Tag Archives: Animal microbiome

April 10, 2024

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Good morning microbiome enthusiasts! Today’s MD is on the shorter side but we still have some really interesting articles picked out for you to peruse – including a microbiome-sparing targeted P. aeruginosa compound, effective probiotics for restoring a healthy coral microbiome, and a study characterizing the microbiome of metastatic cancers in over 4,000 biopsies. Plus, don’t forget that April’s Microbiome Virtual International Forum is happening next week!

Human Microbiome

Longitudinal multi-omics analysis uncovers the altered landscape of gut microbiota and plasma metabolome in response to high altitude – Yang Han et al – BMC Microbiome

Illuminating microflora: shedding light on the potential of blue light to modulate the cutaneous microbiome – Hannah J Serrage et al – Frontiers in Cellular and Infection Microbiology

Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC – Rauf Salamzade et al – Microbial Genomics

A pan-cancer analysis of the microbiome in metastatic cancer – Thomas Battaglia et al – Cell

A Lacticaseibacillus rhamnosus secretome induces immunoregulatory transcriptional, functional and immunometabolic signatures in human THP-1 monocytes – Michael P. Jeffrey et al – Nature Scientific Reports

The oral cavity and intestinal microbiome in children with functional constipation – Monika Kwiatkowska et al – Nature Scientific Reports

Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults – Casper S. Poulsen et al – Nature Scientific Reports

Colonization during a key developmental window reveals microbiota-dependent shifts in growth and immunity during undernutrition – Yadeliz A. Serrano Matos et al – BMC Microbiome

Animal models

Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice – Tatsuya Dokoshi et al – Nature Communications

A folate inhibitor exploits metabolic differences in Pseudomonas aeruginosa for narrow-spectrum targeting – Connor Chain et al – Nature Microbiology

Animal microbiome

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience – Lauren F. Messer et al – Nature Communications

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment – Nathalia Delgadillo-Ordoñez et al – Nature Communications Biology

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation – Daxi Wang et al – BMC Microbiome

Plant, root & soil microbiome

Root volatiles manipulate bacterial biofilms – Waseem Raza & Gaofei Jiang – Nature Ecology & Evolution

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community – Chong-Die Wu et al – BMC Plant Biology

Bioinformatics & tools

Holomics – a user-friendly R shiny application for multi-omics data integration and analysis – Katharina Munk et al – BMC Bioinformatics

April 7, 2024

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Human and General Microbiome

The secreted protein Amuc_1409 from Akkermansia muciniphila improves gut health through intestinal stem cell regulation – Eun-Jung Kang – Nature Communications

A universal plasma metabolites-derived signature predicts cardiovascular disease risk in MAFLD – Zhonglin Li – Atherosclerosis

Oral-gut microbial transmission promotes diabetic coronary heart disease – Yiwen Li – Cardiovascular Diabetology

Comparative analysis of microbial composition and functional characteristics in dental plaque and saliva of oral cancer patients – Man Zhang – BMC Oral Health

Investigating the causal role of the gut microbiota in esophageal cancer and its subtypes: a two-sample Mendelian randomization study – Jia Li – BMC Cancer

Beneficial Microbes and Compounds

Gut bacteria-driven homovanillic acid alleviates depression by modulating synaptic integrity – Mingliang Zhao – Cell Metabolism

Animal Microbiome (model and non-model)

Stress-induced mucin 13 reductions drive intestinal microbiome shifts and despair behaviors – Courtney R Rivet-Noor – Brain, Behavior, and Immunity

Integrated analysis of intestinal microbiota and transcriptome reveals that a coordinated interaction of the endocrine, immune system and gut microbiota response to heat stress in Litopenaeus vannamei – Guowei Liao – Developmental and Comparative Immunology

Associations between the rumen microbiota and carcass merit and meat quality in beef cattle – Devin B Holman – Applied Microbiology and Biotechnology

Characterization of oral microbiota in 6-8-month-old small breed dogs – Masahiro Morita – BMC Veterinary Research

A compendium of ruminant gastrointestinal phage genomes revealed a higher proportion of lytic phages than in any other environments – Yingjian Wu – Microbiome

Effects of fecal microbiota transfer on blood pressure in animal models: A systematic review and meta-analysis – Lingyu Lin – PloS ONE

