Category Archives: Animal experiments

August 16, 2020

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Today’s quite diverse digest features: a study on antimicrobial resistance in the drinking water microbiome in disinfected and disinfection-free drinking water systems, how Antarctic soil microorganisms stay energised and hydrated, and several awesome webinars and podcasts. Happy reading/listening!

General microbiome

Development of Microbiome Biobanks – Challenges and Opportunities – M.J. Ryan – Trends in Microbiology

Review: STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies – Tehmina Bharucha – The Lancet Infectious Diseases

Theme issue: The role of the microbiome in host evolution – compiled and edited by Oren Kolodny, Benjamin J. Callahan and Angela E. Douglas – Philosophical Transactions of the Royal Society B: Biological Sciences

Selected papers:
Review: Microbiota–host interactions shape ageing dynamics – Miriam Popkes and Dario Riccardo Valenzano – Philosophical Transactions of the Royal Society B: Biological Sciences

Opinion: Pathogen resistance may be the principal evolutionary advantage provided by the microbiome – Michael R. McLaren and Benjamin J. Callahan – Philosophical Transactions of the Royal Society B: Biological Sciences

Gut microbiome

A Randomized Clinical Trial of Fecal Microbiota Transplant for Alcohol Use Disorder – Jasmohan S Bajaj – Hepatology

Urogenital microbiome

Comparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality – Catherine Putonti – mSphere

Vaginal Estrogen Therapy Is Associated with Increased Lactobacillus in the Urine of Post-Menopausal Women with OAB Symptoms – Dr. Krystal Thomas-White – American Journal of Obstetrics and Gynecology

Vaginal microbiome

Vaginal microbiota, genital inflammation, and neoplasia impact immune checkpoint protein profiles in the cervicovaginal microenvironment – Paweł Łaniewski –npj Precision Oncology

Lateral Gene Transfer Shapes Diversity of Gardnerella spp. – Lindsey L. Bohr – Frontiers in Cellular and Infection Microbiology

Variation of the vaginal microbiome during and after pregnancy in Chinese women – Xiaoai Zhang – medRxiv

Review: Diversity of Vaginal Microbiome in Pregnancy: Deciphering the Obscurity – Parakriti Gupta – Frontiers in Public Health

Pregnancy and early life

Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota – Rémi Gschwind – PlosOne

Respiratory microbiome

A Novel Description of the Human Sinus Archaeome During Health and Chronic Rhinosinusitis – Brett Wagner Mackenzie – Frontiers in Cellular and Infection Microbiology

Animal microbiome

Temporal changes in the gut microbiota in farmed Atlantic cod (Gadus morhua) outweigh the response to diet supplementation with macroalgae – Ciara Keating – bioRxiv

Broiler Chickens and Early Life Programming: Microbiome transplant-induced cecal bacteriome dynamics and phenotypic effects – Gustavo A. Ramírez – bioRxiv

Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits – Thea Os Andersen – Methods

Fast and Slow-Growing Management Systems: Characterisation of Broiler Caecal Microbiota Development throughout the Growing Period – Laura Montoro-Dasi – animals

Animal experiment

Mucosal or systemic microbiota exposures shape the B cell repertoire – Hai Li – Nature

The immune system fails to mount a protective response to Gram-positive or Gram-negative bacterial prostatitis – Federico Lupo – bioRxiv

Oncogenic Gene Fusions in Non-Neoplastic Precursors as Evidence that Bacterial Infection Initiates Prostate Cancer – Eva Shrestha – bioRxiv

Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy – Lukas F. Mager – Science

Lung and gut microbiota are altered by hyperoxia and contribute to oxygen-induced lung injury in mice – Shanna L. Ashley – Science Translational Medicine

Plant/root/soil microbiome

*A genome compendium reveals diverse metabolic adaptations of Antarctic soil microorganisms – Maximiliano Ortiz – bioRxiv

Healthy soils for healthy plants for healthy humans – Heribert Hirt – EMBO reports

