May 13, 2020

Happy Wednesday, y’all! Before we get to today’s papers, I wanted to let everyone know about a webinar happening on June 3rd at 12:00 PM E.T. called “Unraveling the link between the gut microbiome, human health, and disease.” Tomoya Yamashita, M.D., Ph.D. from Kobe University Graduate School of Medicine and Meredith Hullar, Ph.D. from the Fred Hutchinson Cancer Research Center will both be speaking. If you’re interested you can register here.

Now onto the highlights! We have some super interesting research to share with you today including an examination of the efficacy of transplanting the human gut microbiota into mice and its impact on studying immunological responses; evidence that early-life intestinal colonizers may influence brain development; and a new tool, pepFUNK, which uses a peptide-centric approach to identify KEGG pathways in metaproteomic datasets. Enjoy!

General microbiome
Human Microbiota-Transplanted C57BL/6 Mice and Offspring Display Reduced Establishment of Key Bacteria and Reduced Immune Stimulation Compared to Mouse Microbiota-Transplantation. Lundberg, R. et al. Scientific Reports.

Review: The role of the microbiome in the neurobiology of social behaviour. Sarkar, A. et al. Biological Reviews.

Pregnancy and early life
Neonatal diet alters fecal microbiota and metabolome profiles at different ages in infants fed breast milk or formula. Brink, L.R. et al. The American Journal of Clinical Nutrition.

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers. Lugli, A.G. et al. FEMS Microbiology Ecology.

Human respiratory microbiome
Bioorthogonal Non-Canonical Amino Acid Tagging Reveals Translationally Active Subpopulations of the Cystic Fibrosis Lung Microbiota. Valentini, T.D. et al. Nature Communications.

Human gut microbiome
Longitudinal Analysis of Serum Cytokine Levels and Gut Microbial Abundance Links IL-17/IL-22 With Clostridia and Insulin Sensitivity in Humans. Zhou, X. et al. Diabetes.

Berberine and Its Structural Analogs Have Differing Effects on Functional Profiles of Individual Gut Microbiomes. Li, L. et al. Gut Microbes.

Animal experiments
Developmental Signatures of Microbiota-Derived Metabolites in the Mouse Brain. Swann, J.R. et al. Metabolites.

Bifidobacteria Shape Host Neural Circuits During Postnatal Development by Promoting Synapse Formation and Microglial Function. Luck, B. et al. Scientific Reports.

Glycerol Monolaurate, an Analogue to a Factor Secreted by Lactobacillus, Is Virucidal Against Enveloped Viruses, Including HIV-1. Welch, J.L. et al. mBio.

Gut Microbiome Communication With Bone Marrow Regulates Susceptibility to Amebiasis. Burgess, S.L. et al. The Journal of Clinical Investigation.

The Protective Effects of 2′-Fucosyllactose Against E. Coli O157 Infection Are Mediated by the Regulation of Gut Microbiota and the Inhibition of Pathogen Adhesion. Wang Y. et al. Nutrients.

Capsaicin Improves Glucose Homeostasis by Enhancing Glucagon-Like peptide-1 Secretion Through the Regulation of Bile Acid Metabolism via the Remodeling of the Gut Microbiota in Male Mice. Hui, S. et al. FASEB Journal.

Microbiota-Induced Type I Interferons Instruct a Poised Basal State of Dendritic Cells. Schaupp L. et al. Cell.

Intratumoral Accumulation of Gut Microbiota Facilitates CD47-based Immunotherapy via STING Signaling. Shi, Y. et al. Journal of Experimental Medicine.

Animal microbiome
Housefly (Musca domestica L.) associated microbiota across different life stages. de Jonge, N. et al. Scientific Reports.

Honey-bee–associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. Deboutte, W. et al. PNAS.

Bayesian Modeling Reveals Host Genetics Associated With Rumen Microbiota Jointly Influence Methane Emission in Dairy Cows. Zhang, Q. et al. ISME Journal.

Review: The role of the gut microbiome in sustainable teleost aquaculture. Perry, W.B. et al. Proceedings of the Royal Society B.

Interactions between social groups of colobus monkeys (Colobus vellerosus) explain similarities in their gut microbiomes. Wikberg E.C. Animal Behaviour.

