February 20, 2023

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Human and General Microbiome

Review: Controlling the human microbiome – Yang-Yu Liu – Cell Systems

Review: Metabolic models of human gut microbiota: Advances and challenges – Daniel Rios Garza – Cell Systems

The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes that reflect dietary intakes and fecal water content – Nikki Renall – Gut Microbes

Identifying the Novel Gut Microbial Metabolite Contributing to Metabolic Syndrome in Children Based on Integrative Analyses of Microbiome-Metabolome Signatures – Jia Wei – Microbiology Spectrum

Gut Microbiome and Risk of Ischemic Stroke: A Comprehensive Mendelian Randomization Study – Changjiang Meng – European Journal of Preventive Cardiology

Ancient Microbiome

Metagenomic analysis of Ancient Egyptian canopic jars – Enrique Rayo – American Journal of Biological Anthropology

Animal Model Microbiome

Preprint: Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model – Marlyd E Mejia – bioRxiv

Plant Microbiome

Multidisciplinary evaluation of plant growth promoting rhizobacteria on soil microbiome and strawberry quality – Jun Haeng Nam – AMB Express

Environmental Microbiome

Unravelling microalgal-bacterial interactions in aquatic ecosystems through 16S rRNA gene-based co-occurrence networks – B L D Uthpala Pushpakumara – Scientific Reports

Microbiome Analysis and Techniques

gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota – Victòria Pascal Andreu – Nature Biotechnology

Reliability of species detection in 16S microbiome analysis: Comparison of five widely used pipelines and recommendations for a more standardized approach – Andreas Hiergeist – PloS One

Preprint: Impact of experimental bias on compositional analysis of microbiome data – Yingtian Hu – 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 13, 2023

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Today’s reading recommendation is a microbiota review collection edited by Lindsay Hall and Melanie Schirmer.

Happy Monday and see you at #MVIF!

Vaginal microbiome

Gardnerella Diversity and Ecology in Pregnancy and Preterm Birth – Hanna L. Berman – bioRxiv

Heterogeneity of the group B streptococcal type VII secretion system and influence on colonization of the female genital tract – Brady L. Spencer – bioRxiv

Urinary microbiome

Comparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains – Ananya Prasad – mSphere

Human gut

Gut microbes predominantly act as symbiotic partners rather than raw nutrients – Nuno Felipe da Silva Soares – bioRxiv

Antibiotic resistance in the commensal human gut microbiota – Lisa E Lamberte, Willem van Schaik – Current Opinion in Microbiology

Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting – Lharbi Dridi – Nature Communications

Animal experiments

Over supplementation with vitamin B12 alters microbe-host interactions in the gut leading to accelerated Citrobacter rodentium colonization and pathogenesis in mice – Andrew J. Forgie – Microbiome

Disturbance of lipid metabolism in germ-free mice transplanted with gut microbiota of DSS-induced colitis mice – Chungho Lee – Plos One

Bioinformatics

Accurate and fast graph-based pangenome annotation and clustering with ggCaller – Samuel T. Horsfield – bioRxiv

Brief report: uBin – a manual refining tool for genomes from metagenomes – Till L V Bornemann – Environmental Microbiology

In-situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day – Javier Tamames – bioRxiv

The virtual microbiome: A computational framework to evaluate microbiome analyses – Belén Serrano-Antón – Plos One

February 8, 2023

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Human gut microbiome

Gut microbiota of Parkinson’s disease in an appendectomy cohort: a preliminary study – Nakahara et al. – Scientific Reports

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

Microbiota-derived acetate enhances host antiviral response via NLRP3 – Niu et al. – Nature Communications

Gut microbiota remodeling improves natural aging-related disorders through Akkermansia muciniphila and its derived acetic acid – Ma et al. – Pharmacological Research

Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation – Wang et al. – Microbiome

Animal microbiome (for animals in the wild)

[PREPRINT]Impacts of Age on the Gut Microbiota in Captive Giant Pandas – Li, Lui & Zhang – bioRxiv

Bioinformatics

[PREPRINT]Strain Tracking with Uncertainty Quantification – Kim et al. – bioRxiv

Efficient computation of contributional diversity metrics from microbiome data with FuncDiv – Douglas et al. – Bioinformatics

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

February 1, 2023

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General microbiome

Multi-dimensional experimental and computational exploration of metabolism pinpoints complex probiotic interactions – Zampieri, Efthimiou & Angione – Metabolic Engineering

