Category Archives: Human gut

October 16, 2023

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Human and General Microbiome

A Sedentary Lifestyle Changes the Composition and Predicted Functions of the Gut Bacterial and Fungal Microbiota of Subjects from the Same Company – Longwei Xu – Current Microbiology

Animal Microbiome

Effect of urbanization and parasitism on the gut microbiota of Darwin’s finch nestlings – Gabrielle Solomon – Molecular Ecology

Metabarcoding using nanopore long-read sequencing for the unbiased characterization of apicomplexan haemoparasites – Lucas G Huggins – Molecular Ecology Resources

Bacterial networks in Atlantic salmon with Piscirickettsiosis – Yoandy Coca – Scientific Reports

Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions that respond to ovulation regulation in the mouse endometrium – Sisi Pu – BMC Genomics

Beneficial Microbes, Foods and Compounds

Probiotic-fermented tomato alleviates high-fat diet-induced obesity in mice: Insights from microbiome and metabolomics – Benliang Wei – Food Chemistry

Lactobacillus rhamnosus Modulates Lung Inflammation and Mitigates Gut Dysbiosis in a Murine Model of Asthma-COPD Overlap Syndrome – Jéssica Aparecida Vasconcelos – Probiotics and Antimicrobial Proteins

Fermented Goat’s Milk Contributes to the Recovery of Iron Deficiency Anemia via Modulation of the Gut Microbiome – Ana Soriano-Lerma – Journal of Agricultural and Food Chemistry

Environmental Microbiome

Coexistence of specialist and generalist species within mixed plastic derivative-utilizing microbial communities – Laura Schaerer – Microbiome

Review: A critical review of the recent trends in source tracing of microplastics in the environment – Kiruthika K M – Environmental Research

Keystone taxa of phoD-harboring bacteria mediate alkaline phosphatase activity during biochar remediation of Cd-contaminated soil – Qiang Wang – The Science of the Total Environment

Plant Microbiome

Maintaining beneficial alga-associated bacterial communities under heat stress: Insights from controlled co-culture experiments using antibiotic-resistant bacterial strains – Elham Karimi – FEMS Microbiology Ecology

Review: Deep discovery informs difficult deployment in plant microbiome science – Dor Russ – Cell

Highlights: Plant cell wall component induced bacterial development – Ákos T Kovács – Trends in Microbiology

Microbiome Analysis: Tools, Techniques and Resources

MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile – Pieter-Jan Van Camp – Microbiome

Subgroup Identification Using Virtual Twins for Human Microbiome Studies – Hyunwook Koh – IEEE/ACM Transactions on Computational Biology and Bioinformatics

October 13, 2023

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Today’s digest features the Chinese Gut Microbiome Resource, plate readers in the anaerobic chamber, seasonal stability of sponge microbiomes, and more.

Also, you can support the outreachy bugsigdb project by sharing your study to be curated (more info here https://www.outreachy.org/apply/project-selection/#bioconductor or contact me). See you at #MVIF next week!

General

From hype to hope: considerations in conducting robust microbiome science – Amelia J McGuinness – Brain, Behavior, and Immunity

Global

Unraveling the functional dark matter through global metagenomics – Georgios A. Pavlopoulos – Nature

Human gut microbiome

Integration of 168,000 samples reveals global patterns of the human gut microbiome – Richard J. Abdill – bioRxiv

Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets – Anna C. Salvador – Microbiome

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects – Pan Huang – bioRxiv

Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index – Sofía Tesolato – PlosOne

Tracking gut microbiome and bloodstream infection in critically ill adults – Christopher H. Gu – PlosOne

Human milk

Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy – Martin F. Laursen & Henrik M. Roager – The ISME Journal

Antibiotic Resistome

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments – Jessica Subirats – Applied and Environmental Microbiology

Plant microbiome

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods – Sabin Khana – bioRxiv

Animal microbiome

Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa – Claire E. Lamb & Joy E. M. Watts – Environmental Microbiome

An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management – Rita A. H. Hoving-Bolink – PlosOne

Technique

Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers – Oona L.O. Snoeyenbos-West – bioRxiv

Bioinformatics

On the relationship between protist metabarcoding and protist metagenome-assembled genomes – Daryna Zavadska – bioRxiv

Track, Analyze, Visualize: Unravel Your Microbiome’s Temporal Tale with MicrobiomeStat – Chen Yang & MicrobiomeStat team

October 11, 2023

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General microbiome

Major data analysis errors invalidate cancer microbiome findings – Gihawi et al. – mBio

Relative abundance data can misrepresent heritability of the microbiome – Bruihning et al. – Microbiome

