October 2, 2020

Today’s exciting updates – FMT method to restore normal microbial development in caesarean-born infants, mechanism unveiled how dietary tryptophan improves alcohol induced liver injury, advance in droplet based microfluidics to study host-microbiome interactions, prebiotics encapsulation of probiotic to suppress colon cancer and new hope to curb plastic waste by discovery of plastic-eating enzyme cocktail. Happy weekend, stay safe!

General microbiome

Eligible blood donors’ decisions about donating stool for fecal microbiota transplantation: Does ambivalence play a role? – Melissa K. Hyde – Transfusion

Microbiota-Dependent Effects of IL-22 – Morsal Sabihi – Cells

Human microbiome

Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study – Katri Korpela – Cell

Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases – Ji In Park – Scientific Reports

Dysbiosis in the oral microbiomes of anti-CCP positive individuals at risk of developing rheumatoid arthritis – Zijian Cheng – Annals of the Rheumatic Diseases

Animal microbiome

Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol-induced liver injury – Laura Wrzosek – Gut

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato – Microbiome

Competitive reduction of poultry-borne enteric bacterial pathogens in chicken gut with bioactive Lactobacillus casei – Zajeba Tabashsum – Scientific Reports

Offspring susceptibility to metabolic alterations due to maternal high-fat diet and the impact of inhaled ozone used as a stressor – Samantha J. Snow – Scientific Reports

Beneficial effects of mung bean seed coat on the prevention of high-fat diet-induced obesity and the modulation of gut microbiota in mice – Dianzhi Hou – European Journal of Nutrition

Prebiotics‐Encapsulated Probiotic Spores Regulate Gut Microbiota and Suppress Colon Cancer – Di‐Wei Zheng – Advanced Materials

Multi-Omic Analysis Reveals Different Effects of Sulforaphane on the Microbiome and Metabolome in Old Compared to Young Mice – Se-Ran Jun – Microorganisms

Plant microbiome

Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes – Stefan Geisen – Isme Journal

Techniques

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin – Microbiome

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis – Sidney P. Walker – Scientific Reports

Non-microbiology picks

Plastic-eating enzyme ‘cocktail’ heralds new hope for plastic waste – Science Daily

August 16, 2020

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

July 10, 2020

Today’s digest contains many exciting articles – gut microbiome in precision medicine for cancer, important review on patent protection in microbiome therapeutics, role of the gut microbiota in sympathetic neurons, interaction of pacemaker neurons with the gut microbiota, gut dysbiosis in lupus and many more….Enjoy reading and happy weekend!

General microbiome

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

Co-evolution and Co-speciation of Host-Gut Bacteria Systems – Mathieu Groussin – Cell Host and Microbe

Microbiome therapeutics and patent protection – Mark J. FitzGerald – Nature Biotechnology

Human microbiome

Fecal Microbiota Transplantation is Safe and Effective in Patients with Clostridioides difficile Infection and Cirrhosis – Yao-WenCheng – CLinial Gastroenterology and Hepatology

Association of Gut Microbiota-Dependent Metabolite Trimethylamine N-Oxide with First Ischemic Stroke – Taoping Sun – Journal of Atherosclerosis and Thrombosis

Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet? – Konstantinos Gkikas – Nutrients

The duodenal microbiome is altered in small intestinal bacterial overgrowth – Gabriela Leite – PlosOne

Faecal microbiota transplantation: A life-saving therapy challenged by commercial claims for exclusivity – Christian LodbergHvas – EClinical Medicine

Animal experiments

Microbiota modulate sympathetic neurons via a gut–brain circuit – Paul A. Muller – Nature

Prototypical pacemaker neurons interact with the resident microbiota – Alexander Klimovich – PNAS

Gut microbiota dysbiosis and altered tryptophan catabolism contribute to autoimmunity in lupus-susceptible mice – Seung-Chul Choi – Science Translational Medicine

The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease – Yu Liu – Faseb Journal

