Category Archives: Human gut

April 12, 2024

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Today’s digest features human gut microbiome studies on dietary fiber and fasting glucose, ocean microbiome, pangenome approaches, and more.

See you at #MVIF!

Oral microbiome

Saliva sampling method influences oral microbiome composition and taxa distribution associated with oral diseases – Cristian Roca – PlosOne

Gut microbiome

Changes in the intestinal microbiota of individuals with non-alcoholic fatty liver disease based on sequencing: An updated systematic review and meta-analysis – Wenpin Cai – PlosOne

Gut microbiota differences in stunted and normal-lenght children aged 36–45 months in East Nusa Tenggara, Indonesia – Ingrid S. Surono – PlosOne

Integrating research on bacterial pathogens and commensals to fight infections—an ecological perspective – Lisa Maier – The Lancet Microbe

Recommendations for the Use of Dietary Fiber to Improve Blood Pressure Control – Hamdi A. Jama – Hypertension

Review: Prebiotic selection influencing inflammatory bowel disease treatment outcomes: a review of the preclinical and clinical evidence – Amin Ariaee – eGastroenterology

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments – Torben Soelbeck Rasmussen – bioRxiv

Continuous glucose monitoring and intrapersonal variability in fasting glucose – Smadar Shilo – Nature Medicine

Animal microbiome

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens – Seyed Hossien Kairmi – PlosOne

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency – Naomi Sarpong – Frontiers in Microbiology

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

Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants – Zhe Pan – ISME Communications

Ocean microbiome

Decoding populations in the ocean microbiome – Ramiro Logares – Microbiome

Bioinformatics

High-resolution Profiling of Bacterial and Fungal Communities using Pangenome-Informed Taxon-Specific Long-Read Amplicons – Luzia Stalder – bioRxiv

CELEBRIMBOR: Pangenomes from metagenomes – Joel Hellewell – bioRxiv

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 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 20, 2024

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Human gut and general microbiome

Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition – Hao-Wei Chang et al – Nature Microbiology

Outcomes after Fecal Microbiota Transplantation in combination with Bezlotoxumab for Inflammatory Bowel Disease and Recurrent C. difficile Infection – Jessica R Allegretti – American Journal of Gastroenterology

Diosmin alleviates ulcerative colitis in mice by increasing Akkermansia muciniphila abundance, improving intestinal barrier function, and modulating the NF-κB and Nrf2 pathways – Maha Badr Salem et al – Cell Heliyon

Gut microbiota profiling in obese children from Southeastern China – Jingjing Wang et al – BMC Pediatrics

A flexible high-throughput cultivation protocol to assess the response of individuals’ gut microbiota to diet-, drug-, and host-related factors – Janina N Zünd et al – ISME Communications

Animal experiments

Intact lung tissue and bronchoalveolar lavage fluid are both suitable for the evaluation of murine lung microbiome in acute lung injury – Lijun Zheng et al – BMC Microbiome

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

Plant, soil, and environmental microbiome

Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development – Chao Xiong et al – mSystems

Bacterial communities associated with an island radiation of lichen-forming fungi – Miguel Blázquez et al – PLOS ONE

Built environment microbiome

Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing – Enoch Narh Kudjordjie et al – PLOS One

The composition of the bacterial communities collected from the PM10 samples inside the Seoul subway and railway station – Shambhavi Sharma et al – Nature Scientific Reports

Bioinformatics

Differential network connectivity analysis for microbiome data adjusted for clinical covariates using jackknife pseudo-values – Seungjun Ahn & Somnath Datta – BMC Bioinformatics

Beneficial microbes & microbial metabolites
Natural intestinal metabolite xylitol reduces BRD4 levels to mitigate renal fibrosis – Zhouke Tan et al – Clinical and Translational Science

Probiotics supplementation during pregnancy or infancy on multiple food allergies and gut microbiota: a systematic review and meta-analysis – Lan Jiang et al – Nutrition Reviews

Non-Microbiome Microbiology

Koch’s curse: How models of extreme pathology bias studies of host–pathogen interactions – Kalyan K. Dewan & Eric T. Harvill – PLOS Pathogens

March 18, 2024

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Today’s digest features the human gut microbiome atlas of Africa, sociobiome, a large human gut Bacteroidales culture collection, Patescibacteria in global waste water treatment plants, and more.

This month, the May 2024 contribution period of Outreachy started! Outreachy, as an internship program, supports diversity in open source & open science!

See you at #MVIF!

Gut microbiome

Expanding the human gut microbiome atlas of Africa – Dylan G Maghini – bioRxiv

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

The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study – Leon Peto – medRxiv

Multi-omics analysis of the gut microbiome and metabolites associated with the psychoneurological symptom cluster in children with cancer receiving chemotherapy – Jinbing Bai – Journal of Translational Medicine

Longitudinal analysis of the gut microbiome in adolescent patients with anorexia nervosa: microbiome-related factors associated with clinical outcome – Nadia Andrea Andreani – Gut Microbes

Healthy microbiome – moving towards functional interpretation – Kinga Zielińska – bioRxiv

Sociobiome – Individual and neighborhood socioeconomic status influence the gut microbiome in a multi-ethnic population in the US – Soyoung Kwak – npj Biofilms and Microbiomes

Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans – Sarah Morais – Science

Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution – Zhenrun J. Zhang – bioRxiv

Animal experiment

A history of repeated antibiotic usage leads to microbiota-dependent mucus defects – Kertu Liis Krigul – bioRxiv

Water microbiome

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – Microbiome

Bioinformatics

Review: Challenges in computational discovery of bioactive peptides in ’omics data – Luis Pedro Coelho – Proteomics

For long-term sustainable software in bioinformatics – Luis Pedro Coelho – Plos Computational Biology

Data-driven prediction of colonization outcomes for complex microbial communities – Lu Wu – Nature Communications

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