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

June 12, 2020

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Buenos dias and greetings from Spain!

Today we can announce a Virtual Skin Microbiome Symposium held by New York Society of Cosmetic Chemists (NYSCC), that will start on June 15 to June 22, 2020, will include five on-demand sessions, a live panel Q&A and the Suppliers’ Day Digital Pop-Up & Solutions Center.

COVID-19

Epidemiological models are important tools for guiding COVID-19 interventions – Robin N. Thompson – BMC Medicine

Diagnosis of COVID-19 in children: the story evolves – R. Harwood and I. Sinha – BMC Medicine

Africa’s response to COVID-19 – Chikwe Ihekweazu and Emmanuel Agogo – BMC Medicine

Evaluation of the potential incidence of COVID-19 and effectiveness of containment measures in Spain: a data-driven approach – Alberto Aleta and Yamir Moreno – BMC Medicine

Pre-print – Identification of unique mutations in SARS-CoV-2 strains isolated from India suggests its attenuated pathotype – Shubham Gaurav – bioRxiv

General microbiome

Feasibility of collection and analysis of microbiome data in a longitudinal randomized trial of community gardening – Mireia Gascon – Future microbiology

Targeted microbiome depletion – A Du Toit – Nature Reviews Microbiology

Combining proteogenomics and metaproteomics for deep taxonomic and functional characterization of microbiomes from a non-sequenced host D Gouveia et al. – Biofilms and Microbiomes

Microbiome factors in HPV-driven carcinogenesis and cancers D Lin et al. – Plos Pathogens

Human respiratory microbiome

Clinical diagnostic application of metagenomic next-generation sequencing in children with severe nonresponding pneumonia – Heping Wang – PLOS ONE

Human vaginal microbiome

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis – Anna-Ursula Happel – PLOS ONE

Human nearly-sterile sites

Parapseudoflavitalea muciniphila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a human peritoneal tumour and reclassification of Pseudobacter ginsenosidimutans as Pseudoflavitalea ginsenosidimutans comb. nov. – Paul A. Lawson et al. – Microbiology society

Draft Genome Sequence of Escherichia coli UMB1353, Isolated from the Female Urinary Tract – T Crawford et al. – Microbiology Resource Announcements

Human gut microbiome

Pre-print – The effect of short-course antibiotics on the resistance pro le of colonizing gut bacteria in the ICU: a prospective cohort study – C Munck et al. – Research Square

Pre-print – Dietary sphinganine is selectively assimilated by members of the gut microbiome – Min-Ting Lee et al. – bioRxiv

Pre-print – Nutritional combinatorial impact on the gut microbiota and plasma short-chain fatty acids levels in the prevention of mammary cancer in Her2/neu estrogen receptor-negative transgenic mice – Manvi Sharma et al. – bioRxiv

Animal experiments

Evaluation of the bacterial ocular surface microbiome in ophthalmologically normal dogs prior to and following treatment with topical neomycin-polymyxin-bacitracin – Callie M Rogers et al. – PLOS ONE

Short-chain fructo-oligosaccharides supplementation to suckling piglets: Assessment of pre- and post-weaning performance and gut health – Miriam Ayuso – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen et al. – PLOS ONE

Effect of dietary gossypol supplement on fermentation characteristics and bacterial diversity in the rumen of sheep – CaiDie Wang – PLOS ONE

Polysaccharides isolated from Cordyceps Sinensis contribute to the progression of NASH by modifying the gut microbiota in mice fed a high-fat diet – Lei Chen – PLOS ONE

β-glucan administration improves growth performance and gut health in New Zealand White and APRI rabbits with different breed responses – Mahmoud M Abo Ghanima – PLOS ONE

Comparative study of gut microbiota in Tibetan wild asses (Equus kiang) and domestic donkeys (Equus asinus) on the Qinghai-Tibet plateau – H Liu, X Zhao – PeerJ

Pre-print – Differential genes and microbiota revealed by serum metabolomics of obese rats after intervention by Rhizoma Coptidis – K Luo et al. – Research Square

Pre-print – Quantifying fluorescent glycan uptake to elucidate strain-level variability in foraging behaviors of rumen bacteria – Leeann Klassen et al. – bioRxiv

Animal microbiome

Characterizing the microbiome of ectoparasitic louse flies feeding on migratory raptors – Rebecca A McCabe et al. – PLOS ONE

Characterization of the microbiota of commercially-traded finfish fillets – HR Shehata et al. – Food Research International

A bug’s life-delving into the challenges of helminth microbiome studies – F Formenti et al. – PLoS Neglected Tropical Diseases

