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 microbiome
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
March 1, 2022
General microbiome
Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses – Ramaloko et al. – Environmental Microbiology
Global diversity and distribution of mushroom-inhabiting bacteria – Gohar et al. – Environmental Microbiology Reports
Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on blaNDM Transmission – Dong et al. – Microbiology Spectrum
Multi-site human microbiome
Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis – Cai et al. – Microbiology Spectrum
Human respiratory microbiome
Early life inter-kingdom interactions shape the immunological environment of the airways – C Pattaroni et al. – Microbiome
Human gut microbiome
Altered gut metabolites and microbiota interactions are implicated in colorectal carcinogenesis and can be non-invasive diagnostic biomarkers – Coker et al. – Microbiome
Animal experiments
Development of a rational framework for the therapeutic efficacy of fecal microbiota transplantation for calf diarrhea treatment – Islam et al. – Microbiome
Animal microbiome
Comparative microbiome analysis of Diaphorina citri and its associated parasitoids Tamarixia radiata and Diaphorencyrtus aligarhensis reveals Wolbachia as a dominant endosymbiont – Ashraf et al. – Environmental Microbiology
Plant, root, and soil microbiome
Core arbuscular mycorrhizal fungi are predicted by their high abundance-occupancy relationship while host-specific taxa are rare and geographically structured – Kajihara et al. – New Phytologist
Embracing mountain microbiome and ecosystem functions under global change – Wang et al. – New Phytologist
Nitrogen fertilization disrupts the temporal dynamics of arbuscular mycorrhizal fungal hyphae but not spore density and community composition in a wheat field – Babalola et al. – New Phytologist
Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain – Pang et al. – Microbiology Spectrum
Seed microbiota revealed by a large-scale meta-analysis including 50 plant species – Simonin et al. – New Phytologist
Viewpoint: Plant–microbe eco-evolutionary dynamics in a changing world – Angulo et al. – New Phytologist
Stem traits, compartments, and tree species affect fungal communities on decaying wood – Yang et al. – Environmental Microbiology
Microplastics reduce soil microbial network complexity and ecological deterministic selection – Shi et al. – Environmental Microbiology
The core root microbiome of Spartina alterniflora is predominated by sulfur-oxidizing and sulfate-reducing bacteria in Georgia salt marshes, USA – Rolando et al. – Microbiome
Water and extremophile
“Boom-and-busted-dynamics” of phytoplankton-virus interactions explain the paradox of the plankton – Flynn et al. – New Phytologist
Communality in microbial stress response and differential metabolic interactions revealed by time-series analysis of sponge symbionts – Taylor et al. – Environmental Microbiology
Global 16S rRNA diversity of provannid snail endosymbionts from Indo-Pacific deep-sea hydrothermal vents – Breusing et al. – Environmental Microbiology Reports
Sources of protein diet differentially stimulate the gut and water microbiota under freshwater crayfish, marron (Cherax cainii, Austin 2002) culture – Foysal et al. – Environmental Microbiology Reports
November 6, 2020
Shalom from Israel!
While the eyes of the world are looking at the US elections results, it’s good to know that the world of microbiome research is stable and produces great scientific discoveries. So stop refreshing the news websites, grab yourself a cup of cofee and enjoy your Saturday.
Today’s digest has some great papers about memory in microboimes, factors that shapes bacterial growth, infant skin microbial communities, degraded soils restoration using self-assembly communities, songbirds microbiome, antiSMASH3 is out (!), useful youtube video for metagenome ML analysis in MATLAB and more. Reminding those of you who are intrested in agriculture-related microbioe studies to stop by and follow my bot agmicroPapers
General microbiology
Memory shapes microbial populations, Chaitanya S Gokhale , bioRxiv
Bacterial–fungal interactions revealed by genome-wide analysis of bacterial mutant fitness, Emily C. Pierce, Nature Microbiology
Environmental and Physiological Factors Affecting High-Throughput Measurements of Bacterial Growth, Esha Atolia , mBio
Human microbiome
Host variables confound gut microbiota studies of human disease, Ivan Vujkovic-Cvijin, Nature
Infant Skin Bacterial Communities Vary by Skin Site and Infant
Age across Populations in Mexico and the United States, Melissa B. Manus, mSystems
Plant and soil microbiome
Microbiome manipulation by a soil-borne fungal plant pathogen using effector proteins, Nick C. Snelders, Nature Plants
Assembly and variation of root-associated microbiota of rice during their vegetative growth phase with and without lindane pollutant, Jiayin Feng, Soil Ecology Letters
Restoring degraded microbiome function with self-assembled communities, Carlos Fernando Gutierrez Landazuri , FEMS Micro. Eco.
