January 26, 2022

General microbiome

[PREPRINT]Arresting microbiome development limits immune system maturation and resistance to infection – Lubin et al. – bioRxiv

Pregnancy and early life

Transcription shifts in gut bacteria shared between mothers and their infants – Vatanen et al. – Scientific Reports

Human urinary tract microbiome

Immune milieu and microbiome of the distal urethra in Ugandan men: impact of penile circumcision and implications for HIV susceptibility – Galwango et al. – Microbiome

Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states – Adu-Oppong et al. – Microbiome

Longitudinal variability in the urinary microbiota of healthy premenopausal women and the relation to neighboring microbial communities: A pilot study – Biehl et al. – PLOS One

Human vaginal microbiome

molBV reveals immune landscape of bacterial vaginosis and predicts human papillomavirus infection natural history – Usyk et al. – Nature Communications

Human gut microbiome

Differences in gut microbiome by insulin sensitivity status in Black and White women of the National Growth and Health Study (NGHS): A pilot study – Price et al. – PLOS One

Changes in the gut microbiota and risk of colonization by multidrug-resistant bacteria, infection and death in critical care patients – Rubio et al. – Clinical Microbiology and Infection

[PREPRINT]Gut Microbiome of Helminth Infected Indigenous Malaysians Is Context Dependent – Tee et al. – bioRxiv

Assessing the joint effects of brain aging and gut microbiota on the risks of psychiatric disorders – Zhang et al. – Brain Imaging and Behavior

Animal microbiome

Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing – Xue et al. – Microbiome

The influence of food processing methods on serum parameters, apparent total-tract macronutrient digestibility, fecal microbiota and SCFA content in adult beagles – Cai et al. – PLOS One

Kaempferol acts on bile acid signaling and gut microbiota to attenuate the tumor burden in ApcMin/+ mice – Li et al. – European Journal of Pharmacology

[PREPRINT]Diet outweighs genetics in shaping gut microbiomes in Asian honeybee – Su et al. – bioRxiv

Changes of Gut Microbiota by Natural mtDNA Variant Differences Augment Susceptibility to Metabolic Disease and Ageing – Künstner et al. – Int. J. Mol. Sci.

Diet Prevents Social Stress-Induced Maladaptive Neurobehavioural and Gut Microbiota Changes in a Histamine-Dependent Manner – Costa et al. – Int. J. Mol. Sci.

Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms – Schugar et al. – eLife

Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota – Perez-Lamarque – mSystems

Parkinson’s Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats – van Kessel et al. – mSystems

Multi-omics Analysis Revealed Coordinated Responses of Rumen Microbiome and Epithelium to High-Grain-Induced Subacute Rumen Acidosis in Lactating Dairy Cows – Mu et al. – mSystems

Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians – Chen et al. – Molecular Ecology

Commensal oral microbiota induces osteoimmunomodulatory effects separate from systemic microbiome in mice – Hathaway-Schrader et al. – JCI insight

Plant, root, and soil microbiome

Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota – Duran et al. – Nature Communications

[PREPRINT]Biodiversity of the Genus Trichoderma in the Rhizosphere of Coffee (Coffea arabica) Plants in Ethiopia and their Potential Use in Biocontrol of Coffee Wilt Disease – Mulatu et al. – bioRxiv

Built environment (subways, indoor surfaces)

A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms – Lim et al. – PLOS One

Techniques

[PREPRINT]Choice of 16S ribosomal RNA primers impacts urinary microbiota profiling – Heidrich et al. – bioRxiv

December 15, 2021

Nasal microbiome

Deep nasal sinus cavity microbiota dysbiosis in Parkinson’s disease – Pal et al – NPJ Parkinson’s disease

Pregnancy and early life

Influence of Family Integrated Care on the Intestinal Microbiome of Preterm Infants With Necrotizing Enterocolitis and Enterostomy: A Preliminary Study – Yang et al. – Front. Pediatr.

