September 01, 2021

General microbiome

Circulating microbiome DNA: An emerging paradigm for cancer liquid biopsy – Chen et al. – Cancer letters

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics – Letten et al. – The ISME Journal

[PERSPECTIVE]Crosstalk between γδ T cells and the microbiota – Papotto, Yilmaz & Silva-Santos – Nature Microbiology

Pregnancy and early life

Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life – Tsukuda et al. – The ISME Journal

Deterministic transition of enterotypes shapes the infant gut microbiome at an early age – Xiao et al. – Genome Biology

Human oral microbiome

[REVIEW]Association between metabolic syndrome and periodontitis: The role of lipids, inflammatory cytokines, altered host response, and the microbiome – Pirih et al. – Periodontology 2000

[REVIEW]Fungal diseases: Oral dysbiosis in susceptible hosts – Villar & Dongari-Bagtzoglou – Periodontology 2000

[REVIEW]The oral microbiome: Role of key organisms and complex networks in oral health and disease – Sedghi et al. – Periodontology 2000

Human gut microbiome

Human reference gut microbiome catalog including newly assembled genomes from under-represented Asian metagenomes – Kim et al. – Genome Medicine

[REVIEW]The promise of the gut microbiome as part of individualized treatment strategies – Schupack et al. – Nature Reviews Gastroenterology & Hepatology

[REVIEW]The gut microbiome and efficacy of cancer immunotherapy – Robiello et al. – Pharmacology & Therapeutics

Integrated analysis of the faecal metagenome and serum metabolome reveals the role of gut microbiome-associated metabolites in the detection of colorectal cancer and adenoma – Chen et al. – Gut

Animal/Insect microbiome

Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes – Gupta et al. – Microbiome

Social networks strongly predict the gut microbiota of wild mice – Raulo et al. – The ISME Journal

Genetic identity and genotype × genotype interactions between symbionts outweigh species level effects in an insect microbiome – Smee, Raines & Ferrari – The ISME Journal

[REVIEW]The effects of raw-meat diets on the gastrointestinal microbiota of the cat and dog: a review – Butowski et al. – New Zealand Veterinary Journal

Plant, root, and soil microbiome

Predicting spatial patterns of soil bacteria under current and future environmental conditions – Mod et al. – The ISME Journal

Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype – Stopnisek & Shade – The ISME Journal

Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota – Wippel et al. – Nature Microbiology

Bioinformatics/Techniques

Functional meta-omics provide critical insights into long- and short-read assemblies – Galata et al. – Briefings in Bioinformatics

[PREPRINT]BiomeHorizon: visualizing microbiome time series data in R – Fink et al. – bioRxiv

Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Shibata et al. – PLOS ONE

MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data – Mongad et al. – Genomics

August 22nd, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains a selection of really interesting preprints and published studies. If you are interested in soil microbiology, take a look at the preprint by Nelson and collaborators, who characterized the soil microbiome across a wildfire burn severity gradients in coniferous forests and made their dataset available in the Fire Responding Ecogenomic database (FiRE-db).

Looking at a large variety of ecosystems, Rodriguez-Gijon and collaborators used a vast collection of Metagenomes Assembled Genomes (MAGs), to investigate the genomes size of prokaryotes in these ecosystems. They show that, while the environment of origin can be linked to genome size, it seems like evolutionary phylogenetic history is in many cases a stronger predictor.

Finally, today’s non-microbiology pick is a great “10 simples rules” paper reviewing best practices on organizing bioinformatics workshops in low and middle-income countries.

Have a great Weekend!


General microbiome

Preprint: A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked to ecosystem type and trophic strategy – Rodriguez-Gijon et al. – BioRXiV

Multi-site human microbiome

Review : Host-Microbe Metagenomics: a Lens To Refocus Our Perspective
on Infectious and Inflammatory Diseases – Kalantar and Langelier – mSystems

Human gut microbiome

Rectal bacteriome and virome signatures and clinical outcomes in community-acquired pneumonia: An exploratory study – Kullberg et al. – EClinicalMedicine

Review: The important role of fungi in inflammatory bowel diseases – Wang et al. – Scandinavian Journal of Gastroenterology


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

Preprint: A bacterial genome and culture collection of gut microbial in weanling piglet – Dong et al. – BioRXiV

