendelian randomization – Yaoxian Xiang – Journal of Translational Medicine

Bacterial amylases enable glycogen degradation by the vaginal microbiome – Dominick J Jenkins – Nature Microbiology

Babies, bugs and brains: How the early microbiome associates with infant brain and behavior development – Sebastian Hunter – PloS One

A retrospective analysis of vitamin B6 deficiency and associated changes of gut microbes in Crohn’s disease – Zhongsheng Feng – European Journal of Clinical Nutrition

The intestinal microbiota predicts COVID-19 severity and fatality regardless of hospital feeding method – Vanni Bucci – mSystems

Commentary and Views: The importance of the gut microbiome in the pathogenesis and transmission of SARS-CoV-2 – Carlo Brogna – Gut Microbes

Meta-analysis: Perturbations in gut microbiota composition in patients with polycystic ovary syndrome: a systematic review and meta-analysis – Pan Li – BMC Medicine

Letter: Caution regarding the specificities of pan-cancer microbial structure – Abraham Gihawi – Microbial Genomics

Review: Gut microbial beta-glucuronidase: a vital regulator in female estrogen metabolism – Shiwan Hu – Gut Microbes

Review: Three specific gut bacteria in the occurrence and development of colorectal cancer: a concerted effort – Dengmei Gong – PeerJ

Animal Microbiome (models and non-model organisms)

Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China – Michelle Baker – Nature Food

The enhancement in toxic potency of oxidized functionalized polyethylene-microplastics in mice gut and Caco-2 cells – Ji Wang – The Science of the Total Environment

Review: Geroprotective potential of microbiome modulators in the Caenorhabditis elegans model – Brandi C Miller – GeroScience

Microbiome Ecology and Evolution

Macroevolutionary constraints on global microbial diversity – Ford J Fishman – Ecology and Evolution

Evolutionary dynamics on sequential temporal networks – Anzhi Sheng – PLoS Computational Biology

Nutritional and host environments determine community ecology and keystone species in a synthetic gut bacterial community – Anna S Weiss – Nature Communications

Extremophiles

Earth to Mars: A Protocol for Characterizing Permafrost in the Context of Climate Change as an Analog for Extraplanetary Exploration – Kimberley R Miner – Astrobiology

Bioleaching of polymetallic sulphidic mining residues: influence of increasing solid concentration on microbial community dynamics and metal dissolution – Catherine Joulian – Research in Microbiology

Environmental Microbiome

Multidimensional specialization and generalization are pervasive in soil prokaryotes – Damian J Hernandez – Nature Ecology & Evolution

Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity – Brajogopal Samanta – Current Microbiology

Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study – Dámaris Núñez-Gómez – Environmental Microbiome

Opinion: New microbial tools to boost restoration and soil organic matters – Tadeo Sáez-Sandino – Microbial Biotechnology

Microbiome Research: Resources, Tools and Techniques

Optimization of fecal sample homogenization for untargeted metabolomics – Kieran Tarazona Carrillo – Metabolomics : Official Journal of the Metabolomic Society

metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering – Chunlin Hao – Microbiome

sccomp: Robust differential composition and variability analysis for single-cell data – Stefano Mangiola – PNAS

Metagenome sequencing and 103 microbial genomes from ballast water and sediments – Zhaozhao Xue – Scientific Data

August 6, 2023

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Human and General Microbiome

Methionine restriction-induced sulfur deficiency impairs antitumour immunity partially through gut microbiota – Ming Ji – Nature Metabolism

Total RNA sequencing reveals gene expression and microbial alterations shared by oral pre-malignant lesions and cancer – Mohammed Muzamil Khan – Human Genomics

Metagenomics revealed a correlation of gut phageome with autism spectrum disorder – Khashayar Shahin – Gut Pathogens

The cervical microbiota of Hispanics living in Puerto Rico is nonoptimal regardless of HPV status – Daniela Vargas-Robles – mSystems

Illuminating the Oral Microbiome: Cellular Microbiology – Richard J Lamont – FEMS Microbiology Reviews

Meeting report of the sixth annual tri-service microbiome consortium symposium – Ida G Pantoja-Feliciano De Goodfellow – Environmental Microbiome

Evaluation of Intestinal Microbiota in Children With Sickle Cell Disease – Feryal Karahan – Journal of Pediatric Hematology/Oncology

Genetic and gut microbiome determinants of SCFA circulating and fecal levels, postprandial responses and links to chronic and acute inflammation – Ana Nogal – Gut Microbes

