August 8, 2024

Human respiratory, skin, and gut microbiome

Nurturing futures through the maternal microbiome – Roberta Pala & Katherine Kenny – Sociology of Health & Illness

The skin microbiota of preterm infants and impact of diaper change frequency – Noelle E. Younge et al – PLOS One

Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity – Ana M. Valdes et al – BMC Medicine

Gut microbial composition is altered in sarcopenia: A systematic review and meta-analysis of clinical studies – Xiaohong Mai et al – PLOS One

Associations of upper respiratory mucosa microbiota with Rheumatoid arthritis, autoantibodies, and disease activity – Young Bin Joo et al – PLOS One

Effect of β-lactam antibiotics on the gut microbiota of term neonates – Hongdan Gu et al – BMC Annals of Clinical Microbiology & Antimicrobials

Clinical efficacy of a multilamellar cream on skin physiology and microbiome in an epidermal stress model: A controlled double-blinded study – Joachim W Fluhr et al – Int. Journal of Cosmetic Science

Animal experiments

Mouse adaptation of human inflammatory bowel diseases microbiota enhances colonization efficiency and alters microbiome aggressiveness depending on the recipient colonic inflammatory environment – Simon M. Gray et al – BMC Microbiome

Animal microbiome

Gut microbiota composition of the isopod Ligia in South Korea exposed to expanded polystyrene pollution – Young-Mi Lee et al – PLOS One

Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome – Patrizia Robino et al – BMC Biological Research

Survey of antimicrobial and probiotic use practices in wildlife rehabilitation in the United States – Elizabeth A. Miller et al – PLOS One

The impact of management on the fecal microbiome of endangered greater sage-grouse (Centrocercus urophasianus) in a zoo-based conservation program – Emma Vaasjo et al – Conservation Physiology

Water & extremophile microbiome

Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome – Pablo Suárez-Moo et al – Environmental Microbiology

Production of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column – Su Ding et al – ISME Journal

Plant, root & soil microbiome

Characterization of fungal microbiome structure in leaf litter compost through metagenomic profiling for harnessing the bio-organic fertilizer potential – Sophayo Mahongnao et al – 3Biotech

Plant species influences the composition of root system microbiome and its antibiotic resistance profile in a constructed wetland receiving primary treated wastewater – Valentina Riva et al – Frontiers in Microbiology

DNA stable isotope probing reveals the impact of trophic interactions on bioaugmentation of soils with different pollution histories – Esteban E. Nieto et al – BMC Microbiome

Seed endophytes and rhizosphere microbiome of Imperata cylindrica, a pioneer plant of abandoned mine lands – Wenqin Mao et al – Frontiers in Microbiology

Temperature-dependent trophic associations modulate soil bacterial communities along latitudinal gradients – Xing Huang et al – ISME Journal.

Microbial ecology

[PREPRINT] Models of microbiome evolution incorporating host resource provisioning – Yao Xiao et al – bioRxiv

Beneficial microbes & compounds

Combining Bifidobacterium longum subsp. infantis and human milk oligosaccharides synergistically increases short chain fatty acid production ex vivo – Florac De Bruyn et al – Nature Communications Biology

June 19, 2024

Oral and respiratory microbiota

Safety, Feasibility, and Advantages of Oral Microbiota Transplantation: The First Clinical Case – Oleg V. Goloschapov – Journal of Pediatric Hematology/Oncology

Oral microbial dysbiosis in patients with oral cavity cancers – Ozge Unlu – Clinical Oral Investigations

Nasal cathelicidin is expressed in early life and is increased during mild, but not severe respiratory syncytial virus infection – Sofia Sintoris – Nature Scientific Reports

Human gut microbiome

Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges – Lucas Masier – Nature Metabolism

Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice – Yohannes Seyoum – Nature Communications

Beneficial microbes and compounds

Short-chain fatty acid valerate reduces voluntary alcohol intake in male mice – Suresh C. Bokoliya – BMC Microbiome

