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
Category Archives: Animal experiments
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 18, 2024
Today’s digest features the human gut microbiome atlas of Africa, sociobiome, a large human gut Bacteroidales culture collection, Patescibacteria in global waste water treatment plants, and more.
This month, the May 2024 contribution period of Outreachy started! Outreachy, as an internship program, supports diversity in open source & open science!
See you at #MVIF!
Gut microbiome
Expanding the human gut microbiome atlas of Africa – Dylan G Maghini – bioRxiv
Review: The individual response to antibiotics and diet — insights into gut microbial resilience and host metabolism – Lars M. M. Vliex – Nature Reviews Endocrinology
The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study – Leon Peto – medRxiv
Multi-omics analysis of the gut microbiome and metabolites associated with the psychoneurological symptom cluster in children with cancer receiving chemotherapy – Jinbing Bai – Journal of Translational Medicine
Longitudinal analysis of the gut microbiome in adolescent patients with anorexia nervosa: microbiome-related factors associated with clinical outcome – Nadia Andrea Andreani – Gut Microbes
Healthy microbiome – moving towards functional interpretation – Kinga Zielińska – bioRxiv
Sociobiome – Individual and neighborhood socioeconomic status influence the gut microbiome in a multi-ethnic population in the US – Soyoung Kwak – npj Biofilms and Microbiomes
Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans – Sarah Morais – Science
Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution – Zhenrun J. Zhang – bioRxiv
Animal experiment
A history of repeated antibiotic usage leads to microbiota-dependent mucus defects – Kertu Liis Krigul – bioRxiv
Water microbiome
Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants – Huifeng Hu – Microbiome
Bioinformatics
Review: Challenges in computational discovery of bioactive peptides in ’omics data – Luis Pedro Coelho – Proteomics
For long-term sustainable software in bioinformatics – Luis Pedro Coelho – Plos Computational Biology
Data-driven prediction of colonization outcomes for complex microbial communities – Lu Wu – Nature Communications
March 7, 2024
General microbiome
[OPINION]Toward an integrative framework for microbial community coalescence – Custer, Bresciani & Dini-Andreote – Trends in Microbiology
Studying mixed-species biofilms of Candida albicans and Staphylococcus aureus using evolutionary game theory – Dühring & Schuster – PLOS One
Human oral microbiome
Microbial Communities and Functional Genes in Periodontitis and Healthy Controls – Ma et al. – International Dental Journal
Human gut microbiome
[REVIEW]Unlocking the secrets: exploring the influence of the aryl hydrocarbon receptor and microbiome on cancer development – Rayan et al. – Cellular & Molecular Biology Letters
Short term supplementation with cranberry extract modulates gut microbiota in human and displays a bifidogenic effect – Lessard-Lord et al. – npj Biofilms and Microbiomes
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
Fecal microbiota impacts development of Cryptosporidium parvum in the mouse – Widmer & Creasey – Scientific reports
High fat diet is associated with gut microbiota dysbiosis and decreased gut microbial derived metabolites related to metabolic health in young Göttingen Minipigs – Lützhøft et al. – PLOS One
Animal microbiome (for animals in the wild)
Gustatory Responsiveness of Honey Bees Colonized with a Defined or Conventional Gut Microbiota – Suenami, Sato & Miyazaki – Microbes and Environments
[REVIEW]Fungal infection of insects: molecular insights and prospects – Hong et al. – Trends in Microbiology
Plant, root, and soil microbiome
Microbiome sequencing revealed the abundance of uncultured bacteria in the Phatthalung sago palm-growing soil – Nutaratat et al. – PLOS One
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)
Assigning the unassigned: A signature-based classification of rDNA metabarcodes reveals new deep-sea diversity – Angeles et al. – PLOS One
February 29, 2024
Human oral microbiome
Using formalin fixed paraffin embedded tissue to characterize the microbiota in p16-positive and p16-negative tongue squamous cell carcinoma: a pilot study – Yuanbo et al. – BMC Oral Health
Human gut microbiome
Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota – Carasso et al. – Cell Host & Microbe
Integrated multi-omics analysis reveals gut microbiota dysbiosis and systemic disturbance in major depressive disorder – Xie et al. – Psychiatry Research
Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection – Nooij et al. – Genome Medicine
Bacteroides salyersiae is a potent chondroitin sulfate-degrading species in the human gut microbiota – Wang et al. – Microbiome
Elemental iron protects gut microbiota against oxygen-induced dysbiosis – Ostrov et al. PLOS One
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
Fecal microbiota transplantation ameliorates abdominal obesity through inhibiting microbiota-mediated intestinal barrier damage and inflammation in mice – Zhu et al. – Microbiological Research
Animal microbiome (for animals in the wild)
Exploring the modulatory effects of brown seaweed meal and extracts on intestinal microbiota and morphology of broiler chickens challenged with heat stress – Oretomiloye & Adewole – Poultry Science
Plant, root, and soil microbiome
Synthetic microbe-to-plant communication channels – Boo et al. Nature Communications
Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil – Li et al. – Microbiome
Influence of climatic variation on microbial communities during organic Pinot noir wine production – Ohwofasa et al. – PLOS One
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
February 23, 2024
Today’s digest features the MetaPhlAn v4.1 & viral module, early life gut microbiome and diabetes, human milk oligosaccharides study, and more.
