August 4, 2020

Greetings Everyone. Today’s Microbiome Digest comprises of a wide variety of topics covering soil microbiota, tumor to water to extremophile microbiome. The digest has some reviews, books, as well as interesting articles on how synthetic microbial communities facilitate sustainable growth and the role of microbial communities in balancing the environment. A terrific news article covering the isolation of microbes buried beneath the sea floor for more than 100 million years. Today’s digest can be summarized by a quote by Julie Morley.

“Every being devotes and dedicates itself to some innate purpose. Single cells, microbes, plants, insects, animals – every being makes it own unique contribution” – Julie J. Morley

General microbiome

*Shifts in the microbiota associated with male mosquitoes (Aedes aegypti) exposed to an obligate gut fungal symbiont (Zancudomyces culisetae) – Jonas Frankel-Bricker – Scientific Reports

Microbiome-derived metabolites reproduce the mitochondrial dysfunction and decreased insulin sensitivity observed in type 2 diabetes – Ormsby et al – bioRxiv

*Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth – Zuñiga et al – Nature Communications

Multi-site human microbiome

Microbiome harbored within tumors: a new chance to revisit our understanding of cancer pathogenesis and treatment – Zhao et al – Signal Transduction and Targeted Therapy

Human skin microbiome
Paradigms and Perspectives: The skin microbiome as a clinical biomarker in atopic eczema: Promises, navigation, and pitfalls – Reiger et al – The journal of Allergy and Clinical Immunology

Human gut microbiome
Review: Gut microbiota and atherosclerosis: role of B cell for atherosclerosis focusing on the gut-immune-B2 cell axis – Chen et al – Journal of Molecular Medicine

Gut microbiome a promising target for management of respiratory diseases – Trivedi et al – Biochemical Journal

*A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota – Aakko et al – Scientific Reports

Effects of antibiotic treatment on gut microbiota and how to overcome its negative impacts on human health – Ribeiro et al – ACS Infect. Dis

Animal experiments
Dynamics of uterine microbiota in postpartum dairy cows with clinical or subclinical endometritis – Pascottini et al – Scientific Reports

Plant, root, and soil microbiome
Book chapter: The Extended Microbiota: How Microbes Shape Plant-Insect Interactions – Mayoral-Peña et al – Evolutionary Ecology of Plant-Herbivore Interaction

Response of Soil Microbial Community to C:N:P Stoichiometry along a Caragana korshinskii Restoration Gradient on the Loess Plateau, China – Zhang et al – forests

Review: The endosphere microbial communities, a great promise in agriculture – Adeleke et al – International Microbiology

Water and extremophile microbiome
Influence of microorganisms on initial soil formation along a glacier forefield on King George Island, maritime Antarctica – Krauze et al – Biogeosciences

Review: Microbial communities of soda lakes and pans in the Carpathian Basin: a review – Tamás Felföldi – Biologia Futura

Fungal Community in Antarctic Soil Along the Retreating Collins Glacier (Fildes Peninsula, King George Island) – dos Santos et al – microorganims

Culture Independent Diversity of Bacterial Communities Indigenous to Lower Altitude at Laohugou Glacial Environment – Ali et al – Geomicrobiology Journal

Review: Methanosarcina acetivorans: A Model for Mechanistic Understanding of Aceticlastic and Reverse Methanogenesis – James G. Ferry – Front.Microbiol

The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation – Chung et al – Front.Microbiol

Food microbiology
FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation – Vaccalluzzo et al – Food Microbiology


Bioinformatics
Book: A Bioinformatics Primer for the Analysis of Illumina MiSeq Data of Litter-Associated Fungi and Bacteria – Seena et al – Methods to Study Litter Decomposition

Techniques
Review: Method development for cross-study microbiome data mining: challenges and opportunities – Su et al – Computational and Structural Biotechnology Journal

Microbes in the news
*Scientists pull living microbes, possibly 100 million years old, from beneath the sea – Elizabeth Pennnisi – Science

July 31, 2020

Today’s digest features studies on hospital-associated bacterial communities on window components, the effect of urbanization on the vaginal microbiota of Amerindians, nitrate as a potential prebiotic for oral health, and the latest news in bioinformatics. Happy reading!