The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer – James P. J. Hall – Frontiers in Microbiology

Review: Plant–microbiome interactions: from community assembly to plant health – Pankaj Trivedi – Nature Reviews Microbiology

Water microbiome

*Differential prevalence and host-association of antimicrobial resistance traits in disinfected and non-disinfected drinking water systems – Maria Sevillano – Science of The Total Environment

MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge – Marta Nierychlo – Water Research

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in two sequential rapid sand filters – Lianna Poghosyan – Water Research

Shotgun metagenomics of indigenous bacteria collected from the banks of the San Jacinto River for biodegradation of aromatic waste – Rupa Iyer and Ashish Damania – FEMS Microbiology Letters

Viruses and phages

Viruses in wastewater: occurrence, abundance and detection methods – Mary Vermi Aizza Corpuz – Science of The Total Environment

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities – Christian Santos-Medellin – bioRxiv

Techniques

Correlative Light Electron Ion Microscopy reveal in vivo localisation of bedaquiline in Mycobacterium tuberculosis infected lungs – Antony Fearns – bioRxiv

Label-free smartphone quantitation of bacteria by darkfield imaging of light scattering in fluoropolymer micro capillary film allows portable detection of bacteriophage lysis – Sultan İlayda Dönmez – Sensors and Actuators B: Chemical

Bioinformatics

Raven: a de novo genome assembler for long reads – Robert Vaser and Mile Sikic – bioRxiv

SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis – Stevenn Volant – BMC Bioinformatics

Rapid discovery of novel prophages using biological feature engineering and machine learning – Kimmo Sirén – bioRxiv

Critical Relevance of Stochastic Effects on Low-Bacterial Biomass 16S rRNA Gene Analysis – John R. Erb-Downward – mBio

On the complexity of haplotyping a microbial community – Samuel M Nicholls – bioRxiv

Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system – Will A. Overholt – Environmental Microbiology

Webinar

Microbiome, machine learning and network models – Amy Willis and Ben Bloem-Reddy – Northwest Data Science Seminar Series

The Gut Brain Axis across the Life Span – John Cryan – iScience webinar

Pushing the Envelope: Remodeling the Gram-negative Outer Membrane – M. Stephen Trent – SG BUG (Singapore Bacterial Ultra Group) seminar series

Podcast

Getting to Know Your Friendly Neighbourhood Microbiologist – Lucie Semenec and Amy Cain – The Joint Academic Microbiology Seminars podcast

Does not compute – Sanjay Srivastava, Alexa Tullett, and Simine Vazire – The Black Goat podcast

August 14, 2020

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Good morning from Massachusetts! Dr. Elisabeth Bik will be giving a Zoom talk today on research misconduct in biomedical research. You can register at the link under events. Fittingly, today’s digest includes a preprint on the effects of retraction after misconduct on citations. Other highlights today include an entire theme issue on the microbiome and host evolution and a paper on phylogenomic analyses of archaea attempting to elucidate the DPANN lineage. In early life, the placental microbiome debate rages on with a paper demonstrating evidence for contamination rather than an actual placental microbiome. Finally, I have highlighted a paper studying whether soil archives can give us a glimpse into soil microbial communities of the past.

Have a great weekend!

Events

Dr. Bik is discussing “The Dark Side of Science: Misconduct in Biomedical Research” today at 12PM EDT! Register here.

General microbiome

Theme Issue: The role of the microbiome in host evolution – Philosophical Transactions of the Royal Society B

Pregnancy and early life

Evidence for contamination as the origin for bacteria found in human placenta rather than a microbiota – Rémi Gschwind – PloS One

Human milk microbiome

SARS-CoV-2 in human milk is inactivated by Holder pasteurization but not cold storage – Gregory J. Walker – Journal of Paediatrics and Child Health

Human oral microbiome

Review: Oral microbiome geography: Micron-scale habitat and niche – Jessica L. Mark Welch – Cell Host & Microbe

