November 8, 2022

Greetings from Pittsburgh, PA!

It’s election day here, which means I have low grade nausea and am looking for a distraction. If you’re in the same boat, check out today’s awesome articles on a holobiont deep sea shrimp, plant-microbiome assemblies of poplar trees, and viral community-wide auxiliary metabolic genes. I also included a few interesting preprints, my favorite of which is noted below and uses a microbiome public dataset to compare different normalization and transformation methods.

Animal microbiome

A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata – Aubé et al. – Microbiome

Plant, root, and soil microbiome

Plant sex affects plant-microbiome assemblies of dioecious Populus cathayana trees under different soil nitrogen conditions – Guo et al. – Microbiome

Phages and viruses

Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts – Luo et al. – Microbiome


*Preprint: Alpha and beta-diversities performance comparison between different normalization methods and centered log-ratio transformation in a microbiome public dataset – Bars-Cortina – bioRxiv

Preprint: Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts – McCallum et al. – bioRxiv

Preprint: Targeted metagenomics using probe capture detects a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics – Siljanen et al. – bioRxiv

October 17, 2022

Human and General Microbiome

Comparison of microbial signatures between paired faecal and rectal biopsy samples from healthy volunteers using next-generation sequencing and culturomics – Indrani Mukhopadhya – Microbiome

Depression and fatigue in active IBD from a microbiome perspective-a Bayesian approach to faecal metagenomics – Anne Kerstin Thomann – BMC Medicine

Dynamics of human milk oligosaccharides in early lactation and relation with growth and appetitive traits of Filipino breastfed infants – Tinu M Samuel – Scientific Reports

The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis – Efrat Muller – NPJ Biofilms and Microbiomes

Review: Strains to go: interactions of the skin microbiome beyond its species – Ryan Caldwell – Current Opinion in Microbiology

Gut bacterial extracellular vesicles: important players in regulating intestinal microenvironment – Xiao Liang – Gut Microbes

Brief overview of dietary intake, some types of gut microbiota, metabolic markers and research opportunities in sample of Egyptian women – Nayera E Hassan – Scientific Reports

Profile of gut microbiota and serum metabolites associated with metabolic syndrome in a remote island most afflicted by obesity in Japan – Tsugumi Uema – Scientific Reports

The intestinal clock drives the microbiome to maintain gastrointestinal homeostasis – Marjolein Heddes – Nature Communications

Identification of bacterial lipopeptides as key players in IBS – Camille Petitfils – Gut

Gut-innervating nociceptors regulate the intestinal microbiota to promote tissue protection – Wen Zhang – Cell

BefA, a microbiota-secreted membrane disrupter, disseminates to the pancreas and increases β cell mass – Jennifer Hampton Hill – Cell Metabolism

Alterations in the nasopharyngeal microbiome associated with SARS-CoV-2 infection status and disease severity – Nick P G Gauthier – PloS one

preprint: Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes – Bryan D Merrill – bioRxiv

Beneficial Microbes and Compounds

Long-term use of Lacticaseibacillus paracasei N1115 from early life alleviates high-fat-diet-induced obesity and dysmetabolism in mice – Z H Miao – Beneficial Microbes

Animal Model Microbiome

Trimethylamine, a gut bacteria metabolite and air pollutant, increases blood pressure and markers of kidney damage including proteinuria and KIM-1 in rats – Klaudia M Maksymiuk – Journal of Translational Medicine

Animal Microbiome

Molecular detection of Coxiella-like endosymbionts and absence of Coxiella burnetii in Amblyomma mixtum from Veracruz, Mexico – Estefanía Grostieta – Experimental & Applied Acarology

Environmental Microbiome

An enriched ammonia-oxidizing microbiota enables high removal efficiency of ammonia in antibiotic production wastewater – Jiamin Chen – Chemosphere

October 14, 2022

Today’s digest features manipulation of crop microbiome to minimise impact of climate change on agricultural productivity, turtle microbiome, #microber2022, and more. Happy Friday!

See you next week at #MVIF!