General microbiome

Microbial species interactions determine community diversity in fluctuating environments – Shota Shibasaki – bioRxiv

Review: The host-associated archaeome – Guillaume Borrel – Nature Reviews Microbiology

Oral microbiome

*Nitrate as a potential prebiotic for the oral microbiome – Bob T. Rosier – Scientific Reports

Skin microbiome

Deep skin dysbiosis in vitiligo patients: link with mitochondrial and immune changes – Hanene Bzioueche – medRxiv

Gut microbiome

Review: The microbiome: An emerging key player in aging and longevity– Minhoo Kim and Bérénice A. Benayoun – Translational Medicine of Aging

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Kelsey E. Huus – Microbiome

Vaginal microbiome

*Changes in the vaginal microbiota across a gradient of urbanization – Daniela Vargas-Robles – Scientific Reports

Comparison between a novel molecular tool and conventional methods for diagnostic classification of bacterial vaginosis: is integration of the two approaches necessary for a better evaluation? – Margherita Scapaticci – New Microbiologica

Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence – Norhan Alhajjar – bioRxiv

Association between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization – McKenna C Eastment – The Journal of Infectious Diseases

Urinary microbiome

Review: The microbiome in urological diseases – Kwang Woo Lee – Investigive and Clinical Urology

Review: FimH and Anti-Adhesive Therapeutics: A Disarming Strategy Against Uropathogens – Meysam Sarshar – Antibiotics

Characterization of urinary microbiome in patients with bladder cancer: Results from a single-institution, feasibility study – Juan Chipollini – Urologic Oncology: Seminars and Original Investigations

Animal microbiome

Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage – Jolinda Pollock – Scientific Reports

Vaginal Microbiota Changes During Estrous Cycle in Dairy Heifers – Juan J. Quereda – Frontiers in Veterinary Science

Animal experiment

The gut microbiome switches mutant p53 from tumour-suppressive to oncogenic – Eliran Kadosh – Nature

An Enteric Pathogen Subverts Colonization Resistance by Evading Competition for Amino Acids in the Gut – Gustavo Caballero-Flores – Cell Host & Microbe

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin – Damien J. Cabral – mSystems

Water and extremophile microbiome

Determining the primary sources of fecal pollution using microbial source tracking assays combined with land-use information in the Edwards Aquifer – Jessica Hinojosa – Water Research

Diverse Microorganisms in Sediment and Groundwater Are Implicated in Extracellular Redox Processes Based on Genomic Analysis of Bioanode Communities – Tyler J. Arbour – Frontiers in Microbiology

Food microbiome

Discovering microbiota and volatile compounds of surströmming, the traditional Swedish sour herring – Luca Belleggia – Food Microbiology

Built environment

*Viable bacterial communities on hospital window components in patient rooms – Patrick F. Horve – PeerJ

Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation – Ganesh Babu Malli Mohan – mSystems

Phages and viruses

Viral Metagenomic Content Reflects Seawater Ecological Quality in the Coastal Zone – Anastasia Tsiola – Viruses

Bioinformatics

Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets – Yi Yue – BMC Bioinformatics

Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach – Christian Milani – mSystems

Automated prediction and annotation of small proteins in microbial genomes– Matthew G Durrant and Ami S Bhatt – bioRxiv

Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing data – Abigail L. Lind – bioRxiv

MicrobeAnnotator: a user-friendly, comprehensive microbial genome annotation pipeline – Carlos A. Ruiz-Perez – bioRxiv

Topological and kernel-based microbial phenotype prediction from MALDI-TOF mass spectra – Caroline Weis – Bioinformatics

NetCoMi: Network Construction and Comparison for Microbiome Data in R – Stefanie Peschel – bioRxiv

Review: Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses – Ana Elena Pérez-Cobas – Microbial Genomics

Podcast

Machine learning for drug development with Marinka Zitnik – Jacob Schreiber – The Bioinformatics Chat

June 17, 2020

Hello and welcome to Wednesday’s Digest! Today’s selection includes two separate but complementary papers from Cell Host & Microbe. The first, from Brett Finlay’s lab, investigates what drives the loss of Immunoglobulin A recognition by beneficial bacteria in the gut of undernourished children. The second, from Jeffrey Gordon’s lab, examines the impact of prebiotic and microbial interventions on oral vaccination responses in a mouse model of childhood undernutrition. These papers both highlight the important relationship between nutrition, the microbiota, and host mucosal immunity.

There are also a few fungi-focused papers today as well as some interesting animal microbiome research. Tan et al. compare the microbiome of pigs and their farmers and Andrade-Oliveira et al. found that antimicrobial resistance genes from a feline oral commensal can be transferred to a human-associated staphylococci. I also want to call attention to the techniques section, especially a paper by Song and Xie in which they used CRISPR/Cas9 to deplete host contamination in 16S rRNA gene amplicon samples.

Happy reading, y’all!