Human gut microbiome

Epidemiology and associated microbiota changes in deployed military personnel at high risk of traveler’s diarrhea – William A. Walters – PloS One

Animal experiments

Differential alteration in gut microbiome profiles during acquisition, extinction, and reinstatement of morphine-induced CPP – Jianbo Zhang – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Modulation of the intestinal microbiota of broilers supplemented with monensin or functional oils in response to challenge by Eimeria spp. – Alexandre Maciel Vieira – PloS One

Herpes simplex virus infection, Acyclovir and IVIG treatment all independently cause gut dysbiosis – Chandran Ramakrishna – PloS One

Animal microbiome

Raw milk and fecal microbiota of commercial Alpine dairy cows varies with herd, fat content and diet – Francesca Albonico – PloS One

Hydrolytic bacteria associated with natural helminth infection in the midgut of Red Sea marbled spinefoot rabbit fish Siganus rivulatus – Ghada Abd-Elmonsef Mahmoud – Microbial Pathogenesis

Plant, root, and soil microbiome

Book: Agriculturally Important Fungi for Sustainable Agriculture Vol 2: Functional Annotation for Crop Protection – Eds. Ajar Nath Yadav et al. – Springer

Patient propagules: Do soil archives preserve the legacy of fungal and prokaryotic communities? – Gian Maria Niccolò Benucci – PloS One

Labile carbon limits late winter microbial activity near Arctic treeline – Patrick F. Sullivan – Nature Communications

Enhanced biodegradation of crude oil by constructed bacterial consortium comprising salt-tolerant petroleum degraders and biosurfactant producers – Weiwei Chen – International Biodeterioration & Biodegradation

Plant–archaea relationships: a potential means to improve crop production in arid and semi-arid regions – Elizabeth Temitope Alori – World Journal of Microbiology and Biotechnology

First report of Fusarium equiseti causing crown rot and damping-off on durum wheat in Algeria – Amor Bencheikh – Archives of Phytopathology and Plant Protection

Soil microbial diversity and composition: Links to soil texture and associated properties – Qing Xia – Soil Biology and Biochemistry

Water, air, and extremophile microbiome

Effects of different habitats on the bacterial community composition in the water and sediments of Lake Taihu, China – Wenjie Chang – Environmental Science and Pollution Research

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea – Shanshan Yang – Nature Communications

Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution – Nina Dombrowski – Nature Communications

Preprint: Occurrence, identification and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa – Fadare Temitope Folake — BioRxiv

Built environment

The microbiome of drinking water biofilters is influenced by environmental factors and engineering decisions but has little influence on the microbiome of the filtrate – Ben Ma – Environmental Science & Technology

In-situ remediation of acid mine drainage from abandoned coal mine by filed pilot-scale passive treatment system: Performance and response of microbial communities to low pH and elevated Fe – Haiyan Chen – Bioresource Technology

Bioinformatics and other techniques

De novo sequence assembly requires bioinformatic checking of chimeric sequences – Laila Sara Arroyo – PloS One

Review on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the rapid screening of microbial species: A promising bioanalytical tool – Suresh Kumar Kailasa – Microchemical Journal

Microbes in the News

Using the infant stool microbiome to predict NEC: New machine learning tool predicts devastating intestinal disease in premature infants – Science Daily

Science Publishing and Career

Preprint: Does retraction after misconduct have an impact on citations? A pre-post study – Cristina Candal-Pedreira – bioRxiv

August 13, 2020

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Today’s updates – microbiome connections in various disease cohorts such as gastric cancer, IBD, anorexia nervosa, obesity and diabetes; information on gut bacterial polyphosphates and o-glycanases and their role in host immunity and mucin breakdown; and new sequencing strategies to identify antibiotic-resistant genes. Happy reading!