Fish skin and gut microbiomes show contrasting signatures of host species and habitat – FÉ Sylvain et al. – Applied and Environmental

Plant, root, and soil microbiome

Isolation, Screening and Identification of Free-Living Diazotrophic Bacteria from Salinated Arid Soils – SA Begmatova et al. – Microbiology

Eukaryotic Microbial Communities in Japanese Arable AndisolsInvestigated by Amplicon Sequencing of 18S rRNA – GenesKazumori Mise et al. – American Society for microbiology

Combined effects of green manure returning and addition of sewage sludge compost on plant growth and microorganism communities in gold tailings. – YJ Ai et al. – Environmental Science and Pollution

Taxonomic shifts in arbuscular mycorrhizal fungal communities with shade and soil nitrogen across conventionally managed and organic coffee agroecosystems. – L Aldrich-Wolfe et al. – Mycorrhiza

Metagenomics Framework for the study of Soil Microbial Communities Based 16s rRNA Gene profiling approach – A Basu et al. – International Journal of Biotechnology

Soil microbial communities in the rhizosphere of Robinia pseudoacacia L. after being exposed to elevated atmospheric CO2 and cadmium for 4 years – X Jia et al. – Applied Soil Ecology

Soil aggregates by design: Manufactured aggregates with defined microbial composition for interrogating microbial activities in soil microhabitats – HJ Harvey et al – Soil Biology and Biochemistry

Would fertilization history render the soil microbial communities and their activities more resistant to rainfall fluctuations? J Kátai et al. – biorxiv

Pre-print – Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae – Justine Charon et al. – bioRxiv

Water and extremophile microbiome

Comparative metagenomics reveals the microbial diversity and metabolic potentials in the sediments and surrounding seawaters of Qinhuangdao mariculture area – Shuping Wang et al. – PLOS ONE

Spatial dynamics of eukaryotic microbial communities in the German Bight – PAA Sprong et al. – Journal of Sea Research

Temporal distribution of microbial community in an industrial wastewater treatment system following crash and during recovery periods – H Barak et al. – Chemosphere

Pre-print – Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbiome structure and key drivers – Chenjing Jiang et al. – bioRxiv

Pre-print – Ozone nanobubble treatment effectively reduced pathogenic Gram positive and negative bacteria in freshwater and safe for tilapia – Chayuda Jhunkeaw et al. – bioRxiv

Pre-print – Impact of trimethoprim on the river microbiome and antimicrobial resistance. James Delaney et al. – bioRxiv

Bioinformatics

gutMEGA: a database of the human gut MEtaGenome Atlas – Q Zhang et al. – Briefings in Bioinformatics

June 10, 2020

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Greetings from Western New York! This is my first post to Microbiome Digest and I hope it turns out well as I have been busy trying to learn the nuances of publishing on WordPress over the past few months. As a retired Ophthalmologist with a Laboratory Medicine background and research studies in Microbiology I have a distinct affinity for microbiome-related research as it pertains to dysbiosis and pathogenesis. I have included some interesting articles on the association of the microbiome in gallstone disease, gastric and esophageal cancers as well as in HPV cancers. There is also a brief news article pertaining to handwashing of significance in the COVID-19 world we are currently living in. Stay safe and enjoy!

COVID-19

Novel Coronavirus disease 2019 (COVID-19): new challenges and new responsibilities in developing countries. FR Anjum, et al.- Human Vaccines & Immunotherapeutics

APPLIED MICROBIOLOGY

Microplastics provide new microbial niches in aquatic environments. Y Yang, et al.- Applied Microbiology and Biotechnology

GENERAL MICROBIOME

Gallstone Disease and Microbiome. IN Grigor’eva, et al.- Microorganisms

PREGNANCY AND EARLY LIFE

Bacterial Peptidoglycans from Microbiota in Neurodevelopment and Behavior. A Gonzalez-Santana,et al.- Trends in Molecular Medicine

HUMAN SKIN MICROBIOME

News Article: You Need To Use Soap & Sanitizer — But You Also Need To Tend To Your Microbiome

HUMAN GUT MICROBIOME

Comparison of the gut microbiome composition among individuals with acute or long-standing spinal cord injury vs. able-bodied controls. J Li, W Van Der Pol, et al. – The Journal of Spinal Cord …

Influence of microbiota on immunity and immunotherapy for gastric and esophageal cancers. X Zhang, et al.- Gastroenterology Report

ANIMAL MICROBIOME

Exposure of CuO nanoparticles and their metal counterpart leads to change in the gut microbiota and resistome of collembolans. J Ding, et al.- Chemosphere

