Tag Archives: Animal microbiome

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

March 3, 2024

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Human and General Microbiome

The influence of placenta microbiota of normal term pregnant women on immune regulation during pregnancy – Ping Yang – BMC Pregnancy and Childbirth

Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial – Mary Ni Lochlainn – Nature Communications

A metagenomic catalog of the early-life human gut virome – Shuqin Zeng – Nature Communications

Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study – Paula Istvan – Nature Communications

Bisphenol A exposure affects specific gut taxa and drives microbiota dynamics in childhood obesity – Ana Lopez-Moreno – mSystems

Prevotella, a dominant bacterium in young people with stage Ⅲ periodontitis, related to the arachidonic acid metabolism pathway – Qin Ye – Microbes and Infection

Dual membrane-spanning anti-sigma factors regulate vesiculation in Bacteroides thetaiotaomicron – Evan J Pardue – PNAS

Beneficial Microbes and Compounds

Blautia coccoides is a Newly Identified Bacterium Increased by Leucine Deprivation and has a Novel Function in Improving Metabolic Disorders – Yuguo Niu – Advanced Science

Fecal Microbiota Transplantation in Amyotrophic Lateral Sclerosis: Clinical Protocol and Evaluation of Microbiota Immunity Axis – Elena Niccolai – Methods in Molecular Biology

Effect of Lactobacillus reuteri NCIMB 30351 drops on symptoms of infantile functional gastrointestinal disorders and gut microbiota in early infants: Results from a randomized, placebo-controlled clinical trial – Oleg Yu Tyrsin – European Journal of Pediatrics

Animal Microbiome

Gut microbiota facilitate adaptation of invasive moths to new host plants – Shouke Zhang – The ISME Journal

Plant Microbiome

A Synthetic Microbiome Based on Dominant Microbes in Wild Rice Rhizosphere to Promote Sulfur Utilization – Changji Wang – Rice

Environmental Microbiome

Life at the borderlands: microbiomes of interfaces critical to One Health – Simon R Law – FEMS Microbiology Reviews

Neural network establishes co-occurrence links between transformation products of the contaminant and the soil microbiome – Yuhui Xiang – The Science of the Total Environment

Microbiome Analysis: Tools, Protocols, Techniques and Resources

Review: Transforming Big Data into AI-ready data for nutrition and obesity research – Diana M Thomas – Obesity

Explainable artificial intelligence for microbiome data analysis in colorectal cancer biomarker identification – Pierfrancesco Novielli – Frontiers in Microbiology

A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass – Joana Pereira-Marques – Gut Microbes

On the limits of 16S rRNA gene-based metagenome prediction and functional profiling – Monica Steffi Matchado – Microbial Genomics


February 28, 2024

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Human gut microbiome

Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging – Shalini Singh – BMC Microbiome

Safety, feasibility, and impact on the gut microbiome of kefir administration in critically ill adults – Vinod K. Gupta – BMC Medicine

Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip – Jeeyon Lee – Advanced Science

Animal experiments

CRB1-associated retinal degeneration is dependent on bacterial translocation from the gut – Shanzhen Peng – Cell

Amino acid formula induces microbiota dysbiosis and depressive-like behavior in mice – Ji Hu – Cell Reports

Bacteroides fragilis aggravates high-fat diet-induced non-alcoholic fatty liver disease by regulating lipid metabolism and remodeling gut microbiota – Yumei Huang – Microbiology Spectrum

Animal microbiome

Gut microbiota modulation enhances the immune capacity of lizards under climate warming – Jing Yang – BMC Microbiome

Gut microbiota contribute to variations in honey bee foraging intensity – Cassondra L Vernier – ISME Journal

Virome diversity shaped by genetic evolution and ecological landscape of Haemaphysalis longicornis – Run-Ze Ye – BMC Microbiome

Multi-omics reveal mechanisms of high enteral starch diet mediated colonic dysbiosis via microbiome-host interactions in young ruminant – Chunjia Jin – BMC Microbiome

Plant, root, and soil microbiome

[PREPRINT] Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils – Valerie A Seitz – Research Square

Stronger compensatory thermal adaptation of soil microbial respiration with higher substrate availability – Lingrui Qu – ISME Journal

Built environment

Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants – Yulin Zhang – mSystems

Water and extremophile microbiome

Novel functional insights into the microbiome inhabiting marine plastic debris: critical considerations to counteract the challenges of thin biofilms using multi-omics and comparative metaproteomics – Lauren F. Messer – BMC Microbiome

Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides – Feng-Qing Wang – BMC Microbiome

Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea – Tianshuo Zu – Microbial Ecology

Beneficial microbes

[PREPRINT] 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

Neuroprotective Effects of Bifidobacterium animalis subsp. lactis NJ241 in a Mouse Model of Parkinson’s Disease: Implications for Gut Microbiota and PGC-1α – Yuxuan Dong – Molecular Neurobiology

February 15, 2024

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Human and General Microbiome

Review: Gastrointestinal and brain barriers: unlocking gates of communication across the microbiota-gut-brain axis – María R Aburto – Nature Reviews Gastroenterology & Hepatology

Alterations of gut microbiota in infants with biliary atresia identified by 16S rRNA-sequencing – Fei Liu – BMC Pediatrics

Culture- and non-culture-based approaches reveal unique features of the ocular microbiome in dry eye patients – Maria Naqvi – The Ocular Surface

Animal Microbiome

Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria – Lluvia Vargas-Gastélum – mSphere

Beneficial Microbes 

Colonic probiotic insufflation: clinical proposal for an economical game-changer for restoration of the gut microbiome in colorectal cancer and beyond – Ryan Varghese – International Journal of Surgery

Neuroprotective Effect of a Multistrain Probiotic Mixture in SOD1(G93A) Mice by Reducing SOD1 Aggregation and Targeting the Microbiota-Gut-Brain Axis – Zikai Xin – Molecular Neurobiology

Plant Microbiome

Metagenomic and biochemical analyses reveal the potential of silicon to alleviate arsenic toxicity in rice (Oryza sativa L.) – Temoor Ahmed – Environmental Pollution

Mechanisms on salt tolerant of Paenibacillus polymyxa SC2 and its growth-promoting effects on maize seedlings under saline conditions – Chengqiang Wang – Microbiological Research

Environmental Microbiome

Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones – Hao Sun – Microbiome

Biogeography and assembly processes of abundant and rare soil microbial taxa in the southern part of the Qilian Mountain National Park, China – Zhilin Feng – Ecology and Evolution


Microbiome Analysis: Tools, Techniques and Resources

A Clinical Breathomics Dataset – Ping-Hung Kuo – Scientific Data

DeepMPTB: a vaginal microbiome-based deep neural network as artificial intelligence strategy for efficient preterm birth prediction – Oshma Chakoory – Biomarker Research

MicroMPN: methods and software for high-throughput screening of microbe suppression in mixed populations – Karla Franco Meléndez – Microbiology Spectrum

Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario – Manna Zhao – Frontiers in Cellular and Infection Microbiology