October 13, 2020

Today’s mid-week digest is about – meta analysis of metabolic benefits of probiotics, probiotics and synbiotics, microbiome association with narcolepsy type 1, design of microbial consortium for reduced C. difficle colonization, new sequencing technique for pathogen identification in cerebrospinal fluid and many more… Happy reading!

Human microbiome

The effect of probiotics, prebiotics or synbiotics on metabolic outcomes in individuals with diabetes: a systematic review and meta-analysis – Patricia M. Bock – Diabetologia

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D. Gerson – American Journal of Perinatology

Targeting the microbiome-gut-brain axis for improving cognition in schizophrenia and major mood disorders: A narrative review – Miquel Bioque – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Inflammatory Bowel Disease Environmental Risk Factors: Diet and Gut Microbiota – Sarah Altajar – Current Gastroenterology Reports

Co‐ and polymicrobial infections in the gut mucosa: the host‐microbiota‐pathogen perspective – Teresa Frisan – Cellular Microbiology

Gut microbiota composition is associated with narcolepsy type 1 – Alexandre Lecomte – Neurology

A parental transcriptional response to microsporidia infection induces inherited immunity in offspring – Alexandra R. Willis – BioRxiv

Melamine contamination and associated health risks: Gut microbiota does make a difference – Meenakshi Rajpoot – Biotechnology and Applied Biochemistry

Animal microbiome

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization – Fátima C. Pereira – Nature Communications

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

Bacterial community analysis on the different mucosal immune inductive sites of gastrointestinal tract in Bactrian camels – Wang-Dong Zhang – PlosOne

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Larivière‐Gauthier – Letters in Applied Microbiology

Plant, root and soil microbiome

Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow – Ruifen Zhu – Scientific Reports

Evidence for signatures of ancient microbial life in paleosols – Katharina Frindte – Scientific Reports

Techniques

Pathogen identification in culture-negative cerebrospinal fluid specimens of patients with purulent meningitis using next-generation sequencing technology – Xin Men – International Journal of Clinical Experimental Pathology

October 1, 2020

Greetings, friends!

Today’s digest contains a wealth of microbiology articles focused on everything from the dog ear canal microbiome to estuarine methanogen communities. Rather than highlight a specific research article, today I’d like to encourage you to check out this week’s New York Times article profiling the organizers of Black in Micro Week and this commentary published by one of the organizers in mSphere. Black in Micro week began this Monday and programming is scheduled to continue through October 4th. If you missed earlier events, you’re in luck! The organizers have already uploaded videos of all completed events at the Black in Micro youtube channel.

Enjoy!


Events

Black in Micro Week is this week (September 28 – October 4th, 2020) on your favorite social media platforms! Check out the Black in Microbiology website for additional information, including a full programming schedule, and follow @BlackinMicro and #BlackinMicro on Twitter and Instagram.

Human respiratory microbiome

Airway microbiota is associated with the severity of non‐CF bronchiectasis – Li et al. – The Clinical Respiratory Journal

Human gut microbiome

Systematic analysis of gut microbiota in pregnant women and its correlations with individual heterogeneity – Yang et al. – npj Biofilms and Microbiomes

Review: Implication of gut microbiota in cardiovascular diseases – Zhou et al. – Oxidative Medicine and Cellular Longevity

Animal experiments

Changes in the ear canal microbiota of dogs with otitis externa – Kasai et al. – Journal of Applied Microbiology

Plant, root, and soil microbiome

Soil borne Fusarium solani exhibited pathogenic effect on tomato cultivars in Nigeria – Abiala et al. – Archives of Phytopatholgy and Plant Protection

A symbiotic nutrient exchange within the cyanosphere microbiome of the biocrust cyanobacterium, Microcoleus vaginatus – Nelson et al. – The ISME Journal

Successional change of the fungal microbiome pine seedling roots inoculated with Tricholoma matsutake – Park et al. – Frontiers in Microbiology

