Category Archives: Metagenomics & Bioinformatics

July 8, 2020

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Good morning! Today’s digest includes a broad selection of interesting research. Particular highlights include a study in rats that found microbiota transplantation attenuated neuroinflammation, a human study on the dramatic microbiome effects of dietary glycans, and a new technique for using drones to collect dolphin microbiome samples.

Pregnancy and early life

History of breastfeeding but not mode of delivery shapes the gut microbiome in childhood, Camille C. Cioffi et al., PLOS ONE

Preprint: Gut microbiota and fecal short-chain fatty acids are not associated with bone mass in healthy Chinese children: a cross-sectional study, Fengyan Chen et al., Research Square

Impact of Long-Term and Low-Dose Antibiotic Prophylaxis on Gut Microbiota in Children, Yuko Akagawa et al., The Journal of Urology

Human gut microbiome

Microbiome and health implications for ethnic minorities after enforced lifestyle changes, David M. Keohane et al., Nature Medicine

Preprint: Metaproteomics reveals potential signatures of disease-specific alterations in the gut microbial proteolytic events in inflammatory bowel disease, Zhixiang Yan et al., Research Square

High-resolution temporal profiling of the human gut microbiome reveals consistent and cascading alterations in response to dietary glycans, Richard Creswell et al., Genome Medicine

Preprint: High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota, Andres Aranda-Diaz et al., bioRxiv

Preprint: pH-dependent spontaneous hydrolysis rather than gut bacterial metabolism reduces levels of the ADHD treatment, Methylphenidate, Julia Aresti et al., bioRxiv

Animal experiments

The gut microbiota attenuate neuroinflammation in manganese exposure by inhibiting cerebral NLRP3 inflammasome, Wang and Yang et al., Biomedicine & Pharmacotherapy

Magnetic fields modulate metabolism and gut microbiome in correlation with Pgc‐1α expression: Follow‐up to an in vitro magnetic mitohormetic study, Yee Kit Tai et al., The FASEB Journal

Preprint: Multi-omics analysis of aspirin treatment response in mice provide molecular insights and targets linked to liver fibrosis regression, Adil Bhat et al., bioRxiv

Animal microbiome

Limited influence of the microbiome on the transcriptional profile of female Aedes aegypti mosquitoes, Josephine Hyde et al., Scientific Reports

The gut bacterial microbiota of sea turtles differs between geographically distinct populations, T. Franciscus Scheelings et al., Endangered Species Research

Bioinformatics

Sparse reduced-rank regression for integrating omics data, Hilafu, Safo and Haine, BMC Bioinformatics

Techniques

An ecological framework to understand the efficacy of fecal microbiota transplantation, Yandong Xiao et al., Nature Communications

The use of Unmanned Aerial Vehicles (UAVs) to sample the blow microbiome of small cetaceans, Cinzia Centelleghe et al., PLOS ONE

July 7, 2020

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Today’s digest features the mighty sourdough microbiome, AGNOSTOS (a computational workflow for genes annotation using clustering and remote homology detection, contextualizing them with genomic and environmental information), and a new episode of the Bioinformatics Chat podcast about reproducible pipelines and NGLess (a user-friendly domain-specific programming language for NGS data processing), and more. Happy reading/listening!

General microbiome

Microbiome definition re-visited: old concepts and new challenges – Gabriele Berg – Microbiome

Positive interactions are common among culturable bacteria – Jared Kehe – bioRxiv

Gut microbiome

An emerging role of Prevotella histicola on estrogen-deficiency induced bone loss through the gut microbiota-bone axis – Zhongxiang Wang – bioRxiv

Identifying novel high-impact rare disease-causing mutations, genes and pathways in exomes of Ashkenazi Jewish inflammatory bowel disease patients – Yiming Wu – medRxiv

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting – Yang Liu – medRxiv

GWAS of stool frequency reveals genes, pathways, and cell types relevant to human gastrointestinal motility and irritable bowel syndrome – Ferdinando Bonfiglio – medRxiv

Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in Parkinson’s disease – Velma Aho – medRxiv

Lung microbiome

Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung – Adrian Kordes – Nature Communications

Genitourinary microbiome

Architecture and function of human uromodulin filaments in urinary tract infections – Gregor L. Weiss – Science

The structure and diversity of strain level variation in vaginal bacteria – Brett A. Tortelli – bioRxiv

Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease – Andrew J. Cohen – World Journal of Urology

Human urine 1H NMR metabolomics reveals alterations of the protein and carbohydrate metabolism when comparing habitual Average Danish diet vs. healthy New Nordic diet – Alessia Trimigno – Nutrition

Animal experiments

Lactobacillus rhamnosus probiotic prevents airway function deterioration and promotes gut microbiome resilience in a murine asthma model – Irina Spacova – Gut Microbes

Food microbiome

*The Sourdough Microbiome – Justine Dees – ASM

Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function – Brittany A. Niccum – mSystems

Bioinformatics

*Light into the darkness: Unifying the known and unknown coding sequence space in microbiome analyses – Chiara Vanni – bioRxiv

Welcome to the dark side of genomes and metagenomes – a blog post about the above mentioned study – Antonio Fernandez-Guerra

GraphBin: refined binning of metagenomic contigs using assembly graphs – Vijini Mallawaarachchi – Bioinformatics

Podcast

*Reproducible pipelines and NGLess with Luis Pedro Coelho – Roman Cheplyaka – The Bioinformatics Chat

July 4, 2020

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Greetings from Santiago, Chile! Today in this Digest, we have studies about the influence of alcohol use disorder on the microbiota, several papers about the influence of different compounds (from allicin to DAV132, a colon-targeted antibiotic adsorbent) on the microbiota. Today we have several papers about different models of plant- or soil- associated microbiomes, and a couple of papers from studies with SIV infection models. Have a nice weekend!

Human and General Microbiome

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity – Nancy Ames et al., – Gut Microbes

Comparative evaluation of peptidome and microbiota in different types of saliva samples – Ce Zhu et al., – Annals of Translational Medicine

Preprint: Microbial control over host diet selection – Brian K Trevelline and Kevin D Kohl – BioRxiv

Functional Compounds and the Microbiome

Hemolysin BL from novel Bacillus toyonensis BV-17 induces antitumor activity both in vitro and in vivo – Jiajia Chen et al., – Gut Microbes

Modeling the effect of DAV132, a novel colon-targeted adsorbent, on fecal concentrations of moxifloxacin and gut microbiota diversity in healthy volunteers – Jinju Guk et al., – Clinical Pharmacology and Therapeutics

Allicin-induced host-gut microbe interactions improves energy homeostasis – Chuanhai Zhang et al., – The FASEB Journal

Evidence of Microbiome-Drug Interactions between the Antimalarial Lumefantrine and Gut Microbiota in Mice – Matthew M. Ippolito et al., – The American Society of Tropical Medicine and Hygiene

Contrasting effects of viscous and particulate fibers on colonic fermentation in vitro and in vivo, and their impact on intestinal water studied by MRI in a randomized trial – David Gunn et al., – The American Journal of Clinical Nutrition

Animal Microbiome / Animal Models

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques – Wendy Li and Zhanshan (Sam) Ma – FEMS Microbiology Ecology

Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota – Fengze Miao et al., – Current Microbiology 

Osmotic stress induces gut microbiota community shift in fish – Keng Po Lai et al., – Environmental Microbiology

The Gut-Eye Axis: Lessons Learned from Murine Models – Jason L. Floyd & Maria B. Grant – Ophthalmology and Therapy 

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage – Kristina Allers et al., – Scientific Reports  

Plant or Soil Microbiomes

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition – Seok-Won Jang et al, – Rice 

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations – Ryan S. McClure et al., – Scientific Reports 

