Tag Archives: Animal microbiome

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 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

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

December 2, 2022

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Human and General Microbiome

Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis – Shuwen Han – Microbiology Spectrum

The Spatial Features and Temporal Changes in the Gut Microbiota of a Healthy Chinese Population – Wen Zhang – Microbiology Spectrum

The Gut Microbiota is Important for the Maintenance of Blood-Cerebrospinal Fluid Barrier Integrity – Emily G Knox – The European Journal of Neuroscience

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections – James B Thissen – PloS One

A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics – Margot Delavy – mBio

Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species – Shushan Sargsian – Cell Reports

Genome Watch: Zooming into the structure of the microbiome – Gemma G R Murray – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Saussurea involucrata oral liquid regulates gut microbiota and serum metabolism during alleviation of collagen-induced arthritis in rats – Shan Cong – Phytotherapy Research

Prebiotic oligofructose protects against high-fat diet-induced obesity by changing the gut microbiota, intestinal mucus production, glycosylation and secretion – Paola Paone – Gut Microbes

Review: Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health – Car Reen Kok – Annual Review of Food Science and Technology

Animal Microbiome

Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia – Caijun Zhao – Microbiome

Chronic clinical signs of upper respiratory tract disease associate with gut and respiratory microbiomes in a cohort of domestic felines – Holly Kristin Arnold – PloS One

Plant and Soil Microbiome

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions – Zhonghua Wang – Microbiology Spectrum

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites – Keke Li – Environmental Microbiology

Environmental Microbiome

Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt – Ricardo Amils – Environmental Microbiology

Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes – N V Patin – mSystems

Bioinformatics and Microbiome Analysis

The Application of Spearman Partial Correlation for Screening Predictors of Weight Loss in a Multiomics Dataset – Joel Correa da Rosa – Omics

Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals – Benjamin Torres Salazar – Methods in Molecular Biology

September 3, 2022

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Highlights!!!

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome – Shuqin Zeng – Nature Communications → Authors presented and described the main features of the  Early-Life Gut Genomes (ELGG) catalog: a dataset of 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3-years old from different regions.

A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond – Brendon J Medley – The Journal of Biological Chemistry → AMUC_1438, a previously uncharacterized gene from A. muciniphila, encodes an O-glycopeptidase with mucin degrading capacity. This article shows relevant aspects of its enzymatic function. 

Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression – David Jose Delgado-Diaz – Microbiome → metaproteomic analysis on vaginal swab samples and transcriptomics analysis of cervicovaginal epithelial cell cultures showed that lactic acid, a commonly produced metabolite by the vaginal lactobacilli, is capable of enhancing genital epithelial barrier integrity; this microbial feature may help prevent invasion by sexually transmitted pathogens.

Human and General Microbiome

Review: A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections – A Review – Rigoberto Pallares-Mendez – Current Urology Reports

Review: Methanogenic archaea in the human gastrointestinal tract – Christoph Hoegenauer – Nature Reviews. Gastroenterology & Hepatology

Meta-analysis of caries microbiome studies can improve upon disease prediction outcomes – Mark C Butcher – APMIS

Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure – Tatiana V Karpinets – BMC Cancer

Horizontal gene transfer enables programmable gene stability in synthetic microbiota – Teng Wang – Nature Chemical Biology

A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota – David M Versluis – mSystems

Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation – J Casper Swarte – Science Translational Medicine

Beneficial Microbes and Compounds

Intestinal Microbiomics and Metabolomics Insights into the Hepatoprotective Effects of Lactobacillus paracasei CCFM1222 Against the Acute Liver Injury in Mice – Weiling Guo – Probiotics and Antimicrobial Proteins

An Alternative Oat-Containing Ready-To-Use Therapeutic Food Does Not Alter Intestinal Permeability or the 16S rRNA Fecal Microbiome Configuration Among Children With Severe Malnutrition in Sierra Leone: A Randomized Controlled Trial – D Taylor Hendrixson – The Journal of Nutrition

Study on the Effect of Molecular Weight on the Gut Microbiota Fermentation Properties of Blackberry Polysaccharides In Vitro – Qiao-Yun Li – Journal of Agricultural and Food Chemistry

Animal Model Microbiome

Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition – Iman Zarei – Scientific Reports

Gut microbiota mediates the inhibition of lymphopoiesis in dietary-restricted mice by suppressing glycolysis – Si Tao – Gut Microbes

Non-Model Animal Microbiome

Limited microbiome differences in captive and semi-wild primate populations consuming similar diets – Sahana Kuthyar – FEMS Microbiology Ecology

Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome – Kathrin Busch – Nature Communications

Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts – Yujie Meng – Microbiome

Mucin O-glycan-microbiota axis orchestrates gut homeostasis in a diarrheal pig model – Bing Xia – Microbiome

Plant Microbiome

Stressful, isolated, yet diverse: Green roofs have rich microbiomes that are not dominated by oligotrophic taxa – Antoine Hénault – Environmental Microbiology Reports

Nodulation and nitrogen fixation in Medicago truncatula strongly alters the abundance of its root microbiota and subtly affects its structure – Andrzej Tkacz – Environmental Microbiology