Review: Arbuscular mycorrhizal fungi: an ecological accelerator of phytoremediation of metal contaminated soils – Tiwari et al. – Archives of Agronomy and Soil Science

Co‐occurrence history increases ecosystem stability and resilience in experimental plant communities – van Moorsel et al. – Ecology

Quantitative estimation of stochastic and deterministic processes for soil prokaryotic community assembly in the Yellow River floodplain – Yu et al. – European Journal of Soil Science

Water and extremophile microbiome

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre – Allen et al. – Molecular Ecology

An unexpectedly broad thermal and salinity-tolerant estuarine methanogen community – Blake et al. – Microorganisms

Microbial communities responded to tetracyclines and Cu(II) in constructed wetlands microcosms with Myriophyllum aquaticum – Guo et al. – Ecotoxicology and Environmental Safety

Built environment

Microbial community and function in nitrogen transformation of ectopic fermentation bed system for pig manure composting – Chen et al. – Bioresource Technology

Effect of hydrothermal hot-compression method on the antimicrobial performance of green building materials from heterogeneous cellulose wastes – Echeverria et al. – Journal of Cleaner Production

Nitrous oxide emission and microbial community of full-scale anoxic/aerobic membrane bioreactors at low dissolved oxygen setpoints – Wen et al. – Journal of Water Process Engineering

Response of Cyperus involucratus to sulfamethoxazole and ofloxacin-contaminated environments: Growth physiology, transportation, and microbial community – Xu et al. – Ecotoxicology and Environmental Safety

Microbes in the news

Black microbiologists push for visibility amid a pandemic – Wu – New York Times

Science, publishing, and career

Commentary: mSphere of influence: That’s racist—COVID-19, biological determinism, and the limits of hypotheses – Taylor – mSphere

September 10, 2020

Good morning from smokey, apocalyptic San Francisco! The world outside my window may be in sepia tones, but the articles I’m highlighting here are helping to brighten my day. Today’s digest has some fascinating insect and environmental microbiome research including a paper about the gut microbiota of a beetle that lives in the mixed forest of northeastern Asia and its capacity to efficiently degrade polystyrene. Additionally, there’s a paper characterizing the community structure and metabolic capacity of a biofilm-like microbial community lining the wall of the Yumugi river cave in a remote part of Western New Guinea. I’ve also included a paper examining availability of microbial community sequencing data which found that much of this data is not available and offers suggestions for improving data archiving practices. Finally, there is a very interesting technique paper about an orally ingestible microdevice that can be used to sample the gut microbiota in the upper gastrointestinal tract. Happy reading!

General Microbiome
Influence of Intratumor Microbiome on Clinical Outcome and Immune Processes in Prostate Cancer. – Ma, J. et al., Cancers

Experimental (co)evolution in a multi-species microbial community results in local maladaptation. – Castledine, M. et al., Ecology Letters

Pregnancy and Early Life
Mothers of Preterm Infants Have Individualized Breast Milk Microbiota that Changes Temporally Based on Maternal Characteristics. – Asbury, M.R et al., Cell Host Microbe

The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota. – He, Q. et al., Gut Microbes

Skin microbiome
Stratum Corneum Lipidomics Analysis Reveals Altered Ceramide Profile in Atopic Dermatitis Patients Across Body Sites With Correlated Changes in Skin Microbiome. – Emmert, H. et al., Experimental Dermatology

Vaginal microbiome
Diverse vaginal microbiome was associated with pro-inflammatory vaginal milieu among pregnant women in Uganda. – Bayigga, L. et al. Human Microbiome Journal

Gut microbiome
Diet Diurnally Regulates Small Intestinal Microbiome-Epithelial-Immune Homeostasis and Enteritis. – Tuganbeav, T. et al., Cell

Microbiota-modulated CART + enteric neurons autonomously regulate blood glucose. – Muller, P.A. et al., Science

Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. -Banerjee, A. et al., Gastroenterology

Animal Experiments
Gut microbiome improves postoperative cognitive function by decreasing permeability of the blood-brain barrier in aged mice. – Wen, J. et al., Brain Research Bulletin

