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: gut-health
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 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 6, 2024
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
February 28, 2024
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
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