Category Archives: Human gut

September 1, 2020

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Today’s post consists of review article on short chain fatty acids, research articles on efficacy of fecal microbiota transplant in patients with C. difficle infection and comorbities, identification of potential microbial biomarkers for preterm birth and a new technique to perform ultrafast microbial community analysis. Happy reading!

General microbiome

A systematic review of the effect of dietary pulses on microbial populations inhabiting the human gut – C.P.F. Marinangeli – Beneficial Microbes

Short chain fatty acids in human gut and metabolic health – E E Blaak – Beneficial Microbes

Human microbiome

The gut microbiome–derived metabolite trimethylamine N-oxide modulates neuroinflammation and cognitive function with aging – Vienna E. Brunt – Geroscience

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak – Microbiome

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Patients With Multiple Comorbidities: Long-Term Safety and Efficacy Results From a Tertiary Care Community Hospital – Charumathi Raghu Subramanian – Gastroenterology Research

Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection – Matthew Magruder – Gut Microbes

Leveraging sequence‐based faecal microbial community survey data to identify alterations in gut microbiota among patients with Parkinson’s disease – Tianyi Ji – European Journal of Neuroscience

Plasma enterobacterial ClpB levels and ClpB- and α-MSH–reactive immunoglobulins in lung cancer patients with and without anorexia – Alessio Molfino – Nutrition

Identification of Potential Biomarkers in the Cervicovaginal Fluid by Metabolic Profiling for Preterm Birth – AbuZar Ansari – Metabolites

Plant microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied and Environmental Microbiology

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth – Inga Tamošiūnė – Frontiers in Plant Science

Water microbiome

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu – Microbiome

Techniques

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Non-microbiology picks

Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study – Olivia V Swann – BMJ

August 28, 2020

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Greetings!

Today’s microbiome digest has something for everyone. We have several articles focused on the human microbiome, a few animal studies, and quite a few articles focused on environmental bacteria found in soil, water, and even a cave! I want to highlight one article focused on the impact of spatial proximity on territory among bacteria. Although the article specifically focuses on skin bacteria, it’s relevant to anyone studying microbial communities!

Enjoy!

General microbiome

Horizontal transmission and recombination maintain forever young bacterial symbiont genomes – Russel et al. – PLOS GENETICS

Human skin microbiome

Impact of spatial proximity on territoriality among human skin bacteria – Hernandez-Valdes et al. – npj BIofilms and Microbiomes

Human gut microbiome

Gut microbiota and dysbiosis in Alzheimer’s disease: Implications for pathogenesis and treatment – Liu et al. – Molecular Neurobiology

Animal experiments

Caecal microbiota compositions from 7-day-old chicks reared in high-performance and low-performance industrial farms and systematic culturomics to select strains with anti-Campylobacter activity – Duquenoy et al. – PLOS ONE

Effect of FHA and Prn on Bordetella pertussis colonization of mice is dependent on vaccine type and anatomical site – Zeddeman et al. – PLOS ONE

Animal microbiome

Lactobacilli and other gastrointestinal microbiota of Peromyscus leucopus, reservoir host for agents of Lyme disease and other zoonoses in North America – Milovic et al. – PLOS ONE

Plant, root, and soil microbiome

Simple kinetics, assay, and trends for soil microbial catalases – Chabot et al. – Analytical Biochemistry

Sustaining the growth of Pinaceae trees under nutrient-limited edaphic conditions via plant-beneficial bacteria – Puri et al. – PLOS ONE

Soil properties, bacterial and fungal community compositions and the key factors after 5-year continuous monocropping of three minor crops – Yang et al. – PLOS ONE

Water and extremophile microbiome

Oleaginous potential of indigenously isolated fresh water microalgae for biofuel production – Saraf & Dutt – International Journal of Sustainable Energy

Bacteria and archaea communities in Cerrado natural pond sediments – Silveira et al. – Microbiology of Aquatic Systems

The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea – Turrini et al. – Microbiological Research

On microbial community of Pyropia haitanensis by metagenomic analysis – Wang et al. – Journal of Oceanology and Limnology

August 21, 2020

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Events
HAPPENING TODAY: Microbiome sequencing in high-host and low biomass samples. August 21, 2020.

Webinar Series on the Gut-Brain Axis and the Microbiome
August 28, 2020 – September 25, 2020

Funding
Functional effects of the human gut microbiome on autism. Biocodex Microbiota Foundation

Human microbiome
Focus on Microbiome in Health and Disease – A special microbiome issue in Cell Host Microbe

REVIEW: The Impact of the Microbiome on Immunity to Vaccination in Humans. Sanne E. de Jong et al. Cell Host & Microbe.