Characterization of the fecal microbiota of sows and their offspring from German commercial pig farms – Lührmann et al. – Plos One

Plant, root, and soil microbiome

Preprint: Does plant diversity determine the diversity of the rhizosphere microbial community? – Zverev et al. – BioRXiV

Preprint: Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire – Nelson et al. – BioRXiV

Peatland microbial community responses to plant functional group and drought are depth-dependent – Lamit et al. – Molecular ecology

Soil pH determines bacterial distribution and assembly processes in natural mountain forests of eastern China – Ni et al. – Global ecology and Biogeography

Water and extremophile microbiome

Preprint: The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments – Nishimura et al. – BioRXiV

Food microbiology

Preprint: Mixed culture metagenomics of the microbes making sour beer – Piraine et al. – BioRXiV

Preprint: Insights into the nutritional properties and microbiome diversity in sweet and sour yogurt manufactured in Bangladesh – Tanzina et al. – BioRXiV

Preprint: Microbial communities in retail draft beers and the biofilms they produce – Bose et al. – BioRXiV


Bioinformatics

Book chapter: Bioinformatics Tools and Software – Gupta et al. – Advances in Bioinformatics, Springer, Singapore

MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes – Lee et al. – New biotechnology


My non-microbiology picks

Ten simple rules for organizing a bioinformatics training course in low and middle-income countries – Moore et al. – PLOS computational biology

May 29, 2021

General microbiome

Biogeochemical dynamics and microbial community development under sulfate- and iron-reducing conditions based on electron shuttle amendment – TM Flynn et al. – PLOS ONE

Human skin microbiome

Composition of cutaneous bacterial microbiome in seborrheic dermatitis patients: A cross-sectional study – MGH Sanders et al. – PLOS ONE

Human gut microbiome

Host specificity of the gut microbiome – EK Mallot & KR Amato – Nature Reviews Microbiology

Animal experiments

Influence of genetic background and dietary oleic acid on gut microbiota composition in Duroc and Iberian pigs – A López-Garcí et al. – PLOS ONE

Animal microbiome

Compartmentalization of bacterial and fungal microbiomes in the gut of adult honeybees – M Callegari et al. – npj Biofilms and Microbiomes

Plant, root, and soil microbiome

Saprotrophic fungal diversity predicts ectomycorrhizal fungal diversity along the timberline in the framework of island biogeography theory – T Yang et al. – ISME Communications

Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land – N Yayi et al. – PLOS ONE

Specificity of assemblage, not fungal partner species, explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants – Z Zhao et al. – The ISME Journal

Water and extremophile microbiome

Abundant and rare bacterial taxa structuring differently in sediment and water in thermokarst lakes in the Yellow River Source area, Qinghai-Tibet Plateau – Z Ren et al. – bioRxiv

Phages and viruses

Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes – Y Liu et al. – bioRxiv

Integrating Viral Metagenomics into an Ecological Framework – P Sommers et al. – Annual Review of Virology

Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Z Cao et al. – bioRxiv

May 17, 2021

Good morning from Pittsburgh.

Today’s digest is preprint-heavy and has quite a few articles focused on soil, plants, and agriculture. If you aren’t interested in those areas of research, we also have articles with topics spanning the 1918 pandemic to multi-donor fecal transplants to carbohydrate utilization by marine fungi.

Happy reading!

General microbiome

Fresh extension of Vibrio cholerae competence type IV pili predisposes them for motor-independent retraction – Chlebek et al. – Appl Environ Microbiol

Preprint: Coordination of gene expression with cell size enables Escherichia coli to efficiently maintain motility across conditions – Honda et al. – bioRxiv

Preprint: Archival influenza virus genomes from Europe reveal genomic and phenotypic variability during the 1918 pandemic – Patrono et al. – bioRxiv

Preprint: Fluorescent protein expression as a proxy of bacterial fitness in a high throughput assay – Schlechter et al. – bioRxiv

Preprint: Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units – Viana de Siqueira et al. – bioRxiv

Human skin microbiome

Preprint: Anatomy promotes neutral coexistence of strains in the human skin microbiome – Conwill et al. – bioRxiv

Preprint: Gene- and genome-centric dynamics shape the diversity of oral bacterial populations – Utter et al. – bioRxiv

