Category Archives: Pregnancy and birth

March 15, 2023

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Pregnancy and early life

The impact of prenatal dog keeping on infant gut microbiota development – Panzer et al. – Clinical & Experimental Allergy

Human oral microbiome

Host microbiome interactions in apical periodontitis: the endodontic microbiome in relation to circulatory immunologic markers – Georgiou et al. – International Endodontic Journal

Human gut microbiome

[REVIEW]Microbiota dysbiosis and myasthenia gravis: Do all roads lead to Rome? – Kapoor et al. – Autoimmunity Reviews

Metabolomic interplay between gut microbiome and plasma metabolome in cardiac surgery-associated acute kidney injury – Bai et al. – Rapid Communications in Mass Spectrometry

A non-antibiotic-disrupted gut microbiome is associated with clinical responses to CD19-CAR-T cell cancer immunotherapy – Stein-Thoeringer et al. – Nature Medicine

The gut microbiome modulates the transformation of microglial subtypes – Huang et al. – Molecular Psychiatry

Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the “microworld” age – Wang et al. – Molecular Omics

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

A Longitudinal Characterization of the Seminal Microbiota and Antibiotic Resistance in Yearling Beef Bulls Subjected to Different Rates of Gain – Webb et al. – Microbiology Spectrum

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

Abiotic selection of microbial genome size in the global ocean – Ngugi et al. – Nature Communications

Bioinformatics

Benchmarking genome assembly methods on metagenomic sequencing data – Zhang et al. – Briefings in Bioinformatics

March 8, 2023

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Pregnancy and early life

[PREPRINT]The influence of early life exposures on the infant gut virome – Zhang et al. – bioRxiv

[PREPRINT]Maternal diet and gut microbiome composition modulate early life immune responses – Grant et al. – bioRxiv

Human oral microbiome

Smoking-induced subgingival dysbiosis precedes clinical signs of periodontal disease – Tamashiro et al. – Scientific Reports

Human gut microbiome

Gut microbiota and risk of five common cancers: A univariable and multivariable Mendelian randomization study – Wei et al. – Cancer Medicine

The role of the sex hormone-gut microbiome axis in tumor immunotherapy – Wang et al. – Gut Microbes

[REVIEW]The Influence of the Microbiome on Aggressive Behavior: an Insight into Age Related Aggression – Gulledge, Oyebode & Donaldson – FEMS Microbiology Letters

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

Gnotobiotic mice housing conditions critically influence the phenotype associated with transfer of faecal microbiota in a context of obesity – Daoust et al. – Gut

Animal microbiome (for animals in the wild)

[REVIEW]The coral microbiome: Towards an understanding of the molecular mechanisms of coral-microbiota interactions – Mohamed et al. – FEMS Microbiology Reviews

Comparison of the gut microbiome and resistome in captive African and Asian elephants on the same diet – Feng et al. – Front. Vet. Sci.

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

Core and conditionally rare taxa as indicators of agricultural drainage ditch and stream health and function – Shi et al. – BMC Microbiology

Species invasions shift microbial phenology in a two-decade freshwater time series – Rohwer et al. – PNAS

Bioinformatics

Controlling taxa abundance improves metatranscriptomics differential analysis – Ji & Ma – BMC Microbiology

coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies – Luz Calle, Pujolassos & Susin – BMC Bioinformatics

[PREPRINT]You can move, but you can’t hide: identification of mobile genetic elements with geNomad – Camargo et al. – bioRxiv

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing – Wick, Judd & Holt – PLOS Computational Biology

February 25th, 2023

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Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! Fontana and collaborator performed a fascinating meta-analysis of publicly datasets obtained from fecal samples of healthy athletes and healthy sedentary adults and revealed the microbiota changes associated with competitive athletes lifestyle.