Pregnancy and Early-life
Analysis of Immune, Microbiota and Metabolome Maturation in Infants in a Clinical Trial of Lactobacillus Paracasei CBA L74-fermented Formula. Roggero, P. et al. Nature Communications.

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth. Rasmussen, M.A. et al. The ISME Journal.

Neonatal Diet Alters Fecal Microbiota and Metabolome Profiles at Different Ages in Infants Fed Breast Milk or Formula. Brink, L.R. et al. American Journal of Clinical Nutrition.

Human Milk Fungi: Environmental Determinants and Inter-Kingdom Associations With Milk Bacteria in the CHILD Cohort Study. Moossavi, S. et al. BMC Microbiology.

Profiles of Human Milk Oligosaccharides and Their Relations to the Milk Microbiota of Breastfeeding Mothers in Dubai. Ayoub, C. et al. Nutrients.

Human Milk Microbiota Development During Lactation and Its Relation to Maternal Geographic Location and Gestational Hypertensive Status. Wan, Y. et al. Gut Microbes.

Skin Microbiome
Skin Microbiota Analysis-Inspired Development of Novel Anti-Infectives. Liu, Y. et al. Microbiome.

Review: Skin Microbiome Analysis for Forensic Human Identification: What Do We Know So Far? Tozzo, P. et al. Microorganisms.

Review: Protecting the Outside: Biological Tools to Manipulate the Skin Microbiota. O’Sullivan, J.N. et al. FEMS Microbiology and Ecology.

Vaginal Microbiome
Recovery of Vaginal Microbiota After Standard Treatment for Bacterial Vaginosis Infection: An Observational Study. Lehtoranta, L. et al. Microorganisms.

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure. Fu, M. et al. mBio.

Gut Microbiome
Alterations of the Gut Microbiota in Patients With COVID-19 or H1N1 Influenza. Gu, S. et al. Clinical Infectious Diseases.

Alterations in the Gut Microbiome and Suppression of Histone Deacetylases by Resveratrol Are Associated with Attenuation of Colonic Inflammation and Protection Against Colorectal Cancer. Alrafas, H.R. et al. Journal of Clinical Medicine.

Long-term Dietary Intervention Reveals Resilience of the Gut Microbiota Despite Changes in Diet and Weight. Fragiadakis, G.K. et al. American Journal of Clinical Nutrition.

Oral Microbiome
Intraoral Microbial Metabolism and Association With Host Taste Perception. Gardner, A. et al. Journal of Dental Research.

Animal Experiments
Combined Prebiotic and Microbial Intervention Improves Oral Cholera Vaccination Responses in a Mouse Model of Childhood Undernutrition. Di Luccia, B. et al. Cell Host & Microbe.

Commensal Bacteria Modulate Immunoglobulin A Binding in Response to Host Nutrition. Huus, K.E. et al. Cell Host & Microbe.

The interplay between the gut microbiota and NLRP3 activation affects the severity of acute pancreatitis in mice. Xueyang, L. et al. Gut Microbes.

Structural and functional changes of gut microbiota in ovariectomized rats and their correlations with altered bone mass. Ma, S. et al. Aging (Albany NY).

Animal Microbiome
Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control. Tan, S.C. et al. Scientific Reports.

Staphylococcus nepalensis, a Commensal of the Oral Microbiota of Domestic Cats, Is a Reservoir of Transferrable Antimicrobial Resistance. Andrade-Oliveira, A.L. et al. Microbiology.

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function. Pi, Y. mSystems.

The Microbial Biogeography of the Gastrointestinal Tract of Preterm and Term Lambs. Chong, C.Y.L. et al. Scientific Reports.

Microbial Ecology of Atlantic Salmon (Salmo Salar) Hatcheries: Impacts of the Built Environment on Fish Mucosal Microbiota. Minich, J.J. et al. Applied and Environmental Microbiology.

Dysbiosis in the Gut Microbiota of Soil Fauna Explains the Toxicity of Tire Tread Particles. Ding, J. et al. Environmental Science and Technology.

Insect Microbiome
Dietary Adaptation of Microbiota in Drosophila Requires NF-κB-Dependent Control of the Translational Regulator 4E-BP. Vandehoef, C. et al. Cell Reports.

Responses of soil and earthworm gut bacterial communities to heavy metal contamination. Liu, P. et al. Environmental Pollution.

Effect of Life Stage and Pesticide Exposure on the Gut Microbiota of Aedes Albopictus and Culex Pipiens L. Juma, E.O. et al. Scientific Reports.