Multi-site human microbiome

[PREPRINT]Alternations of fecal microbes and lung tissue microbes in Lung Cancer patients is more consistent than that of sputum – Yanze et al. – bioRxiv

Human oral microbiome

[PREPRINT]A core salivary microbiome shows the high prevalence of bacterial members yet variability across human populations – Ruan et al. – bioRxiv

Human eye microbiome

Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease – Liang et al. – Front. Cell Dev. Biol.

Human vaginal microbiome

[REVIEW]Beyond bacterial vaginosis: vaginal lactobacilli and HIV risk – Armstrong & Kaul – Microbiome

Human gut mycobiome/microbiome

The fecal mycobiome in non-alcoholic fatty liver disease – Demir et al. – Journal of Hepatology

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

Intermittent Fasting Reshapes the Gut Microbiota and Metabolome and Reduces Weight Gain More Effectively Than Melatonin in Mice – Liu et al. – Front. Nutr.

Analyzing gut microbiota composition in individual Anopheles mosquitoes after experimental treatment – Fofana et al. – iScience

Microbial interaction-driven community differences as revealed by network analysis – Pan et al. – Computational and Structural Biotechnology Journal

[PREPRINT]Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle – Hoces et al. – bioRxiv

[PREPRINT]Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community – Lyalina et al – bioRxiv

Gut microbiota modulates weight gain in mice after discontinued smoke exposure – Fluhr et al. – Nature

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

[PREPRINT]Stratified microbial communities are highly sensitive towards multiple combined global change factors, revealing antagonistic and synergistic effects – Suleiman et al. – bioRxiv

Bioinformatics / Databases

Cow Rumen v1.0 – Database

[REVIEW]A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data – Yang et al. – Computational and Structural Biotechnology Journal

Microbiome podcast

The Microbiome Facts, Not the Hype – Kristina Campbell

November 26, 2021

General microbiome

Metabolomics-Microbiome Crosstalk in the Breast Cancer Microenvironment – Al-Ansari – Metabolites

Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection – Barber et al. – Nature Microbiology

Human gut microbiome

Human gut bacterial metabolism drives Th17 activation and colitis – Alexander et al. – Cell Host & Microbiome

Integrative Analysis of Metabolome and Microbiome in Patients with Progressive Alcohol-Associated Liver Disease – Gao et al. – Metabolites

Human Fecal Metabolome Reflects Differences in Body Mass Index, Physical Fitness, and Blood Lipoproteins in Healthy Older Adults – Cui et al. – Metabolites

[REVIEW]Gut Microbiota, Microbial Metabolites and Human Physical Performance – Lensu & Pekkala – Metabolites

[Editorial]Next steps after 15 stimulating years of human gut microbiome research – Clavel et al. – Microbial Biotechnology

[REVIEW]The microbiome, Gastrointestinal cancer and immunotherapy – Newsome, Yang & Jobin – Journal of Gastroenterology and Hepatology

Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease – Doron et al. – Nature Microbiology

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

Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-brain axis – Zhao et al. – Microbiome

Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs – Wang et al. Microbiome

Animal microbiome (for animals in the wild)

Circadian dynamics of the teleost skin immune-microbiome interface – Ellison, Wilcockson & Cable – Microbiome

Honey bee genetics shape the strain-level structure of gut microbiota in social transmission – Wu et al. – Microbiome

Plant, root, and soil microbiome

Evidence for host–microbiome co-evolution in apple – Abdelfattah et al. – New Phytologist

Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen – Vogel et al. – Nature Microbiology

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis – Yang et al. – npj Biofilms and Microbiomes

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

Cross-regional scale pollution of freshwater biofilms unveiled by antibiotic resistance genes – Yao et al. – Science of The Total Environment

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community – Tan et al. – npj Biofilms and Microbiomes

Bioinformatics

Multivariable association discovery in population-scale meta-omics studies – Mallick et al. – PLOS Computational Biology

Techniques

Assessing saliva microbiome collection and processing methods – Armstrong, Parmar & Blaser – npj Biofilms and Microbiomes

October 29, 2021

Sorry for the delayed post, WordPress was playing some mean tricks on me today and there were no treats! Good morning all and happy spooky season! It’s been a moment since I’ve written a post and I write to you now as a freshly (pepper)minted PhD! I’m feeling gourd and can’t wait to pumpkin spice things up with some fangtastic papers.