Human microbiome

Review: Microbiome epidemiology and association studies in human health – Hannah VanEvery – Nature Reviews Genetics

Gut microbiome

The effects of fermented vegetable consumption on the composition of the intestinal microbiota and levels of inflammatory markers in women: A pilot and feasibility study – Amy E. Galena – PlosOne

Functional screens of barcoded expression libraries uncover new gene functions in carbon utilization among gut Bacteroidales – Yolanda Y. Huang – bioRxiv

Advancing human gut microbiota research by considering gut transit time – Nicola Procházková – Gut

Food Additive Emulsifiers and Their Impact on Gut Microbiome, Permeability, and Inflammation: Mechanistic Insights in Inflammatory Bowel Disease – Aaron S Bancil – Journal of Crohn’s and Colitis

Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome – Lianmin Chen – Nature Medicine

Vaginal microbiome

N-glycosylation of cervicovaginal fluid reflects microbial community, immune activity, and pregnancy status – Gang Wu – Scientific Reports

Animal microbiome

*More than just hitchhikers: a survey of bacterial communities associated with diatoms originating from sea turtles Get access Arrow – Klara Filek – FEMS Microbiology Ecology

Plant microbiome

*Next generation tools for crop-microbiome manipulation to mitigate the impact of climate change – Bruna D. Batista & Brajesh K. Singh – Environmental Microbiology

Soil microbiome

Defending Earth’s terrestrial microbiome – Colin Averill – Nature Microbiology


GTDB-Tk v2: memory friendly classification with the Genome Taxonomy Database – Pierre-Alain – Bioinformatics

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets – Oskar Hickl – bioRxiv

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes – Josh L. Espinoza & Chris L. Dupont – BMC Bioinformatics

September 22, 2022

Happy almost Friday! Today’s digest includes a time series tracking changes after fecal transplant, biofilm-formation analysis from isolations from swine slaughterhouses as well as techniques to improve computational notebooks, rapid genotyping, and more.


Human gut microbiome

Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains – Koo & Morrow – PLOS One

Animal experiments

Microbiome complexity shapes metabolism – Litichevskiy & Thaiss – PLOS Biology

Minimal overall divergence of the gut microbiome in an adaptive radiation of Cyprinodon pupfishes despite potential adaptive enrichment for scale-eating – Heras & Martin – PLOS One

Molecular characterization and biofilm-formation analysis of Listeria monocytogenes, Salmonella spp., and Escherichia coli isolated from Brazilian swine slaughterhouses – Santos et al. – PLOS One

Animal microbiome

Ecology and distribution of Leptospira spp., reservoir hosts and environmental interaction in Sri Lanka, with identification of a new strain – Sluydts et al. – PLOS Neglected Tropical Diseases


A simple kit to use computational notebooks for more openness, reproducibility, and productivity in research – Figueiredo et al. – PLOS Computational Biology

Bacterial concentration and Campylobacter spp. quantification differ when fresh or ultra-frozen samples are analysed over time using molecular biology and culture-based methods – Khattak et al. – Plos One

Robust inference of population size histories from genomic sequencing data – Upadhya & Steinrücken – PLOS Computational Biology

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data – Váradi et al. – PLOS One

Improved assessments of bulk milk microbiota composition via sample preparation and DNA extraction methods – Xue & Marco – PLOS ONE

September 8, 2022

Today’s microbiome digest includes ten rules for teaching yourself R, food safety profiles of ready-to-eat raw minced meat, teaching that addresses eco-anxiety, as well as both pathogenic and entomopathogenic fungi!

Human gut microbiome

Meals, Microbiota and Mental Health in Children and Adolescents (MMM-Study): A protocol for an observational longitudinal case-control study – Asbjornsdottir et al. – PLOS One

Strongyloides stercoralis infection induces gut dysbiosis in chronic kidney disease patients – Hai et al. – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Mycoparasitism capability and growth inhibition activity of Clonostachys rosea isolates against fungal pathogens of grapevine trunk diseases suggest potential for biocontrol – Geiger et al. – PLOS One

Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae – Wilberts et al. – PLOS One

Food microbiology

Bacteriological quality and antimicrobial susceptibility profiles of isolates of ready-to-eat raw minced meat from hotels and restaurants in Arba Minch, Ethiopia – Tonjo et al. – PLOS One


Ten simple rules for teaching yourself R – Lawlor et al. – PLOS Computational Biology


Laboratory evaluation of RealStar Yellow Fever Virus RT-PCR kit 1.0 for potential use in the global yellow fever laboratory network – Basile et al. – PLOS Neglected Tropical Diseases

Science, publishing, and career )

Insufficient yet improving involvement of the global south in top sustainability science publications – Dangles et al. – PLOS One

Adapt conservation biology teaching to address eco-anxiety in students – São Pedro et al. – PLOS Biology

August 19, 2022

Today’s digest is short and sweet! We have articles on the gut microbiota in rats, the influence of host genetics on the leaf fungal microbiome, and biofilm fouling in drinking water. There are also two manuscripts which provide tips for pathway enrichment analysis and biomarker discovery.