Human gut microbiome

Discrimination exposure impacts unhealthy processing of food cues: crosstalk between the brain and gut – Zhang et al. – Nature Mental Health

[REVIEW]The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective – Leigh et al. – The Journal of Physiology

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

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]The role of family and environment in determining the skin microbiome of captive aquatic frogs, Xenopus laevis – Chapman et al. – bioRxiv

Vertical transmission of gut bacteria in commercial chickens is limited – Shterzer et al. – Animal Microbiome

Bioinformatics/Techiques

[PREPRINT]MetaQuad: Shared Informative Variants Discovery in Metagenomic Samples – Xu et al. – bioRxiv

[PREPRINT]Insertion sequence driven evolution of the microbiota revealed by a novel metagenomics pipeline – Kirsch, Hryckowian & Duerkop

[PREPRINT]A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics – Eisenhofer et al. – bioRxiv

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Zhang et al. – Applied and Environmental Microbiology

[PERSPECTIVE]Challenges and opportunities in sharing microbiome data and analyses – Huttenhower, Finn & McHardy – Nature Microbiology

October 9, 2023

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Human and General Microbiome

Mitochondrial dysfunction promotes microbial composition that negatively impacts on ulcerative colitis development and progression – Ainize Peña-Cearra – NPJ Biofilms and Microbiomes

The recovery of the microbial community after plaque removal depends on periodontal health status – Xiaoqing Li – NPJ Biofilms and Microbiomes

Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 +  – Massimo Bellato – Scientific Reports

COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition – Shilin Zhao – NPJ Vaccines

Spatial diversity of the skin bacteriome – Marcos Pérez-Losada – Frontiers in Microbiology

Microbiota-gut-brain axis drives overeating disorders – Sijia Fan – Cell Metabolism

Review: Human-gut bacterial protein-protein interactions: understudied but impactful to human health – Diana Balint – Trends in Microbiology

Review: Progress of linking gut microbiota and musculoskeletal health: casualty, mechanisms, and translational values – Yu Wang – Gut Microbes

Review: The microbial landscape of colorectal cancer – Maxwell T White – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Probiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties – Juan Carlos Ariute – Probiotics and Antimicrobial Proteins

Faecalibacterium prausnitzii, Bacteroides faecis and Roseburia intestinalis attenuate clinical symptoms of experimental colitis by regulating Treg/Th17 cell balance and intestinal barrier integrity – Nooshin Mohebali – Biomedicine & Pharmacotherapy 

Simulated gastrointestinal digestion of beer using the simgi® model. Investigation of colonic phenolic metabolism and impact on human gut microbiota – Magaly Rodriquez-Saavedra – Food Research International

Animal Microbiome (Model and Non-model organisms)

High temperatures augment inhibition of parasites by a honey bee gut symbiont – Evan C Palmer-Young – Applied and Environmental Microbiology

The maternal microbiome promotes placental development in mice – Geoffrey N Pronovost – Science Advances

Omics-Based Mathematical Modeling Unveils Pathogenesis of Periodontitis in an Experimental Murine Model – C Fujihara – Journal of Dental Research

Environmental Microbiome

Compost, plants and endophytes versus metal contamination: choice of a restoration strategy steers the microbiome in polymetallic mine waste – Martina Kracmarova-Farren – Environmental Microbiome

Litter decomposition and nutrient release are faster under secondary forests than under Chinese fir plantations with forest development – Shuaijun Li – Scientific Reports

Microbiome Analysis: Tools, Techniques and Resources

PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation – Guangping Huang – Microbiome

The newest Oxford Nanopore R10.4.1 full-length 16S rRNA sequencing enables the accurate resolution of species-level microbial community profiling – Tianyuan Zhang – Applied and Environmental Microbiology

October 4, 2023

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General microbiome

[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology

Statistically learning the functional landscape of microbial communities – Skwara et al. – Nature Ecology & Evolution

Human skin microbiome

Skin microbiota secretomes modulate cutaneous innate immunity against Borrelia burgdorferi s.s – Baquer et al. – Scientific Reports

Human gut microbiome

Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort – Galperine et al. – BMC Infectious Diseases

Association Between Bowel-Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome – Ma et al. – Neurology

[REVIEW]The gut microbiome tango in the progression of chronic kidney disease and potential therapeutic strategies – Tang, Yu & Pan – Journal of Translational Medicine

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

Microbiota-gut-brain axis drives overeating disorder – Fan et al. – Cell Metabolism

Animal microbiome (for animals in the wild)

Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics – Wang et al. – Animal Microbiome

Plant, root, and soil microbiome

Using wasps as a tool to restore a functioning vine grape mycobiota and preserve the mycobial “terroir” – Di Paola et al. – Scientific Reports

Soil microbes mediate the effects of resource variability on plant invasion – Zhang et al. – Ecology

Bioinformatics

[PREPRINT]Deepurify: a multi-modal deep language model to remove contamination from metagenome-assembled genomes – Zou et al. – bioRxiv

[PREPRINT]BATTER: Accurate Prediction of Rho-dependent and Rho-independent Transcription Terminators in Metagenomes – Jin et al. – bioRxiv

[PREPRINT]Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles – Chang et al. – bioRxiv

Techniques

INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution – Nino et al. – Nature Protocols

October 2, 2023

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Highlights!

Review: A relational framework for microbiome research with Indigenous communities – Alyssa C Bader – Nature Microbiology

Review: Microbiome ownership for Indigenous peoples – Matilda Handsley-Davis – Nature Microbiology

Human and General Microbiome

Expanded microbiome niches of RAG-deficient patients – Ryan A Blaustein – Cell Reports Medicine

Low dietary fiber intake impairs small intestinal Th17 and intraepithelial T cell development over generations – Charlotte J Royer – Cell Reports

Iron acquisition by a commensal bacterium modifies host nutritional immunity during Salmonella infection – Luisella Spiga – Cell Host & Microbe

Microbiome profile and calprotectin levels as markers of risk of recurrent Clostridioides difficile infection – Silvia Vázquez-Cuesta – Frontiers in Cellular and Infection Microbiology

Safety and tolerability of frozen, capsulized autologous faecal microbiota transplantation. A randomized double blinded phase I clinical trial – Måns Stefansson – PloS One

Metabolism of azo food dyes by bacterial members of the human gut microbiome – Riley Elder – Anaerobe

Genetic risk score in multiple sclerosis is associated with unique gut microbiome – Noha S Elsayed – Scientific Reports

Antisense inhibition of RNA polymerase α subunit of Clostridioides difficile – Rusha Pal – Microbiology Spectrum

Review: Metabolic signature for a dysbiotic microbiome in the female genital tract: A systematic review and meta-analysis – Biban Gill – American Journal of Reproductive Immunology

Review: Influence of Plant-Based Diet on the Cardiovascular System: A Narrative Review – Gurusha Jangid – Cardiology in Review

Review: Bile acid and its bidirectional interactions with gut microbiota: a review – Shuqi He – Critical Reviews in Microbiology

Animal Microbiome

Population mixing mediates the intestinal flora composition and facilitates invasiveness in a globally invasive fruit fly – Yidan Wang – Microbiome

Diet-related factors strongly shaped the gut microbiota of Japanese macaques – Wanyi Lee – American Journal of Primatology

Skin and gut microbiomes of tadpoles vary differently with host and water environment: a short-term experiment using 16S metabarcoding – Bárbara Santos – Scientific Reports

Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats – Dangdang Wang – Microbiome

The multi-kingdom microbiome of the goat gastrointestinal tract – Yanhong Cao – Microbiome

Multi-breed host rumen epithelium transcriptome and microbiome associations and their relationship with beef cattle feed efficiency – P A S Fonseca – Scientific Reports

Animal Model Microbiome

Select symbionts drive high IgA levels in the mouse intestine – Shanshan Zhang – Cell Host & Microbe

Blocked conversion of Lactobacillus johnsonii derived acetate to butyrate mediates copper-induced epithelial barrier damage in a pig model – Yang Wen – Microbiome

Laboratory mice with a wild microbiota generate strong allergic immune responses – Junjie Ma – Science Immunology

Plant Microbiome

Host genetic variation drives the differentiation in the ecological role of the native Miscanthus root-associated microbiome – Niuniu Ji – Microbiome

Changes in structure and assembly of a species-rich soil natural community with contrasting nutrient availability upon establishment of a plant-beneficial Pseudomonas in the wheat rhizosphere – Daniel Garrido-Sanz – Microbiome

Microbially produced fertilizer provides rhizobacteria to hydroponic tomato roots by forming beneficial biofilms – Yuya Sato – Applied Microbiology and Biotechnology

Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities – Ming-Yi Chou – Microbiology Spectrum 

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development – Ella T Sieradzki – mSystems

Environmental Microbiome

The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea – Wei-Wei Liu – Microbiology Spectrum

Microbial biogeography of pit mud from an artificial brewing ecosystem on a large time scale: all roads lead to Rome – Jun-Lan Mei – mSystems

Stable microbial community in compacted bentonite after 5 years of exposure to natural granitic groundwater – Katja Engel – mSphere

Microbiome Analysis Tools, Techniques and Resources

Impact of Experimental Bias on Compositional Analysis of Microbiome Data – Yingtian Hu – Genes

happi: a hierarchical approach to pangenomics inference – Pauline Trinh – Genome Biology

Integrating a tailored recurrent neural network with Bayesian experimental design to optimize microbial community functions – Jaron C Thompson – PLoS Computational Biology

Review: Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics – Koji Arikawa – Computational and Structural Biotechnology Journal

September 25, 2023

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Highlights!