Zoonotic bacteria in the vicinity of animal farms as a factor disturbing the human microbiome: a review – Anna Kozajda – International Journal of Occupational Medicine and Environmental Health

Metagenomic insights into jellyfish-associated microbiome dynamics during strobilation – Saijun Peng – ISME Communications

Host evolution shapes gut microbiome composition in Astyanax mexicanus – Misty R Riddle – Ecology and Evolution

Environmental Microbiome

Heavy metal induced shifts in microbial community composition and interactions with dissolved organic matter in coastal sediments – Yu Wang – The Science of the Total Environment

Long-term and combined heavy-metal contamination forms a unique microbiome and resistome: A case study in a Yellow River tributary sediments – Yu Cao – Environmental Research

Deciphering the impact of cold-adapted bioinoculants on rhizosphere dynamics, biofortification, and yield of kidney bean across varied altitudinal zones – Amir Khan – The Science of the Total Environment

Plant Microbiome

Analysis of microbial dynamics in the soybean root-associated environments from community to single-cell levels – Masako Kifushi – Journal of Bioscience and Bioengineering

Microbiome Analysis: Tools, Protocols, Techniques and Resources

phylaGAN: Data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data – Divya Sharma – Bioinformatics

April 3, 2024

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Human Microbiome

Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria – Chenhao Li et al – Cell


Small Intestine Bacterial Overgrowth is associated with increased Campylobacter and epithelial injury in duodenal biopsies of Bangladeshi children – Shah Mohammad Fahim et al – PLOS Neglected Tropical Diseases


Placental TLR recognition of salivary and subgingival microbiota is associated with pregnancy complications – Kazune Pax et al – BMC Microbiome


Ecological patterns and processes of temporal turnover within lung infection microbiota – Helen Gavillet et al – BMC Microbiome


Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis – Jinlin Zhu et al – Gut Microbes


A comparative study on dietary diversity and gut microbial diversity in children with autism spectrum disorder, attention-deficit hyperactivity disorder, their neurotypical siblings, and non-related neurotypical volunteers: a cross-sectional study – Shunya Kurokawa et al – Journal of Child Psychology & Psychiatry


Disrupted gut microecology after high-dose 131I therapy and radioprotective effects of arachidonic acid supplementation – Ganghua Lu et al – European Journal of Nuclear Medicine & Molecular Imaging


Pathogen-specific alterations in intestinal microbiota precede urinary tract infections in preterm infants: a longitudinal case-control study – Luyang Hong et al – Gut Microbes



Plant, soil, and root microbiome

Soil fungal communities varied across aspects of restored grassland in former mining areas of the Qinghai-Tibet Plateau – Xioqing Li et al – PLOS One


Integrated rice-yellow catfish farming resulting in variations in the agricultural environment, rice growth performance, and soil bacterial communities – Yiran Hou et al – Environmental Science & Pollution Research


Microbial terroir: associations between soil microbiomes and the flavor chemistry of mustard (Brassica juncea) – Corinne Walsh et al – New Phytologist


Animal experiments

The gut metabolite indole-3-propionic acid activates ERK1 to restore social function and hippocampal inhibitory synaptic transmission in a 16p11.2 microdeletion mouse model – Jian Jiang et al – BMC Microbiome


[PREPRINT] Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors – Zachary L. McAdams et al – bioRxiv


Water & extremophile microbiome

Phenology and ecological role of aerobic anoxygenic phototrophs in freshwaters – Cristian Villena-Alemany et al – BMC Microbiome


The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats – Sara M E Rassner et al – Environmental Microbiology


Animal Microbiome

Molecular-Weight-Dependent Degradation of Plastics: Deciphering Host-Microbiome Synergy Biodegradation of High-Purity Polypropylene Microplastics by Mealworms – Lei He et al – Environmental Science & Technology


Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment – Daniel Scicchitano et al – BMC Animal Microbiome


Tools & techniques

[PREPRINT] rRNA Operon Improves Species-Level Classification of Bacteria and Microbial Community Analysis Compared to 16S rRNA – Sohyoung Won et al – bioRxiv

March 31, 2024

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Human Microbiome

The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children – Sarah M Heston – Gut Microbes

Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung – Patrick J Dörner – Nature Communications

The gut metabolite indole-3-propionic acid activates ERK1 to restore social function and hippocampal inhibitory synaptic transmission in a 16p11.2 microdeletion mouse model – Jian Jiang – Microbiome

