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

June 19, 2023

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Highlights!

A data-driven approach for predicting the impact of drugs on the human microbiome – Yadid M Algavi – Nature Communications

CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection – Lingdi Zhang – Microbiome

Human and General Microbiome

Gut and oral microbiome modulate molecular and clinical markers of schizophrenia-related symptoms: A transdiagnostic, multilevel pilot study – Jakleen J Lee – Psychiatry Research

Effects of vaginal microbiota transfer on the neurodevelopment and microbiome of cesarean-born infants: A blinded randomized controlled trial – Lepeng Zhou – Cell Host & Microbe

Metaproteomics Characterizes the Human Gingival Crevicular Fluid Microbiome Function in Periodontitis – Xiaolian Xiao – Journal of Proteome Research

Generation of dysbiotic microbiota in cutaneous leishmaniasis and enhancement of skin inflammation – Shumaila Naz – Microbial Pathogenesis

Oral microbiota may affect osteoradionecrosis following radiotherapy for head and neck cancer – Zhengrui Li – Journal of Translational Medicine

Oral microbial communities in 5-year-old children with versus without dental caries – Zhengyan Yang – BMC Oral Health

Analysis of gut microbiota in patients with Williams-Beuren Syndrome reveals dysbiosis linked to clinical manifestations – Federica Del Chierico – Scientific Reports

Review: Aspects of oral streptococcal metabolic diversity: Imagining the landscape beneath the fog – Peter Zuber – Molecular Microbiology

Review: Challenges and strategies for preventing intestinal damage associated to mercury dietary exposure – Pilar Rodríguez-Viso – Toxicology

Animal Microbiome

Phylogenetic comparative approach reveals evolutionary conservatism, ancestral composition, and integration of vertebrate gut microbiota – Benoît Perez-Lamarque – Molecular Biology and Evolution

Social transmission of bacterial symbionts homogenizes the microbiome within and across generations of group-living spiders – Clémence Rose – ISME Communications

Rookery through rehabilitation: Microbial community assembly in newborn harbour seals after maternal separation – Alexandra D Switzer – Environmental Microbiology

Microbiome Research Tools and Techniques

The TaxUMAP atlas: Efficient display of large clinical microbiome data reveals ecological competition in protection against bacteremia – Jonas Schluter – Cell Host & Microbe

MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets – Matthys G Potgieter – PLoS Computational Biology

Methods for Analyzing the Gut Microbiota in Diabetic Retinopathy – Yinhua Huang – Methods in Molecular Biology

Using nanopore sequencing to identify fungi from clinical samples with high phylogenetic resolution – Atsufumi Ohta – Scientific Reports

June 16, 2023

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Thank you for answering my question above.

Today’s digest features indigenous chicken in Ethiopia, drug effects on gut microbiome, beach water microbial risk assessment, and more. See you at #MVIF next week!

Microbial ecology

Guild and Niche Determination Enable Targeted Alteration of the Microbiome – Oriane Moyne – bioRxiv

Genital microbiome

Interaction of genital microbiota in infertile couples – David Baud – bioRxiv

Gut microbiome

Emergence of community behaviors in the gut microbiota upon drug treatment – Sarela Garcia-Santamarina – bioRxiv

Skin microbiome

Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons – Marcus H. Y. Leung – Microbiome

Animal microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning – bioRxiv

Animal experiments

Effects of fenbendazole on fecal microbiome in BPH/5 mice, a model of hypertension and obesity, a brief report – Kalie F. Beckers – Plos One

Gut microbiota and cognitive development in infant mice: Quantity and source of potable water – Chong-Su Kim and Dong-Mi Shin – Plos One

Plant microbiome

Globally consistent response of plant microbiome diversity across hosts and continents to soil nutrients and herbivores – Eric W. Seabloom – Nature Communications

Methodology

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

QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification – Yu Yang – Water Research

Bioinformatics

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics – Rémi Gschwind – Nucleic Acids Research

June 13, 2023

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Today’s microbiome digest includes quite a few host-microbe studies, including one published by my colleague and highlighted below which focuses on the hindgut microbiome of the American cockroach.

Human gut microbiome

Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics – Hromada – and Venturelli – PLOS Biology

Construction of model animals to explore intestinal microbiome for detection of breast cancer – Ji et al. – PLOS One

Animal experiments

**Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics – Dukes et al. – Frontiers in Microbiology

Evaluation of microbial and vancomycin treatments in ulcerative colitis in murine models – Hasan and Yang – PLOS One

Animal microbiome

Geography, not lifestyle, explains the population structure of free-living and host-associated deep-sea hydrothermal vent snail symbionts – Hauer et al. – Microbiome

Insect phylogeny structures the bacterial communities in the microbiome of psyllids (Hemiptera: Psylloidea) in Aotearoa New Zealand – Martoni et al. – PLOS One

Water and extremophile microbiome

In the right place, at the right time: the integration of bacteria into the Plankton Ecology Group model – Park et al. – Microbiome