Sodium Butyrate Alleviates Mouse Colitis by Regulating Gut Microbiota Dysbiosis – Xiujing Dou – Animals

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome – Min-Ting Lee – Journal of Lipid Research

Commentary: Modulating microbiome metabolites in vivo – Chun-Jun Guo – Science

Plant, root and soil microbiome

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history – Martinus Schneijderberg – ISME Journal

Water microbiome

Anthropogenic dissolved organic carbon and marine microbiomes – Maria Vila-Costa – ISME Journal

Functional foods

Effect of a functional fibre supplement on glycemic control when added to a year-long medically supervised weight management program in adults with type 2 diabetes – Raylene A. Reimer – European Journal of Clinical Nutrition

Prenatal exposure to the probiotic Lactococcus lactis decreases anxiety-like behavior and modulates cortical cytoarchitecture in a sex specific manner – Natalia Surzenko – PlosOne

Non microbiology picks

SARS-CoV-2 is transmitted via contact and via the air between ferrets – Mathilde Richard – Nature Communications

July 1, 2020

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


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

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

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

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

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

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

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


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

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


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

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


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

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

Probiotics to precision probiotics

After “precision medicine”, it is now time to conceptualize the term “precision probiotics”. In simple words, fundamental idea of precision medicine is to develop “new taxonomy” of disease employing molecular characterization of disease based on individual data that will enable better stratification of patients and determining most effective treatments. On similar lines, Veiga and colleagues offer strategies to develop precision probiotics, combine with multi-omics host response data to find most optimal probiotic modality in stratified individuals/populations.

I would recommend to read the review in full. To motivate you, following are some excerpts from the review:

“Historically, the discovery of probiotics relied on a top-down approach, where a microorganism enriched in healthy individuals (compared to an altered health state) is suggested to be beneficial and correlates with a health benefit upon administration to humans…While this empirical top-down approach provides robust leads for the development of probiotics, in the absence of prior mechanistic information, it inherently necessitates multiple cycles of trial and error to identify health benefits.”

Problems with top-down approach

  • “Probiotic efficacy being both strain- and indication-specific
  • Person-specific factors also contribute to heterogeneity in the outcome of probiotic supplementations, including diet, age and the microbiome. Colonization-resistant microbiomes are more resilient to probiotic interventions compared to colonization-permissive individuals.”

Bottom up approach

“The phenotypic approach is based on screening for probiotic effects using in vitro and ex vivo cell cultures as well as animal models with immune, neuronal, metabolic or microbial read-outs.

Target-based discovery relies on the selection of probiotic candidates based primarily on in silico prediction of their capacity to produce molecular effectors that are potentially able to modulate host or microbial pathways, which are foreseen to play a critical role in health or disease. Such in silico predictions would require the use of multi-omics (such as genomics, transcriptomics, metabolomics and proteomics) possibly coupled to metabolic reconstruction to infer the metabolic capacity of the screened microorganisms.”

Challenges with bottom-up approach

  • “A greater challenge lies in applying a person-specific approach to predict efficacy, which likely requires obtaining profound individualized host data (including genetics, anthropometrics and immune profiling) and microbiome data (such as strain-level composition, transcriptomics and metabolomics), as well as identifying relevant biomarkers that predict colonization resistance and/or a health outcome.
  • As stool samples do not accurately reflect colonization and impact on the gut microbiota along the gastrointestinal tract during probiotic supplementation, there is a great need to devise non-invasive means for identifying compatible probiotic–individual matches.
  • Another important factor to consider is safety, as exogenous microorganisms can have unexpected effects on the microbiome, and can even compromise the health of vulnerable subjects and result in bacteraemia or fungaemia.”

I believe that these challenges also hold true for top-down approach

Precision probiotics strategies

The big aim

“…developing algorithms that, when provided with these individualized parameters, can suggest the optimal probiotic modality that would result in a beneficial outcome.”