Vaginal microbiomes of breast cancer survivors treated with aromatase inhibitors with and without vulvovaginal symptoms – Pimpun Prasanchit – Scientific Reports

Integrated analysis of gut metabolome, microbiome, and brain function reveal the role of gut-brain axis in longevity – Bin Jiao – Gut Microbes

Exploring the diversity of vaginal microbiota between healthy women and cervical cancer patients in India – Ashwini Kamble – Journal of Medical Microbiology

Oral pathobiont Klebsiella chaperon usher pili provide site-specific adaptation for the inflamed gut mucosa – Yijie Guo – Gut Microbes

Hypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut – Yi Han Tan – The ISME Journal

Review: Microbiome bacterial influencers of host immunity and response to immunotherapy – Yeganeh Yousefi – Cell Reports. Medicine

Beneficial Microbes

Review: Unlocking the Potential of Probiotics: A Comprehensive Review on Research, Production, and Regulation of Probiotics – Tales Fernando da Silva – Probiotics and Antimicrobial Proteins

Mulberry leaf and konjac flour compound dietary fiber improves digestion and metabolism in elderly mice with high-fish-protein diet by regulating gut microbiota structure and intestinal tissue repair – Liling Deng – Food Chemistry: X

Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes – Zheng Wang – Circulation Research

Animal Microbiome (model and non-model)

Colitis reduces active social engagement in mice and is ameliorated by supplementation with human microbiota members – D Garrett Brown – Nature Communications

Disentangling direct vs indirect effects of microbiome manipulations in a habitat-forming marine holobiont – Alexander Harry McGrath – NPJ Biofilms and Microbiomes

Microplastics dampen the self-renewal of hematopoietic stem cells by disrupting the gut microbiota-hypoxanthine-Wnt axis – Lingli Jiang – Cell Discovery

Review: Immune interactions between mosquitoes and microbes during midgut colonization – Julia A Cai – Current Opinion in Insect Science

Microbiome Analysis

A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts – Jie Pan – Briefings in Bioinformatics

Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes – Zhanshan Sam Ma – BMC Bioinformatics

An in-depth evaluation of metagenomic classifiers for soil microbiomes – Niranjana Rose Edwin – Environmental Microbiome

Generalized reporter score-based enrichment analysis for omics data – Chen Peng – Briefings in Bioinformatics

March 27, 2024

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Built environment microbiome

Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station – Pratyay Sengupta et al – BMC Microbiome

An overview of the bacterial microbiome of public transportation systems-risks, detection, and countermeasures – Yen-Tran Ly et al – Frontiers in Public Health

Bioinformatics and computational methods

Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics – Enhui Wu et al – BMC Microbiome

Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes – Jasper van Bemmelen et al – BMC Bioinformatics

Multi-omic integration of microbiome data for identifying disease-associated modules – Efrat Muller – Nature Communications

Animal experiments

Gender affirming hormone therapy preserves skeletal maturation in young mice via the gut microbiome – Subhashis Pal et al – Journal of Clinical Investigation

Microbiota-derived indoles alleviate intestinal inflammation and modulate microbiome by microbial cross-feeding – Gang Wang et al – BMC Microbiome

[PREPRINT] Akkermansia muciniphila identified as key strain to alleviate gut barrier injury through Wnt signaling pathway – Xin Ma et al – bioRxiv

Microbiota from human infants consuming secretors or non-secretors mothers’ milk impacts the gut and immune system in mice – Manoj Gurung et al – mSystems

Plant and soil microbiome

Lose-lose consequences of bacterial community-driven invasions in soil – Xipeng Liu & Joana Falcão Salles – BMC Microbiome

Manipulating the physical distance between cells during soil colonization reveals the importance of biotic interactions in microbial community assembly – Sana Romdhane et al – BMC Environmental Microbiome

Soil fungal communities varied across aspects of restored grassland in former mining areas of the Qinghai-Tibet Plateau – Xioaqing Li et al – PLOS One

Animal microbiome

Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota – Marie Bouilloud et al – BMC Animal Microbiome

Bats, Bacteria, and Bat Smell V.2.0: Repeatable Sex-Specific Differences in Scent Organ Microbiota – Öncü Maraci et al – Microbial Ecology

Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs – Jacoba I. Bromfield et al – mSphere

Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin – M.S. Pankey et al – Molecular Ecology

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition – C. E. Dubé et al – Nature Communications

March 24, 2024

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Human Microbiome

A host-microbiota interactome reveals extensive transkingdom connectivity – Nicole D Sonnert – Nature

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche – Martha Zepeda-Rivera – Nature

Cluster-specific associations between the gut microbiota and behavioral outcomes in preschool-aged children – Marcel van de Wouw – Microbiome

Association between oral and fecal microbiome dysbiosis and treatment complications in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation – M Faraci – Scientific Reports

Design of a proteolytic module for improved metabolic modeling of Bacteroides caccae – Amandine Paulay – mSystems

Cataloging the phylogenetic diversity of human bladder bacterial isolates – Jingjie Du – Genome Biology

Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis – Jianjun Liu – NPJ Biofilms and Microbiomes

Extracellular vesicles from vaginal Gardnerella vaginalis and Mobiluncus mulieris contain distinct proteomic cargo and induce inflammatory pathways – Andrea Joseph – NPJ Biofilms and Microbiomes

A specific enterotype derived from gut microbiome of older individuals enables favorable responses to immune checkpoint blockade therapy – Xiaoqiang Zhu – Cell Host & Microbe

Opposing diet, microbiome, and metabolite mechanisms regulate inflammatory bowel disease in a genetically susceptible host – Gabriel Vasconcelos Pereira – Cell Host & Microbe

HPV-associated cervicovaginal microbiome and host metabolome characteristics – Yao Zhang – BMC Microbiology

Review: Mediterranean diet: a potential player in the link between oral microbiome and oral diseases – Giuseppina Augimeri – Journal of Oral Microbiology

Beneficial Microbes and Compounds

Exopolysaccharides Produced by Bifidobacterium longum subsp. longum YS108R Ameliorates DSS-Induced Ulcerative Colitis in Mice by Improving the Gut Barrier and Regulating the Gut Microbiota – Huizhen Li – Journal of Agricultural and Food Chemistry

Lactobacillus rhamnosus GG ameliorates hyperuricemia in a novel model – Yang Fu – NPJ Biofilms and Microbiomes

Specific vaginal and gut microbiome and the anti-tumor effect of butyrate in cervical cancer women – Mengzhen Han – Translational Oncology

Harnessing the Power Within: Engineering the Microbiome for Enhanced Gynecologic Health – Caitriona Brennan – Reproduction & Fertility

Animal Microbiome (including Model species)

Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice – Rebecca H Gellman – Cell Reports

The crosstalk between intestinal microbiota and MDSCs fuels colitis associated cancer development – Hadas Ashkenazi-Preiser – Cancer Research Communications

Integrating microbial abundance time series with fermentation dynamics of the rumen microbiome via mathematical modelling – Mohsen Davoudkhani – PloS ONE

Plant and Soil Microbiome

Heritable microbiome variation is correlated with source environment in locally adapted maize varieties – Xiaoming He – Nature Plants

The evolutionary genomics of adaptation to stress in wild rhizobium bacteria – Hanna Kehlet-Delgado – PNAS

Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system – Kristin Barbour – The ISME Journal

Environmental Microbiome

Genome analysis and biogeographic distribution of the earliest divergent Frankia clade in the southern hemisphere – Fede Berckx – FEMS Microbiology Ecology

Host population crashes disrupt the diversity of associated marine microbiomes – William S Pearman – Environmental Microbiology

Microplastic-antifouling paint particle contamination alters microbial communities in surrounding marine sediment – A S Tagg – The Science of the Total Environment

Microbiome Analysis

MCSS: microbial community simulator based on structure – Xingqi Hui – Frontiers in Microbiology

Datathons: fostering equitability in data reuse in ecology – Stephanie D Jurburg – Trends in Microbiology

March 17, 2024

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Human Microbiome

Stratification of Fusobacterium nucleatum by local health status in the oral cavity defines its subspecies disease association – Madeline Krieger – Cell Host & Microbe

Bile acids modified by the intestinal microbiota promote colorectal cancer growth by suppressing CD8(+) T cell effector functions – Jingjing Cong – Immunity

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease – Xin Zhou – Cell Host & Microbe

Body mass index can mediate the interplay between gut microbiome and sleep disorders – Lng Adami – Sleep Medicine