NEWS
MVIF has launched their crowdfunding campaign https://www.gofundme.com/f/me-mvif
See you at #MVIF next week!
Oral microbiome
Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Davide Bazzani – npj Biofilms and Microbiomes
Nasal microbiome
Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Y Zhao – bioRxiv
Semen microbiome
Characterisation and comparison of semen microbiota and sperm function in men with infertility, recurrent miscarriage, or proven fertility – Shahriar Mowla – bioRxiv
Gut microbiome
CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei – Sivan Kijner – Nature Communications
Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study – Kinga Humińska-Lisowska – Plos One
The impact of iron supplementation on the preterm neonatal gut microbiome: A pilot study – Matthew VanOrmer – Plos One
Early-life exposures to specific commensal microbes prevent type 1 diabetes – Jamal Green – bioRxiv
Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing – Philipp Spohr – Scientific Reports
Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome – Qiyi Chen – Cell Host & Microbe
Animal experiment
The gut ileal mucosal virome is disturbed in patients with Crohn’s disease and exacerbates intestinal inflammation in mice – Zhirui Cao – Nature Communications
Animal microbiome
Gut microbiome diversity and function during hibernation and spring emergence in an aquatic frog – Ji-Eun Lee – Plos One
Unraveling the gut microbiota of Tibetan chickens: insights into highland adaptation and ecological advantages – Tao Zeng – bioRxiv
Water microbiome
A difficult coexistence: resolving the iron-induced nitrification delay in groundwater filters – Francesc Corbera-Rubio – bioRxiv
Human virome
Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Moreno Zolfo – bioRxiv
February 21, 2024
Human nasal microbiome
[PREPRINT]Nasal commensals reduce Staphylococcus aureus proliferation by restricting siderophore availability – Zhao et al. – bioRxiv
Human oral microbiome
Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases – Bazzani et al. – npj Biofilms and Microbiomes
Human gut microbiome
Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity – Behling et al. – Microbiome
Animal microbiome
Psychological stress-induced microbial metabolite indole-3-acetate disrupts intestinal cell lineage commitment – Wei et al. – Cell Metabolism
Gut microbiota contributes to bisphenol A-induced maternal intestinal and placental apoptosis, oxidative stress, and fetal growth restriction in pregnant ewe model by regulating gut-placental axis – Zhang et al. – Microbiome
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)
Novel insights into the rhizosphere and seawater microbiome of Zostera marina in diverse mariculture zones – Sun et al. – Microbiome
Alteration of bacterial community composition in the sediments of an urban artificial river caused by sewage discharge – Li et al. – PeerJ
The exometabolome of microbial communities inhabiting bare ice surfaces on the southern Greenland Ice Sheet – Doting et al. – Environmental Microbiology
Searching for microbial contribution to micritization of shallow marine sediments – Garuglieri et al. – Environmental Microbiology
Food microbiology
Unveiling the microbial communities and metabolic pathways of Keem, a traditional starter culture, through whole-genome sequencing – Rana et al. – Scientific Reports
Phages and viruses
[PREPRINT]Fecal Virome Transplantation (FVT) from healthy humans remodels the gut bacteriome and virome and reduces metabolic syndrome in mice – Cervantes-Echeverría et al. – bioRxiv
[PREPRINT]Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples – Zolfo et al. – bioRxiv
Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)
Why addressing how our brain and our gut talk to each other matter for IBS – Gut microbiota for health
February 13, 2024
General microbiome
Model-free prediction of microbiome compositions – Asher & Bashan – Microbiome
Pregnancy and early life
Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition – Mercer et al. – Microbiome
Human airway microbiome
Genomic attributes of airway commensal bacteria and mucosa – Cuthbertson et al. – Communications Biology
Human skin microbiome
[REVIEW]Triggers for the onset and recurrence of psoriasis: a review and update – Liu et al. – Cell Communication and Signaling
Human vaginal microbiome
Uterine fibroids and longitudinal profiles of the vaginal microbiota in a cohort presenting for transvaginal ultrasound – Robbins – PLOS One
Human gut microbiome
Microbial-derived imidazole propionate links the heart failure-associated microbiome alterations to disease severity – Raju et al. – Genome Medicine
Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity – Behling et al. – Microbiome
Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe – Colorado et al. – Microbiome
Gut microbiome signature of metabolically healthy obese individuals according to anthropometric, metabolic and inflammatory parameters – Lee et al. – Scientific Reports
Animal microbiome
Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties – Shen et al. – Microbiome
Falcon gut microbiota is shaped by diet and enriched in Salmonella – Ahmad et al. – PLOS One
Sex differences in colonic gene expression and fecal microbiota composition in a mouse model of obesity-associated colorectal cancer – Chang et al. – Scientific Reports
Cadaver decomposition microbiome
A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables – Burcham et al. – Nature Microbiology
Bioinformatics
YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample – Koslicki et al. – Bioinformatics
Gut microbiome-metabolome interactions predict host condition – Shtossel et al. – Microbiome
Techniques
Fecal microbiome composition and diversity of cryopreserved canine stool at different duration and storage conditions – Barko et al. – PLOS One
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