Bioinformatic Tools and Microbiome Analysis Techniques

Gut bacterial nutrient preferences quantified in vivo – Xianfeng Zeng – Cell

Metric learning for comparing genomic data with triplet network – Zhi Ma – Briefings in Bioinformatics

STENSL: Microbial Source Tracking with ENvironment SeLection – Ulzee An – mSystems

Review: Emerging microfluidic technologies for microbiome research – Yue Yu – Frontiers in Microbiology

August 13, 2022

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Human and General Microbiome

Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer – Cheng Kong – Gut

A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients – Soon Kyu Lee – Gut Microbes

Longitudinal study of the vaginal microbiome in pregnancies involving preterm labor – Yoshiko Sakabe – Fujita Medical Journal

Oral microbiome and serological analyses on association of Alzheimer’s disease and periodontitis – Kuan-Lun Fu – Oral Diseases

Review: Ultra-processed foods and human health: from epidemiological evidence to mechanistic insights – Bernard Srour – The Lancet. Gastroenterology & Hepatology

Beneficial Microbes, Compounds and Interventions

Dietary Fiber Modulates the Release of Gut Bacterial Products Preventing Cognitive Decline in an Alzheimer’s Mouse Model – Daniel Cuervo-Zanatta – Cellular and Molecular Neurobiology

Functional and safety characterization of beneficial vaginal lactic acid bacteria for the design of vaginal hygiene products – Jessica Alejandra Silva – Journal of Applied Microbiology

Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis – Haiyang Lu – Cell host & Microbe

Review: The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management – Ali Nabavi-Rad – Gut Microbes

Non-Model Animal Microbiome

Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen – Matthew Grisnik – Microbial Ecology

Non-steroidal anti-inflammatory drugs caused an outbreak of inflammation and oxidative stress with changes in the gut microbiota in rainbow trout (Oncorhynchus mykiss) – N Hodkovicova – The Science of the Total Environment

Bees under interactive stressors: The novel insecticides flupyradifurone and sulfoxaflor along with the fungicide azoxystrobin disrupt the gut microbiota of honey bees and increase opportunistic bacterial pathogens – Yahya Al Naggar – The Science of the Total Environment

Plant Microbiome

Host genotype controls ecological change in the leaf fungal microbiome – Acer VanWallendael – PLoS Biology

Suaeda salsa Root-Associated Microorganisms Could Effectively Improve Maize Growth and Resistance under Salt Stress – Yongdong Wang – Microbiology Spectrum

Review: Regulation of immune complex formation and signalling by FERONIA, a busy goddess in plant-microbe interactions – Zhikun Duan – Molecular Plant Pathology

Food Microbiome

A systematic, complexity-reduction approach to dissect the kombucha tea microbiome – Xiaoning Huang – eLife

Bioinformatic Tools and Microbiome Analysis Techniques

ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa – Kevin S Kuchinski – BMC Genomics

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications – Maaly Nassar – GigaScience

MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening – Caitlin M A Simopoulos – mSystems

December 17, 2021

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Human and General Microbiome

Association of microbial dynamics with urinary estrogens and estrogen metabolites in patients with endometriosis – Nhung Le – PloS ONE

Gut Microbiome in Probable Intestinal Tuberculosis and Changes following Anti-Tuberculosis Treatment – Hyuk Yoon – Yonsei Medical Journal

Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis – Tomohiro Hayashi – Frontiers in Cardiovascular Medicine

Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community – Yongyong Kang – Microbiology Spectrum

Stability of healthy subgingival microbiome across space and time – Ryan Tamashiro – Scientific Reports

Successional Stages in Infant Gut Microbiota Maturation – Leen Beller – mBio

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Peng Zhang – The ISME Journal

Bacterial vaginosis and health-associated bacteria modulate the immunometabolic landscape in 3D model of human cervix – Paweł Łaniewski – NPJ Biofilms and Microbiomes

Acute malnutrition and its determinants of preschool children in Bangladesh: gender differentiation – Md Reazul Karim – BMC Pediatrics

SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts – M Nazmul Hoque – Scientific Reports

Gut Mycobiota Dysbiosis in Pulmonary Tuberculosis Patients Undergoing Anti-Tuberculosis Treatment – Demin Cao – Microbiology Spectrum

Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid – Michael E J Buhl – International Journal of Systematic and Evolutionary Microbiology

Human and General Microbiome – Reviews

Review: The Role of Gut Microbiota and Genetic Susceptibility in the Pathogenesis of Pancreatitis – Fumin Xu – Gut and Liver

Review: Transcript host-RNA signatures to discriminate bacterial and viral infections in febrile children – Danilo Buonsenso – Pediatric Research

Review: The role of anaerobic bacteria in the development and prevention of colorectal cancer: A review study – Mehrdad Mohammadi – Anaerobe

Review: Lung microbiome, gut-lung axis and chronic obstructive pulmonary disease – Kuppan Gokulan – Current Opinion in Pulmonary Medicine

Systematic review: Gut microbiota modulation as a possible mediating mechanism for fasting-induced alleviation of metabolic complications: a systematic review – Pooneh Angoorani – Nutrition & Metabolism