General microbiome

Gut microbiota and COVID-19: A superfluous diagnostic biomarker or therapeutic target? – Emily Klann – Clinical Infectious Diseases

Engineered Live Biotherapeutics: Progress and Challenges – Yang Tan – Biotechnology Journal

Human microbiome

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity – Lianmin Chen – Nature Communications

Multi-omics data integration in anorexia nervosa patients before and after weight regain: A microbiome-metabolomics investigation – Alessio Maria Monteleone – Clinical Nutrition

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci – Bruno Cavadas – Microorganisms

Faecal microbiota signatures of IBD and their relation to diagnosis, disease phenotype, inflammation, treatment escalation and anti-TNF response in a European Multicentre Study (IBD-Character) – S. Vatn – Scandinavian Journal of Gastroenterology

A randomized crossover trial on the effect of plant-based compared with animal-based meat on trimethylamine-N-oxide and cardiovascular disease risk factors in generally healthy adults: Study With Appetizing Plantfood—Meat Eating Alternative Trial (SWAP-MEAT) – Anthony Crimarco – Americal Journal of Clinical Nutrition

Whole-blood transcriptome profiling reveals signatures of metformin and its therapeutic response – Monta Ustinova – PlosOne

Microbial Profile During Pericoronitis and Microbiota Shift After Treatment – Xiuling Huang – Frontiers in Microbiology

Animal experiments

Unraveling the camel rumen microbiome through metaculturomics approach for agriculture waste hydrolytic potential – Shweta Srivastava – Archives of Microbiology

Bacterial polyphosphates interfere with the innate host defense to infection – Julian Roewe – Nature Communications

Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown – Lucy I. Crouch – Nature Communications

Nostoc sphaeroids Kütz polysaccharide and powder enrich a core bacterial community on C57BL/6j mice – Meixia Li – International Journal of Biological Macromolecules

Maternal dietary omega-3 deficiency worsens the deleterious effects of prenatal inflammation on the gut-brain axis in the offspring across lifetime – Q. Leyrolle – Neuropsychopharmacology

Water microbiome

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community – Pratibha Panwar – Microbiome

Techniques

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

Metagenomic next-generation sequencing of rectal swabs for the surveillance of antimicrobial-resistant organisms on the Illumina Miseq and Oxford MinION platforms – Rebecca Yee – European Journal of Clinical Microbiology & Infectious Diseases

August 6, 2020

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Good morning from Minnesota! A broad selection of papers to share with you today: Immune responses in lung transplant patients, an examination of how hurricanes can alter the soil microbiome, and a cool preprint on host–microbe interactions in stickleback, plus 10 more—

Human respiratory microbiome

(Preprint) Nasal commensal, Staphylococcus epidermidis shapes the mucosal environment to prevent influenza virus invasion through Serpine1 induction, Ara Jo et al., bioRxiv

Cystic Fibrosis Lung Transplant Recipients Have Suppressed Airway Interferon Responses during Pseudomonas Infection, Daniel T. Dugger et al., Cell Reports Medicine

Human gut microbiome

The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients, Qianqian Zeng et al., Scientific Reports

Home, Sweet Home: How Mucus Accommodates our Microbiota, Benjamin X Wang et al., The FEBS Journal

Animal experiments

Preprint: Immune gene expression covaries with gut microbiome composition in stickleback, Lauren E Fuess et al., bioRxiv

Transient neonatal antibiotic exposure increases susceptibility to late-onset sepsis driven by microbiota-dependent suppression of type 3 innate lymphoid cells, Xinying Niu et al., Scientific Reports

Animal microbiome

Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire, Robert Pieper et al., The ISME Journal

Plant, root, and soil microbiome

Major changes in grapevine wood microbiota are associated with the onset of esca, a devastating trunk disease, Emilie Bruez et al., Environmental Microbiology

Increase in abundance and decrease in richness of soil microbes following Hurricane Otto in three primary forest types in the Northern Zone of Costa Rica, William D. Eaton et al., PLOS ONE

Water and extremophile microbiome

Planet Microbe: a platform for marine microbiology to discover and analyze interconnected ‘omics and environmental data, Alise J Ponsero et al., Nucleic Acids Research

Microbial communities can predict the ecological condition of headwater streams, Robert H. Hilderbrand et al., PLOS ONE

Bioinformatics

(Preprint) Snipe: Highly sensitive pathogen detection from metagenomic sequencing data, Lihong Huang et al., bioRxiv

Techniques

Impact of time and temperature on gut microbiota and SCFA composition in stool samples, Janet L. Cunningham et al., PLOS ONE

August 4, 2020

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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

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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

July 27, 2020

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Greetings from Pittsburgh!