Multi-species relationships in legume roots: From pairwise legume-symbiont interactions to the plant – microbiome – soil continuum, Myrto Tsiknia, FEMS Micro. Eco.
Animal microbiome
Evidence supporting the microbiota–gut–brain axis in a songbird, Morgan C. Slevin, Biology Letters
Comparative Analysis of the Fecal Microbiota of Wild and Captive Beal’s Eyed Turtle (Sacalia bealei) by 16S rRNA Gene Sequencing, Jonathan J. Fong , Front. Micro.
High-Throughput Cultivation for the Selective Isolation of Acidobacteria From Termite Nests, Markus Oberpaul , Front. Micro.
Bioinformatics
EUKulele: Taxonomic annotation of the unsung
eukaryotic microbes, Arianna I. Krinos, JOSS
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes, Kai Blin, Nucleic Acids Research
**Youtube Video- Microbiome: How to Navigate Through Matlab to Perform Machine Learning Analysis on Metagenomics Data
**Help questionnaire! Natural Products – Data Repositories Questionnaire
October 3, 2020
Shalom and good morning from Israel!
Today’s digest is highly diverse, with papers about naming microbes (bottom line- be creative and interesting!), human hair microbiome, the role of one single bacteria in plant growth, how phages weaponizes host bacteria and much more.
Lastly, a bit of ‘self promotion’- the lockdown in Isrel encouraged me to finally create AgrimicroPapers, a twitter-bot (using this great manual) for agriculture- and plant microbiome-realted papers. Feel free to follow and DM papers if they were missed by the bot. Enjoy!
General microbiology
Prokaryotic names: the bold and the beautiful, Aharon Oren, FEMS Micro. Letters
Human and animal microbiome
**Understanding the impact of antibiotic perturbation on the human microbiome, D.J. Schwartz, Genome Medicine
Salivary microbiome in patients undergoing hemodialysis and its associations with the duration of the dialysis, Xiaobo Duan, BMC Nephrology
Phytochemicals as modifiers of gut microbial communities, Giulia Dingedo, Food & Function
Relationship between the bacterial community structures on human hair and scalp, Kota Watanabe, Biosc. Biotech. Bioche
Pangenome sequence evolution within human gut microbiomes is explained by gene-specific rather than host-specific selective pressures, Arnaud N’Guessan, bioRxiv
Changes in dietary fiber intake in mice reveal
associations between colonic mucin Oglycosylation and specific gut bacteria, Hasinika Gamage, Gut Microbes
Gut metabolites are more predictive of disease- and cohoused- states than gut bacterial features in a mouse model of polycystic ovary syndrome, Bryan Ho, bioRxiv
Environmental microbiome
**A single bacterial genus maintains root growth in a complex microbiome, Omri Finkel, Nature
The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future, Peter H.A.M Bakker, Molecular Plant (Cell)
Quantification of Extracellular Proteases and Chitinases from Marine Bacteria, Yang Zou, Current Micro.
Characterization of microbial communities in commercial bee pollen used for mass rearing of Bombus impatiens,Vicente D. Moreno Andrade, J. Apicultural Research
Phages
Phages weaponize their bacteria with biosynthetic gene clusters, Anna Dragos, bioRxiv
Microbiome news
Biotechs have big ambitions for the microbiome, SFBT
Core metagenomic functions of the poultry microbiome, Poultry World
September 20, 2020
Shalom from Israel and have a happy Jewish New Year!