Today’s non-microbiology pick is an preprint exploring postdoctoral and PhD student’s career self-efficacy in US biological sciences and showed how women and non US citizen have a significant lower level of career self-efficacy compared to their male and US citizen peers. The authors discuss potential causes for these differences and offer recommendations for increasing trainee career self-efficacy.

Have a great Saturday!

Pregnancy and early life

Preprint: Co-localization of antibiotic resistance genes is widespread in the infant gut microbiome and associates with an immature gut microbial composition – Li et al. – BioRXiv

Human gut microbiome

The human gut microbiome of athletes: metagenomic and metabolic insights – Fontana et al. – Microbiome

Review: Gut microbiome-based strategies for host health and disease – Wang et al. – Critical Reviews in Food Science and Nutrition

The role of diet in shaping human gut microbiota – Rinninella et al. – Best practive & Research clinical Gastroenterology

Preprint: Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria – Robitaille et al. – BioRXiv

Genetic-Phenotype Analysis of Bifidobacterium bifidum and Its Glycoside Hydrolase Gene Distribution at Different Age Groups – Wei et al. – Foods

Animal microbiome

Preprint: Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) – Andres et al. – BioRXiv

Plant, root, and soil microbiome

Preprint: Short- and long-term effects of continuous compost amendment on soil microbiome community – Kraut-Cohen et al. – BioRXiv

Awaking the Dormant Virome in the Rhizosphere – Braga and Schumacher – Molecular ecology

Water and extremophile microbiome

Preprint: A novel order-level lineage of ammonia-oxidizing Thaumarchaeota is widespread in marine and terrestrial environments – Zheng et al. – BioRXiv

Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics – Dart et al. – Viruses

Food microbiology

Analysis of the core bacterial community associated with consumer-ready Eastern oysters (Crassostrea virginica) – Hines et al. – Plos One

Phages and viruses

Review: The Role of Temperate Phages in Bacterial Pathogenicity – Gummalla et al. – Microorganisms

Bioinformatics

Review: Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses – Ibanez-Lligona et al – Viruses

Non microbiology pick

Preprint: Citizenship status and career self-efficacy: An intersectional study of biomedical trainees in the United States – Chatterjee et al. – BioRXiv

February 18th, 2023

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Bonjour from Paris, France !

In today’s digest you will find a broad range of amazing preprints and published papers! An amazing read is a fresh preprint from Fritz and collaborator describing an exciting method of sampling in difficult to reach environments. The authors used army ants of the genus Dorylus which are foragers to survey the viral diversity of plants, vertebrate and invertebrates of the tropical forest!

Today’s non-microbiology pick is an opinion piece on the current state and limitation of viral taxonomy. In this piece, Simmonds and collaborators, provide concrete recommendations to guide the development of a coherent and comprehensive virus taxonomy.

Have a great Saturday!

Pregnancy and early life

The investigation of the association of pregnancy weight gain on maternal and neonatal gut microbiota composition and abundance using 16sRNA sequencing – Song and Liu – BMC Pregnancy and Childbirth

Human gut microbiome

The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population – Bourdeau-Julien et al. – Microbiome

Review: Conversations in the Gut: The Role of Quorum Sensing in Normobiosis – Markus et al. – International Journal of Molecular Sciences

Review: Gut Microbiome and Neurodevelopmental Disorders: A Link Yet to Be Disclosed – Illiodromiti et al. – Microorganisms

Natural Green Spaces, Sensitization to Allergens, and the Role of Gut Microbiota during Infancy – Buchholz et al. – mSystems

Animal experiments

Mimicking seasonal changes in light-dark cycle and ambient temperature modulates gut microbiome in mice under the same dietary regimen – Matsumoto et al – Plos One

Animal microbiome

Preprint: Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta – Moeller et al. – BioRxiV

Plant, root, and soil microbiome

Preprint: Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype – Simonin et al. – BioRxiV

Preprint: Viral but not bacterial community succession is characterized by extreme turnover shortly after rewetting dry soils – Santos-Medellin et al. – BioRxiV