Saturday and Sunday’s digests were packed full of great articles, which means the week is off to a slower start than usual. We’ve got two environmentally focused preprints that I am super excited about, a paper demonstrating how microbiota can be dosed in order to help mice mitigate intestinal cancer and inflammation, and a paper focused on the eco-thermodynamics of methanogenic bioprocesses. Enjoy!

Animal experiments

Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis – Zhang et al. – Microbiome

Water and extremophile microbiome

Preprint: Distinct microbial communities along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents – Somee et al. – BioRxiv

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses – Nobu et al. – Microbiome

Preprint: Freshwater monitoring by nanopore sequencing – Urban et al. – bioRxiv

July 25, 2020

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Good morning and happy Saturday y’all! Today’s digest is brief, but covers some fascinating papers including: small RNAs regulating gut microbe metabolism; epigenetics linking the early-life airway microbiota with allergic rhinitis; and the impact of gut microbial composition on vagal innervation. I’ve also included a non-microbiome pick discussing how to spot and resolve common statistical mistakes in research manuscripts. The authors of the article hope this will help improve robustness of scientific research. Happy reading!

Gut Microbiome
A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron. Ryan, D. et al. Nature Communications.

Depicting SARS-CoV-2 faecal viral activity in association with gut microbiota composition in patients with COVID-19. Zuo, T. et al. Gut.

High microbiota reactivity of adult human intestinal IgA requires somatic mutations. Kabbert, J. et al. Journal of Experimental Medicine.

A unified catalog of 204,938 reference genomes from the human gut microbiome. Almeida, A. et al. Nature Biotechnology.

Airway Microbiome
Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age. Morin, A. et al. Journal of Allergy and Clinical Immunology.

Early-Life Microbiome
Butyrate producing colonic Clostridiales metabolise human milk oligosaccharides and cross feed on mucin via conserved pathways. Pichler, M.J. et al. Nature Communications.

Animal Experiments
Bile acids drive the newborn’s gut microbiota maturation. van Best, N. et al. Nature Communications.

Gut microbiota composition modulates inflammation and structure of the vagal afferent pathway. Kim, J.S. et al. Physiology & Behavior.

TNFα regulates intestinal organoids from mice with both defined and conventional microbiota. Sun, L. et al. International Journal of Biological Macromolecules.

Water Microbiome
Nutrient and microbial water quality of the upper Ganga River, India: identification of pollution sources. Bowed, M.J. et al. Environmental Monitoring and Assessment.

Plant, Root, and Soil Microbiome
Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment. Aydogan, E.L. FEMS Microbiology and Ecology.

Non-Microbiome Pick
Science Forum: Ten common statistical mistakes to watch out for when writing or reviewing a manuscript. Makin, T.R. and Orban de Xivry, JJ. eLife.

July 23, 2020

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In today’s digest – duodenal microbiota linked to stunting in children, differential effects of germfree and antibiotic treated mouse models on social behavior, microbial metabolite receptor GPBAR and its interaction with bile acids, review article on engineering microbes to treat diseases and many more…happy reading!