Phages and viruses

Beyond pathogenesis: Detecting the full spectrum of ecological interactions in the virosphere – Jurburg et al. – PLOS Biology

Phage therapy and the public: Increasing awareness essential to widespread use – McCammon et al. – PLOS One

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

June 5, 2023

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Human and General Microbiome

Altered gut microbiota as potential biomarker biomarkers for autism spectrum disorder in early childhood – Yingxin Zhao – Neuroscience

The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination – M Laura Rolon – Microbiome

Succession and determinants of the early life nasopharyngeal microbiota in a South African birth cohort – Shantelle Claassen-Weitz – Microbiome

Secreted Akkermansia muciniphila threonyl-tRNA synthetase functions to monitor and modulate immune homeostasis – Su-Man Kim – Cell Host & Microbe

Gut Microbiome Composition is associated with future onset of Crohn’s Disease in Healthy First-Degree Relatives – Juan Antonio Raygoza Garay – Gastroenterology

Metagenome Investigation of Ocular Microbiota of Cataract Patients With and Without Type 2 Diabetes – Zheng Shao – Translational Vision Science & Technology

Longitudinal Gut Microbiota Dysbiosis Underlies Olanzapine-Induced Weight Gain – Li Qian – Microbiology Spectrum

Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut – Ida Ormaasen – BMC Genomics

Review: The Microbiome in Advanced Melanoma: Where Are We Now? – Dylan D Fortman – Current Oncology Reports

Review: Human gut microbiome: A primer for the clinician – Saurabh Kedia – JGH Open

Review: Role of gut microbiota and bacterial metabolites in mucins of colorectal cancer – Ming Gu – Frontiers in Cellular and Infection Microbiology

Beneficial Microbes and Compounds

Bacteriophage targeting microbiota alleviates non-alcoholic fatty liver disease induced by high alcohol-producing Klebsiella pneumoniae – Lin Gan – Nature Communications

Clostridium butyricum improves cognitive dysfunction in ICV-STZ-induced Alzheimer’s disease mice via suppressing TLR4 signaling pathway through the gut-brain axis – Yunfang Su – PloS One

Review: Regulation of gut microbiota by vitamin C, vitamin E and β-carotene – Xin-Yu Li – Food Research International

Animal Microbiome

Diversity of the Pacific Ocean coral reef microbiome – Pierre E Galand – Nature Communications

Effects of Aeromonas hydrophila infection on the intestinal microbiota, transcriptome, and metabolomic of common carp (Cyprinus carpio) – Lan Zhang – Fish & Shellfish Immunology

Genital tract microbiome dynamics are associated with time of Chlamydia infection in mice – Lihong Zhao – Scientific Reports

Environmental Microbiome

The core mangrove microbiome reveals shared taxa potentially involved in nutrient cycling and promoting host survival – Benjamin J Wainwright – Environmental Microbiome

Microbiome Research Tools and Techniques

Formation and Analysis of Mono-species and Polymicrobial Oral Biofilms in Flow-Cell Models – Jessica Neilands – Methods in Molecular Biology

MAIRA: Protein-based Analysis of MinION Reads on a Laptop – Caner Bağcı – Methods in Molecular Biology 

Recovery and Analysis of Long-Read Metagenome-Assembled Genomes – Krithika Arumugam – Methods in Molecular Biology 

Evaluation of 96-well high-throughput DNA extraction methods for 16S rRNA gene metabarcoding – Marie-Pierre Chapuis – Molecular Ecology Resources

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

May 22, 2023

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Have a nice day. Today we have a long list!

Highlights!

Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease – Weijie Liang – Cell Host & Microbe

An integrated tumor, immune and microbiome atlas of colon cancer – Jessica Roelands – Nature Medicine

General and Human Microbiome 

Skin microbiome alterations in upper extremity secondary lymphedema – Adana-Christine Campbell – PloS One

Isolation and identification of hyaluronan-degrading bacteria from Japanese fecal microbiota – Hazuki Akazawa – PloS One

Bacterial and metabolic phenotypes associated with inadequate response to ursodeoxycholic acid treatment in primary biliary cholangitis – Laura Martinez-Gili – Gut Microbes

Gut microbiota and its relation to inflammation in patients with bipolar depression: a cross-sectional study – Tingting Huang – Annals of General Psychiatry

Alterations in the Gut Microbiome and Metabolisms in Pregnancies with Fetal Growth Restriction – Zixin Tao – Microbiology Spectrum

16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients – Maartje Kristensen – Microbiology Spectrum

Single-Molecule Approach to 16S rRNA for Vaginal Microbiome Signatures in Response to Metronidazole Treatment – Hanyu Qin – Microbiology Spectrum

The presence of intratumoral Porphyromonas gingivalis correlates with a previously defined pancreatic adenocarcinoma, immune cell expression phenotype and with tumor resident, adaptive immune receptor features – Jacob C Kinskey – Carcinogenesis