Review: Microbiota associated with peri-implantitis-A systematic review with meta-analyses – Érika B S Carvalho – Clinical Oral Implants Research

Review: Exploration of Gut Microbiome Research in Africa: A Scoping Review – Abdulkadir Yusif Maigoro – Journal of Medicinal Food

Animal Microbiome

Exploration of the candidate beneficial bacteria for P. vannamei culture by core microbiome analysis using amplicon sequencing – Natarajan Lalitha – Letters in Applied Microbiology

Plant Microbiome

A symbiotic footprint in the plant root microbiome – Kyle Hartman – Environmental Microbiome

Review: Towards integrative plant pathology – Tatiana Ruiz-Bedoya – Current Opinion in Plant Biology

More about the Microbes

Sodium levels and grazing pressure shape natural communities of the intracellular pathogen Legionella – Oded Bergman – Microbiome

Review: Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait – Maria Esteban-Torres – Gut Microbes

Microbiome Research: Resources, Tools and Techniques

ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization – Chen Yang – Bioinformatics

July 30, 2023

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Human and General Microbiome

Resistome expansion in disease-associated human gut microbiomes – Simen Fredriksen – Microbiome

A microbial causal mediation analytic tool for health disparity and applications in body mass index – Chan Wang – Microbiome

Alterations of gut microbiota in biopsy-proven diabetic nephropathy and a long history of diabetes without kidney damage – Xiao Lu – Scientific Reports

Assessment of infant outgrowth of cow’s milk allergy in relation to the faecal microbiome and metaproteome – Diana M Hendrickx – Scientific Reports

Analysis of bacterial vaginosis, the vaginal microbiome, and sexually transmitted infections following the provision of menstrual cups in Kenyan schools: Results of a nested study within a cluster randomized controlled trial – Supriya D Mehta – PLoS Medicine

Evolutionary modeling suggests that addictions may be driven by competition-induced microbiome dysbiosis – Ohad Lewin-Epstein – Communications Biology

Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes – Kelsey N Thompson – Science Translational Medicine

Increased genital mucosal cytokines in Canadian women associate with higher antigen-presenting cells, inflammatory metabolites, epithelial barrier disruption, and the depletion of L. crispatus – Christina Farr Zuend – Microbiome

Insulin alleviates murine colitis through microbiome alterations and bile acid metabolism – Shuying He – Journal of Translational Medicine

The Vaginal Microbiota of Pregnant Women Varies with Gestational Age, Maternal Age, and Parity – Roberto Romero – Microbiology Spectrum

Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections – Hui Li – Microbiome

Systematic Review: Probiotics to prevent necrotising enterocolitis in very preterm or very low birth weight infants – Sahar Sharif – The Cochrane Database of Systematic Reviews

Comment: A gut feeling for drugs that have metabolic benefits – Eryun Zhang – Nature Communications

Review: Antibiotic perturbations to the gut microbiome – Skye R S Fishbein – Nature Reviews. Microbiology

Review: The global human gut microbiome: genes, lifestyles, and diet – Mona Parizadeh – Trends in Molecular Medicine

Beneficial Microbes and Compounds

5-Aminosalicylic acid alters the gut microbiota and altered microbiota transmitted vertically to offspring have protective effects against colitis – Haruka Wada – Scientific Reports

Food Microbiome

Presence of an ultra-small microbiome in fermented cabbages – Hae-Won Lee – PeerJ

Animal Microbiome

The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels – Simone Anzà – Microbiome

Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks – Xianghui Liang – Microbiome

Human-influenced diets affect the gut microbiome of wild baboons – Madelyn Moy – Scientific Reports

Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics – Barbara P Brito – Microbiome

Social network position is a major predictor of ant behavior, microbiota composition, and brain gene expression – Tomas Kay – PLoS Biology

Plant Microbiome

The root microbiome: techniques for exploration and agricultural applications – Ashling Cannon – BioTechniques

Environmental Microbiome

Recently-formed Antarctic lakes host less diverse benthic bacterial and diatom communities than their older counterparts – Jan Kollár – FEMS Microbiology Ecology

Microbiome Research: Resources, Tools and Techniques

Greengenes2 unifies microbial data in a single reference tree – Daniel McDonald – Nature Biotechnology

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning – Alex Chklovski – Nature Methods

Lectin-Seq: A method to profile lectin-microbe interactions in native communities – Robert L McPherson – Science Advances

A mixed-model approach for estimating drivers of microbiota community composition and differential taxonomic abundance – Amy R Sweeny – mSystems

July 23, 2023

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Highlights!

Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome – Mohammad H Mirhakkak – Nature Communications

Depletion of butyrate-producing microbes of the Firmicutes predicts nonresponse to FMT therapy in patients with recurrent Clostridium difficile infection – Hongliang Tian – Gut Microbes

Chagas disease is related to structural changes of the gut microbiota in adults with chronic infection (TRIPOBIOME Study) – José A Pérez-Molina – PLoS Neglected Tropical Diseases

Human and General Microbiome

Study of the gut microbiome in Egyptian patients with Parkinson’s Disease – Mohammad Mehanna – BMC Microbiology

Intestinal microbiota controls graft-versus-host disease independent of donor-host genetic disparity – Motoko Koyama – Immunity

A systematic review exploring the association between the human gut microbiota and brain connectivity in health and disease – Danique Mulder – Molecular Psychiatry

A macroecological perspective on genetic diversity in the human gut microbiome – William R Shoemaker – PloS One

Gut microbiota metabolites mediate the interplay between childhood maltreatment and psychopathology in patients with eating disorders – Giovanni Castellini – Scientific Reports

In-depth metataxonomic investigation reveals low richness, high intervariability, and diverse phylotype candidates of archaea in the human urogenital tract – Yeon Bee Kim – Scientific Reports

Host microbiome-pathogen interactions in pediatric infections – Jillian H Hurst – Current Opinion in Infectious Diseases

Intratumoural microbiome can predict the prognosis of hepatocellular carcinoma after surgery – Lejia Sun – Clinical and Translational Medicine

A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis – Brett A McGregor – Parasites & Vectors

Microbiome-derived cobalamin and succinyl-CoA as biomarkers for improved screening of anal cancer – Sergio Serrano-Villar – Nature Medicine

Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease – Gemma L D’Adamo – Cell Reports. Medicine

Multimodal immune cell phenotyping in GI biopsies reveals microbiome-related T cell modulations in human GvHD – Sebastian Jarosch – Cell Reports. Medicine

Beneficial Microbes and Compounds

Prebiotics and the risk of upper digestive tract and stomach cancers: the PrebiotiCa study – Federica Turati – Journal of the Academy of Nutrition and Dietetics

Plant Microbiome

Disturbance of eucalypt forests alters the composition, function, and assembly of soil microbial communities – Ernest D Osburn – FEMS Microbiology Ecology

Reciprocal influence of soil, phyllosphere, and aphid microbiomes – Adrian Wolfgang – Environmental Microbiome

Review: Co-evolution within the plant holobiont drives host performance – Fantin Mesny – EMBO Reports

Environmental Microbiome

May microbial ecological baseline exist in continental groundwater? – Sining Zhong – Microbiome

Evolutionary patterns of archaea predominant in acidic environment – Rafael Bargiela – Environmental Microbiome

Microbiome Research: Resources, Tools and Techniques

Machine learning-based approaches for cancer prediction using microbiome data – Pedro Freitas – Scientific Reports

Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products – Maria Victoria Fernandez-Cantos – Frontiers in Microbiology

A bioinformatic analysis of zinc transporters in intestinal Lactobacillaceae – Uyen Huynh – Metallomics

Uncovering the Carboxylated Metabolome in Gut Microbiota-Host Co-metabolism: A Chemical Derivatization-Molecular Networking Approach – Yan-Zhen Wang – Analytical Chemistry

July 16, 2023

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Human and General Microbiome

A two-sample mendelian randomization analysis investigates associations between gut microbiota and infertility – Taozhi Li – Scientific Reports

Targeting gut microbiota-derived kynurenine to predict and protect the remodeling of the pressure-overloaded young heart – Bozhong Shi – Science Advances

Intratumoral Microbiota Composition Regulates Chemoimmunotherapy Response in Esophageal Squamous Cell Carcinoma – Hong Wu – Cancer Research

Metabolic and inflammatory profiles, gut microbiota and lifestyle factors in overweight and normal weight young thai adults – Surasawadee Somnuk – PloS One

Metagenomic assessment of gut microbial communities and risk of severe COVID-19 – Long H Nguyen – Genome Medicine

Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics – Arianna Basile – Gut Microbes