General microbiome

The Microbiota-Gut-Immune-Glia (MGIG) Axis in Major Depression – Leszek Rudzki – Molecular Neurobiology

Engineering the gut microbiota to treat chronic diseases – Noura S. Dosoky – Applied Microbiology and Biotechnology

Human microbiome

Acute and chronic improvement in postprandial glucose metabolism by a diet resembling the traditional Mediterranean dietary pattern: Can SCFAs play a role? – Marilena Vitale – Clinical Nutrition

Linking the duodenal microbiota to stunting in a cohort of undernourished Bangladeshi children with enteropathy – Robert Y. Chen – New England Journal of Medicine

Enterobacterales Infection after Intestinal Dominance in Hospitalized Patients – Krishna Rao – mSphere

Differences in the gut Firmicutes to Bacteroidetes ratio across age groups in healthy Ukrainian population – Alexander Vaiserman – BMC Microbiology

Preprint- Association of gut microbiota with cerebral cortex and cerebrovascular abnormality in human mild traumatic brain injury – Lijun Bai – BioRxiv

Real-world study in infants fed an infant formula with two human milk oligosaccharides – Enriqueta Román – Nutricion Hospitalaria

Animal experiments

Gut microbiome composition differences among breeds impact feed efficiency in swine – Matteo Bergamaschi – Microbiome

Opposing effects of antibiotics and germ-free status on neuropeptide systems involved in social behaviour and pain regulation – Katerina V. A. Johnson – BMC Neuroscience

Local Necrotic Cells Trigger Systemic Immune Activation via Gut Microbiome Dysbiosis in Drosophila – Hina Kosakamoto – Cell Reports

Peanut skin extract ameliorates the symptoms of type 2 diabetes mellitus in mice by alleviating inflammation and maintaining gut microbiota homeostasis – Lan Xiang – Aging

Preprint- Community composition and development of the post-weaning piglet gut microbiome – D. Gaio – BioRxiv

Gut microbiota regulate tumor metastasis via circRNA/miRNA networks – Zhuxian Zhua – Gut Microbes

Porcine circovirus type 2 (PCV2) and Campylobacter infection induce diarrhea in piglets: Microbial dysbiosis and intestinal disorder – Gang Yang – Animal Nutrition

Plant, root and soil microbiome

Populations of the Parasitic Plant Phelipanche ramosa Influence Their Seed Microbiota – Sarah Huet – Frontiers in Plant Science

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat – Aymé Spor – Scientific Reports

Water microbiome

Preprint- Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs – A. Meziti – BioRxiv

Preprint- Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing – Kimothy L. Smith – BioRxiv

Phages and Viruses

Preprint- Targeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal Tract – Sabrina I. Green – BioRxiv

Techniques
Structural basis of GPBAR activation and bile acid recognition – Fan Yang – Nature

Microbes in News

Machine learning analysis reveals less diverse microbiome in children with type 1 diabetes – Healio

July 15, 2020

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There are several notable entries in today’s digest. Registration is open for the European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” virtual training course. The course is for European secondary school science teachers and is 5 weeks long. The 3rd Microbiome Movement will also be held this year, both virtually and in-person. Links are in the Events section.  

Today I’ve highlighted a bioinformatics paper on variant calling for cpn60 barcode sequencing and an early life paper on pre-term infant stem cell proliferation upregulated by microbial metabolites. While putting this digest together, I learned algae turns snow different colors! This is so cool to me that I’ve highlighted that paper as well. Finally, the News section includes an article for Smithsonian Magazine by Rob Dunn on quarantine’s effects on our microbial passengers.  

Happy reading!

Events

3rd Microbiome Movement – Animal Health & Nutrition Summit, taking place in North Carolina as well as digitally October 19-21, 2020.

European Learning Laboratory for the Life Sciences’ “Introducing Your Microbiome” November 2-December 7, 2020. Applications are due October 15 and the course is free.