Review: Postbiotic butyrate: role and its effects for being a potential drug and biomarker to pancreatic cancer – Abinaya Elango – Archives of Microbiology

Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease – Filippo Martinelli – Scientific Reports

Antibacterial activity of nonantibiotics is orthogonal to standard antibiotics – Mariana Noto Guillen – Science

Defining Porphyromonas gingivalis strains associated with periodontal disease – Vijaya Murugaiyan – Scientific Reports

Review: The individual response to antibiotics and diet – insights into gut microbial resilience and host metabolism – Lars M M Vliex – Nature Reviews Endocrinology

Unveiling the immunomodulatory effect of the novel probiotic Akkermansia muciniphila and its protective effect in vitro – Alba Calvo – Microbiological Research

Microbial metabolite enhances immunotherapy efficacy by modulating T cell stemness in pan-cancer – Dingjiacheng Jia – Cell

Animal Microbiome

Rice straw ash and amphibian health: A deep dive into microbiota changes and potential ecological consequences – Wen-Jing Dong – The Science of the Total Environment

Microbial community composition in the dung of five sympatric European herbivore species – Xingzhao Sun – Ecology and Evolution

Antibiotics treatment promotes vasculogenesis in the brain of glioma-bearing mice – Maria Rosito – Cell Death & Disease

Environmental Microbiome

Microecological characteristics of water bodies/sediments and microbial remediation strategies after 50 years of pollution exposure in ammunition destruction sites in China – Xu Yang – Environmental Research

Microbiome Analysis: Tools, Protocols, Techniques and Resources

Review: Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions – Nolan K Newman – Nature Protocols

Resource competition predicts assembly of gut bacterial communities in vitro – Po-Yi Ho – Nature Microbiology

March 13, 2024

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Human gut microbiome

Gut microbiota–tryptophan metabolism–GLP-1 axis participates in β-cell regeneration induced by dapagliflozin – Yafei Jiang et al – Diabetes

Inhibition of inosine metabolism of the gut microbiota decreases testosterone secretion in the testis – Lei Tang et al – mSystems

[REVIEW] Exploring the gut microbiota and its potential as a biomarker in gliomas – Dana Aljarrah et al – Biomedicine & Pharmacotherapy

Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin and acacia gum in Kenyan infant gut microbiota during iron supplementation – Paula Momo Cabera et al – ISME Communications

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Ekaterina Buzun et al – Cell Host and Microbe

Animal Microbiome

Dietary carbohydrate sources differently prime the microbial ecosystem but not the epithelial gene expression profile along the complete gut of young calves – Thomas Hartinger et al – BMC Animal Microbiome

Multi-omics reveals that alkaline mineral water improves the respiratory health and growth performance of transported calves – Jiancheng Qi et al – BMC Microbiome

Efficacy of a novel multi-enzyme feed additive on growth performance, nutrient digestibility and gut microbiome of weanling pigs fed corn-wheat or wheat-barley based diet – Ayodeji S Aderibigbe et al – Journal of Animal Science

Plant and soil microbiome

Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition – Jia Wang et al – mSystems

Plasma Treatment Modifies Element Distribution in Seed Coating and Affects Further Germination and Plant Growth through Interaction with Soil Microbiome – Tetiana Kalachova et al – Journal of Agricultural and Food Chemistry

Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils – Prinpida Sonthiphand et al – Bulletin of Environmental Contamination and Toxicology

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria – Katarina Hrovat et al – ISME Communications

Root microbiota analysis of Oryza rufipogon and Oryza sativa reveals an orientation selection during the domestication process – Liqun Jiang et al – Microbiology Spectrum

Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes – Ziguo Zhang et al – mSystems

Sugar transporters spatially organize microbiota colonization along the longitudinal root axis of Arabidopsis – Eliza P.-I. Loo et al – Cell Host and Microbe

Built environment microbiome

Microbiome analysis of the restricted bacteria in radioactive element-containing water at the Fukushima Daiichi Nuclear Power Station – Tomoro Warashina et al – Applied and Environmental Microbiology

Bioinformatics and Techniques

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes – Thibaut Dumas et al – BMC Microbiome

Proportion-based normalizations outperform compositional data transformations in machine learning applications – Aaron Yerke et al – BMC Microbiome

A method to correct for local alterations in DNA copy number that bias functional genomics assays applied to antibiotic-treated bacteria – Geraldine J. Sullivan et al – mSystems