Plant, root, and soil microbiome
Global Warming Shifts the Composition of the Abundant Bacterial Phyllosphere Microbiota as Indicated by a Cultivation Dependent and Independent Study of the Grassland Phyllosphere of a Long-Term Warming Field-Experiment. Aydogan, E.L. et al. FEMS Microbiology Ecology.

Probiotics / prebiotics
A Human-Origin Probiotic Cocktail Ameliorates Aging-Related Leaky Gut and Inflammation via Modulating the Microbiota/Taurine/Tight Junction Axis. Ahmadi, S. et al. JCI Insight.

Bioinformatics
SHOGUN: A Modular, Accurate, and Scalable Framework for Microbiome Quantification. Hillmann, B. et al. Bioinformatics.

pepFunk: A Tool for Peptide-Centric Functional Analysis of Metaproteomic Human Gut Microbiome Studies. Simopoulos, C.M.A. et al. Bioinformatics.

Microbes in the news
Mapping the Microbiome in Saliva of COVID-19 Patients.

Inside the Belly of the Horse – Doctoral candidate Alexa Johnson goes inside the gut to investigate equine health.

May 12, 2020

Buenos dias!! Greetings from Spain.

Today we can highlight a very interesting article of gut–brain modulation of a monkey model of human depression, MELODY a new trial to improve the future microbiome of the offspring of mothers with Crohn’s disease, or how It’s the fertilization the main agent in rhizosphere composition.

I hope you enjoy reading this as much as I did making it!
Stay safe, Jose

COVID-19

Pre-print: Prediction analysis of SARS-COV-2 entry in Livestock and Wild animals – Manas Ranjan Praharaj et al. – bioRxiv

Pre-print: Clinical performance of SARS-CoV-2 IgG antibody tests and potential protective immunity – Niko Kohmer et al. – bioRxiv

Pre-print: The role of high cholesterol in age related COVID19 lethality. – Hao Wang et al. – bioRxiv

Human vaginal microbiome

Effect of commercial vaginal products on the growth of uropathogenic and commensal vaginal bacteria – Kristin J. Hung et al. – Scientific Reports

Human respiratory microbiome

Differences in airway microbiome and metabolome of single lung transplant recipients – Nirmal S. Sharma et al. – Respiratory Research

Pre-print: Assessing the variation within the oral microbiome of healthy adults – Jacob T. Nearing et al. – bioRxiv

Microbiome profile associated with malignant pleural effusion – Samira Shojaee et al. – PLOS ONE

Composition and function of oral microbiota between gingival squamous cell carcinoma and periodontitis – Yuchao Li et al. – Oral Oncology

Esophageal microbiome signature in patients with Barrett’s esophagus and esophageal adenocarcinoma – Loris Riccardo Lopetuso et al. – PLOS ONE

Human gut microbiome

Subtle Variations in Dietary-Fiber Fine Structure Differentially Influence the Composition and Metabolic Function of GutMicrobiota – Tuncil, Y. E et al. – mSphere

Intestinal parasites in rural communities in Nan Province, Thailand: Changes in bacterial gut microbiota associated with minute intestinal fluke infection – Ajala Prommi et al. – Cambridge University Press

Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease – Michelle R et al. – Journal of the American Society of Nephrology

The gut microbiome modulates gut–brain axis glycerophospholipid metabolism in a region-specific manner in a non-human primate model of depression – Peng Zheng et al. – Molecular Psychiatry

A dietary intervention to improve the microbiome composition of pregnant women with Crohn’s disease and their offspring: The MELODY (Modulating Early Life Microbiome through Dietary Intervention in Pregnancy) trial design – Peter Inga et al. – Contemporary Clinical Trials Communications

Gut Microbiota Dysbiosis Associated with Bile Acid Metabolism in Neonatal Cholestasis Disease – Meng Li et al. – Scientific Reports

Individual and cohort-specific gut microbiota patterns associated with tissue-specific insulin sensitivity in overweight and obese males – Gerben D. A. Hermes et al. – Scientific Reports

Fecal microbiota composition is linked to the postoperative disease course in patients with Crohn’s disease – Anna Strömbeck et al. – BMC Gastroenterology

Human skin microbiome

Diversity of navel microbiome in young adults Free – Shreya Shah et al. – Journal of Medical Microbiology