Exploring Co-occurrence patterns and microbial diversity in the lung microbiome of patients with non-small cell lung cancer – Sadaf Najafi – BMC Microbiology

Aerobic exercise training and gut microbiome-associated metabolic shifts in women with overweight: a multi-omic study – Jukka E Hintikka – Scientific Reports

Glycogen availability and pH variation in a medium simulating vaginal fluid influence the growth of vaginal Lactobacillus species and Gardnerella vaginalis – Stephany Navarro – BMC Microbiology

Antibiotic-induced gut microbiota dysbiosis has a functional impact on purine metabolism – Xin Liu – BMC Microbiology

Coarse graining the human gut microbiome – Christian Diener – Cell Host & Microbe

Review: Intestinal mucus and their glycans: A habitat for thriving microbiota – Ana S Luis – Cell host & Microbe

Review: https://www.cell.com/trends/immunology/fulltext/S1471-4906(23)00111-4 – Isabel Tarrant – Trends in Immunology

Review: A comprehensive perspective on the interaction between gut microbiota and COVID-19 vaccines – Ming Hong – Gut Microbes

Beneficial Microbes and Compounds

Bacillus coagulans MZY531 alleviates intestinal mucosal injury in immunosuppressive mice via modulating intestinal barrier, inflammatory response, and gut microbiota – Zhongwei Zhao – Scientific Reports

Microbiome Engineering Using Probiotic Yeast: Saccharomyces boulardii and the Secreted Human Lysozyme Lead to Changes in the Gut Microbiome and Metabolome of Mice – Jungyeon Kim – Microbiology Spectrum

Animal Microbiome

Neotropical bee microbiomes point to a fragmented social core and strong species-level effects – Jordan G Kueneman – Microbiome

Multi-Omics Reveals the Impact of Exogenous Short-Chain Fatty Acid Infusion on Rumen Homeostasis: Insights into Crosstalk between the Microbiome and the Epithelium in a Goat Model – Yongkang Zhen – Microbiology Spectrum

Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats – Huasong Bai – Microbiology Spectrum

First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome – J Eduardo Martinez-Hernandez – PeerJ

Plant Microbiome

The predictive power of phylogeny on growth rates in soil bacterial communities – Jeth Walkup – ISME Communications

Potential relevance between soybean nitrogen uptake and rhizosphere prokaryotic communities under waterlogging stress – Tengxiang Lian – ISME Communications

Effects of nitrogen reduction combined with bio-organic fertilizer on soil bacterial community diversity of red raspberry orchard – Xu Yuan – PloS One

Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome – Wenke Smets – mBio

Environmental Microbiome

Pathogen resistance in soils associated with bacteriome network reconstruction through reductive soil disinfestation – Weijing Zhu – Applied Microbiology and Biotechnology

Microbiome Research: Resources, Tools and Techniques

Detection of Microorganisms in Body Fluid Samples – Xin Ji – Methods in Molecular Biology 

Guidelines for Microbiome Studies in Renal Physiology – Rikeish R Muralitharan – American Journal of Physiology. Renal Physiology

Quantitative differences in synthetic gut microbial inoculums do not affect the final stabilized in vitro community compositions – Thiyagarajan Gnanasekaran – mSystems

Review: Activity-based protein profiling in microbes and the gut microbiome – Lin Han – Current Opinion in Chemical Biology

July 10, 2023

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Last week’s highlights

Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial – Bertrand Routy – Nature Medicine

Top-down identification of keystone taxa in the microbiome – Guy Amit – Nature Communications

Sources of gut microbiota variation in a large longitudinal Finnish infant cohort – Roosa Jokela – EBioMedicine

Events

11th Microbiome R&D and Business Collaboration Forum and 5th Probiotics & Prebiotics Congress: USA – San Diego, CA – October, 19 – 20, 2023

Human and General Microbiome

Essay: A microbiome exercise – Christoph A Thaiss – Science

Mendelian randomisation analysis reveals the possible causal relationship between infections, microbiota and clinical disease – Shifang Li – Gut

Microbiome variance of the small bowel in Crohn’s disease – Lucas Wauters – Gut

Metagenomics analysis of the neonatal intestinal resistome – Stefano Leo – Frontiers in Pediatrics

Development of the intestinal microbiome in cystic fibrosis in early life – Courtney E Price – mSphere

Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease – Yogesh Singh – Molecular Neurodegeneration

Male-Biased Gut Microbiome and Metabolites Aggravate Colorectal Cancer Development – Ling Wang – Advanced Science