REVIEW: The Gut Microbiota and Unhealthy Aging: Disentangling Cause from Consequence. Erica N. DeJong et al. Cell Host & Microbe.

Helminth coinfection and COVID-19: An alternate hypothesis. Russell Hays et al. PLoS Negleced Tropical Diseases.

Gut microbiome
REVIEW: Mitochondria, the gut microbiome and ROS. and ROS. J. William O.Ballard & Samuel G. Towarnicki. Cellular Signalling.

Stool Microbiome Profiling of Patients with Metastatic Renal Cell Carcinoma Receiving Anti–PD-1 Immune Checkpoint Inhibitors. Nicholas J. Salgia et al. European Urology.

Programing of an Intravascular Immune Firewall by the Gut Microbiota Protects against Pathogen Dissemination during Infection. Braedon McDonald et al. Cell Host & Microbe

Oral microbiome
Analysis of microbial changes in the tonsillar formalin-fixed paraffin-embedded tissue of Chinese patients with IgA nephropathy. Anchao Zhu. Pathology – Research and Practice

Early life microbiome
Breastmilk Feeding Practices Are Associated with the Co-Occurrence of Bacteria in Mothers’ Milk and the Infant Gut: the CHILD Cohort Study. Kelsey Fehr et al. Cell Host & Microbe.

Animal microbiome
Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows. Mae Berlow. Microbial Ecology

Built environment
Passenger-surface microbiome interactions in the subway of Mexico City. Daniela Vargas-Robles et al. PLoS One.

Plant, root, and soil microbiome
Plant resistance and leaf chemical characteristic jointly shape phyllosphere bacterial community. Tian Xueliang. World Journal of Microbiology and Biotechnology.

The role of land management and elevation in shaping soil microbial communities: Insights from the Central European Alps. Nadine Praega. Soil Biology and Biochemistry.

Composition, predicted functions, and co-occurrence networks of fungal and bacterial communities_ Links to soil organic carbon under long-term fertilization in a rice-wheat cropping system. Jie Chen. European Journal of Soil Biology

Diversity and structure of prokaryotic communities within organic and conventional farming systems in central highlands of Kenya. Edward Nderitu Karanja et al. PLoS One.

Water and wastewater
Turning harmful algal biomass to electricity by microbial fuel cell: A sustainable approach for waste management. Jafar Ali. Environmental Pollution.

Combining physicochemical properties and microbiome data to evaluate the water quality of South African drinking water production plants. Tawanda E. Maguvu et al. PLoS One.

Viruses
They are what you eat: Shaping of viral populations through nutrition and consequences for virulence. Rebekah Honce & Stacey Schultz-Cherry. PLoS Pathogens.

Bioinformatics
Assembly methods for nanopore-based metagenomic sequencing: a comparative study. Adriel Latorre-Pérez. Scientific Report.

Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools. Hooman Derakhshani et al. BMC Genomics.

Modeling microbial cross-feeding at intermediate scale portrays community dynamics and species coexistence. Chen Liao et al. PLoS Computational Biology

Pre-print
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. Cameron Martino et al. bioRxiv

Evaluation of Compatibility of 16S rRNA V3V4 and V4 Amplicon Libraries for Clinical Microbiome Profiling. Po-Yu Liu et al.bioRxiv

Shirin’s non-microbiology picks
MICROBIOME ART: François-Joseph Lapointe, when biology meets art. Jihane Mossalim. Convergence Initiative.

BEHIND THE PAPER: Early-life microbiota diversification facilitates enterocyte proliferation. Michael Dougherty. Nature Microbiology Research Community

JOP OPPURTUNITY: PhD positions in the ecology and evolution of metabolic cross-feeding interactions in soil-living bacterial communities and the gut microbiota in protecting the host against intestinal colonisation by multidrug-resistant organisms

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 10th, 2020

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God morgon!

Good morning from Sweden. Today’s digest is a light one but carries a preprint with some very important findings. The study has suggested that the nCoV can potentially hijack the immune system completely by infecting the lymphocytes. This might lead to impaired antibody and T-cell response, something that could have a serious implication on the success of the much-awaited vaccine. (Unfortunately, for some unknown reasons, the PDF of the preprint is inaccessible to me! Let me know down in the comments if you are able to download it.)