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest – Laura M. Mason et al.,– Journal of Applied Microbiology

Phylogenetic signals and predictability in plant-soil feedbacks – Elizabeth M. Wandrag et al., – New Phytologist

Genomics / Bioinformatics

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites – Feifei Xu et al., – Microbial Genomics 

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey et al., – Genome Research

Other papers

Preprint: Metagenome-assembled genomes from Monte Cristo Cave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars – Amanda G Bendia et al., – BioRxiv 

Preprint: Exploring metal resistance genes and mechanisms in copper enriched metal ore metagenome – Esmaeil Forouzan Sr. et al., – BioRxiv

SARS-CoV-2 Preprints

Preprint: Alpha-1 antitrypsin inhibits SARS-CoV-2 infection – Lukas Wettstein et al., – BioRxiv

July 3rd, 2020

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General microbiome

Microbiome definition re-visited: old concepts and new challenges – Berg et al. Microbiome

Large-scale metabolic interaction network of the mouse and human gut microbiota. – Lim et al. Scientific Data

Early life microbiome

Very early-life exposure to microbiota-induced TNF drives the maturation of neonatal pre-cDC1 – Kohler et al. Gut.

Human gut microbiome

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes – Reitmeier et al. Cell Host & Microbe

Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study – Clooney et al. Gut

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level – Kenny et al. Cell Host & Microbe

Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer – Yang et al. Nature Cancer

Animal microbiome

A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity – Ganley et al. Cell Chemical Biology

Extremophile microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Hou et al. BMC Microbiome

Phages and viruses

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron – Porter et al. Nature Microbiology

Bioinformatics

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data – Kieser et al. BMC Bioinformatics

Techniques

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens – Gonzalez et al. mSystems

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture – Villa et al. mSystems

July 1, 2020

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Greetings Everyone,
I want to began the month of July on a note that diversity is the basis for life. I can’t think of anything better to teach us about diversity, co-existence, and evolution than the fascinating Microbiome.
The microbiome affects us right from our birth till the end affecting our mental as well as physical health. The microbiome exhibits all sorts of differences in shape, size, color, metabolic functions in order to sustain life.
Much to learn from these tiny beings!!!!
Today’s Digest comprises of some interesting studies about effect of microbiome on chemotherapy and studies on tumor microbiome. It also includes articles exploring genetics of gut microbiome and the role of microbiome in inflammatory bowel disease. Additionally has a news article about taking microbiome therapies to clinical trials.
Hope you enjoy reading today’s digest!!
“Life on earth is such a good story you cannot afford to miss the beginning… Beneath our superficial differences we are all of us walking communities of bacteria. The world shimmers, a pointillist landscape made of tiny living beings”. – Lynn Margulis

General microbiome
Human Microbiota and Effectiveness of Cancer Chemotherapy – Shvets et al – Experimental Oncology

Immunity to commensal skin fungi promotes psoriasiform skin inflammation – Hurabielle et al – PNAS

Human Tumor microbiome
*Perspective: Probing the tumor micro(b)environment – Atreya et al – Science

Human Eye microbiome
Review: Current Knowledge on the Human Eye Microbiome: A Systematic Review of Available Amplicon and Metagenomic Sequencing Data – Delbeke et al – Acta Ophthalmologica

Human nearly-sterile sites (blood, organs, brain)
Blood Bacterial Profiles Associated with HIV Infection and Immune Recovery – Serranno-Villar et al – The Journal of Infectious Diseases

Human gut microbiome
*Genetics of human gut microbiome composition – Kurilshikov et al – bioRxiv

Review: The microbiome in inflammatory bowel diseases: from pathogenesis to therapy – Liu et al – Protein&Cell

Built environment
Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al – bioRxiv

Food microbiology
Food and mood: how do diet and nutrition affect mental wellbeing? – Firth et al – BMJ

Bioinformatics
DRAM for distilling microbial metabolism to automate the curation of microbiome function – Shaffer et al – bioRxiv