Evidence of a causal and modifiable relationship between kidney function and circulating trimethylamine N-oxide – Petros Andrikopoulos – Nature Communications

A blood-based metabolomic signature predictive of risk for pancreatic cancer – Ehsan Irajizad – Cell Reports. Medicine

Enterobacteriaceae growth promotion by intestinal acylcarnitines, a biomarker of dysbiosis in Inflammatory Bowel Disease – Johanna M S Lemons – Cellular and Molecular Gastroenterology and Hepatology

Inducible CRISPR-targeted knockdown of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies – Zachary W Beller – PNAS

Review: The gut microbiota and its biogeography – Giselle McCallum – Nature Reviews. Microbiology

Human and General Microbiome

The role of the gut-microbiota-brain axis via the subdiaphragmatic vagus nerve in chronic inflammatory pain and comorbid spatial working memory impairment in complete Freund’s adjuvant mice – Caibao Yue – Journal of Psychiatric Research

Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection – Leonardo Mancabelli – Microbiology Spectrum

Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota – Eri Komori – Scientific Reports

Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo – Mei Luan – BMC Microbiology

Review: The role of the glycome in symbiotic host-microbe interactions – Rustam Aminov – Glycobiology

Review: Microbiome-targeted interventions for the control of oral-gut dysbiosis and chronic systemic inflammation – Juan Pacheco-Yanes – Trends in Molecular Medicine

Review: The link between the gut microbiome, inflammation, and Parkinson’s disease – Shiqing Nie – Applied Microbiology and Biotechnology

Food Microbiome

The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut – Wisnu Adi Wicaksono – Gut Microbes

Animal Microbiome

Reducing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome – N K Newman – Microbiome

Combined effect of a neonicotinoid insecticide and a fungicide on honeybee gut epithelium and microbiota, adult survival, colony strength and foraging preferences – Riccardo Favaro – The Science of the Total Environment

Glyphosate decreases survival, increases fecundity, and alters the microbiome of the natural predator Harmonia axyridis (ladybird beetle) – Xueke Gao – Environmental Research

Unfolding the secrets of microbiome (Symbiodiniaceae and bacteria) in cold-water coral – Sanqiang Gong – Microbiology Spectrum

Combined oral intake of short and long fructans alters the gut microbiota in food allergy model mice and contributes to food allergy prevention – Hideaki Takahashi – BMC Microbiology

Review: The pivotal roles of gut microbiota in insect plant interactions for sustainable pest management – Yuxin Zhang – NPJ Biofilms and Microbiomes

Plant Microbiome

Review: Endophytes Modulate Plant Genes: Present Status and Future Perspectives – Vivek Kumar – Current Microbiology

Environmental Microbiome

Planktonic and epilithic prokaryota community compositions in a large temperate river reflect climate change related seasonal shifts – Attila I Engloner – PloS One

Thiothrix and Sulfurovum genera dominate bacterial mats in Slovak cold sulfur springs – Lea Nosalova – Environmental Microbiome

Built Environment Microbiome

Innovative strategy for the conservation of a millennial mausoleum from biodeterioration through artificial light management – Yuanyuan Bao – NPJ Biofilms and Microbiomes

More Microbes

In vitro and in silico evaluation of the serrapeptase effect on biofilm and amyloids of Pseudomonas aeruginosa – Georgios Katsipis – Applied Microbiology and Biotechnology

Microbiome Analysis: Tools, Techniques and Resources

Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data – Hunyong Cho – Briefings in Bioinformatics

Review: Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data – Ostaizka Aizpurua – Critical Reviews in Biotechnology

September 20, 2023

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General microbiome

Frequency of change determines effectiveness of microbial response strategies – Li et al. – The ISME Journal

Human gut microbiome

Social and psychological adversity are associated with distinct mother and infant gut microbiome variations – Warner et al. – Nature Communications

Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua – Mills et al. – Microbiome

Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts – Hansen et al. – Scientific Reports