Sleep promoting and omics exploration on probiotics fermented Gastrodia elata Blume – Chao-Qi Zhang – NPJ Science of Food

Animal microbiome

Metagenomic approach revealed the mobility and co-occurrence of antibiotic resistomes between non-intensive aquaculture environment and human – Li Tian – BMC Microbiome

Water and extremophile microbiome

Bacterial community and cyanotoxin gene distribution of the Winam Gulf, Lake Victoria, Kenya – Katelyn M. Brown – Environmental Microbiology

Genome-wide screen of genetic determinants that govern Escherichia coli growth and persistence in lake water – Nataliya Teteneva – ISME Journal

Plant, root, and soil microbiomes

Root-associated Streptomyces produce galbonolides to modulate plant immunity and promote rhizosphere colonization – Clément Nicolle – ISME Journal

Organic fertilization co-selects genetically linked antibiotic and metal(loid) resistance genes in global soil microbiome – Zi-Teng Liu – Nature Communications

Conceptualizing soil fauna effects on labile and stabilized soil organic matter – Gerrit Angst – Nature Communications

Fungi

The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island – Saeed Ullah – Nature Scientific Reports

Archaea

Asgard archaeal selenoproteome reveals a roadmap for the archaea-to-eukaryote transition of selenocysteine incorporation machinery – Biyan Huang – ISME Journal

Microbial Ecology

Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution – Hagay Enav – Nature Biotechnology

Methods

High-throughput single-cell transcriptomics of bacteria using combinatorial barcoding – Karl D. Gaisser – Nature Protocols

Commentary and opinions

SeqCode in the golden age of prokaryotic systematics – Diego Javier Jiménez – ISME Journal

Digestive Disease Week 2024 – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Barriers and enablers to the effective implementation of omics research in low- and middle-income countries – Jacus S. Nacis – Nature Biotechnology

June 5, 2024

Human gut microbiome

Gut microbiome and inflammation among athletes in wheelchair in a crossover randomized pilot trial of probiotic and prebiotic interventions – Ezra Valido – Nature Scientific Reports

A microbiota-directed complementary food intervention in 12-18-month-old Bangladeshi children improves linear growth – Ishita Mostafa – eBioMedicine

Gut microbiome shifts in people with type 1 diabetes are associated with glycaemic control: an INNODIA study – Tommi Vatanen – Diabetologia

Association of methyl donor nutrients dietary intake and sleep disorders in the elderly revealed by the intestinal microbiome – Qianqian Chen – Food & Function

[REVIEW] The human gut microbiome and aging – Evan Bradley & John Haran – Gut Microbes

[REVIEW] Nurturing gut health: role of m6A RNA methylation in upholding the intestinal barrier – Shuaijie Wang – Cell Death Discovery

Persistent dysbiosis of duodenal microbiota in patients with controlled pediatric Crohn’s disease after resolution of inflammation – Rebecca Pierce – Nature Scientific Reports

Dysfunctional circadian clock accelerates cancer metastasis by intestinal microbiota triggering accumulation of myeloid-derived suppressor cells – Jing-Lin Liu – Cell Metabolism

Human respiratory microbiome

Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure – Georgios D. Kitsios – Nature Communications

Lack of correlation between in vitro and within patient measures of P. aeruginosa biofilms in cystic fibrosis – Amanda J Morris – Cell Heliyon

Human oral microbiome

The oral microbiome and oral and upper gastrointestinal diseases – Sifan Liu – Journal of Oral Microbiology

Comprehensive analysis of the oral microbiota and metabolome change in patients of burning mouth syndrome with psychiatric symptoms – Shihong Luo – Journal of Oral Microbiology

Candida albicans natural diversity: a resource to dissect fungal commensalism and pathogenesis – Elena Lindemann-Perez – Current Opinion in Microbiology