  • “To achieve this goal, on one hand, scientists need to better characterize the physiological or pathological pathways that can be modulated by probiotics, in line with the increasing effort to use bottom-up approaches.
  • On the other hand, further digitization of tools for the collection and processing of person-specific data, and their integration with genomic and metabolomic host and microbiome profiles, will be required.
  • Setting up standardized protocols that allow bio-citizens to self-experiment in ‘N-of-1 trials’ and report their experiences with probiotics, coupled with individualized measurements, would greatly expand our understanding of differential probiotic activity in the heterogenous human population. This approach will require devising strict validation and safety measurements for promising centralized data collection while maintaining participants’ anonymity.

“…While today, this (refers to microbiome data) personal information is poorly actionable, tomorrow it could serve as the basis for microbiome-centred precision nutrition and preventive medicine, including precision probiotics.”

May 8, 2020.

The highlighted paper of the day looked at the relationship between statins and gut microbiome / enterotype prevalence, mined from data collected from the MetaCardis study which looked at over 2000 participants all across the EU and collected over 1,400 parameters.

If you’re looking for a review/news article of the paper head to: Statin drugs might boost healthy gut microbes

If you’re looking for the paper: Statin therapy is associated with lower prevalence of gut microbiota dysbiosis – Sara Silva – Nature

COVID-19


Identification of Drugs Blocking SARS-CoV-2 Infection using Human Pluripotent Stem Cell-derived Colonic Organoids – Xiaohua Duan – bioRxiv

Whose coronavirus strategy worked best? Scientists hunt most effective policies – Elizabeth Gibney – Nature

Coronavirus activates a stem cell-mediated defense mechanism that accelerates the activation of dormant tuberculosis: implications for the COVID-19 pandemic – Lekhika Pathak – bioRxiv

General Microbiome

Multi ‘Omics Profiling of the HIV Airway Epithelium: Integration of the Microbiome, Methylome, and Transcriptome – MS Jude – Am J Respir Crit Care Med

Intracellular Staphylococcus aureus persisters upon antibiotic exposure – Frederuc Peyrusson – Nature Communications

Isolation and characterization of bacteriophages that infect Citrobacter rodentium, a model pathogen for investigating human intestinal diseases – Carolina Mizuno – bioRxiv

MiniReview: A toxic environment: a growing understanding of how microbial communities affect Shiga toxin expression by E. coli O157:H7 – Erin M. Nawrocki – American Society for Microbiology, Applied and Environmental Microbiology

Pregnancy and early life

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to- weaning transition – Martin Beaumont – Gut Microbes

Gut Microbiome Derived 12,13 Dihome Promotes Antigen Presenting Cell Dysfunction In Vitro and Airway Allergic Inflammation In Vivo – S Levan – Atsjournal


Multi-site human microbiome

The Microbiome and the Gut‐Liver‐Brain Axis for CNS Clinical Pharmacology: Challenges in Specifying and Integrating In Vitro and In Silico Models – Kyle Hawkins – Clinical Pharmacology and Therapeutics

Gut Check: The Intestinal Microbiome Does Not Predict or Protect from Vancomycin- Resistant Enterococcus Acquisition Among Critically Ill Patients – Chanderraj – Atsjournal

The Tumour-Resident Microbiome Is Associated with Cancer Hypomethylation Status in Lung Adenocarcinoma – Marshall – atsjournal

An association between the gut microbiota and immune cell dynamics in humans. – Jonas Schluter – bioRxiv

Metabolomics

Analyzing the impact of Mycobacterium tuberculosis infection on primary human macrophages by combined exploratory and targeted metabolomics – Vrieling Frank

Review: Metabolome–Microbiome Crosstalk and Human Disease – Kathleen Lee-Sarwar – metabolites

Animal Microbiome

Review – Mycobacterium bovis: From Genotyping to Genome Sequencing – Ana Guimaraeas – Microorganism

Animal experiments

Staphylococcus aureus-induced proteomic changes in the mammary tissue of rats: A TMT-based study – Lirong Cai – Plos One