[REVIEW]Advancing CAR T cell therapy through the use of multidimensional omics data – Yamg et al. – Nature Reviews Clinical Oncology

Pregnancy and early life

[REVIEW]Microbial transmission, colonisation and succession: from pregnancy to infancy – Xiao & Zhai – Gut

Human gut microbiome

Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome – Wang et al. – Microbiology Spectrum

[PREPRINT]Probiotics supplementation to adult human small intestinal stoma microbiota causes dynamic increase in the community resistance to perturbations and nutrient utilization – Jansma et al. – bioRxiv

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

Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice – Vallier et al. – Gut Microbes

Host-microbe co-metabolism via MCAD generates circulating metabolites including hippuric acid – Pruss et al. – Nature Communications

Disruption of the Intestinal Mucosal Barrier Induced by High Fructose and Restraint Stress Is Regulated by the Intestinal Microbiota and Microbiota Metabolites – Yu et al. – Microbiology Spectrum

[PREPRINT]Shift from a Simplified to Complex Gut Microbiota Reduces Adenoma Burden in a Preclinical Rat Model of Colon Cancer – Busi et al. – bioRxiv

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

Viral infection switches the balance between bacterial and eukaryotic recyclers of organic matter during coccolithophore blooms – Vincent et al. – Nature Communications

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. – Microbiome

Bioinformatics

[PREPRINT]Accounting for 16S rRNA copy number prediction uncertainty and its implications in microbial diversity analyses – Gao & Wu – bioRxiv

Techniques

[PREPRINT]Methods for the analysis of skin microbiomes: a comparison of sampling processes and 16S rRNA hypervariable regions – Alyami et al. – bioRxiv

January 27, 2023

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General Microbiome

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies – Kennedy et al. Nature

Microbial foods for improving human and planetary health – Jahn et al. Cell

A tissue atlas of ulcerative colitis revealing evidence of sex-dependent differences in disease-driving inflammatory cell types and resistance to TNF inhibitor therapy – Mayer et al. Science Advances

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults – Larson et al. Nature Aging

Bacteriophage / Virome

Phage therapy: From biological mechanisms to future directions – Strathdee et al. Cell

Mining metatranscriptomes reveals a vast world of viroid-like circular RNAs – Lee et al. Cell

Water and extremophile microbiome

High-resolution metagenomic reconstruction of the freshwater spring bloom – Kavagutti et al. Microbiome

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria – Sereika et al. ISME

Bioinformatics

Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching – Louwen et al. Microbiome

PLSDA-batch: a multivariate framework to correct for batch effects in microbiome data – Wang & Cao. Briefings in Bioinformatics

Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine – Heinken et al. Nature Biotechnology

Non-Microbiome picks

Infection infidelities drive innate immunity – Kagan. Science

Functional T cells are capable of supernumerary cell division and longevity – Soerens et al. Nature

Genetic adaptation to pathogens and increased risk of inflammatory disorders in post-Neolithic Europe – Kerner et al. Cell Genomics

January 25, 2023

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Human oral microbiome

Microbiological profile of peri-implantitis: Analyses of microbiome within dental implants – Kensara et al. – Journal of Prosthodontics

Human gut microbiome

Integrated Multi-Cohort Analysis of the Parkinson’s Disease Gut Metagenome – Boktor et al. – Movement Disorders

Gut microbiota and microbiota-derived metabolites promotes endometriosis – Chadchan et al. – Cell Death Discovery

Immune communication between the intestinal microbiota and the cardiovascular system – Ren et al. – Immunology Letters

Animal microbiome

The structure and diversity of microbial communities in Paederus fuscipes (Coleoptera: Staphylinidae): from ecological paradigm to pathobiome – Chamanakar et al. – Microbiome

The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet – Lin et al. – Microbiome

Fecal Microbiota Was Reshaped in UCP1 Knock-In Pigs via the Adipose-Liver-Gut Axis and Contributed to Less Fat Deposition – Pan et al. – Microbiology Spectrum

Gut microbiota of skywalker hoolock gibbons (Hoolock tianxing) from different habitats and in captivity: Implications for gibbon health – Lan et al. – American Journal of Primatology

Housing temperature plays a critical role in determining gut microbiome composition in research mice: Implications for experimental reproducibility – Hylander et al. – Biochimie