Human gut microbiome

Preprint: Two microbiota subtypes identified in Irritable Bowel Syndrome with distinct responses to the low-FODMAP diet – Vervier et al. – bioRxiv

Strain engraftment competition and functional augmentation in a multi-donor fecal microbiota transplantation trial for obesity – Wilson et al. – Microbiome

Plant, root, and soil microbiome

Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula – Brown et al. – Microbiome

Preprint: A novel dual enrichment strategy provides soil- and digestate-competent N2O-respiring bacteria for mitigating climate forcing in agriculture – Jonassen et al. – bioRxiv

Preprint: Temporal dynamics of microbial transcription in wetted hyperarid desert soils – León-Sobrino et al. – bioRxiv

Preprint: Metagenomic sequencing for rapid identification of Xylella fastidiosa from leaf samples – Roman-reyna et al. – BioRxiv

Preprint: Pseudomonas arenae sp. nov., Pseudomonas glycinis sp. nov. and Pseudomonas harudinis sp. nov., three novel bacterial species and plant endophytes – Seaton et al. – bioRxiv

Preprint: Phage-resistant bacteria reveal a role for potassium in root colonization – Tzipilevich & Benfey – bioRxiv

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems – Qian et al. – Microbiome

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

Potential and expression of carbohydrate utilization by marine fungi in the global ocean – Baltar et al. – Microbiome

Preprint: Syntrophic H2 production enhances the performance of primarily acetate-supplemented reactors treating sulphate contaminated solutions – Hessler et al. – bioRxiv

May 07, 2021

Human gut microbiome

Androgen-induced gut dysbiosis disrupts glucolipid metabolism and endocrinal functions in polycystic ovary syndrome – Han et al. Microbiome

Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model – Newman et al. Microbiome

Metagenomic Analysis of Common Intestinal Diseases Reveals Relationships among Microbial Signatures and Powers Multidisease Diagnostic Models – Jiang et al. mSystems

Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential – Mangalea et al. Cell Host & Microbe. 

Human respiratory microbiome

Integrative microbiomics in bronchiectasis exacerbations – Mac Aogáin et al. Nature Medicine

Probiotics

The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics – Salminen et al. Nature Reviews Gastroenterology & Hepatology

Mycobiota/Fungi

Fungal taxonomy and sequence-based nomenclature – Lucking et al. Nature Microbiology

Host-Microbiota interactions

A Streptococcus Quorum Sensing System Enables Suppression of Innate Immunity – Rahbari et al. mBio

Bioinformatics

Tamock: simulation of habitat-specific benchmark data in metagenomics – Gerner et al. BMC Bioinformatics

Techniques

Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota – Baker et al. Microbiome

April 28, 2021

General microbiome

Microbiota regulate innate immune signaling and protective immunity against cancer – Xing et al. – Cell Host & Microbe

Pregnancy and early life

[PREPRINT]Diet Potentially Drives the Differentiation of Eating Behaviours via Alterations to the Gut Microbiome in Infants – Yan et al. – bioRxiv

[REVIEW]Impact of Maternal Nutritional Supplementation during Pregnancy and Lactation on the Infant Gut or Breastmilk Microbiota: A Systematic Review – Zaidi, Moore & Okala – Nutrients

Infant Gut Microbiome Is Enriched with Bifidobacteria longumssp. infantisin Old Order Mennoniteswith Traditional Farming Lifestyle – Seppo et al. – Allergy

Human skin microbiome

Can antibiotic‐induced changes in the composition of the hair follicle microbiome regulate human hair growth? – Lousada et al. – Experimental Dermatology

Human gut microbiome

Multi-omics study reveals that statin therapy is associated with restoration of gut microbiota homeostasis and improvement in outcomes in patients with acute coronary syndrome – Hu et al. – Theranostics

Alteration of gut microbial profile in patients with diabetic nephropathy – Du et al. – Endocrine

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

Sargassum fusiforme fucoidan modifies gut microbiota and intestinal metabolites during alleviation of hyperglycemia in type 2 diabetic mice – Wu et al. – Food & Function

Bidirectional interaction of nobiletin and gut microbiota in mice fed with a high-fat diet – Zhang et al. – Food & Function