Plant, root, and soil microbiome


Effects of earthworms on the microbiomes and antibiotic resistomes of detritus fauna and phyllosphere – Dong Zhu – Environmental Science and Technology

Surface runoff alters cave microbial community structure and function – Madison Davis – Plos One

Water and extremophile microbiome

Culturing of ‘Unculturable’ Subsurface Microbes: Natural Organic Carbon Source Fuels the Growth of Diverse and Distinct Bacteria from Groundwater – Xiaoqin Wu – bioRxiv

Bioinformatics & Techniques

Sequence count data are poorly fit by the negative binomial distribution – Stjin Hawinkel – Plos One

Book Chappter: Meta-Pangenome: At the Crossroad of Pangenomics and Metagenomics – Bing MA – The Pangenome, Springer.

Snipe: Highly sensitive pathogen detection from metagenomic sequencing data – Lihong Huang – bioRxiv

Validated Method for the Study of Human Lung Microbiota from Excised Tissue – Dumont-Leblond – atsjounal

Microbes in the news

Bad to the Bone – Matthew Greseth- MUSC Health

Meet the ‘psychobiome’: the gut bacteria that may alter how you think, feel, and act – Elizabeth Pennisi – ScienceMag

Decoding the Microbiome: Essential to Advancing Precision Medicine – Heather Hall – rdworldonline

Harithaa’s non-microbiology picks!

Mass spectrometry for future atomic clocks – Marianna Safrova – Nature (news & views)

April 6, 2020

God morgon!

Good morning from Sweden. This is my first post and following the current trend, it starts with some articles on the COVID19 pandemic. Today’s digest is headlined by some interesting preprints reporting inhibitors of SARS-CoV2 virus, followed by another interesting read suggesting the link between the gut microbiome and ADHD, some articles on our struggle against pathogenic bacteria, virus and fungi, and capped off with a small but informative news article on things one should not do during the COVID19 lockdown.

You might notice that today’s post is dominated by preprints. These preprints, while being an excellent way to disperse information as rapidly as it emerges, aren’t peer-reviewed. Hence, always read them with a pinch of salt!

COVID19

Preprint: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication – Franck Touret, et al.

Preprint: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 – Xuesen Zhao, et al.

Preprint: Indomethacin has a potent antiviral activity against SARS CoV-2 in vitro and canine coronavirus in vivo – Tianhong Xu, et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Emily K. Mantlo, et al.

Microbial interactions

Preprint: Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria – Ryan K Fritts, et al.

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics – Weipeng Zhang, et al. – Microbiome

Preprint: Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms – Gabi Steinbach, et al.

Human microbiome

Preprint: Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Anouk C. Tengeler, et al.

Lung function and microbiota diversity in cystic fibrosis – Leah Cuthbertson, et al. – Microbiome

Animal microbiome

Preprint: Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets – Martin Beaumont, et al.

Bacteria Hysteria

Preprint: The adaptive transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress – Crispin Zavala-Alvarado, et al.

Preprint: Cytotoxicity of the effector protein BteA was attenuated in Bordetella pertussis by insertion of an alanine residue – Jan Bayram, et al.

Preprint: Antimicrobial peptide induced-stress renders Staphylococcus aureus susceptible to toxic nucleoside analogues – Alexandro Rodriguez-Rojas, et al.

Preprint: (p)ppGpp and malonyl-CoA set the pace for Staphylococcus aureus adaptation to FASII antibiotics and provide a basis for bi-therapy inhibition – Amit Pathania, et al.

Phages and viruses

Preprint: Viral RNA is a target for Wolbachia-mediated pathogen blocking – Tamanash Bhattacharya, et al.

Preprint: Synchronized infection identifies early rate-limiting steps in the hepatitis B virus life cycle – Anindita Chakraborty, et al.

Techniques

Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Takeo Shibata, et al.

Preprint: Biotinylated surfome profiling identifies potential biomarkers for diagnosis and therapy of Aspergillus fumigatus infection – Lei-Jie Jia, et al.