Indolepropionic Acid, a Metabolite of the Microbiome, Has Cytostatic Properties in Breast Cancer by Activating AHR and PXR Receptors and Inducing Oxidative Stress. – Sári, Z. et al., Cancers

Angiogenin maintains gut microbe homeostasis by balancing α-Proteobacteria and Lachnospiraceae. – Sun, D. et al., Gut

Gut Microbiota-Associated Activation of TLR5 Induces Apolipoprotein A1 Production in the Liver. – Yiu, J.H.C. et al., Circulation Research

Animal and insect microbiome
Cross-generational effects of climate change on the microbiome of a photosynthetic sponge. – Luter, H.M. et al., Environmental Microbiology

Symbionts shape host innate immunity in honeybees. – Horak, R.D. et al., Proceedings Biological Sciences

Parental Microbiota Modulates Offspring Development, Body Mass and Fecundity in a Polyphagous Fruit Fly. – Nguyen, B. et al. Microorganisms

Fast and Facile Biodegradation of Polystyrene by the Gut Microbial Flora of Plesiophthalmus davidis Larvae. – Woo, S. et al., Applied and Environmental Microbiology

Gut microbiota protects honey bees (Apis mellifera L.) against polystyrene microplastics exposure risks. – Wang, K. et al., Journal of Hazardous Materials

Plant, root, and soil microbiome
Characteristics of microbial community of soil subjected to industrial production of antibiotics. – Borčinová, M. et al., Folia Microbiologica

Host selection shapes crop microbiome assembly and network complexity. -Xiong, C. et al., The New Phytologist

Microbiome of root vegetables-a source of gluten-degrading bacteria. – Kõiv, V. et al., Applied Microbiology and Biotechnology

Water and extremophile microbiome
Environmental stability impacts the differential sensitivity of marine microbiomes to increases in temperature and acidity. – Wang, Z. et al., ISME Journal

Insights into the Vertical Stratification of Microbial Ecological Roles across the Deepest Seawater Column on Earth. – Xue, C-X et al., Microorganisms

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

Built environment
Airborne bacteria in outdoor air and air of mechanically ventilated buildings at city-scale in Hong Kong across seasons. – Zhou, Y. et al., Environmental Science and Technology

Phages and viruses
Review: Phages and their potential to modulate the microbiome and immunity. Federici, S. et al., Cellular and Molecular Immunology

Bioinformatics
Generalized estimating equation modeling on correlated microbiome sequencing data with longitudinal measures. – Chen, B. and Xu, W., PLoS Computational Biology

The Nubeam reference-free approach to analyze metagenomic sequencing reads. – Dai, H. and Guan, Y., Genome Research

The archives are half-empty: an assessment of the availability of microbial community sequencing data. – Jurburg, S.D. et al., Communications Biology

Techniques
An effective culturomics approach to study the gut microbiota of mammals. – Pereira, A.C. and Cunha, M.V., Research in Microbiology

Activity-based cell sorting reveals responses of uncultured archaea and bacteria to substrate amendment. – Reichart, N.J. et al., ISME Journal

An Ingestible Self-Polymerizing System for Targeted Sampling of Gut Microbiota and Biomarkers. – Chen, L. et al., ACS Nano

May 5, 2020

Events

The Virtual Microbiome Summit – May 19-22, 2020

Multi-site human microbiome

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

Human gut microbiome

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

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

Animal experiments

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

Techniques

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

April 24, 2020

Events

Virtual Podium 2020 – Session 5 (Microbiome) – April 24, 2020

Scientific career and work-life balance – April 24, 2020

World Malaria Day – April 25, 2020 – Draws attention to the impact of the disease and (re)urges us to find a way to overcome it once and for all.
Join the #talkingmalaria tweetchat on April 24, 2020 at 12 noon BST.