Caterpillar Gut and Host Plant Phylloplane Mycobiomes Differ: A New Perspective on Fungal Involvement in Insect Guts. Višňovská, D. et al. FEMS Microbiology Ecology.

Plant, Root, and Soil Microbiome
The Response of Soil and Phyllosphere Microbial Communities to Repeated Application of the Fungicide Iprodione: Accelerated Biodegradation or Toxicity? Katsoula, A. et al. FEMS Microbiology Ecology.

Host Genotype Explains Rhizospheric Microbial Community Composition: The Case of Wild Cotton Metapopulations (Gossypium Hirsutum L.) in Mexico. Hernández-Terán, A. et al. FEMS Microbiology Ecology.

Review: Microbiome Approaches Provide the Key to Biologically Control Postharvest Pathogens and Storability of Fruits and Vegetables. Kusstatscher, P. et al FEMS Microbiology and Ecology.

Review: The Plant Microbiome: From Ecology to Reductionism and Beyond. Fitzpatrick, C.R. et al. Annual Review of Microbiology.

Water Microbiome
Persistence of Wastewater Antibiotic Resistant Bacteria and Their Genes in Human Fecal Material. Scaccia, N. et al. FEMS Microbiolgy Ecology.

Review: Microorganisms Populating the Water-Related Indoor Biome. Babič, M.N. et al. Applied Microbiology and Biotechnology.

Phage
Introducing Lu-1, a Novel Lactobacillus Jensenii Phage Abundant in the Urogenital Tract. Miller-Ensminger, T. et al. PLoS ONE.

Review: Bacteriophage-mediated Manipulation of the Gut Microbiome – Promises and Presents Limitations. Rasmussen, T.S. et al. FEMS Microbiology Reviews.

Bioinformatics
gutMEGA: A Database of the Human Gut MEtaGenome Atlas. Zhang, Q. et al. Briefings in Bioinformatics.

Techniques
Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing. Song, L. and Xie, K. Microbiome.

Optimization and Standardization of the Culturomics Technique for Human Microbiome Exploration. Diakite, A. et al. Scientific Reports

Direct detection of mRNA expression in microbial cells by fluorescence in situ hybridization using RNase H-assisted rolling circle amplification. Takahashi, H. et al. Scientific Reports.

June 6, 2020

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 3, 2020

Today’s post covers articles on role of microbiome in sepsis, early life microbiota related to cystic fibrosis and respiratory syncitial virus disease, promise and challenge with cancer microbiome, effect of probiotics on intestinal homeostasis after chemotherapy and many more!

General microbiome

Predictive biology: modelling, understanding and harnessing microbial complexity – Allison J. Lopatkin – Nature Reviews Microbiology

The Gut Microbiome’s Role in the Development, Maintenance, and Outcomes of Sepsis – Max W Adelman – Critical Care

The Promise and Challenge of Cancer Microbiome Research – Sumeed Syed Manzoor – Genome Biology

Antidiabetic Effects of Flavan-3-ols and Their Microbial Metabolites – Estefanía Márquez Campos – Nutrients

Human microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome – Roie Levy – PNAS

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale – Soumaya Zlitni – Genome Medicine

Comparative Assessment of Faecal Microbial Composition and Metabonome of Swine, Farmers and Human Control – Shiang Chiet Tan – Scientific Reports

Matching Between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance After Fecal Microbiota Transplantation – Koki Okahara – Journal of Clinical Medicine

Preganancy and early life

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure – Min Fu – mBio

Development of the Gut Microbiota in Early Life: The Impact of Cystic Fibrosis and Antibiotic Treatment – Maartje Kristensen – Journal of Cystic Fibrosis

Altered Gut Microbiota in Infants Is Associated With Respiratory Syncytial Virus Disease Severity – Jeffrey N Harding – BMC Microbiology

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth – M A Rasmussen – Isme Journal

Animal experiments

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system – R. A. Dowden – Scientific Reports

Repetitive, Mild Traumatic Brain Injury Results in a Progressive White Matter Pathology, Cognitive Deterioration, and a Transient Gut Microbiota Dysbiosis – Mariana Angoa-Pérez – Scientific Reports

Association of Gut Microbiota Composition and Function With an Aged Rat Model of Senile Osteoporosis Using 16S rRNA and Metagenomic Sequencing Analysis – Sicong Ma – Aging

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function – Yu Pi – mSystems

Plant, root and soil microbiome

Using Soil Bacterial Communities to Predict Physico-Chemical Variables and Soil Quality – Syrie M Hermans – Microbiome