Bioinformatics

Preprint: Interpretable machine learning framework reveals novel gut microbiome features in predicting type 2 diabetes – Wanglong Gou, et al.

Preprint: Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis – Jenna N Kelly, et al.

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Eli Levy Karin, et al. – Microbiome

Preprint: Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes – Jacob Stanley Iramiot, et al.

Microbes in news

News article: Experts study banana disease in Tanzania – The Guardian

News article: What not to do while on COVID-19 lockdown – Jamaica Observer

I know a lot of my fellow researchers are unable to continue their experiments and are yearning to get back to their respective labs. It is a testing time and I believe that patience and perseverance are the biggest strengths of a researcher. So, let’s bank on our strength and hope to see each other on the other side of this global pandemic soon!

With new information emerging every day about COVID19, there is a plethora of misinformation and myths surrounding the virus and the disease. As science enthusiasts, it is pertinent for us to dispel these myths. Here is a small list that I complied a few days back. Check it out!

March 23, 2020

In today’s digest, review on biliary tract microbiome, effect of disinfection on water microbiome, resveratrol on adipose tissue browning via gut microbiome modelling and influence of livestock farm environment on human gut microbiota and antibiotic resistome.

Hope all readers are staying safe at home!

General microbiome

Intestinal microbiota and its association with colon cancer and red/processed meat consumption – Nadine Abu‐Ghazaleh – Journal of Gastroenterology and Hepatology

Is it time to consider gut microbiome readouts for precision diagnosis and treatment of alcoholic liver disease? – Gail A.M. Cresci – Hepatology

Biliary tract microbiota: a new kid on the block of liver diseases? – Nicoletti A – European Review for Medical and Pharmacological Sciences

Human microbiome

Characteristics of the urinary microbiome in kidney stone patients with hypertension – Fengping Liu – Journal of Translational Medicine

Pregnancy associates with alterations to the host and microbial proteome in vaginal mucosa – Christina Farr Zuend – American Journal of Reproductive Immunology

Prebiotics inhibit proteolysis by gut bacteria in a host diet-dependent manner: a three stage continuous in vitro gut model experiment – Xuedan Wang – Applied and Environmental Microbiology

Animal experiments

Resveratrol enhances brown adipose tissue activity and white adipose tissue browning in part by regulating bile acid metabolism via gut microbiota remodeling – Suocheng Hui – International Journal of Obesity

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms – Jian Sun – Nature Communications

Effects of the dietary fibre inulin and Trichuris suis products on inflammatory responses in lipopolysaccharide-stimulated macrophages – Laura J. Myhill – Molecular Immunology

Deoxycholic Acid-Induced Gut Dysbiosis Disrupts Bile Acid Enterohepatic Circulation and Promotes Intestinal Inflammation – Mengque Xu – Digestive Diseases and Sciences

Commensal Bacteria Impact a Protozoan’s Integration into Murine Gut Microbiota in a Dietary Nutrient-dependent Manner – Applied and Environmental Microbiology

Plant, root and soil microbiome

Rhizosphere fungal communities of wild and cultivated soybeans grown in three different soil suspensions – Chunling Chang – Applied Soil Ecology

Straw decreased N2O emissions from flooded paddy soils via altering denitrifying bacterial community compositions and soil organic carbon fractions – Ning Wang – FEMS Microbial Ecology

Water microbiome

Microbial communities from subglacial water of naled ice bodies in the forefield of Werenskioldbreen, Svalbard – Sławomir Sułowicz – Science of the Total Environment

Disinfection exhibits systematic impacts on the drinking water microbiome – Zihan Dai – Microbiome

Microbial diversity in deep subsurface hot brines of the North West Poland: from a community structure to isolate characteristics – Agnieszka Kalwasińska – Applied and Environmental Microbiology

Non microbiology picks

Identification of antiviral drug candidates against SARS-CoV-2 from FDA-approved drugs – Sangeun Jeon – BioRxiv

Comparative Pathogenesis Of COVID-19, MERS And SARS In A Non-Human Primate Model – Barry Rockx – BioRxiv

March 20, 2020

Good morning! I hope this post finds you well. There are lots of new microbiome papers to share, including work on the disruption of E. coli biofilms, inconsistent diets used in Drosophila microbiome studies, and the effects of pollution on soil microbial communities.

