Category Archives: Human oral

September 13, 2024

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Happy Friday!
And, see you next week at the MVIF and African Microbiome Day events!

Human microbiome

Gut Microbiome

Transient colonizing microbes promote gut dysbiosis and functional impairment โ€“ Sunjae Lee โ€“ย npj Biofilms and Microbiomes

Cataloging metagenome-assembled genomes and microbial genes from the athlete gut microbiome โ€“ Laura Wosinska โ€“ Microbiome Research Reports

Gut microbiome and schizophrenia: insights from two-sample Mendelian randomization โ€“ Keer Zhou โ€“ Schizophrenia

Disease-associated microbiome signature species in the gut โ€“ Junhui Li โ€“ PNAS Nexus

Nasal microbiome

E-Cigarette Use, Cigarette Smoking, and Sex Are Associated With Nasal Microbiome Dysbiosis Get access Arrow โ€“ Elise Hickman โ€“ Nicotine & Tobacco Research

Urinary microbiome

Review: Synthesis of current pediatric urinary microbiome research โ€“ Layla M. Jeries โ€“ Frontiers in Pediatrics

Skin microbiome

The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival โ€“ Philipp Licht โ€“ npj Biofilms and Microbiomes

Animal microbiome

Antibiotics damage the colonic mucus barrier in a microbiota-independent manner โ€“ Jasmin Sawaed โ€“ Science Advances

Host diet drives gut microbiome convergence between coral reef fishes and mammals โ€“ Samuel Degregori โ€“ Molecular Ecology

Functional insights into the effect of feralisation on the gut microbiota of cats worldwide โ€“ Ostaizka Aizpurua โ€“ bioRxiv

Animal experiments

Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury โ€“ Adam M. Hamilton โ€“ npj Biofilms and Microbiomes

Ketogenic interventions restore cognition and modulate peripheral metabolic dysfunctions in Alzheimerโ€™s disease mouse models โ€“ Paule E. H. Mโ€™Bra โ€“ bioRxiv

Plant microbiome

The influence of plant traits on soil microbial communities varies between arid and mesic grasslands โ€“ย Eleonora Egidi โ€“ Plant and Soil

Enrichment of novel entomopathogenic Pseudomonas species enhances willow resistance to leaf beetles โ€“ Haitao Wang โ€“ Microbiome

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes โ€“ F. Fracchia โ€“ Microbiome

Built environment

Predicting how varying moisture conditions impact the microbiome of dust collected from the International Space Station โ€“ Nicholas Nastasi โ€“ Microbiom

The predicted secreted proteome of activated sludge microorganisms indicates distinct nutrient niches โ€“ Kenneth Wasmund โ€“ Environmental Microbiology

Bioinformatics

Microbial network inference for longitudinal microbiome studies with LUPINE โ€“ Saritha Kodikara, Kim-Anh Le Cao โ€“ bioRxiv

August 8, 2024

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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 ฮฒ-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 Suรกrez-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

August 01, 2024

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Pregnancy and early life

Diet at birth is critical for healthy growth, independent of effects on the gut microbiota – van den Elsen et al. – Microbiome

Human oral microbiome

Comparative analysis of microbiome in coronal and root caries – Gondo et al. – BMC Oral Health

Human gut microbiome

Gut microbiota carcinogen metabolism causes distal tissue tumours – Roje et al. – Nature

Time-Dependent Shifts in Intestinal Bacteriome, Klebsiella Colonization and Incidence of Antibiotic-Resistance Genes after Allogeneic Hematopoietic Stem Cell Transplantation – Moiseev et al. – biomedicines

[PREPRINT]Comparative analysis of the treatment-naive microbiome across rheumatic diseases to predict MTX treatment response – Amend et al. – bioRxiv

Meta-analysis identifies common gut microbiota associated with multiple sclerosis – Lin et al. – Genome Medicine

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

[PREPRINT]Ganoderma lucidum alleviates kidney aging by modulating gut microbiota – Liu et al. – bioRxiv