Animal experiments

Wild primate microbiomes prevent weight gain in germ-free mice – Dimitrios N. Sidiropoulos et al. – Animal Microbiome

Changes in the microbiome of mariculture feed organisms after treatment with a potentially probiotic strain of Phaeobacter inhibens – Karen K. Dittmann et al. – Applied and Environmental Microbiology

Alterations of fecal microbiome characteristics by dietary soy isoflavone ingestion in growing pigs infected with porcine reproductive and respiratory syndrome virus – B N Smith et al. – Journal of Animal Science

Influenza infection elicits an expansion of gut population of endogenous Bifidobacterium animalis which protects mice against infection – Qiang Zhang et al. – Genome Biology

Pre-print: Impact of industrial production system parameters on chicken microbiomes: mechanisms to improve performance and reduce Campylobacter – Aaron McKenna et al. – bioRxiv

Administration of Bifidobacterium bifidum CGMCC 15068 modulates gut microbiota and metabolome in azoxymethane (AOM)/dextran sulphate sodium (DSS)-induced colitis-associated colon cancer (CAC) in mice – Qing Wang et al. – Applied Microbiology and Biotechnology

Animal microbiome

Structure and membership of gut microbial communities in multiple fish cryptic species under potential migratory effects – My Hanh Le et al. – Scientific Reports

Seasonal habitat drives intestinal microbiome composition in anadromous Arctic char (Salvelinus alpinus) – Geraint Element et al. – Envariomental microbiology

Honeybee microbiome is stabilized in the presence of propolisPerot Saelao et al. – Biology letters

Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels – Po-Yu Liu et al. – Scientific Reports

Preprint: Differential Response of Digesta- and Mucosa-Associated Intestinal Microbiota to Dietary Black Soldier Fly (Hermetia illucens) Larvae Meal in Seawater Phase Atlantic Salmon (Salmo salar) – Yanxian Li et al. – bioRxiv

Plant, root, and soil microbiome

Liming reduces N2O emissions from Mediterranean soil after-rewetting and affects the size, structure and transcription of microbial communities – Eduardo Vázquez et al – Soil Biology and Biochemistry

Significant effects on soil microbial communities were not detected after strategic tillage following 44 years of conventional or no-tillage management – Vivian A. Rincon-Florez – Pedobiologia

Seasonal variations in soil microbial communities under different land restoration types in a subtropical mountains region, Southwest China – Denggao Fu et al. – Applied Soil Ecology

Short term effects of biochar with different particle sizes on phosphorous availability and microbial communities – Rubab Sarfraz et al. – Chemosphere

Microbial community responses to different volatile petroleum hydrocarbon class mixtures in an aerobic sandy soil – George Mangse et al.– Environmental Pollution

Plant litter amendments in restored wetland soils altered microbial communities more than clay additions – Christine E. Maietta et al. – Soil Biology and Biochemistry

Long-term fertilization rather than plant species shapes rhizosphere and bulk soil prokaryotic communities in agroecosystems – Mikhail V. Semenov et al. – Applied Soil Ecology

Effect of compost amendment and bioaugmentation on PAH degradation and microbial community shifting in petroleum-contaminated soil – Manli Wu et al. – Chemosphere

Review: The use of -omics tools for assessing biodeterioration of cultural heritage: A review – GutarowskaBeata – Journal of Cultural Heritage

Water and extremophile

Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells – Sara Gallego et al – Science of The Total Environment

High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater–Sediment Interface of a Deep-Sea Cold Seep in South China Sea – Qing-Lei Sun et al. – Microorganisms

Glacial microbiota are hydrologically connected and temporally variable – Karen A Cameron et al. – Enviromental microbiology

Built environment

The microbiome driving anaerobic digestion and microbial analysis – Jun Wei Lim et al. – Advances in Bioenergy

Bioinformatics

MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data – Nathanael J. Bangayan et al. – Microorganisms

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia – Matthew G Jones et al. – Genome Biology

TaxIt: An iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples – Mathias Kuhring et al. Journal of Proteome Research

Review: The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health – Ameen Eetemadi et al. – Frontiers in Microbiology

General microbiology

Review: Diversity, ecology and evolution of Archaea – Brett J. Baker et al – Nature Microbiology

Microbes on the market

Microbiome Sequencing Services Market 2020-2024 – husain – NJ MMA News

March 13, 2020

Good moring y’all!