Some of the highlights include a paper by McAlpine et al. examining interkingdom relationships between bacteria and fungi. Specifically, they found that the gut commensal species Lactobacillus can produce a small molecule that blocks filamentous growth of the opportunistic pathogen Candida albicans. Another interesting paper comes from Michael Adams lab at the University of Georgia, Athens which showed that members of the gut microbiota have the capacity to assimilate the metal tungsten which, in turn, allows these microbes to oxidize a broad range of aldehydes in the gut. Additionally, a paper by Plummer et al. looked at the vaginal microbiota of women who have recurrent bacterial vaginosis as well as the penile microbiota of their partners, and found that when males also underwent antibiotic treatment it led to a decrease in bacterial vaginosis in their female partners.

Hope you enjoy reading these fa-boo-lous papers and may you eat, drink, and be scary this Halloween!

General Microbiome
A small molecule produced by Lactobacillus species blocks Candida albicans filamentation by inhibiting a DYRK1-family kinase. – MacAlpine, J. et al., Nature Communications.

Pregnancy and Early-Life
Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. – Laursen, M.F. et al., Nature Microbiology.

Bifidobacterium catabolism of human milk oligosaccharides overrides endogenous competitive exclusion driving colonization and protection. – Heiss, B.E. et al., Gut Microbes.

Mother’s Milk Microbiome Shaping Fecal and Skin Microbiota in Infants with Food Allergy and Atopic Dermatitis: A Pilot Analysis. – Gołębiewski. M. et al., Nutrients.

Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. – Pärnänen, K.M.M. et al., The American Journal of Clinical Nutrition.

Human Vaginal Microbiome
A Prospective, Open-Label Pilot Study of Concurrent Male Partner Treatment for Bacterial Vaginosis. – Plummer, E.L. et al., mBio.

Human Gut Microbiome
Tungsten enzymes play a role in detoxifying food and antimicrobial aldehydes in the human gut microbiome. – Schut, G.J. et al., PNAS.

Commensal bacteria promote endocrine resistance in prostate cancer through androgen biosynthesis. – Pernigoni, N. et al., Science.

Vertebrate host phylogeny influences gut archaeal diversity. – Youngblut, N.D. et al., Nature Microbiology.

Gut microbiota dysbiosis contributes to the development of chronic obstructive pulmonary disease. – Li, N. et al., Respiratory Research.

Oral Administration of Latilactobacillus sakei ADM14 Improves Lipid Metabolism and Fecal Microbiota Profile Associated With Metabolic Dysfunction in a High-Fat Diet Mouse Model. – Won, S.-M. et al., Frontiers in Microbiology.

Human Oral Microbiome
Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses. – Nemoto, T. et al., mSystems.

Animal Experiments
Commensal segmented filamentous bacteria-derived retinoic acid primes host defense to intestinal infection. – Woo, V. et al., Cell Host & Microbe.

Intestinal microbiota shapes gut physiology and regulates enteric neurons and glia. – Vicentini, F.A. et al., Microbiome.

Lactobacillus rhamnosus GG Derived Extracellular Vesicles Modulate Gut Microbiota and Attenuate Inflammatory in DSS-Induced Colitis Mice. – Tong, L. et al., Nutrients.

Animal Microbiome
Phage Treatment Trial to Eradicate LA-MRSA from Healthy Carrier Pigs. – Tuomala, H. et al., Viruses.

Characterization of the Eukaryotic Virome of Mice from Different Sources. – Zhang, C. et al., Microorganisms.

Supplemental L-Arginine Improves the Embryonic Intestine Development and Microbial Succession in a Chick Embryo Model. – Dai, D. et al., Frontiers in Nutrition.

Water and Extremophile Microbiome
Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. – Zrimec, J. et al., mBio.