Happy reading! Also, if you’re in Scotland, consider checking out the enormous E. coli in Edinburgh this weekend!

Animal experiments

Effects of sea salt intake on metabolites, steroid hormones, and gut microbiota in rats – Chanmuang et al. – PLOS One

Plant, root, and soil microbiome

The changing influence of host genetics on the leaf fungal microbiome throughout plant development – Karasov & Lundberg – PLOS Biology

Water and extremophile microbiome

Impacts of temperature and hydraulic regime on discolouration and biofilm fouling in drinking water distribution systems – Fish et al. – PLOS Water


Nine quick tips for pathway enrichment analysis – Chicco & Agapito – PLOS Computational Biology

Ten quick tips for biomarker discovery and validation analyses using machine learning – Diaz-Uriarte et al. – PLOS Computational Biology

August 17, 2022

Pregnancy and early life

[REVIEW]Special Diets in Infants and Children and Impact on Gut Microbioma – Di Profio et al. – Nutrients

Cervicovaginal Complement Activation and Microbiota During Pregnancy and in Parturition – Livson et al. – Frontiers in Immunology

Human gut microbiome

[REVIEW]Interaction between microbiota and immunity and its implication in colorectal cancer – Xing et al. – Frontiers in Immunology

Mapping the human gut mycobiome in middle-aged and elderly adults: multiomics insights and implications for host metabolic health – Shuai et al. – Gut

Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease – Hellmann et al. – IBD

Pan-cancer analysis of microbiome quantitative trait loci – Chen et al. – Cancer Research

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

A Comparison of the Impact of Restrictive Diets on the Gastrointestinal Tract of Mice – Gregor et al. – Nutirents

High fat diets induce early changes in gut microbiota that may serve as markers of ulterior altered physiological and biochemical parameters related to metabolic syndrome. Effect of virgin olive oil in comparison to butter – Andújar-Tenorio et al. – PLOS One

Animal microbiome (for animals in the wild)

Host-Specific Larval Lepidopteran Mortality to Pathogenic Serratia Mediated by Poor Diet – Mason et al. – Journal of Invertebrate Pathology

Plant, root, and soil microbiome

Chemical and microbial characterization of sugarcane mill mud for soil applications – Uchimiya, Hay & LeBlanc – PLOS One

August 15th, 2022

God morgon!

Good morning from Sweden. Today’s digest is a bag full of articles, mostly preprints, from various fields. A newly published article reports that non-antibiotics, carbamazepine, ibuprofen, naproxen and propranolol, affect the horiontal gene transfer (HGT) and promote sharing of plasmids that encode antibiotic resistance genes. This is an important conclusion as so far we were bothered only about antibiotics but now there is evidence that even non-antibiotics can promote antimicrobial resistance.

Staying with antibiotics, a new preprint reports Ruthenium complexes as potent antibacterial compounds against clinical strains of Pseudomonas aeruginosa. The group was able to demonstrate the mode of action of these compounds and also find mutations that might promote supressor phenotype. These compounds also show synergism with Rifampicin, a known antibiotic. Another preprint about P. aeruginosa reports that the bacterium carries multitude of phage resistance mechanisms to fend of bacteriophages. These mechanisms determine the host specificity of phages as individual resistance mechanism only provide resistance against specific phages. This can be a vital information for planning phage therapies.

Elsewhere in the digest are reports on correlation between the presence of certain microbial species with the presence of Legionella in selected EU cities, importance of gut microbiota on glucose metabolism in offspring, and how the climate change induced influx of Atlantic waters in Arctic affects the microbial diversity.

In the end, there is a special report on how certain dietary compounds can alter the micrbes in our food and result in changes to our food. The scientists have proposed a new field of research – nutrifermentics. They report how Benzoic acid, a common food additive, can induce epigenetic changes in Saccharomyces cerevisiae that alter the characteristic of wine. This has important implications in strain developement where deliberate genetic modifications may be avoided by inducing epigenetic changes using such additives.

I hope you will enjoy reading today’s digest. Have a great week!

Water microbiome

Preprint: Genome-resolved community structure and function of freshwater bacteria at a continental scale – Rebecca E. Garner, et al.