Review: Systematic review: Autism spectrum disorder and the gut microbiota – Jenni Korteniemi – Acta Psychiatrica Scandinavica

Review: Early-life respiratory infections and developmental immunity determine lifelong lung health – Clare M Lloyd – Nature Immunology

Microbiome and Evolution

Ecoevolutionary processes structure milk microbiomes across the mammalian tree of life – Mia M Keady – PNAS

Shared evolutionary path in social microbiomes – Nelson Frazão – Molecular Biology and Evolution

Beneficial Microbes and Compounds

Review: Use of probiotics, prebiotics, and synbiotics in non-alcoholic fatty liver disease: A systematic review and meta-analysis – Lim Rong – Journal of Gastroenterology and Hepatology

Akkermansia muciniphila and Bifidobacterium bifidum Prevent NAFLD by Regulating FXR Expression and Gut Microbiota – Fulin Nian – Journal of Clinical and Translational Hepatology

Limosilactobacillus reuteri inhibits the acid tolerance response in oral bacteria – Gabriella Boisen – Biofilm

Animal Microbiome

Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome – Aravindh Nagarajan – Microbiome

Selection for environmental variance shifted the gut microbiome composition driving animal resilience – Cristina Casto-Rebollo – Microbiome

Plant Microbiome

Metabolic interaction models recapitulate leaf microbiota ecology – Martin Schäfer – Science

Environmental Microbiome

Microeukaryotic predators shape the wastewater microbiome – Nils Heck – Water Research

Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples – Cátia Santos-Pereira – Applied Microbiology and Biotechnology

Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes – Jeanett Daga-Quisbert – FEMS Microbiology Ecology

Built Environment

Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea – E Anders Kiledal – Microbiology Spectrum

Microbiome Research: Resources, Tools and Techniques

A catalog of bacterial reference genomes from cultivated human oral bacteria – Wenxi Li – NPJ Biofilms and Microbiomes

Gene-based microbiome representation enhances host phenotype classification – Thomas Deschênes – mSystems

Integrative meta-omics in Galaxy and beyond – Valerie C Schiml – Environmental Microbiome

Preprint: Compositional analysis of microbiome data using the linear decomposition model (LDM) – Yi-Juan Hu – bioRxiv

Preprint: Processing and Storage Methods Affect Oral and Gut Microbiome Composition – Dorothy K Superdock – bioRxiv

Preprint: A genome catalog of the early-life human skin microbiome – Zeyang Shen – bioRxiv

Review: In vitro models as a tool to study the role of gut microbiota in obesity – Abigail González – Critical Reviews in Food Science and Nutrition

July 3, 2023

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Human and General Microbiome

Bacterial Community Modifies Host Genetics Effect on Early Childhood Caries – F Blostein – Journal of Dental Research

Clostridioides difficile infection in infants: a case report and literature review – Zhirong Li – Gut Pathogens

The microbiota of pregnant women with SARS-CoV-2 and their infants – Heidi K Leftwich – Microbiome

Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles – James T Morton – Nature Neuroscience

Human gut bacteria tailor extracellular vesicle cargo for the breakdown of diet- and host-derived glycans – Mariana G Sartorio – PNAS

Site-specialization of human oral Gemella species – Julian Torres-Morales – Journal of oral Microbiology

Review: Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy – Andrew Maltez Thomas – Nature Reviews. Clinical Oncology

Review: Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics – Teija Ojala – Trends in Genetics

Review: Bacteria from the gut influence the host micronutrient status – Dorgeles Kouakou Dje Kouadio – Critical Reviews in Food Science and Nutrition

Beneficial Microbes and Compounds

Milk kefir alters fecal microbiota impacting gut and brain health in mice – Mariana de Fátima Albuquerque Pereira – Applied Microbiology and Biotechnology

Review: Calorie restriction mimetic drugs could favorably influence gut microbiota leading to lifespan extension – Tomoya Shintani – GeroScience

Are probiotics, prebiotics, and synbiotics beneficial in primary thyroid diseases? A systematic review with meta-analysis – Karolina Zawadzka – Annals of Agricultural and Environmental Medicine

Akkermansia muciniphila and Lactobacillus plantarum ameliorate systemic lupus erythematosus by possibly regulating immune response and remodeling gut microbiota – Mengchen Guo – mSphere

