Tag Archives: microbiome analysis

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

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 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 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 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 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

January 20, 2024

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Human and General Microbiome

Gut microbiome for predicting immune checkpoint blockade-associated adverse events – Muni Hu – Genome Medicine

The fusion of multi-omics profile and multimodal EEG data contributes to the personalized diagnostic strategy for neurocognitive disorders – Yan Han – Microbiome

Prediction of lung cancer using novel biomarkers based on microbiome profiling of bronchoalveolar lavage fluid – Gihyeon Kim – Scientific Reports

Exploring the intestinal ecosystem: from gut microbiota to associations with subtypes of inflammatory bowel disease – Fan Li – Frontiers in Cellular and Infection Microbiology

Simulated digestions of free oligosaccharides and mucin-type O-glycans reveal a potential role for Clostridium perfringens – Andrew G McDonald – Scientific Reports

Oral microbiome associated with differential ratios of Porphyromonas gingivalis and Streptococcus cristatus – Qingguo Wang – Microbiology Spectrum

Impact of intratumoral microbiome on tumor immunity and prognosis in human pancreatic ductal adenocarcinoma – Shohei Abe – Journal of Gastroenterology

Evaluation of gut microbiota predictive potential associated with phenotypic characteristics to identify multifactorial diseases – Danielle Cristina Fonseca – Gut Microbes

Review: The Gut Microbiome Affects Atherosclerosis by Regulating Reverse Cholesterol Transport – Yangyang Jiang – Journal of Cardiovascular Translational Research

Review: Role of vertical and horizontal microbial transmission of antimicrobial resistance genes in early life: insights from maternal-infant dyads – Manuel Bernabeu – Current Opinion in Microbiology

Beneficial Microbes and Compounds

Complement in breast milk modifies offspring gut microbiota to promote infant health – Dongqing Xu – Cell

An Oral Nanomedicine Elicits In Situ Vaccination Effect against Colorectal Cancer – Menghang Zu – ACS Nano

Model and Non-Model Animal Microbiome 

Oral bacteria accelerate pancreatic cancer development in mice – Elias Saba – Gut

Bacterial community and diversity in the rumen of 11 Mongolian cattle as revealed by 16S rRNA amplicon sequencing – Yijiu Jia – Scientific Reports

Novel taxonomic and functional diversity of eight bacteria from the upper digestive tract of chicken – Bibiana Rios-Galicia – International Journal of Systematic and Evolutionary Microbiology

Plant Microbiome

A tripartite bacterial-fungal-plant symbiosis in the mycorrhiza-shaped microbiome drives plant growth and mycorrhization – Changfeng Zhang – Microbiome

Host genotype, soil composition, and geo-climatic factors shape the fonio seed microbiome – Naheed Tabassum – Microbiome

The role of plants in ironstone evolution: iron and aluminium cycling in the rhizosphere – Anat Paz – The Science of the Total Environment

Consistent effects of independent domestication events on the plant microbiota – Riccardo Soldan – Current Biology 

Inactivation of siderophore iron-chelating moieties by the fungal wheat root symbiont Pyrenophora biseptata – Katie S French – Environmental Microbiology Reports

Environmental Microbiome

New insights into inhibition of high Fe(III) content on anaerobic digestion of waste-activated sludge – Xuepeng Wang – The Science of the Total Environment

Microbiome Analysis: Tools, Techniques and Resources

Drying as an effective method to store soil samples for DNA-based microbial community analyses: a comparative study – Emily Smenderovac – Scientific Reports

Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines – E Michael Valencia – Scientific Data

Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics – Georgios Marinos – Microbiology Spectrum

Metagenomes and metagenome-assembled genomes from ex vivo fecal incubations of six unique donors – Adrienne B Narrowe – Microbiology Resource Announcements

Bioinformatic Approach to Investigate Larvae Gut Microbiota Cellulosimicrobium protaetiae via Whole-Genome Analysis – Han Le Ho – Molecular Biotechnology