General microbiome

Biosynthesis of silver nanoparticles by Fusarium scirpi and its potential as antimicrobial agent against uropathogenic Escherichia coli biofilms, Candelario Rodríguez-Serrano et al., PLOS ONE


Human gut microbiome

Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy, Aadra P. Bhatt et al., PNAS

Gut Microbiome Pattern Reflects Healthy Aging and Predicts Extended Survival in Humans (preprint), Tomasz Wilmanski et al., bioRxiv

Propionic Acid Shapes the Multiple Sclerosis Disease Course by an Immunomodulatory Mechanism, Alexander Duscha et al., Cell

Adjusting for age improves identification of gut microbiome alterations in multiple diseases, Tarini S Ghosh et al., eLife

Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms, Jian Sun et al., Nature Communications

Review – Altering Routine Intensive Care Unit Practices to Support Commensalism, Hamilton and Behal, Nutrition in Clinical Practice

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota, Ashley E. Kates et al., Frontiers in Cellular and Infection Microbiology

Meta-analysis – Assessing the efficacy and safety of fecal microbiota transplantation and probiotic VSL#3 for active ulcerative colitis: A systematic review and meta-analysis, Xiaofei Dang et al., PLOS ONE


Other human microbiome

Subgingival Host-Microbial Interactions in Hyperglycemic Individuals, P.S. Kumar et al., Journal of Dental Research

Investigating Bifidobacteria and Human Milk Oligosaccharide Composition of Lactating Mothers, Gabriele Andrea Lugli et al., FEMS Microbiology Ecology


Animal experiments

Effects of intestinal flora on the pharmacokinetics and pharmacodynamics of aspirin in high-altitude hypoxia, Sun and Zhang et al., PLOS ONE

Meta-analysis of diets used in Drosophila microbiome research and introduction of the Drosophila Dietary Composition Calculator (DDCC) (preprint), Broderick and Lesperance, bioRxiv

The Carnivorous Digestive System and Bamboo Diet of Giant Pandas May Shape Their Low Gut Bacterial Diversity, Wei Gui et al., Conservation Physiology


Animal microbiome

Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome, Coleman and Whitfield-Cargile et al., PLOS ONE

Dietary substitution of soybean oil with coconut oil in the absence of dietary antibiotics supports growth performance and immune function in nursery and grower pigs, Andrea G. Braundmeier-Fleming et al., Journal of Animal Science and Biotechnology

Isoflavone supplementation, via red clover hay, alters the rumen microbial community and promotes weight gain of steers grazing mixed grass pastures, Brittany E. Harlow et al., PLOS ONE

Domesticated equine species and their derived hybrids differ in their fecal microbiota, J.E. Edwards et al., Animal Microbiome

Integrative analysis of gut microbiome and metabolites revealed novel mechanisms of intestinal Salmonella carriage in chicken, Khin K.Z. Mon et al., Scientific Reports


Plant, root, and soil microbiome

Acute effects of PAH contamination on microbial community of different forest soils, Enrica Picariello et al., Environmental Pollution

Context-dependent Dynamics Lead to the Assembly of Functionally Distinct Microbial Communities, Leonora S Bittleston et al., Nature Communications

Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases, Eden Zhang et al., Microbiome

Perspective – Toward Comprehensive Plant Microbiome Research, Kari Saikkonen et al., Frontiers in Ecology and Evolution


Water and extremophile microbiome

Deep-sea corals provide new insight into the ecology, evolution, and the role of plastids in widespread apicomplexan symbionts of anthozoans, Samuel A. Vohsen et al., Microbiome