A new paper in BMC microbiome shows a correlation between the indoor dust microbiota and the microbiota of infant airways. A classic example of how our environment impacts our health.  There is another interesting preprint where the authors show that a fungus alters its virulence when it is challenged by predatory amoebae. Perhaps the amoeba challenge selects for the warrior mutants which then carry on their warring ways!

Elsewhere in the digest is a preprint where Plasmodium knowlesi was used as a model to successfully determine new vaccine targets against more dangerous Plasmodium vivax, a paper detailing the effect of polar light cycles on the Antarctic lake microbiome, and identification of haloarchael species in Korean gut microbiota.

COVID-19

Preprint: Infection of human lymphomononuclear cells by SARS-CoV-2 – Marjorie C Pontelli, et al.

General Microbiology

Preprint: Amoeba predation of Cryptococcus neoformans results in pleiotropic changes to traits associated with virulence – Man Shun Fu, et al.

Preprint: Using Plasmodium knowlesi as a model for screening Plasmodium vivax blood-stage malaria vaccine targets reveals new candidates – Duncan N Ndegwa, et al.

General microbiome

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

Environmental shaping of the bacterial and fungal community in infant bed dust and correlations with the airway microbiota – Shashank Gupta, et al. – Microbiome

Archaea/Gut microbiota

The human gut archaeome: identification of diverse haloarchaea in Korean subjects – Joon Yong Kim, et al. – Microbiome

Techniques

Preprint: Successful introduction of the Colour Test into inexperienced settings – Kadri Klaos

Zoom Seminar

How a healthy gut microbe affects your whole body? – Karen Ranzi, Holistic Health Coach, Award-Winning Author, Motivational Speaker, Natural Foods Chef, Speech and Feeding Therapist (phew!)

August 9, 2020

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Good morning and a wonderful Sunday!
While you are eating your Sunday eggs and sipping your coffee, enjoy the small collection of microbiome et al. papers- exactly the right size for a Sunday morning.
Visit the microbial community living at Antarctic volcanoes with the preprint from Benda et al. or read the findings by Gibb et al. that indicate that human-managed ecosystems favor the presence of reservoirs of zoonotic diseases- very interesting in the light of the current pandemic. Enjoy!

Human gut microbiome

Essential oils and microbiota: Implications for diet and weight control – Nurhan Unusan – Trends in Food Science & Technology

Animal microbiome

The Gut Microbiota of Pheasant Lineages Reflects Their Host Genetic Variation – Jinmei Ding et al – Frontiers in Genetics

Water and extremophile microbiome

*Preprint: Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica – Amanda G Benda – BioRxiv

Review: New Microbial Biodiversity in Marine Sediments – Brett J Baker et al. – Annual Review of Marine Science

Bioinformatics

Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities – Lukas Beule et al – PeerJ

Techniques

Ten simple rules for reading a scientific paper – Maureen A. Carey et al – PLOS Computational Biology

Judith’s non-microbiology picks

*Zoonotic host diversity increases in human-dominated ecosystems – Rory Gibb et al – Nature

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 5, 2020

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Today’s Microbiome Digest showcases a study of a microbiota derived metabolite that promotes HDAC3 in the gut indicating an epigenetic senror of the microbiota, as well as several interesting papers from Cell Host & Microbe, Nature Microbiology and mSystems.

Covid-19

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic – Boni et al. Nature Microbiology

Retrospective Multicenter Cohort Study Shows Early Interferon Therapy Is Associated with Favorable Clinical Responses in COVID-19 Patients – Wang et al. Cell Host & Microbe

General microbiome

The human gut archaeome: identification of diverse haloarchaea in Korean subjects – Kim et al. BMC Microbiome. 

Microbiota-derived metabolite promotes HDAC3 activity in the gut – Wu et al. Nature

Antibiotics

Distinct Bacterial Pathways Influence the Efficacy of Antibiotics against Mycobacterium tuberculosis – Bellerose et al. mSystems

Novel Antimicrobials from Uncultured Bacteria Acting against Mycobacterium tuberculosis – Quigley et al. mBio

 

Water and extremophile microbiome

Microbial Metabolic Redundancy Is a Key Mechanism in a Sulfur-Rich Glacial Ecosystem – Trivedi et al. mSystems

Bioinformatics

Precise Species Identification for Enterobacter: a Genome Sequence-Based Study with Reporting of Two Novel Species, Enterobacter quasiroggenkampii sp. nov. and Enterobacter quasimori sp. Nov. – Wu et a. mSystems

Phages and viruses

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome – Wolf et al. Nature Microbiology