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
Tag Archives: bioinformatics
March 31, 2024
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
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
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
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 13, 2024
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
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
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
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
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
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
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