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages – Corinne Biderre-Petit – Fems Microbial Ecology

Water microbiome

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation – Zaisheng Yan – Environmental Microbiology

Functional foods

Effect of Probiotics on the Maintenance of Intestinal Homeostasis After Chemotherapy: Systematic Review and Meta-Analysis of Pre-Clinical Studies – W G Lima – Beneficial Microbes

Non microbiology picks

Racial Disparities in Knowledge, Attitudes and Practices Related to COVID-19 in the USA– Wilson M Alobuia – Journal of Public Health

Ozone Treatment for Elimination of Bacteria and SARS-CoV-2 for Medical Environments – Craig Westover – BioRxiv

May 27, 2020

Good morning everybody. It was a bit calm during the last days. Today’s Microbiome Digest tries to give a nice summary of a broad range of latest microbiome related research. Enjoy it!

General microbiome

A microbiological survey of handwashing sinks in the hospital built environment reveals differences in patient room and healthcare personnel sinks – Franco et al – Scientific Reports

Multi-site human microbiome

REVIEW: Interaction between microbiota and immunity in health and disease – Zheng, Liwinski and Elinav – Cell Research

REVIEW: A Comprehensive Review on Natural Bioactive Compounds and Probiotics as Potential Therapeutics in Food Allergy Treatment – Pratap et al. – Front. Immunol.

Editorial: The intestinal microbiota in health and disease – Day, Keenan and Tannock – Journal of the Royal Society of New Zealand

Human oral microbiome

Longitudinal Study of Oral Microbiome Variation in Twins – Freire et al. – Scientific Reports

Human skin microbiome

Skin Microbiome in Atopic Dermatitis – Edslev, Agner and Andersen – Acta Dermato-venereologica

Human gut microbiome and virome

Preprint: Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation – Sims et al. – medRxiv

The intestinal virome in children with cystic fibrosis differs from healthy controls – Coffey et al. – PLOS One

The human gut microbiota and depression: widely reviewed, yet poorly understood – Simpson, Schwartz and Simmons – Journal of Affective Disorders

The Firmicutes/Bacteroidetes Ratio: A Relevant Marker of Gut Dysbiosis in Obese Patients? – Magne et al. – Nutrients

Book Chapter: Who Inhabits Our Gut? Introducing the Human Gut Microbiota – Flint – Why Gut Microbes Matter

Book Chapter: Variability and Stability of the Human Gut Microbiome – Flint – Why Gut Microbes Matter

Book Chapter: How to Analyse Microbial Communities? – Flint – Why Gut Microbes Matter

Book Chapter: Treating the Gut Microbiome as a System – Flint – Why Gut Microbes Matter

Metabolomics

REVIEW: Application of metabolomics to the study of irritable bowel syndrome – Bennet et al. – Neurogastroenterology & Motility

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

Distinct actions of the fermented beverage kefir on host behaviour, immunity and microbiome gut-brain modules in the mouse – van de Wouw et al. – Microbiology

Preprint: Physical activity shapes the intestinal microbiome and immunity of healthy mice but has no protective effects against colitis in MUC2-/- mice – Estaki et al. – bioRxiv

Synergetic responses of intestinal microbiota and epithelium to dietary inulin supplementation in pigs – He et al. – European Journal of Nutrition

Animal microbiome (for animals in the wild)

No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus) – Scheelings et al. – Scientific Reports

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea – Ma et al. – The ISME Journal

Plant, root, and soil microbiome

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts – Zolti et al. – Microbiology

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

16S rRNA Gene Diversity in the Salt Crust of Salar de Uyuni, Bolivia, the World’s Largest Salt Flat – Pecher et al. – Microbiol Resour Announc

Built environment (subways, indoor surfaces)

Fungal diversity and its contribution to the biodeterioration of mural paintings in two 1700-year-old tombs of China – Ma et al. – International Biodeterioration & Biodegradation

Characterizing Microbial Signatures on Sculptures and Paintings of Similar Provenance – Torralba et al. – Microbial Ecology

Food microbiology

Proteomic and Metabolomic Correlates of Healthy Dietary Patterns: The Framingham Heart Study – Walker et al. – Nutrients

Bioinformatics/Resources

ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining – Mungan et al. – Nucleic Acid Research

Draft Genome Sequence of a Novel Species of Halococcus (Strain IIIV-5B), an Endophytic Archaeon Isolated from the Leaf Tissue of Avicennia germinans – Zayas-Rivera et al. – Microbiol Resour Announc

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 – Asnicar et al. – Nature Communications

May 22, 2020

We’ve got a decently sized digest today with a lot of environmental microbe papers, including descriptions of novel species. There is also the Cell paper (highlighted) from Peter Turnbaugh’s group on ketogenic diets and the gut microbiome, which has been getting a lot of press. For new bioinformatic and other techniques, we have a new R package to predict functional profiles in Tax4Fun2, an assessment of phylogenetic rooting methods for bacteria, and a description of fiber intervention used in undergraduate classes for active learning.