[PREPRINT]Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice – Ozcan et al. – bioRxiv

Effects of antibiotic cocktail on the fecal microbiota and their potential correlation of local immune response – Liu et al. – BMC Microbiology

Plant, root, and soil microbiome

[REVIEW]Practical applications of soil microbiota to improve ecosystem restoration: current knowledge and future directions – Peddle et al. – Biological Reviews

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Impact of host species on assembly, composition, and functional profiles of phycosphere microbiomes – Roager et al. – mSystems

Metaproteomic analysis decodes trophic interactions of microorganisms in the dark ocean – Zhao et al. – Nature Communications

Microbial communities on microplastics from seawater and mussels: Insights from the northern Adriatic Sea – Kolenc et al. – Science of The Total Environment

Built environment (subways, indoor surfaces)

A global metagenomic map of urban microbiomes and antimicrobial resistance – Danko et al. – Cell

Bioinformatics

Solving genomic puzzles: computational methods for metagenomic binning – Mallawaarachchi et al. – Briefings in Bioinformatics

July 24, 2024

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Human microbiome

Gut virome-wide association analysis identifies cross-population viral signatures for inflammatory bowel disease – Xiangge Tian et al – BMC Microbiome

The Role of Gut Microbiota in the Neuroprotective Effects of Selenium in Alzheimerโ€™s Disease – Anatoly V. Skalny et al – Molecular Neurobiology

[REVIEW] The oralโ€“gut microbiome axis in health and disease – Benoit J. Kunath – Nature Reviews Microbiology

Enhancing gut microbiota and microbial function with inulin supplementation in children with obesity – Chonnikant Visuthranukul et al – International Journal of Obesity

Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder – Zaiquan Dong et al – Journal of Affective Disorders

Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health – Na Han et al – Frontiers in Microbiology

Skin locations inference and body fluid identification from skin microbial patterns for forensic applications – Litao Huang et al – Forensic Science International

Animal experiments

Improving insulin resistance by sulforaphane via activating the Bacteroides and Lactobacillus SCFAsโ€“GPRโ€“GLP1 signal axis – Sicong Tian et al – Food & Function

Gastroprotective and microbiome-modulating effects of ubiquinol in rats with radiation-induced enteropathy – Walaa A. Eraqi et al – BMC Animal Microbiome

Animal microbiome

Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses – Mason R. Stothart et al – Nature Communications

Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale – Shuai Du et al – Environmental Science & Technology

Modulation of gut microbiota composition and predicted metabolic capacity after nutritional programming with a plant-rich diet in Atlantic salmon (Salmo salar): insights across developmental stages – Marwa Mamdouh Tawfik et al – BMC Animal Microbiome

Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia – Laura Glendinning et al – BMC Microbiome

Water & extremophile microbiome

Genomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton – Tianyi Chang et al – BMC Microbiome

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake – Arianna I. Krinos et al – BMC Microbiome

Built environment microbiome

[PREPRINT] Utilizing the biosimulator to analyze the environmental microbiome within the intensive care units of a hospital – Sunil Thomas et al – ResearchSquare

Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system – Dou Wang et al – BMC Microbiome

Plant, root, & soil microbiome

Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China – Jie-Liang Liang et al – BMC Microbiome

Bioinformatics tools

MIDASim: a fast and simple simulator for realistic microbiome data – Mengyu He et al – BMC Microbiome

June 19, 2024

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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 – Clรฉment 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 Jimรฉnez – 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 7, 2024

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Today’s digest features AMPSphere, Candida pathogenesis, rhizosphere microbiome in the Himalayas, imaging of oral microbiome, and more.
See you at #MVIF special event on women’s health!