PLANT, ROOT AND SOIL MICROBIOME

Soil Bacterial Diversity and Potential Functions Are Regulated by Long-Term Conservation Tillage and Straw Mulching. C Liu, et al- Microorganisms

WATER AND EXTREMOPHILE MICROBIOME

Patterns of environmental variability influence coral‐associated bacterial and algal communities on the Mesoamerican Barrier Reef. L Speare, et al.- Molecular Ecology

PROBIOTICS / PREBIOTICS

Saccharomyces boulardii: What Makes It Tick as Successful Probiotic?. P Pais, et al. – Journal of Fungi

PHAGES AND VIRUSES

Expression and functional study of VpV262 Pol, a moderately halophilic DNA polymerase from the Vibrio parahaemolyticus phage VpV262. Y Gao, et al.- Enzyme and Microbial Technology

Microbiome factors in HPV-driven carcinogenesis and cancers. D Lin, et al.- Plos Pathogens

BIOINFORMATICS

Gut–Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization. B Tilocca, et al.- Int. J. Mol. Sci

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 09, 2020

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Good morning everyone!

Today’s digest presents several antibiotic resistance papers, as well as hospital ICU microbiome study, a microbial nomenculture paper, bunch of human microbiome papers (both gut and vaginal), as well as two computational platforms for analyzing microbial data.

In a more personal note– recently, my PhD research (at ARO and The Hebrew U, Israel) resulted in two manuscripts dealing with the exciting world of bacterial secondary metabolites. The first one is a review paper where we present state-of-the-art tools and methodologies to study and identify novel secondary metabolites gene clusters within the widely diverse soil and root bacterial communities. We present a conceptual pipeline for an efficient use of these culture-based and culture-independent platforms to identify novel antimicrobials-producing gene clusters in-vivo.

The second one (a bioRxiv pre-print) utilized some of these techniques to explore differences in secondary metabolites gene clusters between soil and roots bacterial communities, in terms of diversity, composition and taxonomy. We then took advantage of this data and deeply focused on root-enriched and abundant sequences (those that were associated with NRPS and PKS, mega-enzymes that produces two very important families of secondary metabolites- nonribosomal peptides and polyketides). Then, we used a unique culture-independent platform (eSNaPD, from Sean Brady lab @ Rockefeller U, NY) and were able to actually recover 5 clones (~40Kb in length) that harbored five novel gene clusters. At least one of these probably encode for an antifungal metabolites (derived from Actinobacteria). This piepline/platform is applicable for other uses of course, depending on your research question and the functions you’re intrested in. I’ll be happy for any feedback regarding the bioRxiv MS (either directly there or via my tweeter).

General microbiology

Roadmap for naming uncultivated Archaea and Bacteria, Alison E. Murray, Nature Microbiology

Human microbiome

Re-evaluating the relationship between missing heritability and the microbiome, Gavin Douglas , Microbiome

Microbes and mental health: Can the microbiome help explain clinical heterogeneity in psychiatry?, Christina L. Hayes, Front. Neuroendocrinology

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations, Nicolai Karcher, Genome Biology

Exploring potential of vaginal Lactobacillus isolates from South African women for enhancing treatment for bacterial vaginosis, Anna Ursula Happel , PLOS Pathogens

Hospital microbiome

Temporal variations in bacterial community diversity and composition throughout intensive care unit renovations, Jessica Chopik , Microbiome

Antibiotic Resistance

The household resistome – frequency of beta-lactamases, class 1 integron and antibiotic resistant bacteria in the domestic environment, Laura S. Schages , bioRxiv

Environmental conditions dictate differential evolution of vancomycin resistance in Staphylococcus aureus, Henrique Machado, bioRxiv

Coexistence of Antibiotic Resistance Genes and Virulence Factors Deciphered by Large-Scale Complete Genome Analysis, Yu Pan, mSystems

Bioinformatics

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems, Begum D. Topcuoglu, mBio

PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing, Alexis Robitaille, BMC Bioinformatics

June 08, 2020

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Today, we present a broad spectrum of new studies covering among others the mycobiome of human milk, gut microbes and their association with brain development and cognitive function, and a catalogue of previously unseen microbial genomes. Of particular interest is a study that integrates different sources of data to model a personalized gut microbiome. Last but not least we selected a pre-print on the design and characterization of multiepitopes vaccine for SARS-CoV.