Reshaping of the gastrointestinal microbiome alters atherosclerotic plaque inflammation resolution in mice – Garshick et al. – Scientif Reports

Animal microbiome (for animals in the wild)

Gut bacterial communities across 12 Ensifera (Orthoptera) at different feeding habits and its prediction for the insect with contrasting feeding habits – Zheng et al. – PLOS One

Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone – Antwis et al. – Journal of Animal Ecology

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

[PREPRINT]A Scenic River in Rural Ohio Shows Elevated Antibiotic Resistance Genes, Including Acinetobacter Tetracycline and Macrolide Resistance, Downstream of Wastewater Treatment Plant Effluent – Murphy et al. – bioRxiv

[PREPRINT]Diversity of free-living prokaryotes on terrestrial and marine Antarctic habitats – Bendia et al. – bioRxiv

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics – Cabello-Yeves – Environmental Microbiome

Techniques

Obtaining deeper insights into microbiome diversity using a simple method to block host and non‐targets in amplicon sequencing – Mayer et al. – Molecular Ecology Resources

April 21, 2021

General microbiome

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection – Mu et al. – Microbiome

Pregnancy and early life

A Microbiota-Directed Food Intervention for Undernourished Children – Chen et al. – The New England Journal of Medicine

Bacterial-fungal interactions in the neonatal gut influence asthma outcomes later in life – Boutin et al. – eLife

Human vaginal microbiome

[REVIEW]The effect of different contraceptive methods on the vaginal microbiome – Bastianelli et al. – Expert Review of Clinical Pharmacology

Human gut microbiome and virome

The Gut Microbiome in Progressive Multiple Sclerosis – Cox et al. – Annals of Neurology

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity – Zuo et al. – Microbiome

[REVIEW]The Gut Microbiome: a New Frontier in Musculoskeletal Research – Li et al. – Current Osteoporosis Reports

[REVIEW]Inflammation‐driven brain and gut barrier dysfunction in stress and mood disorders – Doney et al. – European Journal of Neuroscience

The gut microbiota is associated with clinical response to statin treatment in patients with coronary artery disease – Wang et al. – Atherosclerosis

[REVIEW]Dietary restrictions modulate the gut microbiota: Implications for health and disease – Schmidt and Lorentz – Nutrition Research

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

Altering the microbiome inhibits tumorigenesis in a mouse model of oviductal high-grade serous carcinoma – Chen et al. – Cancer Research

Screening of probiotic candidates in a simulated piglet small intestine in vitro model – Hansen et al. – FEMS Microbiology Letters

Animal microbiome (for animals in the wild)

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history – Carrier et al. – PNAS

[PREPRINT]Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding and that E. coli from these dogs are shared with humans and cause opportunistic infections – Mounsey et al. – bioRxiv

Diversity structure of the microbial communities in the guts of four neotropical termite species – Vikram et al. – PeerJ

Alteration of gut microbiota with a broad‐spectrum antibiotic does not impair maternal care in the European earwig – van Meyel et al. – Journal of Evolutionary Biology

Food microbiology

The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites – Sawada et al. – PeerJ

Techniques

[PREPRINT]Development of Microbiome Biomarkers for IgA: a Joint Modeling Approach – Sengupta et al. – bioRxiv

April 07, 2021

General microbiome

Primate phageomes are structured by superhost phylogeny and environment – Gogarten et al. – PNAS

Fungal‐induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL‐22 – Zhu et al. – The EMBO Journal

A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study – Coryell et al. – The Lancet Microbe

The Ocular Microbiome and Microbiota and their Effects on Ocular Surface Pathophysiology and Disorders – Aragona et al. – Survey of Ophthalmology

Human oral microbiome

Multi-dimensional study of the oral microbiome, metabolite, and immunologic environment in peanut allergy – Ho et al. – Journal of Allergy and Clinical Immunology

Human skin microbiome

Temporal Variation in Staphylococcus aureus Protein A Genotypes from Nose and Skin in Atopic Dermatitis Patients – van Mierlo et al. – Dermatology

Sex‐Based Differences in Fecal Short‐Chain Fatty Acid and Gut Microbiota in Irritable Bowel Syndrome Patients – Sun et al. – Journal of Digestive Diseases