Global microbiome

Discovery of antimicrobial peptides in the global microbiome with machine learning โ€“ Cรฉlio Dias Santos-Jรบnior and Marcelo D.T. Torres โ€“ Cell

Bioenergetic mapping of โ€˜healthy microbiomesโ€™ via compound processing potential imprinted in gut and soil metagenomes โ€“ Craig Liddicoat โ€“ Science of The Total Environment

Infant microbiome

The impact of perinatal maternal stress on the maternal and infant gut and human milk microbiomes: A scoping review protocol โ€“ Niamh Ryan โ€“ Plos One

Oral microbiome

Improved Visualization of Oral Microbial Consortia โ€“ S.T. Ramirez-Puebla โ€“ Journal of Dental Research

Animal microbiome

Changes of faecal bacterial communities and microbial fibrolytic activity in horses aged from 6 to 30 years old โ€“ Marylou Baraille โ€“ Plos One

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization โ€“ Ke Zhang โ€“ Microbiome

Animal experiments

Bacteroides uniformis CECT 7771 requires adaptive immunity to improve glucose tolerance but not to prevent body weight gain in diet-induced obese mice โ€“ Marina Romanรญ-Pรฉrez โ€“ Microbiome

The impact of microplastics polystyrene on the microscopic structure of mouse intestine, tight junction genes and gut microbiota โ€“ Qi-Ling Su โ€“ Plos One

Epithelial hypoxia maintains colonization resistance against Candida albicans โ€“ Hannah P. Savage โ€“ Cell Host & Microbe

Viruses and phages

Characterizing the gut phageome and phage-borne antimicrobial resistance genes in pigs โ€“ Jun Hu โ€“ Microbiome

Water microbiome

Deep long-read metagenomic sequencing reveals niche differentiation in carbon cycling potential between benthic and planktonic microbial populations โ€“ Tomeu Viver โ€“ bioRxiv

Root, soil, plant microbiome

Altitude-Dependent Influence of Artemisia brevifolia on its Rhizosphere Microbiome in Ladakh Region of the Western Himalayas โ€“ Manzoor Hussain โ€“ Rhizosphere

Bioinformatics

Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet โ€“ Nicolae Sapoval โ€“ bioRxiv

Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion โ€“ Xiaofan Jin โ€“ bioRxiv

June 5, 2024

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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 Crohnโ€™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 Rodrรญguez – 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 โ€˜healthy microbiomesโ€™ 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 29, 2024

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Human microbiomes

Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction – Alex E. Mohr – Nature Communications

[PREPRINT] Towards a Health-Associated Core Keystone (HACK) index for the human gut microbiome – Abishek Goel – bioRxiv

Exposure to environmental pollutants selects for xenobiotic-degrading functions in the human gut microbiome – Francesca De Fillipis – Nature Communications

The interrelation between microbial immunoglobulin coating, vaginal microbiota, ethnicity, and preterm birth – H.J. Schuster – BMC Microbiome

Porphyromonas gingivalis, a bridge between oral health and immune evasion in gastric cancer – Matรญas Muรฑoz-Medel – Frontiers in Oncology

Differences in maternal subgingival microbiome between preterm and term births: The MOHEPI study – Jung Soo Park – Journal of Periodontal Resaerch

Animal microbiome

Integrating uterine microbiome and metabolome to advance the understanding of the uterine environment in dairy cows with metritis – S. Casaro – BMC Animal Microbiome

Responses of nutrient utilization, rumen fermentation and microorganisms to different roughage of dairy buffaloes – Shichun He – BMC Microbiology

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis – Yujie Meng – BMC Microbiome

Co-habiting ants and silverfish display a converging feeding ecology – Thomas Parmentier – BMC Biology

Temperature-dependent differences in mouse gut motility are mediated by stress – Alvin Han – Nature Lab Animal

Food microbiome

Evaluation of microbiota-induced changes in biochemical, sensory properties and volatile profile of kombucha produced by reformed microbial community – Hilal Kilmanoglu – Food Chemistry X

Plant, soil, and root microbiome

Microbial polyphenol metabolism is part of the thawing permafrost carbon cycle – Bridget B. McGivern – Nature Microbiology

[PREPRINT] Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils – Samuel E. Barnett & Ashley Shade – bioRxiv