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

The biogeography and co-occurrence network patterns of bacteria and microeukaryotes in the estuarine and coastal waters – Wu et al. – Marine Environmental Research

Bioinformatics

[PREPRINT]Capturing the dynamics of microbiomes using individual-specific networks – Yousefi et al. – bioRxiv

PhaTYP: predicting the lifestyle for bacteriophages using BERT – Shang, Tang & Sun – Briefings in Bioinformatics

January 18, 2023

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Human oral microbiome

[PRIMER]A possible role for taste receptor cells in surveying the oral microbiome – Heisey & McCluskey – PLOS Biology

Type II taste cells participate in mucosal immune surveillance – Qin et al. – PLOS One

Human gut microbiome

[NEWS]How our microbiome is shaped by family, friends and even neighbours – Callaway – Nature

The person-to-person transmission landscape of the gut and oral microbiomes – Valles-Colomer et al. – Nature

[REVIEW]The gut microbiota in obesity and weight management: microbes as friends or foe? – van Hul & Cani – Nature Reviews Endocrinology

Dynamics of the gut microbiome, IgA response, and plasma metabolome in the development of pediatric celiac disease – Girdhar et al. – Microbiome

Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes – Jacobs et al. – Microbiome

Microbiome Features Differentiating Unsupervised-Stratification-Based Clusters of Patients with Abnormal Glycometabolism – Xu et al. – mBio

Gut Bacterial Dysbiosis in Irritable Bowel Syndrome: a Case-Control Study and a Cross-Cohort Analysis Using Publicly Available Data Sets – Kim, Lee & Shim – Microbiology Spectrum

Harnessing gut microbes for glycan detection and quantification – Modesto, Pearce & Townsend Il – Nature Communications

The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles – Malan – Müller et al. – Gut Microbes

Animal microbiome

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse – Li et al. – Microbiome

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions – Bay et al. – Microbiome

Plant, root, and soil microbiome

A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data – Merihu et al. – Microbiome

Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle – Kibegwa et al. – PLOS One

Bioinformatics

Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples – Maki et al. – PLOS One

January 13, 2023

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The very first 2023 digest features HMOs, antimicrobials and the neonatal gut microbiota, cheese community, cow rumen microbiome, SemiBin2, and more. Happy Friday and see you next week at #MVIF!

Food microbiome

*Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities – Christina C. Saak – mSystems

Gut microbiome

*Human milk oligosaccharides, antimicrobial drugs, and the gut microbiota of term neonates: observations from the KOALA birth cohort study – D.J.M Barnett – Gut microbes

The gut microbiota in multiple sclerosis varies with disease activity – Florence Thirion – Genome Medicine

Review: Intestinal gas production by the gut microbiota: A review – Erasme Mutuyemungu – Journal of Functional Foods

Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis – Yishay Pinto – Gut

Review: The gut microbiota is an emerging target for improving brain health during ageing – Marcus Boehme – Gut microbiome

Vaginal microbiome

Commensal Lactobacilli Metabolically Contribute to Cervical Epithelial Homeostasis in a Species-Specific Manner – Nicole R. Jimenez – mSphere

Preterm birth is associated with xenobiotics and predicted by the vaginal metabolome – William F. Kindschuh – Nature Microbiology

Animal experiment

Gut microbiota of the young ameliorates physical fitness of the aged in mice – Kwang H. Kim – Microbiome

Catheterization of mice triggers resurgent urinary tract infection seeded by a bladder reservoir of Acinetobacter baumannii – Jennie E. Hazen – Science Translational Medicine

Prebiotic intervention with HAMSAB in untreated essential hypertensive patients assessed in a phase II randomized trial – Hamdi A. Jama – Nature Cardiovascular Research

Akkermansia muciniphila protects mice against an emerging tick-borne viral pathogen – Jinyan Xie – Nature Microbiology

Animal microbiome

Beehives possess their own distinct microbiomes – Lorenzo A. Santorelli – Environmental Microbiome

*Differential carbon utilization enables co-existence of recently speciated Campylobacteraceae in the cow rumen epithelial microbiome – Cameron R. Strachan – Nature Microbiology

Bioinformatics

Ecological landscapes guide the assembly of optimal microbial communities – Ashish B. George and Kirill S. Korolev – Plos Computational Biology

Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering – Theresa Ullmann – Plos Computational Biology

Ten simple rules for using public biological data for your research – Vishal H. Oza – Plos Computational Biology

*SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing – Shaojun Pan – bioRxiv