Acrylate protects a marine bacterium from grazing by a ciliate predator. – Teng, Z.-J. et al., Nature Microbiology.

Plant, Root, and Soil Microbiome
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. – Mahdi, L.K. et al., ISME Journal.

Spatial Characterization of Microbial Communities on Multi-Species Leafy Greens Grown Simultaneously in the Vegetable Production Systems on the International Space Station. – Hummerick, M.E. et al., Life (Basel).

Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms. – Jones, M.L. et al., Elife.

Probiotics
High-efficiency delivery of CRISPR-Cas9 by engineered probiotics enables precise microbiome editing. – Neil, K. et al., Molecular Systems Biology.

Techniques
Visualizing transfer of microbial biomolecules by outer membrane vesicles in microbe-host-communication in vivo. – Bittel, M. et al., Journal of Extracellular Vesicles.

October 27, 2021

COVID19

Severe dysbiosis and specific Haemophilus and Neisseria signatures as hallmarks of the oropharyngeal microbiome in critically ill COVID-19 patients – de Castilhos et al – Clinical Infectious Diseases

General microbiome

The Role of Microbiota in Infant Health: From Early Life to Adulthood – Yao et al. – Front. Immunol.

The microbiome impacts host hybridization and speciation – Miller et al. – PLOS Biology

Pregnancy and early life

Gut Dysbiosis, Bacterial Colonization and Translocation, and Neonatal Sepsis in Very-Low-Birth-Weight Preterm Infants – Lee et al. – Front. Microbiol.

Multi-site human microbiome

Oral, nasal, and gut microbiota in Parkinson’s disease – Li et al. – Neuroscience

Human respiratory microbiome

[REVIEW]Emerging cellular and molecular interactions between the lung microbiota and lung diseases – Xiang & Meng – Critical Reviews in Microbiology

Human gut microbiome/mycobiome

[REVIEW]Drugs and Bugs: The Gut-Brain Axis and Substance Use Disorders – Simpson et al. – Journal of Neuroimmune Pharmacology

Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes – Carasso et al. – The FASEB Journal

Intestinal mycobiota composition and changes in children with thalassemia who underwent allogeneic hematopoietic stem cell transplantation – Yalcin et al. – Pediatric Blodd & Cancer

Gut microbiota analyses of Saudi populations for type 2 diabetes-related phenotypes reveals significant association – AlAli et al. – bioRxiv

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

Consistent gut bacterial and short-chain fatty acid signatures in hypoabsorptive bariatric surgeries correlate with metabolic benefits in rats – Mukorako et al. – International Journal of Obesity

Microbiota instruct IL-17A-producing innate lymphoid cells to promote skin inflammation in cutaneous leishmaniasis – Singh et al – PLOS Pathogens

Anti-inflammatory effects of purple sweet potato anthocyanin extract in DSS-induced colitis: modulation of commensal bacteria and attenuated bacterial intestinal infection – Mu et al. – Food & Function

Plant, root, and soil microbiome/virome

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil – Trubl et al. – Microbiome

Arabidopsis assemble distinct root-associated microbiomes through the synthesis of an array of defense metabolites – Kudjordjie, Sapkota & Nicolaisen – PLOS One

Microbiome of Pukzing Cave in India shows high antimicrobial activity against plant and animal pathogens – Iquebal et al. – Genomics

[REVIEW]Phyllosphere microbiome: Diversity and functions – Bashir et al. – Microbiological Research

[REVIEW]Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives – Kumawat, Razdan & Saharan – Microbiological Research

Phages and viruses

[REVIEW]The intestinal virome: lessons from animal models – Chaffringeon et al. – Current Opinion in Virology

Bioinformatics

[REVIEW]Application of Deep Learning in Plant–Microbiota Association Analysis – Deng et al. – Frontiers in Genetics

Techniques

Simple solution to preserve plant samples for microbiome analyses – Carvalhais et al. – Molecular Ecology Resources

[REVIEW]Novel methods of microbiome analysis in the food industry – Sabater et al. – nternational Microbiology

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