COVID-19

GRAND CHALLENGE: A billion molecules against COVID-19 – Joint European Disruptive Initiative

General microbiome

Reversibility of propionic acid inhibition to anaerobic digestion: Inhibition kinetics and microbial mechanism – Youl Han – Chemosphere

Responses of microbial structures, functions, metabolic pathways and community interactions to different C/N ratios in aerobic nitrification – Hongwei Sun – Bioresource Technology

PERSPECTIVE: Cultivating fungal research – Heidi H. Kong – Science

Human microbiome

REVIEW: Microbiota–immune interactions in asthma pathogenesis and phenotype – Nicholas W.Lukacs – Current Opinion in Immunology

CANCER IN TRANSLATION: Microbiome genomics for cancer prediction – Lorenz Adlung – Nature Cancer

Human skin microbiome

BOOK CHAPTER: The wound microbiome – Aayushi Uberoi – In: Wound Healing, Tissue Repair, and Regeneration in Diabetes.

Human gut microbiome

BOOK CHAPTER: Dietary Fiber and Gut Microbiota – Carolina Senés-Guerrero – In: Science and Technology of Fibers in Food Systems

Animal experiments

Effect of in feed administration of different butyrate formulations on Salmonella Enteritidis colonization and cecal microbiota in broilers – Lonneke Onrust – Veterinary Research

Stochasticity constrained by deterministic effects of diet and age drive rumen microbiome assembly dynamics – Ori Furman – Nature Communications

Sequence variant analysis reveals poor correlations in microbial taxonomic abundance between humans and mice after gnotobiotic transfer – Farnaz Fouladi – ISME Journal

Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in the cattle rumen – Javad Gharechahi – FEMS Microbiology Ecology

Animal microbiome

Host-microbiota interaction helps to explain the bottom-up effects of climate change on a small rodent species – Guoliang Li – ISME Journal

Plant, root, and soil microbiome

Tapping into the maize root microbiome to identify bacteria that promote growth under chilling conditions – Stien Beirinckx – Microbiome

Regulatory relationship between quality variation and environment of Cistanche deserticola in three ecotypes based on soil microbiome analysis – Xiao Sun – Scientific Reports

Effects of biodegradable plastic film mulching on soil microbial communities in two agroecosystems – Sreejata Bandopadhyay – PeerJ

Water microbiome

Total Microbial Activity and Sulfur Cycling Microbe Changes in Response to the Development of Hypoxia in a Shallow Estuary – Yunjung Park – Ocean Science Journal

Built environment

Associations Between Respiratory Infections and Bacterial Microbiome in Student Dormitories in Northern China – Xi Fu – Indoor Air

Bacterial community analysis of floor dust and HEPA filters in air purifiers used in office rooms in ILAS, Beijing – Jianguo Guo – Scientific Reports

Microbes in space

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation – Camilla Urbaniak – Microbiome

Food microbiology

Insights into the Microbiological Safety of Wooden Cutting Boards Used for Meat Processing in Hong Kong’s Wet Markets: A Focus on Food-Contact Surfaces, Cross-Contamination and the Efficacy of Traditional Hygiene Practices – Patrick T. Sekoai – Microorganisms

Pre-print

MicrobioLink: An integrated computational pipeline to infer functional effects of microbiome-host interactions – Tahila Andrighetti – bioRxiv

Repeatability and reproducibility assessment in a large-scale population-based microbiota study: case study on human milk microbiota – Shirin Moossavi – bioRxiv

Mendelian randomization analysis revealed causal effects from gut microbiota to abdominal obesity – Qian Xu – bioRxiv

A quantitative measure of functional redundancy in microbial ecosystems – Taylor M Royalty – bioRxiv

Host association induces genome changes in Candida albicans which alters its virulence – Amanda C Smith – bioRxiv

Shirin’s non-microbiology picks

CAREER FEATURE: Safely conducting essential research in the face of COVID-19 – Virginia Gewin – Nature

Reaching a Large Urban Undergraduate Population through Microbial Ecology Course-Based Research Experiences – Samantha Parks – Journal of Microbiology & Biology Education