Preprint: Bacterial communities of premise plumbing systems in four European cities, and their association with culturable Legionella – Maria Scaturro, et al.

Preprint: Variations in Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities – Taylor Priest, et al.

Bacteria Hysteria

Non-antibiotic pharmaceuticals promote conjugative plasmid transfer at a community-wide level – Yue Wang, et al. Microbiome

Preprint: Screening Avian Pathogens in Eggs from Commercial Hatcheries in Nepal – an Effective Poultry Disease Surveillance Tool – Shreeya Sharma

Preprint: Negative interactions and virulence differences drive the dynamics in multispecies bacterial infections – Désirée A. Schmitz, Richard C. Allen, and Rolf Kümmerli

Preprint: Growth arrest of Staphylococcus aureus induces daptomycin tolerance via cell wall remodelling – Elizabeth V. K. Ledger and Andrew M. Edwards

Preprint: Polynuclear ruthenium complexes are effective antibiotics against Pseudomonas aeruginosa – Brent S. Weber, et al.

Preprint: Cryo-EM structure of the Type IV pilus extension ATPase from enteropathogenic Escherichia coli – Ashok R. Nayak, et al.

Preprint: Accumulation of defense systems drives panphage resistance in Pseudomonas aeruginosa – Ana Rita Costa, et al.

Preprint: Neisseria gonorrhoeae diagnostic escape from a gyrA-based test for ciprofloxacin susceptibility can lead to increased zoliflodacin resistance – Daniel H. F. Rubin, Tatum D. Mortimer, and Yonatan H. Grad

Preprint: A contractile injection system mediates developmentally regulated intra-strain cell death in Streptomyces coelicolor – Maria Vladimirov, et al.

Gut microbiome

Vertical transmission of the gut microbiota influences glucose metabolism in offspring of mice with hyperglycaemia in pregnancy – Cunxi Xue, et al. Microbiome

Phages and viruses

Preprint: Genetic differences between 129S substrains affect antiretroviral immune responses – Robert Z. Zhang, et al.

Preprint: The dissemination of Rift Valley fever virus to the eye and sensory neurons of zebrafish larvae is stat1 dependent – S. ter Horst, et al.

Preprint: HIV-1 latent infection triggers broader epigenomic and transcriptional changes in protein-coding and long non-coding RNAs than active infection of SupT1 cells – Gabrielle Lê-Bury, et al.

Preprint: Pelagibacter phage Skadi – An abundant polar specialist that exemplifies ecotypic niche specificity among the most abundant viruses on Earth – Holger H Buchholz, et al.

Preprint: A comprehensive single cell data analysis of in lymphoblastoid cells reveals the role of Super-enhancers in maintaining EBV latency – Bingyu Yan, et al.

Preprint: Identification of β2 microglobulin, the product of B2M gene, as a Host Factor for Vaccinia Virus Infection by Genome-Wide CRISPR genetic screens – Alejandro Matía, et al.

Preprint: Generation of Recombinant Rotaviruses Expressing Human Norovirus Capsid Proteins – Asha A. Philip and John T. Patton

Preprit: Distantly related hepaciviruses share common entry factor, Claudin-1 – Kamilla Toon, et al.

Preprint: Organisation of the orthobunyavirus tripodal spike and the structural changes induced by low pH and K+ during entry – Samantha Hover, et al.

General microbiome

Preprint: Effects of Cr stress on bacterial community structure and diversity in rhizosphere soils of Iris pseudacorus – Zhao Wei, et al.

Preprint: Lack of specificity in Geobacter periplasmic electron transfer – Sol Choi, Chi Ho Chan, and Daniel R. Bond

Preprint: Lipidomic analysis reveals differences in Bacteroides species driven largely by plasmalogens, glycerophosphoinositols and certain sphingolipids – Eileen Ryan, et al.

Preprint: Turnover of the extracellular polymeric matrix in an EBPR microbial community – Sergio Tomás-Martínez, et al.

Preprint: An Optimal Regulation of Fluxes Dictates Microbial Growth In and Out of Steady-State – Griffin Chure and Jonas Cremer

Preprint: Cryo-ET of infected cells reveals that a succession of two lattices drives vaccinia virus assembly – Miguel Hernandez-Gonzalez, et al.

Preprint: Soil protists can actively redistribute beneficial bacteria along Medicago truncatula roots – Christopher J. Hawxhurst, et al.