Commentary: Microbiome is the key to preventing anastomotic leak in colorectal surgery – James M Kinross – Gut

Commentary: The aerobiome-health axis: a paradigm shift in bioaerosol thinking – Jake M Robinson – Trends in Microbiology

Review: Impact of the host microbiota on fungal infections: new possibilities for intervention? – Eve W L Chow – Advanced Drug Delivery Reviews

Review: Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition – Helen J Jones – Annual Review of Nutrition

Review: A narrative review from gut to lungs: non-small cell lung cancer and the gastrointestinal microbiome – Hely Shah – Translational Lung Cancer Research

Review: The interplay between oral microbiota, gut microbiota and systematic diseases – Xiujun Tan – Journal of Oral Microbiology

Animal Model Microbiome

Exposing new taxonomic variation with inflammation – a murine model-specific genome database for gut microbiome researchers – Ikaia Leleiwi – Microbiome

Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic – Huan Li – BMC Microbiology

Alterations of the gut microbiome and metabolic profile in CVB3-induced mice acute viral myocarditis – Qing Kong – BMC Microbiology

Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice – Yuanyuan He – Microbial Pathogenesis

Non-model Animal Microbiome

An entomopathogenic fungus exploits its host humoral antibacterial immunity to minimize bacterial competition in the hemolymph – Jia-Lin Wang – Microbiome

Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees – Haoyu Lang – Nature Communications

New insights into microbial and metabolite signatures of coral bleaching – Hao Sun – The Science of the Total Environment

Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota – Thomas M Winders – Scientific Reports

Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation – Farhad M Panah – BMC Microbiology

The microbiome and gene expression of honey bee workers are affected by a diet containing pollen substitutes – J Elijah Powell – PloS One

Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens – Xiang-Yu Wang – BMC Microbiology

Built Environment

Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment – Akinobu Toyoda – Scientific Reports

Plant Microbiome

Review: Engineering the Crop Microbiota Through Host Genetics – Carmen Escudero-Martinez – Annual Review of Phytopathology

Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.) – Angélica Jara-Servin – PloS One

Microbiome Analysis

News: Long-read sequencing for the metagenomic analysis of microbiomes – Tristan Free – BioTechniques

May 16, 2023

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Happy Tuesday! Today’s microbiome digest is microbial ecology heavy, with articles focused on the gut microbiome, Antarctic endoliths’, water microbiomes, and more.

Human gut microbiome

Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer – Alexander et al. – Microbiome

Gut microbiome transitions across generations in different ethnicities in an urban setting—the HELIUS study – van der Vossen et al. – Microbiome

Water and extremophile microbiome

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability – Ettinger et al. – Microbiome

Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes – Vigneron et al. – Microbiome

preprint: Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity – Yanuka-Golub et al. – bioRxiv

Built environment

preprint: Microbial Diversity on Ancestral Halls with Different Visitor Flow Rates Using Amplicon Sequencing – Liu et al. – bioRxiv

Techniques

Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies – Orellana et al. – Microbiome

May 15, 2023

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Human Microbiome

Assessing the relationship between gut microbiota and irritable bowel syndrome: a two-sample Mendelian randomization analysis – Bin Liu – BMC Gastroenterology

The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis – A C Anderson – Annals of Clinical Microbiology and Antimicrobials

New evidence for the role of gut microbiota on atrial fibrillation development – Christopher Papandreou – EBioMedicine

Influence of grape consumption on the human microbiome – Asim Dave – Scientific Reports

Microbiota transplant to control inflammation in a patient with NLRC4 gain-of-function-induced disease – Claudia Bracaglia – The Journal of Allergy and Clinical Immunology

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Animal Microbiome

Integrated microbiome-metabolome-genome axis data of Laiwu and Lulai pigs – Xueshuang Lai – Scientific data

Positive associations matter: Microbial relationships drive tick microbiome composition – Nicholas M Fountain-Jones – Molecular Ecology

In Vitro Ileal Fermentation is Affected More by the Fiber Source Fermented than the Ileal Microbial Composition in Growing Pigs – Anna Me Hoogeveen – Current Developments in Nutrition

Oroxin B improves metabolic-associated fatty liver disease by alleviating gut microbiota dysbiosis in a high-fat diet-induced rat model – Yuhong Huang – European Journal of Pharmacology

Plant Microbiome

Drought stress mediated differences in phyllosphere microbiome and associated pathogen resistance between male and female poplars – Tiantian Lin – The Plant Journal 

Environmental Microbiome

Looking into sewage: how far can metagenomics help to detect human enteric viruses? – Julien Schaeffer – Frontiers in Microbiology

Metagenomic insights into the potential risks of representative bio/non-degradable plastic and non-plastic debris in the upper and lower reaches of Haihe Estuary, China – Xinhai Zhao – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

A Bayesian joint model for compositional mediation effect selection in microbiome data – Jingyan Fu – Statistics in Medicine