Tag Archives: Plant 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 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

June 12, 2023

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Highlights!

A microbiota-modulated checkpoint directs immunosuppressive intestinal T cells into cancers – Marine Fidelle – Science 

Using gut microbiota as a diagnostic tool for colorectal cancer: machine learning techniques reveal promising results – Fang Lu – Journal of Medical Microbiology

Outer membrane utilisomes mediate glycan uptake in gut Bacteroidetes – Joshua B R White – Nature

Human and General Microbiome

Skin maturation from birth to 10 years of age: Structure, function, composition and microbiome – Georgios N Stamatas – Experimental Dermatology

Ecological principles of fecal microbiota transplantation – Francisco Dini-Andreote – Trends in Microbiology

Human Genetics Influences Microbiome Composition Involved in Asthma Exacerbations despite Inhaled Corticosteroid Treatment – Javier Perez-Garcia – The Journal of Allergy and Clinical Immunology

Gut bacterial metabolism contributes to host global purine homeostasis – Kazuyuki Kasahara – Cell Host & Microbe

The relative abundance of fecal bacterial species belonging to the Firmicutes and Bacteroidetes phyla is related to plasma levels of bile acids in young adults – Francisco J Osuna-Prieto – Metabolomics

The effect of vitamin D supplementation on the gut microbiome in older Australians – Results from analyses of the D-Health Trial – Hai Pham – Gut Microbes

Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage – Howell Leung – NPJ Biofilms and Microbiomes

Gut microbiota dysbiosis promotes the development of epithelial ovarian cancer via regulating Hedgehog signaling pathway – Xinyue Hu – Gut Microbes

Preprint: Microbes with higher metabolic independence are enriched in human gut microbiomes under stress – Iva Veseli – bioRxiv

Review: Evolutionary implications of host genetic control for engineering beneficial microbiomes – Lucas P Henry – Current Opinion in Systems Biology

Review: It’s all relative: analyzing microbiome compositions, its significance, pathogenesis and microbiota derived biofilms: Challenges and opportunities for disease intervention – Sahar Zaidi – Archives of Microbiology

Animal Microbiome

Gut microbiome helps honeybee (Apis mellifera) resist the stress of toxic nectar plant (Bidens pilosa) exposure: Evidence for survival and immunity – Qihe Tang – Environmental Microbiology

Regulation of host gene expression by gastrointestinal tract microbiota in Chinook Salmon (Oncorhynchus tshawytscha) – Javad Sadeghi – Molecular Ecology

The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts – Jinlong Li – Environmental Microbiome

Association analysis of gut microbiota-metabolites-neuroendocrine changes in male rats acute exposure to simulated altitude of 5500 m – Jianan Wang – Scientific Reports

Microbiomes of Blood-Feeding Triatomines in the Context of Their Predatory Relatives and the Environment – Hassan Tarabai – Microbiology Spectrum

Beneficial Microbes and Compounds

Probiotic interventions promote metabolic health in high fat-fed hamsters in association with gut microbiota and endocannabinoidome alterations – S Lacroix – Beneficial Microbes

Strains of Faecalibacterium prausnitzii and its extracts reduce blood glucose levels, percent HbA1c, and improve glucose tolerance without causing hypoglycemic side effects in diabetic and prediabetic mice – John Kallassy – BMJ Open Diabetes Research & Care

Effects of a low FODMAP diet on gut microbiota in individuals with treated celiac disease having persistent gastrointestinal symptoms – a randomized controlled trial – Anne Mari Herfindal – The British Journal of Nutrition

Designed α-sheet peptides disrupt uropathogenic E. coli biofilms rendering bacteria susceptible to antibiotics and immune cells – Alissa Bleem – Scientific Reports

Review: ‘Multi-omics’ data integration: applications in probiotics studies – Iliya Dauda Kwoji – NPJ Science of Food

Review: Micro-/bio-/nano-/syn-encapsulations and co-treatments of bioactive microbial feed supplementation in augmenting finfish health and aquaculture nutrition: a review – P Puri – Beneficial Microbes

Plant Microbiome

Taxonomic analysis reveals host preference of rare fungi in endophytes of Vitis vinifera from the Czech Republic – Miroslav Kolařík – Folia Microbiologica

Environmental Microbiome

Metaproteomics reveals functional partitioning and vegetational variation among permafrost-affected Arctic soil bacterial communities – Samuel E Miller – mSystems

Built Environment

A new approach of microbiome monitoring in the built environment: feasibility analysis of condensation capture – Jarrad T Hampton-Marcell – Microbiome

Microbiome Research Tools and Techniques

Preprint: A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset – Cankun Wang – bioRxiv

Preprint: DeepBiomarker2: Prediction of alcohol and substance use disorder risk in post-traumatic stress disorder patients using electronic medical records and multiple social determinants of health – Oshin Miranda – Research Square

Latent Dirichlet Allocation modeling of environmental microbiomes – Anastasiia Kim – PLoS Computational Biology

When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities – Sandra Dedrick – mSystems

May 29, 2023

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Highlights!

Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains – Raymond Kiu – Nature Microbiology

Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach – Conor Feehily – Nature Communications

Human and General Microbiome

Expanding the repertoire of counterselection markers for markerless gene deletion in the human gut bacterium Phocaeicola vulgatus – André Neff – Anaerobe

Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection – Zheng Wang – Microbiome

Symbiotic microbiome Staphylococcus epidermidis restricts IL-33 production in allergic nasal epithelium via limiting the cellular necroptosis – Yung Jin Jeon – BMC Microbiology

Gut microbiome associated with low anterior resection syndrome after rectal cancer surgery – Min Jung Kim – Scientific Reports

Metabolomics Reveals Gut Microbiota Contribute to PPARα Deficiency-Induced Alcoholic Liver Injury – Ting Zhang – Journal of Proteome Research

Following your gut: the emerging role of the gut microbiota in predicting and treating immune-related adverse events – Antoine Desilets – Current Opinion in Oncology

Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma – Spyridon Megremis – Scientific Reports

The causal links between gut microbiota and COVID-19: A Mendelian randomization study – Jukun Song – Journal of Medical Virology

The Sexome – A proof of concept study into microbial transfer between heterosexual couples after sexual intercourse – Ruby Dixon – Forensic Science International

A systematic review of the protein composition of whole saliva in subjects with healthy periodontium compared with chronic periodontitis – Ana G Sánchez-Medrano – PloS ONE

Microbiome, Food and Diet

Metagenomic analysis and antibacterial activity of kefir microorganisms – Brianda D González-Orozco – Journal of Food Science

Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults – Leila M Shinn – The Journal of Nutrition

More Microbes

Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota – Afaf Hamame – Scientific Reports

Animal Microbiome

Gut microbiome signatures of extreme environment adaption in Tibetan pig – Fangfang Zhao – NPJ Biofilms and Microbiomes

Holobiont Evolution: Population Theory for the Hologenome – Joan Roughgarden – The American Naturalist

Plant Microbiome

Integration of Phenotypes in Microbiome Networks for Designing Synthetic Communities: a Study of Mycobiomes in the Grafted Tomato System – Ravin Poudel – Applied and Environmental Microbiology

Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum – Jilu Che – Microbiology Spectrum

Bioinformatics, Microbiome Analysis and Techniques

MDM-Pred: a freely available web application for predicting the metabolism of drug-like compounds by the gut microbiota – A S Kolodnitsky – SAR and QSAR in Environmental Research

HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph – Yuanyuan Ma – Bioinformatics 

Bayesian compositional regression with microbiome features via variational inference – Darren A V Scott – BMC Bioinformatics

The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae – Katherine M Elston – ISME Communications

Review: Unravelling animal-microbiota evolution on a chip – Ostaizka Aizpurua – Trends in Microbiology

March 13, 2023

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Human and General Microbiome

Dysbiosis of a microbiota-immune metasystem in critical illness is associated with nosocomial infections – Jared Schlechte – Nature Medicine

Altered infective competence of the human gut microbiome in COVID-19 – Laura de Nies – Microbiome

Impact of high altitude on composition and functional profiling of oral microbiome in Indian male population – Manisha Kumari – Scientific Reports

Incidence of Breast Cancer and Enterococcus Infection: A Retrospective Analysis – Matthew Cardeiro – World Journal of Oncology

Multi-omics studies in interpreting the evolving standard model for immune functions – Dipyaman Ganguly – Briefings in Functional Genomics

Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans – Jinuk Jeong – Journal of oral Microbiology

A transcriptomic insight into the human sperm microbiome through next-generation sequencing – Celia Corral-Vazquez – Systems Biology in Reproductive Medicine

Beneficial Microbes and Compounds

Metformin alleviates liver fibrosis in mice by enriching Lactobacillus sp. MF-1 in the gut microbiota – Tao Yang – Biochimica et Biophysica Acta

Animal Microbiome

Microbiota alters the metabolome in an age- and sex- dependent manner in mice – Kirsty Brown – Nature Communications

IL-22 alters gut microbiota composition and function to increase aryl hydrocarbon receptor activity in mice and humans – Jordan S Mar – Microbiome

Decreased Paneth cell α-defensins promote fibrosis in a choline-deficient L-amino acid-defined high-fat diet-induced mouse model of nonalcoholic steatohepatitis via disrupting intestinal microbiota – Shunta Nakamura – Scientific Reports

Plant Microbiome

Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants – Ye Li – Microbiome

Non-volatile metabolites mediating plant interactions with insect herbivores – Mei Luo – The Plant Journal

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress – Bo Wang – Frontiers in Microbiology

Review: Emerging Pathways for Engineering the Rhizosphere Microbiome for Optimal Plant Health – Shengdie Yang – Journal of Agricultural and food Chemistry

Microbiome Analysis: Tools and Techniques

A bayesian zero-inflated dirichlet-multinomial regression model for multivariate compositional count data – Matthew D Koslovsky – Biometrics

Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples – Ruben López-Aladid – Scientific Reports