POLICY FORUM: Against pandemic research exceptionalism – Alex John London – Science

WORLD VIEW: On the 50th Earth Day, take collective action for the planet – Emma Marris – Nature

BEHIND THE PAPER: Annotating the unknown: Functional Gene Annotation using Untargeted Metabolomics – Robert Jansen – Nature Microbiology Community

Human microbiota associated-rodent models

I came across brilliant review by Jens Walter et al. that resonates with my thoughts in microbiome field. I also work in the same field doing similar experiments, but sometimes it is better to stop and look back what you have been doing. This review has discussed some important points on the transmissibility of human diseases in human microbiota-associated mouse models. They acknowledge the importance of human microbiota-associated mouse models as valuable resource in the microbiome field. However, through systematic review they demonstrate that according to current literature it is easily possible to transfer (any!) human disease in mice through microbiota transplant. The inflated positivity and hype around these experiments must be criticized. Most importantly, they talk about the relevance of negative transplant studies, which are seldom published, and urge to use rigorous statistics to improve the data interpretation. Following are some excerpts from the review, though reading full review is highly recommended.

The problem with the concept:

“Because a “normal” or “healthy” microbiome has not been defined yet, we use the term dysbiosis to refer solely to an altered microbiome associated with a specific disease or condition as compared to a control. Whether such “dysbiotic” microbiomes are the cause or consequence of disease, or whether both are caused by a third factor, is, in most instances, unproven.”

“There are two well-documented diseases in the microbiome field that link a microbial biomarker with causation in disease: Helicobacter pylori-associated peptic ulceration and gastric cancer, and Clostridium (or Clostridioides) difficile infection-associated diarrhea. However, causal inferences between complex microbiomes and other inflammatory, metabolic, neoplastic, and neuro-behavioral disorders have been neither compelling nor conclusive.”

“A substantial proportion of the taxa that comprise the human gut microbiome fail to colonize in the recipient animals. Most importantly, the ecological factors (such as diet, lifestyle, disease phenotype, and human genotype) that have driven the dysbiosis in humans in the first place are absent in the recipient rodents, making it unlikely that disease-associated alterations are replicated. Taxa that colonize at sufficient levels may not engage in the EVOLUTIONARY routed host-microbe interactions that they establish with their native host.”

“Consider H. pylori and C. difficile, two members of the human microbiome with established causality in human disease, neither of which exhibit sufficient colonization to cause reliable pathology in conventional murine models.”

Results from systematic review:

“Of 38 studies meeting the inclusion criteria, all but two (36/38; 95%) concluded that fecal transfer from diseased donors resulted in at least one phenotype of the human disease being greater in the recipient mice when compared with transfers from healthy donors.”

Of all the studies, 63% (24/38) of the studies tested for a dysbiosis in the original human donor samples, and only 29% (11/38) confirmed that at least some aspect (reduced diversity, ecosystem processes/services, loss or bloom of specific taxa, or shifts in metabolic capacity) of the “human dysbiosis” was replicated in the recipient animals. Consequently, the majority of studies did not attempt to identify the “causal component” of the microbiome. Only a few studies (34%; 13/38) identified potential underlying mechanisms linking the dysbiotic microbiome with disease.”

Issues with statistics 

“Often, a small number (1–5) of human donors is used per human disease and control group, and these “donor microbiomes” are then replicated in a larger number of individual mice, which are then often used for statistical inference.”

“The result is “pseudoreplication,” which artificially inflates the sample size, the chance for “false positive” findings, and the evidence for a scientific claim. This problem is amplified if donor samples are pooled before the inoculation of groups of rodents, which is common practice for both the “diseased” and healthy control samples. We found that 84% (32/38) of the published studies on HMA murine models used the individual animals as the statistical inference, although animal numbers were much higher than the number of human donors and therefore inflated. Only 16% of studies (6/38) were clear in their use of the individual human donor samples as the “N” for statistical inferences or used the same number of rodents as donors.”