Ecological drivers and potential functions of viral communities in flooded arsenic-contaminated paddy soils – Gao et al. – Science of the total environment

Water and extremophile microbiome

Preprint: Redefinition of archetypal phytoplankton-associated bacteria taxa based on globally distributed dinoflagellates and diatoms – Yang et al. – BioRxiV

Preprint: Plastic Leachate Exposure Drives Antibiotic Resistance and Virulence in Marine Bacterial Communities – Vlaanderen et al. – BioRxiV

Phages and viruses

Preprint: African army ants at the forefront of virome surveillance in a remote tropical forest – Fritz et al. – BioRxiV

Techniques

Preprint: Dancing the Nanopore limbo – Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction – Simon et al. – BioRxiV

Preprint: The long and short of it: Benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies – Cook et al. – BioRxiV

Non microbiology pick

Opinion: Four principles to establish a universal virus taxonomy – Simmonds et al. – PLoS Biology

February 4th, 2023

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Bonjour from Paris, France !

In today’s digest you will find a wide variety of interesting preprints and published research papers encompassing very interesting microbiome such as Yak calves rumen, compost, wineyard soil and lichen symbionth microbiota!

If you are interested in virome, I recommend looking at the fascinating preprint from Ha and collaborators investigating the biogeography of giant viruses from the phylum Nucleocytoviricota. They leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to recovered novel genomes from these viruses and identified geographical patterns of distribution.

If you are working on human microbiomes, I recommend checking out a really interesting preprint, comparing the biases and strengths of four commercially available DNA extraction kits frequently used for whole genome shotgun analysis of the human microbiome.

Have a great Saturday!

Events and jobs

Event: Cell Symposia: Infection biology in the age of the microbiome. Paris, France June 7-9

Event: 55th Annual Meeting of the European Society for Paediatric Gastroenterology, Hepatology and Nutrition. Vienna, Austria 17-20 May

Pregnancy and early life

Insufficient Evidence of a Breastmilk Microbiota at Six-Weeks Postpartum: A Pilot Study – Leech et al. – Nutrients

Effects of Perinatal Antibiotic Exposure and Neonatal Gut Microbiota – Morreale et al. – Antibiotics

Necrotizing Enterocolitis: The Role of Hypoxia, Gut Microbiome, and Microbial Metabolites – Kaplina et al. – International Journal of Molecular sciences

Human gut microbiome

Preprint: Functional assignment of gut-specific archaeal proteins in the human gut microbiome – Novikova et al. – BioRxiv

Animal microbiome

Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea – Woo et al. – PLOS ONE

The association between gingivitis and oral spirochetes in young cats and dogs – Yamaki et al. – PLOS ONE

Maternal rumen and milk microbiota shapes the establishment of early-life rumen microbiota in grazing yak calves – Guo et al. – Journal of Dairy Science

Plant, root, and soil microbiome

Preprint: Fundamentals of biofilm formation in soil: From functionalized self-assembled monolayers to rewilding – Hendiani et al. – BioRxiv

Local conditions matter: Minimal and variable effects of soil disturbance on microbial communities and functions in European vineyards – Steiner et al. – PLOS ONE

Preprint: Evidence for a core set of microbial lichen symbionts from a global survey of metagenomes – Tagirdzhanova et al. – BioRxiv

Water and extremophile microbiome

Preprint: Assessing the biogeography of marine giant viruses in four oceanic transects – Ha et al. – BioRxiv

Preprint: Cross-domain interactions induce community stability to benthic biofilms in proglacial streams – Busi et al. – BioRxiv

Opinion: Viral infection in the ocean—A journey across scales – Vincent and Vardi – PLOS biology

Bioinformatics

Preprint: Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome – Van Dijk et al – BioRxiv

Techniques

Preprint: Comparison of commercial DNA extraction kits for whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples – Wright et al – BioRxiv

December 9, 2022

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Today’s digest features global antimicrobial resistance, comammox and anammox bacteria in wastewater treatment, mOTUs3, and more. Check out Elisa Granato & Christoph Ziegenhain’s story about postdoc life. Happy Friday and see you next week at #MVIF!