[PREPRINT] Bacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach – Federica Palma et al – bioRXiv

March 10, 2024

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Human and General Microbiome

A cryptic plasmid is among the most numerous genetic elements in the human gut – Emily C. Fogarty – Cell

Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight – Ricardo García-Gamboa – Scientific Reports

Multicomponent (bio)markers for obesity risk prediction: a scoping review protocol – Farhad Vahid – BMJ Open

Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours – Surbhi Mishra – Journal of Advanced Research

Comparative analysis of the vaginal bacteriome and virome in healthy women living in high-altitude and sea-level areas – Chaoran Li – European Journal of Medical Research

Cas9-assisted biological containment of a genetically engineered human commensal bacterium and genetic elements – Naoki Hayashi – Nature Communications

Review: Unlocking the secrets: exploring the influence of the aryl hydrocarbon receptor and microbiome on cancer development – Menatallah Rayan – Cellular & Molecular Biology Letters

Environmental Microbiome

Review: Multi-omics and gut microbiome: Unveiling the pathogenic mechanisms of early-life pesticide exposure – Yifan Yue – Pesticide Biochemistry and Physiology

Ancient Microbiome

Identification of microbial pathogens in Neolithic Scandinavian humans – Nora Bergfeldt – Scientific Reports

Microbiome Analysis: Tools, Protocols, Techniques and Resources

A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics – Raphael Eisenhofer – Microbiology Spectrum

OMEinfo: global geographic metadata for -omics experiments – Matthew Crown – Bioinformatics Advances

Successful topical treatment of human biofilms using multiple antibiotic elution from a collagen-rich hydrogel – Ayushi D Sharma – Scientific Reports

The astounding exhaustiveness and speed of the Astral mass analyzer for highly complex samples is a quantum leap in the functional analysis of microbiomes – Thibaut Dumas – Microbiome

March 6, 2024

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Vaginal Microbiome

Modeling Healthy and Dysbiotic Vaginal Microenvironments in a Human Vagina-on-a-Chip – Aakanksha Gulati et al – JoVE Bioengineering

Cancer microbiome

Multi-omics analysis elucidates the relationship between intratumor microbiome and host immune heterogeneity in breast cancer – Jia Li et al – Microbiology Spectrum

Human gut microbiome

Protein combined with certain dietary fibers increases butyrate production in gut microbiota fermentation – Rachel Jackson et al – Food & Function

A human milk oligosaccharide prevents intestinal inflammation in adulthood via modulating gut microbial metabolism – Kasey M. Schalich et al – mBio

Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation – Leonardo Mancabelli et al – mSystems

Cadaver microbiome

Decomposer communities are universal in death – Michael S. Strickland – Nature Microbiology

Animal microbiome

The coral microbiome in sickness, in health and in a changing world – Christian R. Voolstra et al – Nature Reviews Microbiology

The effects of hydrolyzed protein on macronutrient digestibility, fecal metabolites and microbiota, oxidative stress and inflammatory biomarkers, and skin and coat quality in adult dogs – Clare Hsu et al – Journal of Animal Science

Host starvation and in hospite degradation of algal symbionts shape the heat stress response of the Cassiopea-Symbiodiniaceae symbiosis – Gaëlle Toullec et al – BMC Microbiome

An engineered bacterial symbiont allows noninvasive biosensing of the honey bee gut environment – Audam Chhun et al – PLOS Biology

From phyllosphere to insect cuticles: silkworms gather antifungal bacteria from mulberry leaves to battle fungal parasite attacks – Pengfei Zhao et al – BMC Microbiome

Phages and viruses

Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis – Dominika Kadlečková et al – mSystems

Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses – Hiroaki Takebe et al – mSystems

Plant, root, and soil microbiome

Microbiome sequencing revealed the abundance of uncultured bacteria in the Phatthalung sago palm-growing soil – Pumin Nutaratat et al – PLOS ONE

The rhizosphere microbiome reduces the uptake of arsenic and tungsten by Blechnum orientale by increasing nutrient cycling in historical tungsten mining area soils – Xiaolong Lan et al – Science of the Total Environment

Non-Microbiology/Science Communication

[PREPRINT] Sci-comm “behind the scenes”: Gendered narratives of scientific outreach activities in the life sciences – Perry G. Beasley-Hall et al – bioRxiv