Techniques
MetaRibo-Seq measures translation in microbiomes – Fremin et al – Nature Communications

Microbes on the market
Enterome Secures €46M to Take Microbiome Therapies to Clinical Trials – Helen Albert – Labiotech.eu

Human Microbiome Therapeutics Market Research: Global Status & Forecast by Geography, Type & Application (2016-2026)

June 21, 2020

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Hello from the Sonoran Desert! In today’s digest, you’ll find two very interesting reviews! Stagaman and collaborators come back on years of Zebra-fish gut microbiome research and explore the insights gleaned from this awesome model animal. On the other hand, François and Pybus review our understanding of avian viromes in both wild and domesticated bird populations, highlighting the current limitations and pitfalls in this research area.

But today’s digest also contains very interesting research papers! Gulino and collaborators are exploring viromes in New York city wastewater systems. This paper is particularly interesting as bacteriophages are typically left out from urban environments microbiomes studies, despite their abundance and importance in ecosystems.

Finally, today’s non-microbiology pick is a review that comes back on how information theory, developped by Claude Shannon in the late 40s, have been used in computational biology. This paper is particularly interesting for readers wanting to learn more about the basics of information theory and how it is applied today in bioinformatics.

Have a great Sunday!

Pregnancy and early life

Review: The microbiome in pediatric oncology – Rotz et al. – Cancer

Human respiratory microbiome

Metagenomic analysis of the lung microbiome in pulmonary tuberculosis – a pilot study – Hu et al. – Emerging Microbes & infections

Human vaginal microbiome

Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development –Nkufi Tange et al. – Scientific reports

Human gut microbiome

Preprint: The gut microbiome regulates memory function – Noble et al. – BioRxiV

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

review: Zebrafish microbiome studies make waves – Stagaman et al. – Lab Animal

Built environment (subways, indoor surfaces)

Revealing antimicrobial resistance in stormwater with MinION – Bialasek et al. – Chemosphere

Phages and viruses

Review: Towards an understanding of the avian virome –François et al. – Journal of general Virology

Initial Mapping of the New York City Wastewater Virome –Gulino et al. – mSystems

Bioinformatics

Higher order Markov models for metagenomic sequence classification – Burks et al. –Bioinformatics

Preprint: Combinatorial Algorithms for Strain Level Metagenomic Microbial Detection and Quantification –Zhu et al. –BioRxiV

Preprint: Ultra-rapid metagenotyping of the human gut microbiome – Shi et al. – BioRxiV

My non-microbiology pick

Review: Information Theory in Computational Biology: Where We Stand Today – Chanda et al. – Entropy

June 13, 2020

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Somewhat of a brief digest for today, but to make up for that, the long-awaited results of the PREDICT I study were published in Nature Medicine!

Human gut microbiome

Human postprandial responses to food and potential for precision nutrition – Berry et al. – Nature Medicine

Insect microbiome

Shotgun sequencing of honey DNA can describe honey bee derived environmental signatures and the honey bee hologenome complexity – Bovo et al. – Scientific Reports

Plant, root, and soil microbiome

Low Turnover of Soil Bacterial rRNA at Low Temperatures – Schostag et al. – Frontiers in Microbiology

Water and extremophile microbiome

Preprint: Diatom Modulation of Microbial Consortia Through Use of Two Unique Secondary Metabolites – Shibl et al. – bioRxiv

Complementary sampling methods for coral histology, metabolomics, and microbiome – Greene et al. – Methods in Ecology and Evolution

Phages and viruses

Preprint: Phage infection mediates inhibition of bystander bacteria – Chatterjee et al. – bioRxiv

Depth-related variability in viral communities in highly stratified sulfidic mine tailings – Gao et al. – Microbiome

Bioinformatics

GAD: A Python Script for Dividing Genome Annotation Files into Feature-Based Files – Yasser et al. – Interdisciplinary Sciences: Computational Life Sciences

Towards virtual physiological humans: integrating metabolism, physiology, and gut-microbiome

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Science communication on a recently published paper

Precision Medicine

A milestone in precision medicine would be the ability to explore generative models that can capture the real-world complexity of human physiology. If computational models can successfully integrate physiology, metabolism, and host-microbiome data – thereby achieving personalization of predictive models of virtual physiological humans – this would be a key stepping-stone in yielding promising therapeutic targets that are both individual-specific and case-specific. Thus, the science (and art) of generating and exploring virtual physiological humans could be a boon to systems physiology and precision medicine.