Today’s digest is relatively short, but rather diverse- from the potential characteristics of scientific tweets readers, through cancer microbiome and horses fecal transplants, as well as endophytes microbiomes in different biomes and plants. Also, if you’re still unfaimilar with the ‘Talking about Biotech’ podcast (by Kevin Folta), I highly recommend to add it to your list. The latest episode talks, of course, about the Corona outbreak, and if you’ll go a bit earlier you will find plenty interesring and insightful episodes.

And lastly- pls stay safe! in Israel, as in other parts of the world, conferences are being cancelled, group meetings are rescheduled and we were highly encouraged to work from home (go bioinformatics!). Remember- there is not a single experiment that is more important than your and your love ones health.

General microbiology

Quantifying and contextualizing the impact of bioRxiv preprints through social media audience segmentation, Jedidiah Carlson , bioRxiv

An optimised saliva collection method to produce high-yield, high-quality RNA for translational research, Roisin Sullivan, PLOS ONE

The Vibrio cholerae Type VI Secretion System: Toxins, Regulators and Consequences, Cristian V. Crisan, Env. Micro.

Human microbiome

Microbiome analyses of blood and tissues suggest cancer diagnostic approach, Gregory D. Poore , Nature

Changes in key vaginal bacteria among postpartum African women initiating intramuscular depot-medroxyprogesterone acetate, Bridget M. Whitney ,PLOS ONE

Animal microbiome

The fecal microbiota of healthy donor horses and geriatric recipients undergoing fecal microbial transplantation for the treatment of diarrhea, Caroline A. McKinney , PLOS ONE

Low mutational load and high mutation rate variation in gut commensal bacteria, Ricardo S. Ramiro, PLOS Biology

Marine microbiome

Diel, daily, and spatial variation of coral reef seawater microbial communities, Laura Weber , PLOS ONE

Short‐term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom, Greta Reintjes, Env. Micro.

Plant and Soil microbiome

The diversity and distribution of endophytes across biomes, plant phylogeny, and host tissues—how far have we come and where do we go from here?, Joshua G. Garrison, Env. Micro.

Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees, Elena Arrigoni , Env. Micro.

Salmonella persistence in soil depends on reciprocal interactions with indigenous microorganisms, Jasper Schierstaedt , Env. Micro.

Bioinformatics

Random sampling in metagenomic sequencing leads to overestimated spatial scaling of microbial diversity, Qichao Tu , Env. Micro.

January 16, 2020

Good morning/night everyone!

What I love about writing for MD is the huge diversity of topics we’re meeting along the process of making the daily digest. Even though I’m mostly working on plant and root microbiome, it’s amazing to see how diverse is the world of microbiome and how much more there is to accomplish. Check out today’s digest- and don’t forget the News section as well! it is highly interesting!

General Microbiology

Detection of phylogenetic core groups in diverse microbial ecosystems, Marcos Parras Molto, bioRxiv

Isolation of an archaeon at the prokaryote–eukaryote interface, Hiroyuki Imachi, Nature

Ferrosomes are iron storage organelles formed by broadly conserved gene clusters in bacteria and archaea, Carly R. Grant , bioRxiv

Human microbiome

Distribution of microbial communities and core microbiome in successive wound grades of diabetic foot ulcer individuals, Apoorva Jnana, AEM

Animal microbiome

Parasites modulate the gut-microbiome in insects: A proof-of-concept study, Brian Fredensborg, PlosONE

The effect of diet on the gastrointestinal microbiome of juvenile rehabilitating green turtles (Chelonia mydas), Jennifer Bloodgood ,PlosONE

Rotten-skin disease significantly changed giant spiny frog(Paa spinosa) gut microbiota, Tuoyu He, bioRxiv

Bacterial Biogeography of the Colon in Dogs With Chronic Inflammatory Enteropathy, Paula Giaretta, Veterniary Pathology

Plant and environmental microbiome

Biostimulants applied to maize seeds modulate the enzymatic activity and metaproteome of the rhizosphere, Monica Mattarozzi, Applied Soil Ecology

Biological inhibition of soil nitrification by forest tree species affects Nitrobacter populations, Amandine Laffite, Environmental Microbiology