 Have a great weekend!

Events

Today is the last day of the Virtual Microbiome Summit.

Pregnancy and early life

Women’s multisite microbial modulation during pregnancy – Luiz G. Sparvoli – Microbial Pathogenesis

Multi-site human microbiome

Review: Bi-Directional Interactions Between Microbiota and Ionizing Radiation in Head and Neck and Pelvic Radiotherapy-Clinical Relevance – Nidhya Teresa Joseph – International Journal of Radiation Biology

Human oral microbiome

Defining the oral microbiome by whole-genome sequencing and resistome analysis: the complexity of the healthy picture – Elisabetta Caselli – BMC Microbiology

Human gut microbiome

Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells – Qi Yan Ang – Cell

Preprint: Host genetic and environmental factors shape the human gut resistome – Caroline I. Le Roy – bioRxiv

MinION Sequencing of colorectal cancer tumour microbiomes—A comparison with amplicon-based and RNA-Sequencing – William S. Taylor – PLOS One (Originally posted to the Digest as a pre-print, now published)

Animal experiments

Broilers divergently selected for digestibility differ for their digestive microbial ecosystems – Marion Borey – PLOS One

Dietary Isomalto/Malto‐Polysaccharides Increase Fecal Bulk and Microbial Fermentation in Mice – Rima H. Mistry – Molecular Nutrition and Food Research

Longitudinal Effects of Dietary Oxidized Lipids on the Gut Microbiome and Mycobiome in Pigs – Folagbayi Arowolo – FASEB Journal

Animal microbiome

Single-cell amplicon sequencing reveals community structures and transmission trends of protist-associated bacteria in a termite host – Michael E. Stephens – PLOS One

Plant, root, and soil microbiome

Xylella fastidiosa subsp. pauca and olive produced lipids moderate the switch adhesive versus non-adhesive state and viceversa – Valeria Scala – PLOS One

Mitochondrial genome sequence of Phytophthora sansomeana and comparative analysis of Phytophthora mitochondrial genomes – Guohong Cai – PLOS One

nirS-type denitrifying bacterial communities in relation to soil physicochemical conditions and soil depths of two montane riparian meadows in North China. – Xiaoli Han – Environmental Science and Pollution Research

Tissue-Specific Dynamics in the Endophytic Bacterial Communities in Arctic Pioneer Plant Oxyria digyna – Cindy Given – Frontiers in Plant Science

Effects of Cultured Root and Soil Microbial Communities on the Disease of Nicotiana tabacum Caused by Phytophthora nicotianae – Tianbo Liu – Frontiers in Microbiology

Novel putative rhizobial species with different symbiovars nodulate Lotus creticus and their differential preference to distinctive soil properties – M Rejili – FEMS Microbiology Letters

Water, air, and extremophile microbiome

The microbiome of alpine snow algae shows a specific inter-kingdom connectivity and algae-bacteria interactions with supportive capacities – Lisa Krug – ISME Journal

Variation of near surface atmosphere microbial communities at an urban and a suburban site in Philadelphia, PA, USA – JD Stewart – Science of the Total Environment

Pilot-scale petroleum refinery wastewaters treatment systems: performance and microbial communities’ analysis – Fatma Karray – Process Safety and Environmental Protection

Adverse effects of levofloxacin and oxytetracycline on aquatic microbial communities – Zhigao Zhou – Science of the Total Environment

Application of microbial network analysis to discriminate environmental heterogeneity in Fildes Peninsula, Antarctica – Qian Liu – Marine Pollution Bulletin

Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium – HS Tee – ISME Journal

Metabolic diversity and co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L. Grettenberger – BMC Microbiology

Halocatena pleomorpha gen. nov. sp. nov., an extremely halophilic archaeon of family Halobacteriaceae isolated from saltpan soil – Ashish Verma – IJSEM

Unveiling Cultivable and Uncultivable Halophilic Bacteria Inhabiting Marakkanam Saltpan, India and Their Potential for Biotechnological Applications – Jojy John – Geomicrobiology Journal

Flavobacterium profundi sp. nov., isolated from a deep-sea seamount – Qian Wang – IJSEM