“When virtually all reports are positive, as in our systematic review, the greater the doubt will be and the more justified the scrutiny should be.”

Suggestions for alternative experimental approach

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Why is it important to change?

“Specifically, the correction of altered microbiomes, be it by FMT, live biotherapeutics, or microbial products, will be beneficial only if the alterations are causal or contributory to the disease rather than a bystander response. Causal claims in the microbiome field are often overstated and disproportional to the experimental evidence from which they are derived, and it has become difficult to identify a disease state in which the microbiome has not been implicated in the scientific literature, a notion amplified in the popular press.”

“Sadly, most researchers and reviewers in the microbiome field, and almost all editors of high-impact journals, seem to regard acceptance of the null hypothesis as a failure. As with all scientific endeavor, our field would be served better if editorial policies of higher tier journals and guidelines of funding agencies discouraged any discrimination against negative data, replications, validations of experimental designs, and statistical analyses.”

September 17, 2018

In today’s Microbiome Digest, look for rhizobacteria that affect plant size, methanogenesis in salt marsh sediments, a murine model for periodontitis, and an exciting preprint that identifies a microbiome in dinosaur bones! Plus, as bonus non-microbiology topics, we consider authorship norms across different disciplines and how forensics might work on Mars.

General Microbiome
(preprint) Life Inside A Dinosaur Bone: A Thriving Microbiome – Evan Thomas Saitta – bioRxiv

Metabolic Interactions of a Chain Elongation Microbiome – Wenhao Han – Applied and Environmental Microbiology

Human Gut Microbiome
Passing the “Acid Test”: Do Proton Pump Inhibitors Affect the Composition of the Microbiome? – Tien Dong – Digestive Diseases and Sciences

The gastric mucosal-associated microbiome in patients with gastric polyposis – Rongrong Ren – Scientific Reports

Animal Experiments
An experimental murine model to study periodontitis – Julie Marchesan – Nature Protocols

The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice – Alida Kindt – Nature Communications

Animal Microbiome
Global Networks of Symbiodinium-Bacteria Within the Coral Holobiont – Rachele Bernasconi – Microbial Ecology

(preprint) Gut microbial compositions mirror caste-specific diets in a major lineage of eusocial insects – Saria Otani -bioRxiv

Plant, Root, and Soil Microbiome
Plant growth-promoting rhizobacteria promote plant size inequality – Alan C. Gange – Scientific Reports

Diversity of active viral infections within the Sphagnum microbiome – Joshua MA Stough – Applied and Environmental Microbiology

The impact of high throughput sequencing on plant health diagnosticsThe impact of high throughput sequencing on plant health diagnostics – Ian Adams -European Journal of Plant Pathology

Deltaproteobacteria (Pelobacter) and Methanococcoides are responsible for choline-dependent methanogenesis in a coastal saltmarsh sediment – Eleanor Jameson – ISME Journal

Water and Extremophile Microbiome
Living at the frontiers of life: extremophiles in Chile and their potential for bioremediation – Roberto Orellana – Frontiers in Microbiology

Spatial structuring of bacterial communities in epilithic biofilms in the Acquarossa river (Italy) – Carolina Chiellini – FEMS Microbial Ecology

Bioinformatics
A small‐sample kernel association test for correlated data with application to microbiome association studies – Xiang Zhan – Genetic Epidemiology

Science, Publishing, and Career
Thousands of scientists publish a paper every five days – John P. A. Ioannidis – Nature

Alyson’s Non-Microbiology Picks
Sensing with tools extends somatosensory processing beyond the body – Luke E. Miller- Nature

How Will Police Solve Murders on Mars? – Geoff Manaugh – The Atlantic

June 25, 2018

Today’s Microbiome Digest features the sea turtle microbiome, the bacteria responsible for degrading bioplastics, a new clinical center for phage therapy, the gut-microbiome-brain axis in an Alzheimer’s Disease model, and a preprint about image duplication in scientific publishing.