Extremophile microalgae: An overview, Veronica Malavasi , Journal of Phycology

Methods in microbiome

**Taxonomic classification method for metagenomics based on
core protein families with Core-Kaiju
, Anna Tovo, bioRxiv

**Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance, Xianding Deng , Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling, Ching Jian, PlosONE

The effect of storage conditions on microbial communities in stool, Kristien Nel Van Zyl, PlosONE

Beyond mass spectrometry, the next step in proteomics, Winston and Gregory Timp, Science Advances

Microbiome in the news

Illumina Announces New Sequencing System, Partnership with Roche and Software Suite to Accelerate Adoption of Genomics

Integrating microbiomes into clinical trials – the importance of time

Bayer and Azitra partnership looks to develop skin microbiome products for eczema

**Please read! our mental health is the MOST important thing in our life! Researchers facing ‘shocking’ levels of stress, survey reveals

December 18, 2019

Good morning/afternoon all microbiome lovers!

Coming back from 4th Thunen Sumposium on Soil Metagenomics (11-13.12, Germany), the first section of today’s digest will highlight some work emphasized during the conference. Pay special attention to Amy Willis work (UoW) dealing with amplification bias in 16S analyses, among else. You are more than welcome to check the conference and the bioinformatic workshops schedule, as you’ll find interesting, inspiring and useful studies and tools that are relevant even if you’re not working on soil-associated habitats.

Have a great day!

Soil Metagenomics insights

Rigorous Statistical Methods for Rigorous Microbiome Science, Amy Willis, mSystems. I highly recommended to be familiar with the Willis lab works and tools, for all of us working with amplicon-sequencing and metagenomics. Amy was kind enough to upload her conference materials to github, using this link.

Additionally, They just started a bio-statistics blog, so check this as well.

Consistent and correctable bias in metagenomic sequencing experiments, Michael R. McLaren, bioRxiv

Understanding and interpreting community sequencing measurements of the vaginal microbiome, HL Berman, BJOG

These two papers are from Benjamin Callahan group (NCSW). Even though he wasn’t at the conference, his work (et al.) were mentioned several times by other speakers, so I decided to emphasize these two papers.

The MG-RAST API explorer: an on-ramp for RESTful query composition, Tobias Paczian, BMC Bioinformatics. Folker Meyer, one of the developers of MG-RAST and its head, was actually at the conference with a great talk about both MG-RAST and the importance of pipelines and common workflow language in computational biology. Check this link and the MG-RAST API explorer, making it so much simpler to search, filter and efficiently use MG-RAST.

TerrestrialMetagenomeDB: a public repository of curated and standardized metadata for terrestrial metagenomes, Felipe B Correa, bioRxiv. An amazing tool for searching and filtering soil-associated metagenomes in different databases, plus simple codes for downloading. Take a look at more papers from the de-Rocha group.

Human microbiomoe

**Molecular messages in human microbiota, Matthew T. Henke and Jon Clardy, Science

Resident microbes of lactation rooms and daycares, Diana H. Taft, PeerJ

Female genital tract microbiota affecting the risk of preterm birth: What do we know so far? A Review, O. Tsonis, European J OBG & Reproductive Biology

Differences in Fecal Microbiomes and Metabolomes of People With vs Without Irritable Bowel Syndrome and Bile Acid Malabsorption, Ian B. Jeffery, Gastroenterology

Soil and Plant microbiome

Comparison of Microbial Community of Rhizosphere and Endosphere in Kiwifruit, Min-Jung Kim, Plant Patho J.

Soil microbial communities in diverse agroecosystems exposed to the herbicide glyphosate, Ryan M. Kepler, AEM

Soil exposed to silver nanoparticles reveals significant changes in community structure and altered microbial transcriptional profiles, Matthew J. Meier, Env. Pollution

Animal microbiome

Effects of disease, antibiotic treatment and recovery trajectory on the microbiome of farmed seabass (Dicentrarchus labrax), Danila Rosado, Scientific Reports

November 2, 2019

Good Weekend morning for all!

Today’s digest is highly rich with plant and soil microbiome papers (notice a great Science paper regarding soil suppressiveness phenomena), as well as bacterial metabolism papers and more. Have a great and peaceful weekend!