As yesterday’s digest was packed with great papers, today’s post is a bit thinner- but still with great material. First, take a look at two virtual and fascinating events to be held in the next months. In addition, you’ll find a mini-review about molecular epidiomiology, locust-related microbiome, a fascinating research paper exploring the actual proportion of sequenced prokaryots and a even a paper focusing on the microbiome of hemp.
Stay healthy, wear a mask.
Events
ISME Virtual Microbial Ecology Summit
Human microbiome
Gut microbiota, NLR proteins, and intestinal homeostasis, Hao Guo, JEM
*Mini-review- Molecular epidemiology in current times, Burkhard Tummler, Env. Micro.
Animal microbiome
Microbiome-related aspects of locust density-dependent phase transition, Omer Levy, bioRxiv
Environmental microbiome
**Estimate of the sequenced proportion of the global prokaryotic genome, Zheng Zhang, Microbiome
Microbial dark matter filling the niche in hypersaline microbial mats, Hon Lun Wong, Microbiome
Pan‐genome study of Thermococcales reveals extensive genetic diversity and genetic evidence of thermophilic adaption, Chaofang Zhong , Env. Micro.
Plant microbiome
Evaluating the microbiome of hemp, Samuel E. Barnett, Phytobiomes
June 27, 2020
Shalom from Israel and a Happy world microbiome day!
Yes, it is a true day! celebrating the huge diversity of microbes around us, above us, below us and inside us. Check the day’s official website for more information, and take the weekend to appreciate this amazing field and your own personal contribution to advancing our knowledge about microbial communities on our planet.
Personally, I did my undergrad in Ecology and Evolution, confidence that I’ll my scientific career will focus on plant ecology and distribution, or at least large animals. Microbiology classes and introduction labs bored me, and I did my best to avoid this topic. But all of a sudden, during my Master’s degree (where I worked on a pathogenicity mechanism of postharvest disease-causing bacteria), I fell in love with microbiology in general, and specific bacterial communities. The huge untapped diversity, the unbelievable functions and the amazing interactions needed to maintain a functional community of these invisible inhabitants just fascinated me. Today, as a Ph.D. student exploring secondary metabolites gene clusters in soil and root microbiome, I’m a super-fan of the bacterial world.
How did you end up being microbiome suckers? Feel free to share your stories here as a comment, on MD FB page, or directly on tweeter.
Today’s digest include several microbimoe papers of animal midels (including ‘dirty mice’), diseased tomatoes taxonomical and functional microbiome profile, AND- a sweet reminder of the pre-COVID-19 world, with an analysis of the dust microbiome of a plane (remember this vehicle?).
Human and Animal Models microbiome
**Microbial transmission in animal social networks and the social microbiome, Amar Sarkar , Nat. Eco. Evo.
Does entry to center-based childcare affect gut microbial colonization in young infants?, Gerben D. A. Hermes, Scientific Reports
Serum metabolites reflecting gut microbiome
alpha diversity predict type 2 diabetes, Cristina Menni, Gut microbes
**New Insights into the Immune System Using Dirty Mice, Sara E. Hamilton, J. Immunology.
Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics,Josefin Olausson , bioRxiv
Sleep fragmentation increases blood pressure and is associated with alterations in the gut microbiome and fecal metabolome in rats, Katherine.Maki, Phys. Geno.
Animal microbiome
Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria, Hamutahl Cohen, Microbial Ecology
The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet, Tahliyah S. Mims, bioRxiv
Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry, Eliane Cristina Gruszka Vendruscolo, Sci. Tot. Env.
Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation, Zhipeng Li, FEMS Micro. Eco.
Soil and Plant microbiome
Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici, Xin Zhou, Microbial Ecology
Insights into drylands biocrust microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA, Nuttapon Pombubpa, FEMS Micro. Eco.
Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach, Laura Díaz-García, Microbial Ecology
Shotgun Metagenomics Of Dust Microbiome From Flight Deck And Cabin In Civil Aviation Aircraft, Yu Sun, Indoor Air
Bioinformatics
MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data, D.R. Finn , FEMS Micro. Eco.
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