Food microbiology

Lactic Acid Bacteria Isolated From Korean Kimchi Activate the Vitamin D Receptor–autophagy Signaling Pathways, Rong Lu et al., Inflammatory Bowel Diseases

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome, Bryn C. Taylor et al., mSystems

Differential Microbial Composition of Monovarietal and Blended Extra Virgin Olive Oils Determines Oil Quality During Storage, Zullo and Ciafardini, Microorganisms


Phages and viruses

Honey bees harbor a diverse gut virome engaging in nested strain-level interactions with the microbiota, Germán Bonilla-Rosso et al., PNAS


Bioinformatics

FORENSIC: an Online Platform for Fecal Source Identification, Adélaïde Roguet et al., mSystems

Review – Accurate and complete genomes from metagenomes, Lin-Xing Chen et al., Genome Research

Powmic: An R Package for Power Assessment in Microbiome Case-Control Studies, Li Chen, Bioinformatics


Techniques

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs, Leyuan Li et al., Microbiome


Non-microbiology picks

Marketplace shrimp mislabeling in North Carolina, Morgan L. Korzik et al., PLOS ONE

March 16, 2020

To all the work-from-home researchers (like me!), today’s digest covers microbiome in memory recognition, enteric neuropathy and neurodevelopmental disorder in rodent models. Gut microbiome in cardiovascular disease, a dual mechanism antibiotic and shifts in human gut microbiome and metabolome following gastric bypass. An important preprint that Covid-19 could not induce reinfection in infected rhesus macaques and that Ibuprofen may aggravate Covid-19 infection.

General microbiome

Gut microbiota and cardiovascular disease: opportunities and challenges – Negin Kazemian – Microbiome

Human microbiome
Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response – Jose U. Scher – Nature Reviews Rheumatology

Long-term metal exposure changes gut microbiota of residents surrounding a mining and smelting area – Mengmeng Shao – Scientific Reports

Temporospatial shifts in the human gut microbiome and metabolome after gastric bypass surgery – Zehra Esra Ilhan – NPJ biofilms and microbiomes

Animal experiments

Habitat and seasonality shape the structure of tench (Tinca tinca L.) gut microbiome – Tomasz Dulski – Scientific Reports

Microecological Koch’s postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome – Zhijian Huang – Microbiome

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis – Jun Miyoshi – BioRxiv

Gut microbiota manipulation during the prepubertal period shapes behavioral abnormalities in a mouse neurodevelopmental disorder model – Justin M. Saunders – Scientific Reports

Minocycline-induced microbiome alterations predict cafeteria diet-induced spatial recognition memory impairments in rats – Sarah-Jane Leigh – Translational Psychiatry

A purified membrane protein from Akkermansia muciniphila or the pasteurised bacterium blunts colitis associated tumourigenesis by modulation of CD8+ T cells in mice – Lijuan Wang – Gut

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice – Jingli Li – Science of The Total Environment

High‐fat diet–induced alterations to gut microbiota and gut‐derived lipoteichoic acid contributes to the development of enteric neuropathy – Yvonne Nyavor – Neurogastroenterology and Motility

Plant, root and soil microbiome

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil – L. V. Alteio – mSystems

Impact of plants on the diversity and activity of methylotrophs in soil – Michael C. Macey – Microbiome

Conserved bacterial genomes from two geographically distinct peritidal stromatolite formations shed light on potential functional guilds – Samantha C. Waterworth – BioRxiv

Techniques

A framework for assessing 16S rRNA marker-gene survey data analysis methods using mixtures – Nathan D. Olson – Microbiome

Antibiotic resistance

A dual-mechanism antibiotic targets Gram-negative bacteria and avoids drug resistance – James K. Martin – BioRxiv

Non microbiology picks

Reinfection could not occur in SARS-CoV-2 infected rhesus macaques – Linlin Bao – BioRxiv

Anti-inflammatories may aggravate Covid-19, France advises – The Guardian