Human and animal microbiome

Studying the gut virome in the metagenomic era: challenges and perspectives, Sanzhima Garmaeva, BMC Biology

Cortisol-induced signatures of stress in the fish microbiome, Tamsyn M Uren Webster, bioRxiv

Influence of pig gut microbiota on Mycoplasma hyopneumoniae susceptibility, Meera Surendran Nair, Veterinary Research

Natural variation in the contribution of microbial density to inducible immune dynamics, Derrick Jent, Molecular Ecology

Metabolism

The ecology and evolution of microbial metabolic strategies, Djordje Bajic & Alvaro Sanchez, Curr. Opin. In. Biotechnology

Is the enzymatic hydrolysis of soil organic phosphorus compounds limited by enzyme or substrate availability?, K.A. Jarosch ,SBB

Plant and Soil microbiome

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome, Victor J. Carrio, Science

Drivers of the composition of active rhizosphere bacterial communities in temperate grasslands, Selma Vieira, ISME

Analysis of soil bacterial communities associated with genetically modified drought-tolerant corn, Jose G. Ibaraa ,Applid Soil Ecology

Phyllosphere of Submerged Plants in Bathing Lakes as a Reservoir of Fungi Potential Human Pathogens, Anna Biedunkiewicz, Microbial Ecology

Bacterial microbiome associated with the rhizosphere and root interior of crops in Saskatchewan, Canada, Jorge Cordero, Can. J. of Microbiology

Comparative metagenomics of two distinct biological soil crusts in the Tengger Desert, China, Jin-Yu Li , SBB

In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions, Tatsuyas Nobori, bioRxiv

Air microbiome

Microbial communities in the tropical air ecosystem follow a precise diel cycle, Elena S. Gusareva, PNAS

Bioinformatics

Evaluating Bioinformatic Pipeline Performance for Forensic Microbiome Analysis, Kierra F. Kaszubinski, J. o. Forensic Sci.

August 23, 2019

Good morning everyone!

This post is written from lovely NYC, quite a distance from my hometown in Israel. If you’re working on microbial ecology in the city and care for a cup of coffee (on me!) and a rather interesting chat about science, entreprenurship and agriculture- please contact me via barakdror@outlook.com or just find me on Linkedin.

Today post will feature highly recommended podcast, a great antimicrobial resistance review paper, Cocaine effect on gut microbiota, some cool bioinformatics tools papers, fascinating animal microbiome studies and more.

Resources and Podcast

I’m a huge fan of the This Week in Microbiology podcast. On their 201 episode the team hosted Prof. Mark Martin (U of Puget Sound) with some great list of papers for 1st year undergrads- but it is a great opportunity to read about general concepts and direction in micrboiology. I truely enjoed both the episode and the recommended papers.

15 Biotech-Themed Online Courses to Try at Home

Antibiotic Resistance

Defining and combating antibiotic resistance from One Health and Global Health perspectives, Sara Hernando-Amado, Nature Microbiology

Bioinformatics

An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data, Chenhao Li, Microbiome

Analysing complex metagenomic data with MicroWineBar, Franziska Klincke ,bioRxiv

A systematic NGS-based approach for contaminant detection and functional inference, Sung-Joon Park, bioRxiv

Human and Animal microbiome

Cocaine Induces Inflammatory Gut Milieu by Compromising the Mucosal Barrier Integrity and Altering the Gut Microbiota Colonization, Ernest T. Chivero, Scientific Reports

Influence of the microbiota-gut-brain axis on behavior and welfare in farm animals: A review, Narjis Kraimi, Physiology & Behavior

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system, Yaron Krotman, bioRxiv

Non‐random associations of maternally transmitted symbionts in insects: The roles of drift versus biased co‐transmission and selection, Hugo Mathe-Hubert, Molecular Ecology

The microbiome of the Melitaea cinxia butterfly shows marked variation but is only little explained by the traits of the butterfly or its host plant, G. Minard, Environmental Microbiology

Food microbiome

The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities, Xiaoqing Tan, Microbiome

Environmental microbiome

Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome, Pedro J. Cabello-Yeves, Microbiome

Taxonomic and functional characterization of a microbial community from a volcanic englacial ecosystem in Deception Island, Antarctica, Emma Martinez-Alonso, Scientific Reports