January 14, 2024

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Human and General Microbiome

Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course – Melanie Schirmer – Cell Host & Microbe

Incorporating metabolic activity, taxonomy and community structure to improve microbiome-based predictive models for host phenotype prediction – Mahsa Monshizadeh – Gut Microbes

Microbiota and mucosal gene expression of fecal microbiota transplantation or placebo treated patients with chronic pouchitis – Anna K Hartikainen – Gut Microbes

A robust microbiome signature for autism spectrum disorder across different studies using machine learning – Lucia N Peralta-Marzal – Scientific Reports

Nasal lavage microbiome, but not nasal swab microbiome, correlates with sinonasal inflammation in children with cystic fibrosis – Jaehi Chung – Journal of Cystic Fibrosis

A Gpr35-tuned gut microbe-brain metabolic axis regulates depressive-like behavior – Lingsha Cheng – Cell Host & Microbe

The salivary microbiota of patients with acute lower respiratory tract infection-A multicenter cohort study – Matthew B Rogers – PloS One

The endometrial microbiota and early pregnancy loss – Joshua Odendaal – Human Reproduction

Multi-omics of the gut microbial ecosystem in patients with microsatellite-instability-high gastrointestinal cancer resistant to immunotherapy – Siyuan Cheng – Cell Reports. Medicine

The microbial metabolite urolithin A reduces Clostridioides difficile toxin expression and toxin-induced epithelial damage – Sweta Ghosh – mSystems

Impact of Periodontitis on the Leakage of Oral Bacteria to the Gut – E Buetas – Journal of Dental Research 

Review: Changes in the fecal microbiota of breast cancer patients based on 16S rRNA gene sequencing: a systematic review and meta-analysis – Biqing Luan – Clinical & Translational Oncology

Review: Bacteroides and related species: The keystone taxa of the human gut microbiota – Jae Hyun Shin – Anaerobe

Review: Enhancing microbiome research in sub-Saharan Africa – Kolawole I Ayeni – Trends in Microbiology

Animal Microbiome (Model and non-model organisms)

Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations – Yizhao Shen – GigaScience

Gut microbiota variations in wild yellow baboons (Papio cynocephalus) are associated with sex and habitat disturbance – Marina Bambi – Scientific Reports

Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet – Tomoya Tsukimi – mSystems

Candidatus Methanosphaera massiliense sp. nov., a methanogenic archaeal species found in a human fecal sample and prevalent in pigs and red kangaroos – Virginie Pilliol – Microbiology Spectrum

Plant and Soil Microbiome

A novel plant growth-promoting rhizobacterium, Rhizosphaericola mali gen. nov., sp. nov., isolated from healthy apple tree soil – Han Sol Kim – Scientific Reports

Manipulation of the seagrass-associated microbiome reduces disease severity – Olivia J Graham – Environmental Microbiology

Microbiome Analysis: Tools, Techniques and Resources

Assessment of DNA extraction methods for human gut mycobiome analysis – Piyapat Rintarhat – Royal Society Open Science

NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing – Yusen Lin – Briefings in Bioinformatics

BactInt: A domain driven transfer learning approach for extracting inter-bacterial associations from biomedical text – Krishanu Das Baksi – Computational Biology and Chemistry

The African Human Microbiome Portal: a public web portal of curated metagenomic metadata – Anmol Kiran – Database 

MK-BMC: a Multi-Kernel framework with Boosted distance metrics for Microbiome data for Classification – Huang Xu – Bioinformatics

December 29, 2023

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Human and General Microbiome

Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults – Xuanji Li – Nature Communications

Social anxiety disorder-associated gut microbiota increases social fear – Nathaniel L Ritz – PNAS

Plasmid-encoded toxin defence mediates mutualistic microbial interactions – Sarah Moraïs – Nature Microbiology

