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 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 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 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
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 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 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
January 31, 2024
General microbiome
Finding Candida auris in public metagenomic repositories – Mario-Vasquez et al. – PLOS One
Pregnancy and early life
A pilot study of fecal pH and redox as functional markers in the premature infant gut microbiome – Letourneau et al. – PLOS One
[PREPRINT]Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother’s milk – Allert et al. – bioRxiv
Human nasal microbiome
A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome – Liu et al. – Communications Biology
Human gut microbiome
Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans – Link et al. – Nature Medicine
Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago – Nishimura et al. – PLOS One
[PREPRINT]Unravelling the ancient fungal DNA from the Iceman’s gut – Oskolkov et al. – bioRxiv
Animal experiments (mouse/rat experiments, chickens/pigs on different diets)
Streptococcus anginosus promotes gastric inflammation, atrophy, and tumorigenesis in mice – Fu et al. – Cell
Gut complement induced by the microbiota combats pathogens and spares commensals – Wu et al. – Cell
Complement in breast milk modifies offspring gut microbiota to promote infant health – Xu et al. – Cell
Antidiabetic effects and mechanism of γ-polyglutamic acid on type II diabetes mice – Li et al. – International Journal of Biological Macromolecules
Bacterial microbiome associated with cigarette beetle Lasioderma serricorne (F.) and its microbial plasticity in relation to diet sources – Srinivasan et al. – PLOS One
Animal microbiome (for animals in the wild)
Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids – Chai et al. – Microbiome
[PREPRINT]Thermal fluctuations independently modulate physiological plasticity and the dynamics of the gut microbiome in a tropical rocky shore oyster – Arromrak et al. – bioRxiv
[PREPRINT]Diversity and structure of the deep-sea sponge microbiome in the equatorial Atlantic Ocean – Williams et al. – bioRxiv
Plant, root, and soil microbiome
[PREPRINT]Temporal and spatial dynamics within the fungal microbiome of grape fermentation – Onetto et al. – bioRxiv
Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)
Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism – Valentin-Alvarado et al. – Microbiome
Phages and viruses
[PREPRINT]Viroid-like colonists of human microbiomes – Zheludev et al. – bioRxiv
Bioinformatics
[PREPRINT]DeepGOMeta: Predicting functions for microbes – Hoehndorf et al. – bioRxiv
[PREPRINT]Predicting microbial genome-scale metabolic networks directly from 16S rRNA gene sequences – Øyås et al. – bioRxiv
Techniques
[REVIEW]Unraveling metagenomics through long-read sequencing: a comprehensive review – Kim et al. – Journal of Translational Medicine
Microbes in the news
Non-prescription therapeutics for IBS: where are we? – Costantino – Gut Microbiota for Health by ESNM
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