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
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 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 17, 2024
Human Microbiome
Stratification of Fusobacterium nucleatum by local health status in the oral cavity defines its subspecies disease association – Madeline Krieger – Cell Host & Microbe
Bile acids modified by the intestinal microbiota promote colorectal cancer growth by suppressing CD8(+) T cell effector functions – Jingjing Cong – Immunity
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease – Xin Zhou – Cell Host & Microbe
Body mass index can mediate the interplay between gut microbiome and sleep disorders – Lng Adami – Sleep Medicine
Review: Postbiotic butyrate: role and its effects for being a potential drug and biomarker to pancreatic cancer – Abinaya Elango – Archives of Microbiology
Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease – Filippo Martinelli – Scientific Reports
Antibacterial activity of nonantibiotics is orthogonal to standard antibiotics – Mariana Noto Guillen – Science
Defining Porphyromonas gingivalis strains associated with periodontal disease – Vijaya Murugaiyan – Scientific Reports
Review: The individual response to antibiotics and diet – insights into gut microbial resilience and host metabolism – Lars M M Vliex – Nature Reviews Endocrinology
Unveiling the immunomodulatory effect of the novel probiotic Akkermansia muciniphila and its protective effect in vitro – Alba Calvo – Microbiological Research
Microbial metabolite enhances immunotherapy efficacy by modulating T cell stemness in pan-cancer – Dingjiacheng Jia – Cell
Animal Microbiome
Rice straw ash and amphibian health: A deep dive into microbiota changes and potential ecological consequences – Wen-Jing Dong – The Science of the Total Environment
Microbial community composition in the dung of five sympatric European herbivore species – Xingzhao Sun – Ecology and Evolution
Antibiotics treatment promotes vasculogenesis in the brain of glioma-bearing mice – Maria Rosito – Cell Death & Disease
Environmental Microbiome
Microecological characteristics of water bodies/sediments and microbial remediation strategies after 50 years of pollution exposure in ammunition destruction sites in China – Xu Yang – Environmental Research
Microbiome Analysis: Tools, Protocols, Techniques and Resources
Review: Transkingdom Network Analysis (TkNA): a systems framework for inferring causal factors underlying host-microbiota and other multi-omic interactions – Nolan K Newman – Nature Protocols
Resource competition predicts assembly of gut bacterial communities in vitro – Po-Yi Ho – Nature Microbiology
March 13, 2024
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 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
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