Pregnancy and early life

Gut microbiota maturation during early human life induces enterocyte proliferation via microbial metabolites – Michael W. Dougherty – BMC Microbiology

Human gut microbiome

Perspective: Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology & Hepatology

Microbiome of death

Characterizing the postmortem human bone microbiome from surface-decomposed remains – Alexandra L. Emmons – PloS One

Animal experiments

Saccharomyces cerevisiae fermentation products (SCFP) stabilize the ruminal microbiota of lactating dairy cows during periods of a depressed rumen pH – Hein M. Tun – BMC Veterinary Research

Animal microbiome

A Shift Pattern of Bacterial Communities Across the Life Stages of the Citrus Red Mite, Panonychus citri – Zhen-yu Zhang – Frontiers in Microbiology

Plant, root, and soil microbiome

Nitrogen enrichment stimulates wetland plant responses whereas salt amendments alter sediment microbial communities and biogeochemical responses – Mary Donato – PloS One

Bioavailable metal (loid) s and physicochemical features co-mediating microbial communities at combined metal (loid) pollution sites – Jiawen Wang – Chemosphere

Assessing the effects of tylosin fermentation dregs as soil amendment on macrolide antibiotic resistance genes and microbial communities: Incubation study – Bo Zhang – Journal of Environmental Science and Health, Part B

Book: Phytobiomes: Current Insights and Future Vistas – Manoj Kumar Solanki – Springer

Early changes in bacterial communities in wound tissues of Pinus massoniana after inoculation with Bursaphelenchus xylophilus – Jinyan Liu – Nematology

Preprint: Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil – Alexa M. Nicolas – bioRxiv

Preprint: A Meta-analysis of the known Global Distribution and Host Range of the Ralstonia Species Complex – Tiffany Lowe-Power – bioRxiv

Water, air, and extremophile microbiome

Lipid Biomarker Record of the Serpentinite-Hosted Ecosystem of the Samail Ophiolite, Oman and Implications for the Search for Biosignatures on Mars – Sharon A Newman – Astrobiology

Metabolic acclimation of anammox consortia to decreased temperature – Tangran Huo – Environment International

Complete Genome Sequences of Two Marine Biofilm Isolates, Leisingera sp. nov. Strains 201A and 204H, Novel Representatives of the Roseobacter Group – Giselle S. Cavalcanti – Microbiology Resource Announcements

Microbial interspecific interaction and nitrogen metabolism pathway for the treatment of municipal wastewater by iron carbon based constructed wetland – Xiao Huang – Bioresource Technology

Biogeographical distribution of dissimilatory nitrate reduction to ammonium (DNRA) bacteria in wetland ecosystems around the world – Huawei Pan – Journal of Soils and Sediments

Molecular diversity of the microbial community in coloured snow from the Fildes Peninsula (King George Island, Maritime Antarctica) – Wei Luo – Polar Biology

Novel arsenic hyper-resistant bacteria from an extreme environment, Crven Dol mine, Allchar, North Macedonia – Vladimir Bermanec – Journal of Hazardous Materials

Built environment

Ozone treatment in a wind tunnel for the reduction of airborne viruses in swine buildings – Jonathan M. Vyskocil – Aerosol Science and Technology

Food microbiology

Correlation between microbial communities and key flavors during post-fermentation of Pixian broad bean paste – Ping Liu – Food Research International

Additives affect the distribution of metabolic profile, microbial communities and antibiotic resistance genes in high-moisture sweet corn kernel silage – Zhe Wu – Bioresource Technology

Shifts in autochthonous microbial diversity and volatile metabolites during the fermentation of chili pepper (Capsicum frutescens L.) – Xinxing Xu – Food Chemistry

Proteomic characterization of extracellular vesicles produced by several wine yeast species – Ana Mencher – Microbioal Biotechnology

Book Chapter: Role of Microbes for Attaining Enhanced Food Crop Production – Pankaj Sharma – Microbial Biotechnology: Basic Research and Applications

Bioinformatics

Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling – Sarah J. Vancuren – PloS One

Techniques

Preprint: Visualization of giant virus particles using BONCAT labeling and STED microscopy – Monica Berjon-Otero – bioRxiv

Microbes in the News

Human Microbiome: 39 trillion microbes and bacteria that call us home – Mun-Keat Looi – Science Focus

What Quarantine is Doing to Your Body’s Wondrous World of Bacteria – Rob Dunn – Smithsonian Magazine