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome – Yoko Masuda – BMC Microbiome

Water & extremophile microbiome

Bacterial dynamics of the plastisphere microbiome exposed to sub-lethal antibiotic pollution – Brune Jounnard & Concepcion Sanchez-Cid – BMC Microbiome

Exploring potential polysaccharide utilization loci involved in the degradation of typical marine seaweed polysaccharides by Bacteroides thetaiotaomicron – Biao Yu – Frontiers in Microbiology

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria – Subhash Yadav – BMC Microbiome

May 17, 2024

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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 โ€“ Christopher P. Mancuso โ€“ bioRxiv

Oral microbiome

Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study โ€“ Memduh Bingรถl โ€“ Journal of Clinical Periodontology

Urinary microbiome

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

Respiratory tract

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

Food microbiome

Microbial community structure of plant-based meat alternatives โ€“ Franz-Ferdinand Rochn โ€“ pj Science of Food

Plan, root, soil

Functional team selection: a framework for local adaptation in plants and their belowground microbiomes โ€“ Nancy Collins Johnson and Cรฉsar Marรญn โ€“ ecoevoRxiv

Life on the edge: microbial diversity, resistome, and virulome in soils from the Union Glacier cold desert โ€“ Patricio Arros โ€“ 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 โ€“ Silke Salavati Schmitz โ€“ Access Microbiology

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

Animal experiment

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

Water microbiome

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

Bioinformatics

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

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

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

Full factorial construction of synthetic microbial communities โ€“ Juan Diaz-Colunga โ€“ bioRxiv

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

April 12, 2024

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Today’s digest features human gut microbiome studies on dietary fiber and fasting glucose, ocean microbiome, pangenome approaches, and more.

See you at #MVIF!

Oral microbiome

Saliva sampling method influences oral microbiome composition and taxa distribution associated with oral diseases โ€“ Cristian Roca โ€“ PlosOne

Gut microbiome

Changes in the intestinal microbiota of individuals with non-alcoholic fatty liver disease based on sequencing: An updated systematic review and meta-analysis โ€“ Wenpin Cai โ€“ PlosOne

Gut microbiota differences in stunted and normal-lenght children aged 36โ€“45 months in East Nusa Tenggara, Indonesia โ€“ Ingrid S. Surono โ€“ PlosOne

Integrating research on bacterial pathogens and commensals to fight infectionsโ€”an ecological perspective โ€“ Lisa Maier โ€“ The Lancet Microbe

Recommendations for the Use of Dietary Fiber to Improve Blood Pressure Control โ€“ Hamdi A. Jama โ€“ Hypertension

Review: Prebiotic selection influencing inflammatory bowel disease treatment outcomes: a review of the preclinical and clinical evidence โ€“ Amin Ariaee โ€“ eGastroenterology

Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments โ€“ Torben Soelbeck Rasmussen โ€“ bioRxiv

Continuous glucose monitoring and intrapersonal variability in fasting glucose โ€“ Smadar Shilo โ€“ Nature Medicine

Animal microbiome

Intestinal microbiome profiles in broiler chickens raised without antibiotics exhibit altered microbiome dynamics relative to conventionally raised chickens โ€“ Seyed Hossien Kairmi โ€“ PlosOne

Microbial signatures and enterotype clusters in fattening pigs: implications for nitrogen utilization efficiency โ€“ Naomi Sarpong โ€“ Frontiers in Microbiology

A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience โ€“ Lauren F. Messer โ€“ Nature Communications

Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants โ€“ Zhe Pan โ€“ ISME Communications

Ocean microbiome

Decoding populations in the ocean microbiome โ€“ Ramiro Logares โ€“ Microbiome

Bioinformatics

High-resolution Profiling of Bacterial and Fungal Communities using Pangenome-Informed Taxon-Specific Long-Read Amplicons โ€“ Luzia Stalder โ€“ bioRxiv

CELEBRIMBOR: Pangenomes from metagenomes โ€“ Joel Hellewell โ€“ bioRxiv