Systematic review: The relation between the gut microbiome and osteoarthritis: A systematic review of literature – Emanuele Chisari – PloS ONE

Outlook: Ovarian cancer and the microbiome: a complex relationship – Julianna Photopoulos – Nature

Beneficial Microbes and Compounds

Oligofructose-enriched inulin intake, gut microbiome characteristics and the V̇O2peak response to high-intensity interval training in healthy inactive adults – Camilla J Williams – The Journal of Nutrition

Lactiplantibacillus plantarum DMDL 9010 alleviates dextran sodium sulfate (DSS)-induced colitis and behavioral disorders by facilitating microbiota-gut-brain axis balance – Yan-Yan Huang – Food & Function

Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial – Dorit Vedel Ankersen – Journal of Medical Internet Research

Effect of dietary selenium intake on gut microbiota in older population in Enshi region – Zi-Xiong Zhang – Genes and Environment

Animal Microbiome

The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface – Siobhon L Egan – Microbial Genomics

The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years – Zhiyuan Lu – PeerJ

You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches – Melissa R Ingala – Animal Microbiome

Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level – Rupert Mazzucco – Proceedings of the Royal Society B. Biological Sciences

Plant and Fungi Microbiome

The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host – Maria J Soto-Giron – Scientific Reports

Autotoxin Rg(1) Induces Degradation of Root Cell Walls and Aggravates Root Rot by Modifying the Rhizospheric Microbiome – Yanguo Xu – Microbiology Spectrum

Multitrophic Interactions Between Arbuscular Mycorrhizal Fungi, Foliar Endophytic Fungi and Aphids – Nadia Ab Razak – Microbial Ecology

Other Microbes

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia – Anna G Burrichter – BMC Microbiology

Methods

Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes – Angie Mordant – Microbiology Spectrum

Sample Processing for Metaproteomic Analysis of Human Gut Microbiota – Carmen García-Durán – Methods in Molecular Biology Enhancing Microbiome Research through Genome-Scale Metabolic Modeling – Nana Y D Ankrah – mSystems

Mycobiome (Early 2021 Semi-Annual Fungal Microbiome Picks)

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It’s been a while, but its time to highlight some recent mycobiome articles!

Human mycobiome

Intestinal mycobiota in health and diseases: from a disrupted equilibrium to clinical opportunities – Wu et al. – Microbiome

Gut mycobiota in immunity and inflammatory disease – Li et al. – Immunity

Response to fungal dysbiosis by gut-resident CX3CR1(+) mononuclear phagocytes aggravates allergic airway disease.- Li et al. – Cell Host Microbe. 

Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. – Bacher et al. – Cell. 

Prevalence and diversity of filamentous fungi in the airways of cystic fibrosis patients – a Dutch, multicentre study. – Engle et al. – J Cyst Fibros.

Early gut mycobiota and mother-offspring transfer. – Schei – Microbiome

Fungi form interkingdom microbial communities in the primordial human gut that develop with gestational age. – Willis et al – FASEB J.

Investigating colonization of the healthy adult gastrointestinal tract by fungi. – Auchtung et al. – mSphere.

CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi. – Leonardi et al. – Science.

Commensal Candida albicans positively calibrates systemic Th17 immunological responses. – Shao et al – Cell Host Microbe. 

Macrophages maintain epithelium integrity by limiting fungal product absorption. – Chikina et al. – Cell.

Fungal symbionts produce prostaglandin E2 to promote their intestinal colonization. – Tan et al. – Front Cell Infect Microbiol.

The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL. – Aykut et al – Nature. 

Fungal microbiota dysbiosis in IBD. – Sokol et al – Gut.

Malassezia is associated with Crohn’s disease and exacerbates colitis in mouse models. – Limon et al – Cell Host Microbe.

Macrophage interactions with fungi and bacteria in inflammatory bowel disease. – Leonardi et al. – Curr Opin Gastroenterol.

Fungi participate in the dysbiosis of gut microbiota in patients with primary sclerosing cholangitis. – Lemoinne et al – Gut

Intestinal fungi contribute to development of alcoholic liver disease. – Yang et al – J Clin Invest.

Animal mycobiome

The gut mycobiome of healthy mice is shaped by the environment and correlates with metabolic outcomes in response to diet – Mims and Al Abdallah et al. – Communications Biology

Profound mycobiome differences between segregated mouse colonies do not influence Th17 responses to a newly introduced gut fungal commensal. – Doron et al. – Fungal Genet Biol.

Season, age, and sex affect the fecal mycobiota of free-ranging Tibetan macaques (Macaca thibetana). – Sun et al – Am J Primatol.

Altered immunity of laboratory mice in the natural environment is associated with fungal colonization. – Yeung et al – Cell Host Microbe. 

Mycobiome techniques

The fungal frontier: a comparative analysis of methods used in the study of the human gut mycobiome. – Huseyin et al. – Front Microbiol. 

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Karen et al. – Microbiome

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing – Lind et al – Microbiome

Tiara: Deep learning-based classification system for eukaryotic sequences –  Karlicki et al – bioRxiv.org

~ Kent Willis, MD