Human gut microbiome

[REVIEW]Ecological and evolutionary responses to antibiotic treatment in the human gut microbiota – Pennycook & Scanlan – FEMS Microbiology Reviews

Animal microbiome (for animals in the wild)

The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics – Yang et al. – Zoological Scienc

Microbes in space

Astrobiology of life on Earth – Hallsworth et al. – Environmental Microbiology
Mars’ surface is not universally biocidal – Hallsworth – Environmental Microbiology

Bioinformatics

Draft Genome Sequences and Antimicrobial Profiles of Three Staphylococcus epidermidis Strains from Neonatal Blood Samples – Afeke et al. – Microbiology Resource Announcements

CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning – Arisdakessian et al. – Bioinformatics

Techniques

Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries – Davis, Huang & Wang – Briefings in Bioinformatics

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing – Tourancheau et al. – Nature Methods

March 31, 2021

Pregnancy and early life

Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries – Sands et al. – Nature Microbiology

Human gut microbiome

The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia – Rettedal at al. – JBMR Plus
[Review]Ageing of the gut microbiome: potential influences on immune senescence and inflammageing – Conway & Duggal – Ageing Research Reviews

Human esophageal microbiome

Esophageal microbiome in active eosinophilic esophagitis and changes induced by different therapies – Laserna-Mendieta et al. – Scientific Reports

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

[PREPRINT]Establishment and Resilience of Transplanted Gut Microbiota in Aged Mice – Wang et al. – bioRxiv

Animal microbiome (for animals in the wild)

Termites Are Associated with External Species-Specific Bacterial Communities – Soukup et al. – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Assessment of fungal diversity in soil rhizosphere associated with Rhazya stricta and some desert plants using metagenomics – Noor et al. – Archives of Microbiology

The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization – Wang et al. – The ISME Journal

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

Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession – Shabarova et al. – Nature Microbiology

Techniques

Reduced metagenome sequencing for strain-resolution taxonomic profiles – Snipen et al. – Microbiome

February 26, 2021

Pregnancy and early life

Multi-kingdom ecological drivers of microbiota assembly in preterm infants – Rao et al. – Nature

Human gut

[PREPRINT]A randomization-based causal inference framework for uncovering environmental exposure effects on human gut microbiota – Sommer et al. – bioRxiv

[PREPRINT]Fiber-associated Lachnospiraceae reduce colon tumorigenesis by modulation of the tumor-immune microenvironment – Almeida et al. – bioRxiv

Animal microbiome/experiments

NLRP6-associated host microbiota composition impacts in the intestinal barrier to systemic dissemination of Brucella abortus – Rungue et al. – PLOS Neglected Tropical Diseases

Effects of sodium butyrate supplementation on inflammation, gut microbiota, and short‐chain fatty acids in Helicobacter pylori‐infected mice – Huang et al. – Helicobacter

The porcine corneal surface bacterial microbiome: A distinctive niche within the ocular surface – Leis et al. – PLOS One

Dysbiosis of fecal microbiota in cats with naturally occurring and experimentally induced Tritrichomonas foetus infection – Bierlein et al. – PLOS One

Hologenome analysis reveals dual symbiosis in the deep-sea hydrothermal vent snail Gigantopelta aegis – Lan et al. – Nature Communications

Plant, root, and soil microbiome

The bacterial communities of Alaskan mosses and their contributions to N2-fixation – Holland-Moritz et al. – Microbiome

Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments – Wyness et al. – PLOS One

[PREPRINT]Rare genera differentiate urban green space soil bacterial communities in three cities across the world – Mills et al. – bioRxiv

Nitrogen and water addition regulate fungal community and microbial co-occurrence network complexity in the rhizosphere of Alhagi sparsifolia seedlings – Zhang et al. – Applied Soil Ecology

Metabolic profiling and antioxidant activity during flower development in Agastache rugosa – Yeo et al. – Physiology and Molecular Biology of Plants

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

Long-term dynamic changes in attached and planktonic microbial communities in a contaminated aquifer – Mujica-Alarcon, Thornton & Rolfe – Environmental Pollution

Phages and viruses

Virome composition in marine fish revealed by meta-transcriptomics – Geoghegan et al. – Virus Evolution

Bioinformatics

Comparison of beta diversity measures in clustering the high-dimensional microbial data – Chen et al. – PLOS One