Effect of prebiotics, probiotics, synbiotics on depression: results from a meta-analysis – Qin Zhang – BMC Psychiatry

Animal Microbiome and Animal Model Microbiome

Patterns and determinants of the global herbivorous mycobiome – Casey H Meili – Nature Communications

Resistant starches from dietary pulses modulate the gut metabolome in association with microbiome in a humanized murine model of ageing – Saurabh Kadyan – Scientific Reports

The microbial composition of larval airways from Drosophila melanogaster differ between specimens from laboratory and natural habitats – Hanna Angstmann – Environmental Microbiome

Plant Microbiome

Different Techniques reveal the Difference of Community Structure and Function of Fungi from Root and Rhizosphere of Salvia miltiorrhiza Bunge – C Li – Plant Biology (Stuttgart, Germany)

Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth – Beatriz Lagunas – Microbiome

Core community drives phyllosphere bacterial diversity and function in multiple ecosystems – Ran Xue – The Science of the Total Environment

Environmental Microbiome

A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment – David Madrigal-Trejo – Microbial Ecology

Microbiome Research: Resources, Tools and Techniques

MetaPro: a scalable and reproducible data processing and analysis pipeline for metatranscriptomic investigation of microbial communities – Billy Taj – Microbiome

Supervised learning and model analysis with compositional data – Shimeng Huang – PLoS Computational Biology

Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities – Qi Wang – Bioinformatics

Creation of a milk oligosaccharide database, MilkOligoDB, reveals common structural motifs and extensive diversity across mammals – Sierra D Durham – Scientific Reports

Review: Genetic Engineering of Resident Bacteria in the Gut Microbiome – Jack Arnold – Journal of Bacteriology

Review: Tutorial: integrative computational analysis of bulk RNA-sequencing data to characterize tumor immunity using RIMA – Lin Yang – Nature Protocols

June 26, 2023

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Highlights!

Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes – Matthew M Carter – Cell

A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression – Lauren E Davey – Nature Microbiology

The first international Rome consensus conference on gut microbiota and faecal microbiota transplantation in inflammatory bowel disease – Loris Riccardo Lopetuso – Gut

Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors – Julien Tap – Nature Communications

Human and General Microbiome

Key bacterial taxa determine longitudinal dynamics of aromatic amino acid catabolism in infants’ gut – Martin F Laursen – Gut Microbes

Low diversity microbiota and an increased metabolism of arginine and aromatic amino acids: a hallmark of hepatic encephalopathy in western Mexican patients with alcohol-associated cirrhosis – Tonatiuh Abimael Baltazar-Díaz – Journal of Applied Microbiology

Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy – Gang Fan – Gut Microbes

Species-Specific Analysis of Bacterial Vaginosis-Associated Bacteria – John Osei Sekyere – Microbiology Spectrum

Gut microbiota in nonalcoholic fatty liver disease: a PREDIMED-Plus trial sub analysis – Ana María Gómez-Pérez – Gut Microbes

Associations of Circulating Estrogens and Estrogen Metabolites with Fecal and Oral Microbiome in Postmenopausal Women in the Ghana Breast Health Study – Zeni Wu – Microbiology Spectrum

Meta-analysis of the effects of proton pump inhibitors on the human gut microbiota – Jiayi Zhang – BMC Microbiology

Animal Microbiome

Gut microbiomes of captive primates show phylosymbiosis, respond to dietary sugar reduction, and select for host-specific dietary microbes – Sally L Bornbusch – FEMS Microbiology Ecology

Environmental Microbiome

Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome – Xiaolan Lin – Microbiome

Microbiome Research: Resources, Tools and Techniques

Inferring microbial co-occurrence networks from amplicon data: a systematic evaluation – Dileep Kishore – mSystems

Human microbiome cultivation expands with AI – Marta Selma-Royo – Nature Biotechnology

GutBug: A Tool for Prediction of Human Gut Bacteria Mediated Biotransformation of Biotic and Xenobiotic Molecules Using Machine Learning – Aditya S Malwe – Journal of Molecular Biology

Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome – Céline Elie – Scientific Reports

Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome – Elliot M Lee – mSystems

Assumptions on decision making and environment can yield multiple steady states in microbial community models – Axel Theorell – BMC Bioinformatics

EMBED: Essential MicroBiomE Dynamics, a dimensionality reduction approach for longitudinal microbiome studies – Mayar Shahin – NPJ Systems Biology and Applications

Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy – Oshrit Shtossel – Gut Microbes