Food microbiology

Molecular epidemiology, genetic diversity and antimicrobial resistance of Staphylococcus aureus isolated from chicken and pig carcasses, and carcass handlers – Onyinye J. Okorie-Kanu – PLOS One

Traditional milk transformation schemes in Côte d’Ivoire and their impact on the prevalence of Streptococcus bovis complex bacteria in dairy products – Aimé R Sanhoun – PLOS One

Comparison of Microbial Communities and Amino Acid Metabolites in Different Traditional Fermentation Starters Used during the Fermentation of Hong Qu Glutinous Rice Wine – Zhang-Cheng Liang – Food Research International

Preprint: Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Kristen L. Beck – bioRxiv

Viruses

Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? – Ping Liu – PLOS Pathogens

Vector competence of Aedes aegypti from New Caledonia for the four recent circulating dengue virus serotypes – Olivia O’Connor – PLOS Neglected Tropical Diseases

Bioinformatics

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences – Franziska Wemheuer – Environmental Microbiome

Techniques

Assessing the accuracy of phylogenetic rooting methods on prokaryotic gene families – Taylor Wade – PLOS One

Science education techniques: Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course – Julia Massimelli Sewall – Journal of Microbiology & Biology Education

Science and art

This photographer creates prints with algae.

Non-microbiology picks:

Herd of fuzzy green “glacier mice” baffles scientists.

May 17, 2020

Hello from the Sonoran Desert! It is a sunny Sunday over Tucson, Az! I find that Sundays are the best to explore new ideas and concepts, and I especially love to take the time to read a good opinion piece or parse few review papers. In today’s digest, you’ll find a fascinating review on the Tara Ocean expedition and how it changed our understanding of marine microbial communities. If you’re more interested in the human-associated microbiome, fear not! There is also great pieces on the gut microbiota in athletes and on the interaction of oral and lung microbiome in the context of lung diseases.

If like me, you are a computational biologist thinking about microbiome data all day, you should enjoy reading today’s non microbiology pick, a great perspective paper discussing the FAIR (Findable, Accessible, Interoperable and Reusable) data principle and what are the current hurdles that limit open data reuse.

Have a great Sunday!


Pregnancy and early life

Review: The impact of maternal and early life malnutrition on health: a diet-microbe perspective – Andrew J. Forgie et al. – BMC Medicine

Multi-site human microbiome

Perspective: Microbial Diagnostics for Cancer: A Step Forward but Not Prime Time Yet –  Cynthia L. Sears et al. – Cancer Cell

Human respiratory microbiome

Review: Oral-lung microbiome interactions in lung diseases –  Manoj J. Mammen et al. – Periodontology

Human gut microbiome

Review: The athletic gut microbiota – Alex E. Mohr et al. – Journal of the International Society of Sports Nutrition

Colorectal cancer occurrence and treatment based on changes in intestinal flora – Huifang Si et al. –  Seminars in cancer Biology


Animal experiments 

Microbial communities modulating brain functioning and behaviors in zebrafish: A mechanistic approach – Larica Mohanta et al. –  Microbial Pathogenesis

Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance – Ming-Yuan Xue et al. – Microbiome

Preprint: Rumen protozoa shape microbiome composition and metabolic output of fermentation – Ronnie Solomon et al. – bioRxiv

Animal microbiome (for animals in the wild)

Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development – Zhongwei Yin et al. – Microbiology

After the bite: bacterial transmission from grey seals (Halichoerus grypus) to harbour porpoises (Phocoena phocoena) – Maarten J. Gilbert et al. – Royal Society open science

Exploration of the virome of the European brown shrimp (Crangon crangon) – Benigna Van Eynde et al. – Journal of General Virology

Plant, root, and soil microbiome

Opinion: The Role of Rhizosphere Bacteriophages in Plant Health – Akbar Adjie Pratama et al. – Trends in Microbiology

Analyzing bacterial community in pit mud of Yibin Baijiu in China using high throughput sequencing –  Li Chen et al. – PeerJ

Shifts of bacterial community structure and function in long-term soybean monoculture – Fengjuan Pan et al. – Archives of Agronomy and Soil Science

Bacterial Diversity in Peat Soils of Forest Ecosystems and Oil Palm Plantation – N. A. Kusai et al. – Soil Biology

Space Is More Important than Season when Shaping Soil Microbial Communities at a Large Spatial Scale – Kaoping Zhang et al. – mSystems

Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil – Lateef B. Salam et al. – Bioresources and Bioprocessing