General microbiome

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer – Costa et al. – Microbiome

REVIEW: Conceptualizing the vertebrate sterolbiome – Ridlon – Applied and Environmental Microbiology

Human milk mycobiome

Human milk fungi: environmental determinants and inter-kingdom associations with milk bacteria in the CHILD Cohort Study – Moossavi et al. – BMC Microbiology

Human skin microbiome

Skin microbiota analysis-inspired development of novel anti-infectives – Liu et al. – Microbiome

Human vaginal microbiome

PREPRINT: Vaginal microbiota of adolescents and their mothers: A preliminary study of vertical transmission and persistence – Bassis – bioRxiv

Human gut microbiome

Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome – Thiele et al. – Mol Syst Biol

REVIEW: The gut microbiota profile of adults with kidney disease and kidney stones: a systematic review of the literature – Stanford et al. – BMC Nephrology

PREPRINT: Gut microbes and their genes are associated with brain development and cognitive function in healthy children – Bonham et al. – bioRxiv

Animal microbiome (for animals in the wild)

Microbial environment shapes immune function and cloacal microbiota dynamics in zebra finches Taeniopygia guttata – van Veelen et al. – Animal Microbiome

PREPRINT: Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity – Youngblut – bioRxiv

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

Novel insights into the Thaumarchaeota in the deepest oceans: their metabolism and potential adaptation mechanisms – Zhong et al. – Microbiome

The role of metal contamination in shaping microbial communities in heavily polluted marine sediments – Di Cesare et al. – Environmental Pollution

Techniques

Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing – Song & Xie – Microbiome

SARS-CoV-2

PREPRINT: In silico design and characterization of multiepitopes vaccine for SARS-CoV from its Spike proteins – Kathwate – bioRxiv

June 7, 2020

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Have a nice Sunday! Today, in this brief Digest, we have few papers about Microbiome and Health, including studies on Fibromyalgia, ALS and Hepatitis E infection. Additionally, we have papers about SARS-CoV-2. Stay safe!  

Microbiome research

Review: Microbiome in Health and Disease – Edward M Giles – Journal of Paediatrics and Child Health

Metabolic Syndrome, Depression, and Fibromyalgia Syndrome Prevalence in Patients With Irritable Bowel Syndrome: A Case-Control Study – Muharrem Bayrak – Medicine

Preprint: Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity – Nicholas D Youngblut – bioRxiv

Amyotrophic Lateral Sclerosis and Intestinal Microbiota-Toward Establishing Cause and Effect – Marc Gotkine – Gut Microbes

Freeze-dried Fecal Samples Are Biologically Active After Long-Lasting Storage and Suited to Fecal Microbiota Transplantation in a Preclinical Murine Model of Clostridioides difficile Infection – Julie Reygner – Gut Microbes

Altered Fecal Microbiota on the Expression of Th Cells Responses in the Exacerbation of Patients With Hepatitis E Infection – Jian Wu – Journal of Viral Hepatitis

Covid-19 papers

Preprint: An OpenData portal to share COVID-19 drug repurposing data in real time – Kyle R. Brimacombe – bioRxiv

Preprint: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type – Paul Robert Lephart – bioRxiv

A Systematic Review of Neurological Manifestations of SARS-CoV-2 Infection: The Devil Is Hidden in the Details – Michele Romoli – European Journal of Neurology

Concomitant Brain Arterial and Venous Thrombosis in a COVID-19 Patient – Maria Malentacchi – European Journal of Neurology

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

June 4, 2020

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General microbiome

Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer – Costa et al. – Microbiome

Human microbiome

Review – Host–microbiota interactions in immune-mediated diseases. Ruff et al. – Nature Reviews Microbiology

Human gut microbiome

Gut microbial diversity, inflammation, and oxidative stress are associated with tacrolimus dosing requirements early after heart transplantation – Jennings et al. PLOS One

Review – Interaction between drugs and the gut microbiome – Weersma et al. – Gut

Mucosal Microbiota and Metabolome along the Intestinal Tract Reveal a Location-Specific Relationship – Yuan et al. mSystems

Animal microbiome

The Gut Microbiota Communities of Wild Arboreal and Ground-Feeding Tropical Primates Are Affected Differently by Habitat Disturbance – Barelli et al. mSystems.

Plant, root and soil microbiome

Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation – Carrion et al. Microbiome

Probiotics

Probiotics for the prevention of antibiotic-associated adverse events in children—A scoping review to inform development of a core outcome set – Lukasik et al. –  PLOS One

Phages and viruses

Predicting host taxonomic information from viral genomes: A comparison of feature representations – Young et al. PLOS Comp Biology. 

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

Bioinformatics

The hidden layers of microbial community structure: extracting the concealed diversity dimensions from our sequencing data – Fasolo et al. – FEMS Microbiology Letters

Compositional Lotka-Volterra describes microbial dynamics in the simplex – Joseph et al. PLOS Computational Biology.

Techniques

Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing – Blattman et al. – Nature Microbiology.