Pregnancy and early life

Late-onset Sepsis in Preterm Infants Can Be Detected Preclinically by Fecal Volatile Organic Compound Analysis: A Prospective, Multicenter Cohort Study. – Daniel J C Berkhout- Clinical Infectious Diseases

Human vaginal microbiome

Abnormal vaginal microbioma is associated with severity of localized provoked vulvodynia. Role of aerobic vaginitis and Candida in the pathogenesis of vulvodynia. – Gilbert G. G. Donders- European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

* Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks – Filipe De Vadder – PNAS

Linking the Gut Microbiota to a Brain Neurotransmitter – Kelly G. Jameson – Trends in Neurosciences

Can epilepsy be treated by antibiotics? – Hilde M. H. Braakman – Journal of Neurology

* Changes in intestinal microbiota in HIV-1-infected subjects following cART initiation: influence of CD4+ T cell count – Yongjia Ji – Emerging Microbes & Infections

Review: Human gut microbiome: hopes, threats and promises – Patrice D Cani – Gut

Review: New treatments and therapeutic targets for IBS and other functional bowel disorders – Magnus Simrén – Nature Reviews Gastroenterology & Hepatology

Animal experiments

Effects of chronic noise exposure on the microbiome-gut-brain axis in senescence-accelerated prone mice: implications for Alzheimer’s disease – Bo Cui – Journal of Neuroinflammation

Bacterial methionine metabolism genes influence Drosophila melanogaster starvation resistance – Alec M. Judd – Applied and Environmental Microbiology

The benign helminth Hymenolepis diminuta ameliorates chemically induced colitis in a rat model system – Kateřina Jirků Pomajbíková – Parasitology

Protective role of commensal bacteria in Sjögren Syndrome – Mahira Zaheer – Journal of Autoimmunity

Lactobacillus murinus HF12 colonizes neonatal gut and protects rats from necrotizing enterocolitis. – Mubina Isani – PLOS One

Animal microbiome

Identification of bacteria present in ulcerative stomatitis lesions of captive sea turtles Chelonia mydas – D. X. Vega-Manriquez – Veterinary Research Communications

Characterization of the Microbiota of Oyster Larvae (Crassostrea virginica) and Tank Water from an Aquaculture System with High and Low Larval Survival Rates – Padmini Ramachandran – Genome Announcements

Early colonisation and temporal dynamics of the gut microbial ecosystem in Standardbred foals – S. Quercia – Equine Veterinary Journal

Plant, root, and soil microbiome

Microbial communities responsible for the degradation of poly(lactic acid)/poly(3-hydroxybutyrate) blend mulches in soil burial respirometric tests – Lenka Jeszeová – World Journal of Microbiology and Biotechnology

Phylogenetic diversity and investigation of plant growth-promoting traits of actinobacteria in coastal salt marsh plant rhizospheres from Jiangsu, China – Yuan Gong – Systematic and Applied Microbiology

Dynamics of soil microbial recovery from cropland to orchard along a 20-year chronosequence in a degraded karst ecosystem. – Hongkai Liao – Science of The Total Environment

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling. – Margarita Lopez-Fernandez – FEMS Microbial Ecology

Distinct impacts of reductive soil disinfestation and chemical soil disinfestation on soil fungal communities and memberships. – Jun Zhao – Applied Microbiology and Biotechnology

* Dispersal-competition tradeoff in microbiomes in the quest for land colonization – Francisco Dini-Andreote – Scientific Reports

Water and extremophile microbiome

Linking patterns of net community production and marine microbial community structure in the western North Atlantic. – Seaver Wang – The ISME Journal

Probiotics/Prebiotics

Composition and metabolism of fecal microbiota from normal and overweight children are differentially affected by melibiose, raffinose and raffinose-derived fructans. – Kaarel Adamberg – Anaerobe

Review: Nutraceuticals in Colorectal Cancer: A Mechanistic Approach – Marco Rossi – European Journal of Pharmacology

Science, publishing, and career

* Analysis and Correction of Inappropriate Image Duplication: The Molecular and Cellular Biology Experience – Arturo Casadevall – bioRxiv

Microbes in the news

U.S. center will fight infections with viruses – Kelly Servick – Science

Alyson’s non-microbiology pick

Neanderthal brain organoids come to life – Jon Cohen – Science

February 24, 2018

100+ alerts today with interesting papers across every category. Some highlights include choosing FMT donors, viral insulin-like peptides, and 2 papers on detecting duplicated figures.