Global microbiome & resistome

Experimental temperatures shape host microbiome diversity and composition – Jingdi Li – Global Change Biology

Global biogeography and projection of soil antibiotic resistance genes – Zheng et al. – Science Advances

*Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance – Patrick Munk – Nature Communications

Blood microbiome

No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C.S. Tan – bioRxiv

Gut microbiome

Effects of dog ownership on the gut microbiota of elderly owners – Chaona Jiang – Plos One

Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases – Yoshihiko Tomofuji – Cell Genomics

Gut microbiome-wide association study of depressive symptoms – Djawad Radjabzadeh – Nature Communications

Development of non-alcoholic steatohepatitis is associated with gut microbiota but not oxysterol synthesis – Jacqueline Wyss – bioRxiv

The microbiome’s fiber degradation profile and its relationship with the host diet – Yotam Cohen & Elhanan Borenstein – BMC Biology

Animal microbiome

Lactobacillus reuteri improves the development and maturation of fecal microbiota in piglets through mother-to-infant microbe and metabolite vertical transmission – Gang Wang – Microbiome

Live biotherapeutics

Development of a live biotherapeutic throat spray with lactobacilli targeting respiratory viral infections – Irina Spacova – Microbial Biotechnology

Soil/root/plant microbiome

Differential microbial assembly processes and co-occurrence networks in the soil-root continuum along an environmental gradient – Yangquanwei Zhong – iMeta

Water microbiome

*Co-occurrence and cooperation between comammox and anammox bacteria in a full-scale attached growth municipal wastewater treatment process – Katherine J Vilardi – bioRxiv

Full-scale activated sludge transplantation reveals a highly resilient community structure – Giulia Dottorini – Water Research

Bioinformatics

Towards complete representation of bacterial contents in metagenomic samples – Xiaowen Feng, Heng Li – arXiv

*Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments – Hans-Joachim Ruscheweyh – Microbiome

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023 – CNCB-NGDC Members and Partners – Nucleic Acids Research

Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes – Lei Liu – Microbiome

November 23, 2022

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General microbiome

[PREPRINT]Patterns and determinants of the global herbivorous mycobiome – Meili et al. – bioRxiv

[EDITORIAL]Helicobacter pylori: Have potential benefits been overlooked? – Schubert et al. – JGH Open

Pregnancy and early life

Mechanisms affecting the gut of preterm infants in enteral feeding trials: a nested cohort within a randomised controlled trial of lactoferrin – Young et al. – Arch Dis Child Fetal Neonatal Ed

Human oral microbiome

Ancient oral microbiomes support gradual Neolithic dietary shifts towards agriculture – Quagliariello et al. – Nature Communications

Human vaginal microbiome

[PREPRINT]Longitudinal dynamics of the human vaginal ecosystem across the reproductive cycle – Costello et al. – bioRxiv

Human gut microbiome

[REVIEW]Maternal obesity and resistance to breast cancer treatments among offspring: Link to gut dysbiosis – Andrade, Verma & Hilakivi-Clark

Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis – Baumgartner et al. – Gut Microbes

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

Impact of antibiotic perturbation on fecal viral communities in mice – Anderson et al. – G3

Animal microbiome (for animals in the wild)

Assessing Fungal Diversity and Abundance in the Black Soldier Fly and its Environment – Vitenberg & Opatovsky – Journal of Insect Science

Plant, root, and soil microbiome

Bacterial communities vary across populations and tissue type in red mangroves (Rhizophora mangle, Rhizophoraceae) along an expanding front – Scherer, Mason & Rast – FEMS Microbiology Ecology

Bioinformatics

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes – Fullam et al. – NAR

[PREPRINT]Sparsification of Large Ultrametric Matrices: Insights into the Microbial Tree of Life – Gorman & Lladser