Developing whole cell standards for the microbiome field – Chrysi Sergaki, et al. Microbiome


Preprint: The capacity to configure the hymenophore is not confined to the pore field in Oak mazegill (Daedalea quercina, Polyporales) – Bjarke Jensen

Preprint: Epigenetic Changes in Saccharomyces cerevisiae Alters the Aromatic Profile in Alcoholic Fermentation – Yanzhuo Kong, et al.

August 13, 2022

Human and General Microbiome

Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer – Cheng Kong – Gut

A decrease in functional microbiomes represented as Faecalibacterium affects immune homeostasis in long-term stable liver transplant patients – Soon Kyu Lee – Gut Microbes

Longitudinal study of the vaginal microbiome in pregnancies involving preterm labor – Yoshiko Sakabe – Fujita Medical Journal

Oral microbiome and serological analyses on association of Alzheimer’s disease and periodontitis – Kuan-Lun Fu – Oral Diseases

Review: Ultra-processed foods and human health: from epidemiological evidence to mechanistic insights – Bernard Srour – The Lancet. Gastroenterology & Hepatology

Beneficial Microbes, Compounds and Interventions

Dietary Fiber Modulates the Release of Gut Bacterial Products Preventing Cognitive Decline in an Alzheimer’s Mouse Model – Daniel Cuervo-Zanatta – Cellular and Molecular Neurobiology

Functional and safety characterization of beneficial vaginal lactic acid bacteria for the design of vaginal hygiene products – Jessica Alejandra Silva – Journal of Applied Microbiology

Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis – Haiyang Lu – Cell host & Microbe

Review: The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management – Ali Nabavi-Rad – Gut Microbes

Non-Model Animal Microbiome

Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen – Matthew Grisnik – Microbial Ecology

Non-steroidal anti-inflammatory drugs caused an outbreak of inflammation and oxidative stress with changes in the gut microbiota in rainbow trout (Oncorhynchus mykiss) – N Hodkovicova – The Science of the Total Environment

Bees under interactive stressors: The novel insecticides flupyradifurone and sulfoxaflor along with the fungicide azoxystrobin disrupt the gut microbiota of honey bees and increase opportunistic bacterial pathogens – Yahya Al Naggar – The Science of the Total Environment

Plant Microbiome

Host genotype controls ecological change in the leaf fungal microbiome – Acer VanWallendael – PLoS Biology

Suaeda salsa Root-Associated Microorganisms Could Effectively Improve Maize Growth and Resistance under Salt Stress – Yongdong Wang – Microbiology Spectrum

Review: Regulation of immune complex formation and signalling by FERONIA, a busy goddess in plant-microbe interactions – Zhikun Duan – Molecular Plant Pathology

Food Microbiome

A systematic, complexity-reduction approach to dissect the kombucha tea microbiome – Xiaoning Huang – eLife

Bioinformatic Tools and Microbiome Analysis Techniques

ProbeTools: designing hybridization probes for targeted genomic sequencing of diverse and hypervariable viral taxa – Kevin S Kuchinski – BMC Genomics

A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications – Maaly Nassar – GigaScience

MetaProClust-MS1: an MS1 Profiling Approach for Large-Scale Microbiome Screening – Caitlin M A Simopoulos – mSystems

August 5, 2022

Today’s digest is brief and includes research examining the association between the gut microbiota and Gulf War illness, determining the distribution of psychrophilic microorganisms in a beef slaughterhouse, measuring the quality of DNA sequences via degradation, and more.

Happy Friday!

General microbiome

Measuring quality of DNA sequence data via degradation – Karr et al. – PLOS One

Atypical integrative element with strand-biased circularization activity assists interspecies antimicrobial resistance gene transfer from Vibrio alfacsensis – Nonaka et al. – PLOS One

Human vaginal microbiome

Association of key species of vaginal bacteria of recurrent bacterial vaginosis patients before and after oral metronidazole therapy with short- and long-term clinical outcomes – Mollin et al. – PLOS One

Human gut microbiome

Examining the association between the gastrointestinal microbiota and Gulf War illness: A prospective cohort study – Kates et al. – PLOS One

Food microbiology

Distribution of psychrophilic microorganisms in a beef slaughterhouse in Japan after cleaning – Nakamura et al. – PLOS One

Science, publishing, and career

Ten simple rules for leveraging virtual interaction to build higher-level learning into bioinformatics short courses – Bacon et al. – PLOS Computational Biology