The Impacts of Fecal Microbiota Transplantation from Same Sex on the Symptoms of Ulcerative Colitis Patients – Shang et al. – Polish Journal of Microbiology

Animal microbiome (for animals in the wild)

Transcriptomic, 16S ribosomal ribonucleic acid and network pharmacology analyses shed light on the anticoccidial mechanism of green tea polyphenols against Eimeria tenella infection in Wuliangshan black-boned chickens – Song et al. – Parasites & Vectors

Dityrosine Aggravates Hepatic Insulin Resistance in Obese Mice by Altering Gut Microbiota and the LPS/TLR4/NF-κB Inflammatory Pathway – Ding et al. – Molecular Nutrition & Food Research

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

[REVIEW]Microbiome-assisted restoration of degraded marine habitats: a new nature-based solution? – Corinaldesi et al. – Frontiers in Marine Science

Bioinformatics

[PREPRINT]Comparison of computational methods for host removal and classification of mycobacteria from clinical metagenomic data – Hall & Coin – bioRxiv

September 18, 2023

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Human and General Microbiome

Ocular microbiome evaluation in dry eye disease and meibomian gland dysfunction: Values of variables – Davide Borroni – Experimental Eye Research

Regulation of psoriasis, colitis, and the intestinal microbiota by clusterin – Yu Kyung Jun – Scientific Reports

Bridging of host-microbiota tryptophan partitioning by the serotonin pathway in fungal pneumonia – Giorgia Renga – Nature Communications

High-throughput sequencing analysis of the characteristics of the gut microbiota in aged patients with sarcopenia – Yiyi Zhang – Experimental Gerontology

Draft genome sequence of a Fusobacterium nucleatum strain isolated from a patient in Kazakhstan with colorectal cancer – Gulmira Kulmambetova – Microbiology Resource Announcements

Review: The impacts of oral and gut microbiota on alveolar bone loss in periodontitis – Nannan Han – Journal of Periodontal Research

Control of Helicobacter pylori with engineered probiotics secreting selective guided antimicrobial peptides – Ankan Choudhury – Microbiology Spectrum

Animal Microbiome

The synthetic food dye, Red 40, causes DNA damage, causes colonic inflammation, and impacts the microbiome in mice – Qi Zhang – Toxicology Reports

Disruption of the microbiota-gut-brain axis is a defining characteristic of the α-Gal A (-/0) mouse model of Fabry disease – C Delprete – Gut Microbes

Review: Neuroactive metabolites modulated by the gut microbiota in honey bees – Amélie Cabirol – Molecular Microbiology

Microbiome and Evolution

Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut – Dámariz González – Frontiers in Microbiology

Food Microbiome

Review: Microbiome Assembly in Fermented Foods – Nicolas L Louw – Annual Review of Microbiology

Plant Microbiome

Engineering the Maize Root Microbiome: A Rapid MoClo Toolkit and Identification of Potential Bacterial Chassis for Studying Plant-Microbe Interactions – John van Schaik – ACS Synthetic Biology

Environmental Microbiome

Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols – Yidan Zhang – The Science of the Total Environment

Combination of sequencing batch reactor activated sludge process with sludge lysis using thermophilic bacterial community for minimizing excess sludge – Baoyan Chi – Journal of Environmental Management

September 15, 2023

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Today’s digest features the BugSigDB, AMPSphere and more. Also, you can check out my tips for online conferencing and how to do it better. See you at #MVIF next week!

Respiratory microbiome

The landscape of antibiotic resistance genes in the nasopharynx of preterm infants: Prolonged signature of hospitalization and effects by antibiotics – Achal Dhariwal – bioRxiv

Breast cancer microbiome

Integrating current analyses of the breast cancer microbiome – Sidra Sohail and Michael B. Burns – Plos One

Vaginal microbiome

Diet influences community dynamics following vaginal group B Streptococcus colonization – Christina J. Megli – bioRxiv

Gut microbiome

Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL – Sheng Liu – Microbiome

Water microbiome

Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean – Mirna Vázquez Rosas Landa – mSystems

Insect microbiome

Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions – Francesca De Filippis – Microbiome

Animal experiment

Enhancing Recovery from Gut Microbiome Dysbiosis and Alleviating DSS-Induced Colitis in Mice with a Consortium of Rare Short-Chain Fatty Acid-Producing Bacteria – Achuthan Ambat – bioRxiv

Bioinformatics

BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures – Ludwig Geistlinger – Nature Biotechnology

Computational exploration of the global microbiome for antibiotic discovery – Célio Dias Santos-Júnior – bioRxiv