Animal experiments

Prevotella copri transplantation promotes neurorehabilitation in a mouse model of traumatic brain injury – Nina Gu – Journal of Neuroinflammation

Spatial recovery of the murine gut microbiota after antibiotics perturbation – M. Taguer – mBio

Water and extremophile microbiome

Global biogeography of microbes driving ocean ecological status under climate change – Zhenyan Zhang – Nature Communications

Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens – Natalia Timanikova – Environmental Microbiology

Viruses & phages

Personalized bacteriophage therapy outcomes for 100 consecutive cases: a multicentre, multinational, retrospective observational study – Jean-Paul Pirnay – Nature Microbiology

Built environment microbiome

Environmental and structural factors associated with bacterial diversity in household dust across the Arizona-Sonora border – Lauren D. Benton – Nature Scientific Reports

Plant, root and soil microbiome

Tibetan Plateau grasslands might increase sequestration of microbial necromass carbon under future warming – Qinwei Zhang – Nature Communications Biology

Assembly of Endophytic Communities of Setaria viridis Plants when Grown in Different Soils and Derived from Different Seeds – Carolina Escobar Rodríguez – Phytobiomes

[PREPRINT] Hybrid xyloglucan utilisation loci are prevalent among plant-associated Bacteroidota – Hannah Martin – bioRxiv

Microbial ecology

Cooperative growth in microbial communities is a driver of multistability – William Lopes – Nature Communications

Bioenergetic mapping of ‘healthy microbiomes’ via compound processing potential imprinted in gut and soil metagenomes – Craig Liddicoat – Science of the Total Environment

Temporal dynamics of fecal microbiota community succession in broiler chickens, calves, and piglets under aerobic exposure – Paul Oladele – Microbiology Spectrum

May 17, 2024

Today’s digest features bioinformatics binning methods, healthy dogs, lakes in South Africa, and more. For the human gut microbiome studies, check out the latest digest (May 15, 2024) by Grace Deitzler.

See you at #MVIF!

Skin microbiome

Intraspecies warfare restricts strain coexistence in human skin microbiomes – Christopher P. Mancuso – bioRxiv

Oral microbiome

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study – Memduh Bingöl – Journal of Clinical Periodontology

Urinary microbiome

Microbroth dilution method for antibiotic susceptibility testing of fastidious and anaerobic bacteria of the urinary microbiome – Wilson Geaman – Microbiology Spectrum

Respiratory tract

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease – Nick Quinn-Bohmann – BMC Biology

Food microbiome

Microbial community structure of plant-based meat alternatives – Franz-Ferdinand Rochn – pj Science of Food

Plan, root, soil

Functional team selection: a framework for local adaptation in plants and their belowground microbiomes – Nancy Collins Johnson and César Marín – ecoevoRxiv

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert – Patricio Arros – bioRxiv

Animal microbiome

Microbiota of healthy dogs demonstrate a significant decrease in richness and changes in specific bacterial groups in response to supplementation with resistant starch, but not psyllium or methylcellulose, in a randomized cross-over trial – Silke Salavati Schmitz – Access Microbiology

Early-life factors shaping the gut microbiota of Common buzzard nestlings – Hugo Pereira – Animal Microbiome

Animal experiment

13C-Stable isotope resolved metabolomics uncovers dynamic biochemical landscape of gut microbiome-host organ communications in mice – Xia Xiao – Microbiome

Water microbiome

Metagenomics datasets of water and sediments from eutrophication-impacted artificial lakes in South Africa – Grace Nkechinyere Ijoma – Scientific Data

Bioinformatics

Fairy: fast approximate coverage for multi-sample metagenomic binning – Jim Shaw and Yun William Yu – bioRxiv

Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods – Daniel M Portik – biorXiv

Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level – Amy S Graham – bioRxiv

Full factorial construction of synthetic microbial communities – Juan Diaz-Colunga – bioRxiv

ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences – Yao Pei – Microbiome

April 30, 2024

Human microbiome

Safety and efficacy of faecal microbiota transplantation in patients with mild to moderate Parkinson’s disease (GUT-PARFECT): a double-blind, placebo-controlled, randomised, phase 2 trial – Anout Bruggeman – eClinicalMedicine

Implications of intestinal microecology and immune function alterations for immunotherapy outcomes in advanced unresectable lung adenocarcinoma – Shuang He – Clinical Respiratory Journal

Recipient microbiome-related features predicting metabolic improvement following fecal microbiota transplantation in adults with severe obesity and metabolic syndrome: a secondary analysis of a phase 2 clinical trial – Zhengxiao Zhang – Gut Microbes

Gut microbiome composition and metabolic activity in women with diverticulitis – Wenjie Ma – Nature Communications

Microbiome confounders and quantitative profiling challenge predicted microbial targets in colorectal cancer development – Raúl Y. Tito – Nature Medicine

Prediction and causal inference of hyperuricemia using gut microbiota – Yuna Miyajima – Scientific Reports

Early-life gut microbiota associates with allergic rhinitis during 13-year follow-up in a Finnish probiotic intervention cohort – Sampo Kallio – Microbiology Spectrum

Food microbiome

The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits – Elena A. Alexa – BMC Microbiome

Animal experiments

Sodium Propionate Oral Supplementation ameliorates Depressive-Like Behavior through Gut Microbiome and Histone 3 Epigenetic Regulation – Luiza Marques Prates Behrens – Journal of Nutritional Biochemistry

Colon impairments and inflammation driven by an altered gut microbiota leads to social behavior deficits rescued by hyaluronic acid and celecoxib – Oryan Agronyoni – BMC Medicine

Dissecting the respective roles of microbiota and host genetics in the susceptibility of Card9−/− mice to colitis – C. Danne – BMC Microbiome

Animal microbiome

Synergistic resistance of honeybee (Apis mellifera) and their gut microorganisms to fluvalinate stress – Jianhui Liu – Pesticide Biochemistry and Physiology

Determinants of microbiome composition: Insights from free-ranging hybrid zebras (Equus quagga × grevyi) – Joel O. Abraham – Molecular Ecology

Water & extremophile microbiomes

Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench – Yan-Ru Dang – BMC Microbiome

Rhizospheric bacteria from the Atacama Desert hyper-arid core: cultured community dynamics and plant growth promotion – Juan Castro-Severyn – Microbiology Spectrum

Tools & techniques

Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols – Samuel P. Forry – Scientific Reports

Nanopore and Illumina sequencing reveal different viral populations from human gut samples – Ryan Cook – Microbial Genomics

April 24, 2024

General microbiome

A naturally isolated symbiotic bacterium suppresses flavivirus transmission by Aedes mosquitoes – Science 

Gut Microbiome

Gut microbial metabolism of 5-aminosalicylic acid in inflammatory bowel disease – Gut

Smoking-related Lactobacillus and immune cell infiltration in colorectal cancer: evidence from a population-based study – Gut. 

Gut microbiota dysbiosis contributes to depression-like behaviors via hippocampal NLRP3-mediated neuroinflammation in a postpartum depression mouse model – Brain, Behavior, and Immunity

Respiratory microbiome

Outlook/Review – Exploring the lung microbiome’s role in disease – Nature

Longitudinal dynamics of farmer and livestock nasal and faecal microbiomes and resistomes – Nature Microbiology

Probiotics

Multi-strain probiotics ameliorate Alzheimer’s-like cognitive impairment and pathological changes through the AKT/GSK-3β pathway in senescence-accelerated mouse prone 8 mice – Brain, Behavior, and Immunity

Lactococcus lactis HkyuLL 10 suppresses colorectal tumourigenesis and restores gut microbiota through its generated alpha-mannosidase – Gut