Competition for iron drives phytopathogen control by natural rhizosphere microbiomes – Shaohua Gu et al. – Nature Microbiology

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

Review: Tara Oceans: towards global ocean ecosystems biology – Shinichi Sunagawa et al. – Nature Reviews Microbiology

Review: Microbial genomics amidst the Arctic crisis – Arwyn Edwards et al. – Microbial genomics

Exceptional but vulnerable microbial diversity in coral reef animal surface microbiomes – Marlène Chiarello et al. – Proceedings of the royal society biological sciences


Bioinformatics

A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals – Hyunwook Koh et al. – Microbiome

Review: A practical guide to amplicon and metagenomic analysis of microbiome data – Yong-Xin Liu et al. – Protein Cell

TAMA: improved metagenomic sequence classification through meta-analysis – Mikang Sim et al. – BMC Bioinformatics

nf-rnaSeqMetagen: A nextflow metagenomics pipeline for identifying and characterizing microbial sequences from RNA-seq data – Phelelani T. Mpangase et al. – Medicine in Microecology


My non-microbiology pick

Perspective: FAIR Data Sharing: The Roles of Common Data Elements and Harmonization – R.D.Kush et al. – Journal of Biomedical Informatics

May 5, 2020

Events

The Virtual Microbiome Summit – May 19-22, 2020

Multi-site human microbiome

Comparison of microbiomes in ulcerative and normal mucosa of recurrent aphthous stomatitis (RAS)-affected patients – Yang et al. – BMC Oral Health

Human gut microbiome

Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile – Arnoriaga-Rodríguez et al. – Microbiome

Preprint: Antibiotics may influence gut microbiome signaling to the brain in preterm neonates – Russell et al. – bioRxiv

Animal experiments

Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts – Cortés et al. – Microbiome

Techniques

Preprint: A study’s got to know its limitations – Gooch et al. – bioRxiv

May 1, 2020

Greetings from Durham, NC!

Hope everyone is doing well and staying healthy. Today’s digest includes several host-microbiome studies, environmental microbiome studies, and an intriguing EurekAlert news article.
In this light digest of today, I wanted to highlight a cool review about correlation of the oral microbiome with children’s health and a very interesting article on cell wall architecture of the gram-positive bacteria.
COVID-19 pandemic has opened a sort of Pandora’s box filled with great science along with pseudoscience. So, the digest has these two great articles from Nature: one about chloroquine and other about the race for coronavirus vaccines.
Staying at home is difficult for everyone, here is a fun activity to do: coloring space microbes book.

Stay Safe and entertained at home!!!!

COVID-19 news articles

The race for coronavirus vaccines: a graphical guide – Callaway – Nature

Chloroquine hype is derailing the search for coronavirus treatments – Ledford – Nature

General microbiome
*The architecture of the Gram-positive bacterial cell wall– Pasquina-Lemonche et al. – Nature

Pregnancy and early life
Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery – Hernandez et al. – Scientific Reports

Metabolic Effects of Bovine Milk Oligosaccharides on Selected Commensals of the Infant Microbiome—Commensalism and Postbiotic Effects – Jakobsen et al. – Metabolites

Multi-site human microbiome
*Review: Oral microbiome: possible harbinger for children’s health – Xiao et al. – Nature International Journal of Oral Science

Animal microbiome
Links between the rumen microbiota, methane emissions and feed efficiency of finishing steers offered dietary lipid and nitrate supplementation – Bowen et al. – PLOS ONE

Plant, root, and soil microbiome
Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean – Han et al. – The ISME Journal

Water and extremophile microbiome
Review: Exopolysaccharides from marine bacteria: production, recovery and applications – Dave et al. – Environmental Sustainability

Stromatolitic digitate sinters form under wide‐ranging physicochemical conditions with diverse hot spring microbial communities – Sriaporn et al. – gebiology

Built environment
Comparative analysis of bacterial community and functional species in oil reservoirs with different in situ temperatures – Tian et al. – International Microbiology

Bioinformatics
Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions – Medlock et al. – PLOS Computational Biology

Review: The National Microbiome Data Collaborative: enabling microbiome science – Wood-Charlson et al. – Nature Reviews Microbiology

Probiotics / prebiotics
Lactobacillus plantarum NA136 ameliorates nonalcoholic fatty liver disease by modulating gut microbiota, improving intestinal barrier integrity, and attenuating inflammation – Zhao et al. -Applied Microbiology and Biotechnology

Microbes in the news
Scientists explore links between genetics, gut microbiome and memory – DOE/PACIFIC NORTHWEST NATIONAL LABORATORY