Techniques

[PREPRINT]Soil metatranscriptomics: An improved RNA extraction method toward functional analysis using nanopore direct RNA sequencing – Poursalavati et al. – bioRxix

November 16, 2022

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General microbiome

Enhancing nutritional niche and host defenses by modifying the gut microbiome – Sun et al. – Molecular Systems Biology

Evolution of immune genes is associated with the Black Death – Klunk et al. – Nature

Pregnancy and early life

Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report – Wei et al. – Microbiome

Multi-site human microbiome

Age-Related Changes, Influencing Factors, and Crosstalk Between Vaginal and Gut Microbiota: A Cross-Sectional Comparative Study of Pre- and Postmenopausal Women – Yoshikata et al. – Journal of Women’s Health

Human oral microbiome

Characterization of oral microbiota in HPV and non-HPV head and neck squamous cell carcinoma and its association with patient outcomes – Chan et al. – Oral Oncology

Human gut microbiome

[REVIEW]Making gut microbiomes from scratch – Tiang & Bisanz – Cell Host &Microbe

Impairments of intestinal arginine and NO metabolisms trigger aging-associated intestinal barrier dysfunction and ‘inflammaging’ – Brandt et al. – Redox Biology

Dietary fiber ameliorates sleep disturbance connected to the gut–brain axis – Tang et al. – Food & Function

Meta-analysis of 16S rRNA microbial data identified alterations of the gut microbiota in COVID-19 patients during the acute and recovery phases – Cheng et al. – BMC Microbiology

Relationships between dietary diversity and gut microbial diversity in the elderly – Amamoto et al. – Beneficial Microbes

Alteration of the faecal microbiota composition in patients with constipation: evidence of American Gut Project – Xu et al. – Beneficial Microbes

Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis – Liang et al. – Translational Neurodegeneration

Microbiome insights into pediatric familial adenomatous polyposis – Attard et al. – Orphanet Journal of Rare Diseases

[REVIEW]The crosstalk between intestinal bacterial microbiota and immune cells in colorectal cancer progression – Wen et al. – Clinical and Translational Oncology

[REVIEW]Epigenetic regulation by metabolites from the gut microbiome – Marin-Tello et al. – Benefical Microbes

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

A tetrapeptide from maize combined with probiotics exerted strong anti-inflammatory effects and modulated gut microbiota in DSS-induced colitis mice – Li et al. – Food & Function

IGF1R is a mediator of sex-specific metabolism in mice: Effects of age and high-fat diet – Perez-Matute et al. – Front. Endocrinol.

Animal microbiome (for animals in the wild)

Nutrient dynamics in coral symbiosis depend on both the relative and absolute abundance of Symbiodiniaceae species – McIlroy et al. – Microbiome

Plant, root, and soil microbiome

Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea – Wicaksono et al. – mSystems

Bioinformatics

Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments – Hempel et al. – NAR

Metagenome-assembled genome extraction and analysis from microbiomes using KBase – Chivian et al. – Nature Protocols

SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies – Aytan-Aktug et al. – Microbiology Spectrum

TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes – Gupta et al. – mSystems

Techniques

Optimization of Low-Biomass Sample Collection and Quantitative PCR-Based Titration Impact 16S rRNA Microbiome Resolution – Clokie et al. – Microbiology Spectrum

September 7, 2022

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General microbiome

Impact of environmental conditions and gut microbiota on the in vitro germination and growth of Clostridioides difficile – Martinez et al. – FEMS Microbiology Letters

[FORUM]Polymorphic microbes: a new emerging hallmark of cancer – Lythgoe et al. – Trends in Microbiology

A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter – Hitch et al. – Systematic and Applied Microbiology

A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome – Martiny et al. – PLOS Biology

Pregnancy and early life

Alterations in Vaginal Microbiota among Pregnant Women with COVID-19 – Velik et al. – Journal of Medical Virology