Virome

Phage predation, disease severity, and pathogen genetic diversity in cholera patients – Science

Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment – Nature Microbiology 

Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia – mSphere 

Bioinformatics

A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota – Cell Host & Microbe 

Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes – Genome Biology

Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes – Genome Biology

Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies – Genome Biology

Non Microbiome Pick

Refining the impact of genetic evidence on clinical success – Nature

April 3, 2024

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

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 17, 2024

Pregnancy and early life

Human milk cream alters intestinal microbiome of preterm infants: a prospective cohort study – Adeniyi-Ipadeola et al. – Pediatric Research

A bacterial sialidase mediates early-life colonization by a pioneering gut commensal – Buzun et al. – Cell Host & Microbe

Multi-site human microbiome

[DATA]Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults – Rashidi et al. – Scientific Data

Human respiratory microbiome

[REVIEW]Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies – Cauwenberghs et al. – Cell Reports Medicine

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

The gut microbiota modulate locomotion via vagus-dependent glucagon-like peptide-1 signaling – Lai et al. – npj Biofilms and Microbiomes volume

Nonylphenol induces depressive behavior in rats and affects gut microbiota: A dose–dependent effect – Pan et al. – Environmental Pollution

Animal microbiome (for animals in the wild)

Ocular mucosal homeostasis of teleost fish provides insight into the coevolution between microbiome and mucosal immunity – Kong et al. – Microbiome

Plant, root, and soil microbiome

Unraveling the interplay between root exudates, microbiota, and rhizosheath formation in pearl millet – Alahmad et al. – Microbiome

Biogeographic survey of soil bacterial communities across Antarctica – Varliero et al. – Microbiome

Microbes in space

[PREPRINT]Testing microbial biomining from asteroidal material onboard the International Space Station – Santomartino et al. – bioRxiv

Bioinformatics

[PREPRINT]AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods – Wei et al. – bioRxiv

Techniques

Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly – Hu et al. – Scientific Reports

December 15, 2023

Today’s digest features house mice gut microbiome, infant gut DNA bacteriophage strain persistence, maternal gut microbiome in pregnancy, and more.

Do not miss Francine Marques’s opinion on rethinking culture to unlock the potential of research.

See you at #MVIF next week!

Respiratory microbiome

Review: Winds of change a tale of: asthma and microbiome – David Galeana-Cadena – Frontiers in Microbiology

Gut microbiome

Review: The maternal gut microbiome in pregnancy: implications for the developing immune system – Omry Koren – Nature Reviews Gastroenterology & Hepatology

Bioactive glycans in a microbiome-directed food for children with malnutrition – Matthew C. Hibberd – Nature

Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients – Zixuan Xie – Microbiome

Gut microbiota-related metabolite alpha-linolenic acid mitigates intestinal inflammation induced by oral infection with Toxoplasma gondii Jing Yang – Microbiome

Fiber-deficient diet inhibits colitis through the regulation of the niche and metabolism of a gut pathobiont – Peter Kuffa – Cell Host & Microbe

Animal microbiome

Subspecies divergence, hybridisation and the spatial environment shape phylosymbiosis in the microbiome of house mice – Susana C. M. Ferreira – bioRxiv

Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers – Gilles L. C. Baud – Genome Biology

Seasonal and environmental factors contribute to the variation in the gut microbiome: a large-scale study of a small bird – Martta Liukkonen – bioRxiv

Plant-Root-Soil microbiome

Genome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota – Nathan Vannier – Nature Communications

Virome

Infant gut DNA bacteriophage strain persistence during the first 3 years of life – Yue Clare Lou – Cell Host & Microbe

Techniques

High-throughput anaerobic screening for identifying compounds acting against gut bacteria in monocultures or communities – Patrick Müller – Nature Protocols

Bioinformatics

MAGqual: A standalone pipeline to assess the quality of metagenome-assembled genomes – James P.J. Chong – bioRxiv