Whole-body metabolic reconstructions

Towards this end, Thiele et al. recently published an intriguing paper. Thiele et al. demonstrate building and validation of sex-specific curated Whole-Body Metabolic (WBM) reconstructions. Computational models derived from such WBM reconstructions offer a novel molecular-level, anatomically and physiologically consistent, sex-specific genome-scale reconstructions of human physiology and metabolism. Thiele et al. further demonstrated that the WBM reconstructions can be ‘personalized’ via integration of quantitative physiological data with multi-omics such as metabolomics, and gut-microbiome. Thus, Thiele et al. introduce Harvey and Harvetta, the male and female WBM reconstructions, respectively. These reconstructions and the derived models and analysis enable novel assessment of, e.g., host-microbiome co-metabolism that is individual-specific and is resolved at an organ-level.

Complexity

The extreme complexity of real-world metabolic modelling of host-microbiome in humans can hardly be overstated. Thiele et al. address this critical challenge via constraint-based reconstruction – their models account for the enormous diversity of microbiome-associated microbial genes that are meaningful both physiologically and is individual-specific such as in host-microbiome co-metabolism. Thus this approach allows case-specific investigation of human metabolism, such as for studying inherited metabolic diseases.

Approach

Previously the Thiele Lab , extensive metabolic modelling of metabolic and physiologically relevant pathways (curated algorithmically and manually) led to a comprehensive model that allows investigation via constraint-based reconstruction of over 80,000 pathways. Thiele et al. approached the problem into a smaller sub-problems that they have previously addressed. First – by compiling organ-specific information from previous literature and including experimental-omics data, Thiele Lab generated WBM reconstructions. Second – Thiele Lab imposed constraints the WBM reconstructions via (large-scale) physiology, dietary constraints and quantitative metabolomic data.

Highlights

A key challenge that Thiele et al. addressed in this current 2020 paper is the integration of more than 80,000 biochemical reactions, that were both anatomically and physiologically consistent. These WBM reconstructions describe 26 organs and 6 blood cell types and capture whole-body organ-resolved metabolism. Importantly, these recapitulate previously known inter-organ metabolic cycles and energy use. Interestingly, WBM models can also predict biomarkers. This might, e.g., elucidate new pathways or targets that are implicated in heritable metabolic diseases.

Take-home-message and future ahead

Exploring such quantitative metabolic models could reveal new molecular insights pertaining to (co-dependence of host-microbiome) metabolism and overall human physiology and homeostasis – both in health and disease. The power of computational models is further exemplified if these allow addressing questions via novel hypothesis-testing that go beyond the scope of wet-lab experiments.

written by: Div Prasad

I’m interested in quantitative biology (at the intersection) of human genetics, machine learning, and host-microbiome interactions.

Twitter: @divyaePrasad
github: divprasad

June 6, 2020

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Short digest for today, but I’d like to draw attention to two studies on creative techniques to reduce contamination by host DNA sequences: one using PCR blocking primers to improve 16S rDNA sequencing, and the other on using CRISPR-Cas systems to assist with 18S rDNA sequencing. Happy reading!