The Global Incidence of Adverse Events Associated with Fecal Microbiota Transplantation in Children over the Past 20 Years: A Systematic Review and Meta-Analysis – Wang et al. – Journal of Gastroenterology and Hepatology

Multi-site human microbiome

Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes – Ke, Weiss & Liu – Nature Communications

Human salivary microbiome

Salivary microbiome in chronic kidney disease: what is its connection to diabetes, hypertension, and immunity? – Liu et al. – Journal of Translational Medicine volume

Human vaginal microbiome

Does exposure to different types of menstrual protections affect the vaginal environment? – Tessandier et al. – Molecular Ecology

Human gut microbiome

High-altitude exposure decreases bone mineral density and its relationship with gut microbiota: Results from the China multi-ethnic cohort (CMEC) study – Zuo et al. – Environmental Research

Animal microbiome

Characterization of the oral and fecal microbiota associated with atopic dermatitis in dogs selected from a purebred Shiba Inu colony – Uchiyama et al. – Letters of Applied Microbiology

Probiotics or synbiotics addition to sows’ diets alters colonic microbiome composition and metabolome profiles of offspring pigs – Zhu et al. – Front. Microbiol.

Longitudinal analysis of the rectal microbiome in dogs with diabetes mellitus after initiation of insulin therapy – Laia et al. – PLOS One

Plant, root, and soil microbiome

Core Microbiota in the Rhizosphere of Heavy Metal Accumulators and Its Contribution to Plant Performance – Luo et al. – Environ. Sci. Technol.

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

Global contribution of pelagic fungi to protein degradation in the ocean -Breyer et al. – Microbiome

August 24, 2022

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General microbiome

[REVIEW]Detecting bacterial adaptation within individual microbiomes – Liebermann – Phil. Trans. R. Soc. B

[REVIEW]Soil microbiomes and one health – Banerjee & van der Heijden – Nature Reviews Microbiology

Pregnancy and early life

Microbial Analysis of Umbilical Cord Blood Reveals Novel Pathogens Associated with Stillbirth and Early Preterm Birth – Vander Haar et al. – mBio

Human respiratory microbiome

The respiratory microbiota alpha-diversity in chronic lung diseases: first systematic review and meta-analysis – Avalos-Fernandez et al. – Respiratory Research

Human saliva microbiome

Saliva microbiome, dietary, and genetic markers are associated with suicidal ideation in university students – Ahrens et al. – Scientific Reports

Human gut microbiome

The gut microbiota is associated with immune cell dynamics in humans – Schluter et al. – Nature

The systemic anti-microbiota IgG repertoire can identify gut bacteria that translocate across gut barrier surfaces – Vujkovic-Cvijin et al. – Science Translational Medicine

Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling – Kim et al. – ISME Communications

Correlation of inflammatory biomarkers with the diversity of Bacteroidaceae, Bifidobacteriaceae, Prevotellaceae and Lactobacillaceae families in the intestinal microbiota of patients with end stage renal disease – Asgharian et al. – Advances in Medical Sciences

Impact of the Host Microbiome on Vaccine Responsiveness: Lessons Learned and Future Perspective – Stefanetti & Kasper – Biochemistry

Location-specific signatures of Crohn’s disease at a multi-omics scale – Gonzalez et al. – Microbiome

Association of food insecurity on gut microbiome and metabolome profiles in a diverse college-based sample – Mohr et al. – Scientific Reports

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

The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes – Miranda et al. – mSystems

Microbes in space

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome – Madrigal et al. – Microbiome

Bioinformatics

[PREPRINT]Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4 – Blanco-Miguez et al. – bioRxiv

Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data – Lin, Eggesbø & Peddada – Nature Communications

Techniques

Primers matter: Influence of the primer selection on human fungal detection using high throughput sequencing – Wiemann et al. – Gut Microbes

Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples – Baker et al. – mSystems