Oral microbiome-driven virulence factors: A novel approach to pancreatic cancer diagnosis – Xuemin Zeng – Biomolecules & Biomedicine

The Gut Microbiome: A Primer for the Clinician – Olga C Aroniadis – The American Journal of Gastroenterology

Exploring the role of gut microbiota in migraine risk: a two-sample Mendelian randomization study – Xiangyue Meng – Scandinavian Journal of Gastroenterology

High-Throughput Combined Analysis of Saliva Microbiota and Metabolomic Profile in Chinese Periodontitis Patients: A Pilot Study – Jing Ding – Inflammation

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research – Jonathan L Golob – Cell Reports. Medicine

Impact of dietary inflammatory index on gingival health – Roberta Andrade Reis – Journal of Periodontology

Air particulate pollution exposure associated with impaired cognition via microbiota gut-brain axis: an evidence from rural elderly female in northwest China – Jia Yuan – Environmental Science and Pollution Research International

Metabolic flux and catabolic kinetics of prebiotic-like dietary polyphenol phlorizin in association with gut microbiota in vitro – Jiang Chen – Food Chemistry

Review: Genital tract microbiota composition profiles and use of prebiotics and probiotics in gynaecological cancer prevention: review of the current evidence, the European Society of Gynaecological Oncology prevention committee statement – Anita Mitra – The Lancet. Microbe

Review: Wound Microbiota and Its Impact on Wound Healing – Małgorzata Zielińska – International Journal of Molecular Sciences

Review: Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem – Shuang Wang – Gut Microbes

Animal Model Studies

Gut microbiome responds to alteration in female sex hormone status and exacerbates metabolic dysfunction – Tzu-Wen L Cross – Gut Microbes

Oral fecal transplantation enriches Lachnospiraceae and butyrate to mitigate acute liver injury – Chun-Ju Yang – Cell Reports 

Impact of various high fat diets on gene expression and the microbiome across the mouse intestines – Jose Martinez-Lomeli – Scientific Reports

Non-Model Animal Microbiome

Characteristics of gut microbiota in captive Asian elephants (Elephas maximus) from infant to elderly – Sarisa Klinhom – Scientific Reports

Honeybee symbiont Bombella apis could restore larval-to-pupal transition disrupted by antibiotic treatment – Chen Xiaowen – Journal of Insect Physiology

Toll receptor ligand Spätzle 4 responses to the highly pathogenic Enterococcus faecalis from Varroa mites in honeybees – Wenhao Zhang – PLoS Pathogens

Plant Microbiome

Review: Unveiling the significance of rhizosphere: Implications for plant growth, stress response, and sustainable agriculture – Wogene Solomon – Plant Physiology and Biochemistry

Environmental Microbiome

Connecting molecular biomarkers, mineralogical composition, and microbial diversity from Mars analog lava tubes – Vera Palma – The Science of the Total Environment

The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome – Ate H Jaarsma – Frontiers in Microbiology

Review: A global review on the abundance and threats of microplastics in soils to terrestrial ecosystem and human health – Wenshan Shi – The Science of the Total Environment

Microbiome analysis: tools, techniques and resources

VIBES: A consensus subtyping of the vaginal microbiota reveals novel classification criteria – Diego Fernández-Edreira – Computational and Structural Biotechnology Journal

Generalized matrix decomposition regression: estimation and inference for two-way structured data – Yue Wang – The Annals of Applied Statistics

Single-cell and spatiotemporal transcriptomic analyses reveal the effects of microorganisms on immunity and metabolism in the mouse liver – Ruizhen Zhao – Computational and Structural Biotechnology Journal

PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions – David Vorländer – Biotechnology and Bioengineering

Mock microbial community meta-analysis using different trimming of amplicon read lengths – Diana Haider – Environmental Microbiology

Review: In Vitro Models for Investigating Intestinal Host-Pathogen Interactions – Reece McCoy – Advanced Science