Human gut microbiome

Review: Gut Microbial Metabolites and Blood Pressure Regulation: Focus on SCFAs and TMAO – Poll et al. – Physiology

Review: Trial Watch: the gut microbiota as a tool to boost the clinical efficacy of anticancer immunotherapy – Daillerè et al. – OncoImmunology

Human oral microbiome

Well‐maintained patients with a history of periodontitis still harbor a more disbiotic microbiome than health – Lu et al. – Periodontology

Plant, root, and soil microbiome

Contrasting soil microbial abundance and diversity on and between pasture drill rows in the third growing season after sowing – Hayes et al. – Renewable Agriculture and Food Systems

A novel PCR clamping assay reducing plant host DNA amplification significantly improves prokaryotic endo-microbiome community characterization – Lefèvre et al. – FEMS Microbiology Ecology

Water and extremophile microbiome

Diverse viruses have restricted biogeography in deep-sea hydrothermal vent fluids – Thomas et al. – bioRxiv

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria – Lin et al. – bioRxiv

Phages and viruses

A tissue level atlas of the healthy human virome – Kumata et al. – BMC Biology

Review: Deep Roots and Splendid Boughs of the Global Plant Virome – Dolja et al. – Annual Review of Phytopathology

Bioinformatics

An empirical Bayes approach to normalization and differential abundance testing for microbiome data – Liu et al. – BMC Bioinformatics

Techniques

The use of CRISPR-Cas Selective Amplicon Sequencing (CCSAS) to reveal the eukaryotic microbiome of metazoans – Zhong et al. – bioRxiv

June 5, 2020

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Today’s digest features a review on genetic variability within species in microbiomes, a study on Lactobacilli in the human nose, a new episode of Microbiology Lab Pod with the latest science news on functional metagenomics, a novel resistance gene called GAR, and more. Happy reading/listening!

General microbiome

*Diversity within species: interpreting strains in microbiomes – Thea Van Rossum – Nature Reviews

Earth microbial co-occurrence network reveals interconnection pattern across microbiomes – Bin Ma – Microbiome

Oral and nasal microbiome

Local oral and nasal microbiome diversity in age-related macular degeneration – Jacob Rullo – Scientific Reports

*Lactobacilli Have a Niche in the Human Nose – Ilke De Boeck – Cell Reports

Gut microbiome

Resistant maltodextrin intake reduces virulent metabolites in the gut environment: randomized control study in a Japanese cohort – Yuichiro Nishimoto – MedRxiv

Pregnancy and early life

One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces – Ana Paula Christoff – PlosOne

Animal microbiome

Cecal microbiome composition and metabolic function in probiotic treated broilers – Denise R. Rodrigues – PlosOne

Characterization of native Escherichia coli populations from bovine vagina of healthy heifers and cows with postpartum uterine disease – Candelaria Gonzalez Moreno – PlosOne

Animal experiments

Structural and Functional Changes of Gut Microbiota in Ovariectomized Rats and Their Correlations With Altered Bone Mass – Sicong Ma – Aging

Plant, root, and soil microbiome

Dissecting the effect of continuous cropping of potato on soil bacterial communities as revealed by high-throughput sequencing – Jing Zhao – Plos One

Water microbiome

Increasing flow rate reduces biofouling and colonization by filamentous bacteria in drippers fed with reclaimed wastewater – Kevin Lequette – bioRxiv

Phages and viruses

Integration of phage and yeast display platforms: A reliable and cost effective approach for binning of peptides as displayed on-phage – Priyanka Pandya – PlosOne

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes – Kira Moon – Microbiome

Bioinformatics

Estimating Microbial Interaction Network: Zero-inflated Latent Ising Model Based Approach– Jie Zhou – bioRxiv

Assessment of statistical methods from single cell, bulk RNA-seq and metagenomics applied to microbiome data – Matteo Calgaro – bioRxiv

Metabolomics

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power– Jasmin Hafner – Synthetic Biology

Inferring Active Metabolic Pathways from Proteomics and Essentiality Data – Ariadna Montero-Blay – Cell Reports

Podcast

*May 2020 Pod: Discovering novel resistance genes and how bacteria become virulent – Bengtsson-Palme Lab and Marlies Böhm – Microbiology Lab Pod