General microbiome
Review: The microbiome in precision medicine: the way forward. – Joseph F Petrosino – Genome Medicine

Motivations of participants in the citizen science of microbiomics: data from the British Gut Project. – Lorenzo Del Savio – Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Pregnancy and early life
The Role of the Genitourinary Microbiome in Pediatric Urology: a Review. – Daniel Gerber – Current Urology Reports

Review: Reproductive outcome of patients undergoing in vitro fertilization treatment and diagnosed with bacterial vaginosis or abnormal vaginal microbiota: a systematic PRISMA review and meta-analysis. – Thor Haahr – Bjog : An International Journal Of Obstetrics And Gynaecology

Multi-site human microbiome
Review: The Vagus Nerve at the Interface of the Microbiota-Gut-Brain Axis. – Bruno Bonaz – Frontiers In Neuroscience

Human vaginal microbiome
Protein Content of Cervicovaginal Fluid Is Altered During Bacterial Vaginosis. – Carolina Sanitá Tafner Ferreira – Journal Of Lower Genital Tract Disease

Human nearly-sterile sites
Microbiome-Host Interactions in Hematopoietic Stem-Cell Transplant Recipients. – Tessa Andermann – Biology Of Blood And Marrow Transplantation : Journal Of The American Society For Blood And Marrow Transplantation

Human gut microbiome
** Competitively Selected Donor Fecal Microbiota Transplantation: Butyrate Concentration and Diversity as Measures of Donor Quality. – Danielle Barnes – Journal Of Pediatric Gastroenterology And Nutrition

Metagenomic Characterization of the Human Intestinal Microbiota in Fecal Samples from STEC-Infected Patients. – Federica Gigliucci – Frontiers In Cellular And Infection Microbiology

ReviewHuman Gut Microbiota and Gastrointestinal Cancer. – Changting Meng – Genomics, Proteomics & Bioinformatics

Review: Impact of the Gut Microbiota on Intestinal Immunity Mediated by Tryptophan Metabolism. – Jing Gao – Frontiers In Cellular And Infection Microbiology

Microbial interactions
Competitive resource allocation to metabolic pathways contributes to overflow metabolisms and emergent properties in cross-feeding microbial consortia. – Ross P Carlson – Biochemical Society Transactions

Worlds Apart – Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions. – Zhi-Luo Deng – Frontiers In Microbiology

Using niche breadth theory to explain generalization in mutualisms – Rebecca T. Batstone – Ecology

Metabolic division of labor in microbial systems – Ryan Tsoi – PNAS

Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle – Karthik Anantharaman – ISME

Review: Bacterial – Fungal Interactions: ecology, mechanisms and challenges. – A Deveau – Fems Microbiology Reviews

Role of extracellular polymeric substances in polymicrobial biofilm infections of Staphylococcus epidermidis and Candida albicans modelled in the nematode Caenorhabditis elegans. – Jillian E Holt – Pathogens And Disease (older, from July 2017)

Animal experiments
Acute and repeated exposure to social stress reduces gut microbiota diversity in Syrian hamsters. – Katherine A Partrick – Behavioural Brain Research

1H NMR based identification of intestinally-absorbed metabolites by Ussing chamber analysis of the rat cecum. – Meredith Dinges – Analytical Chemistry

Influence of gemcitabine chemotherapy on the microbiota of pancreatic cancer xenografted mice. – Concetta Panebianco – Cancer Chemotherapy And Pharmacology

Grape seed proanthocyanidins influence gut microbiota and enteroendocrine secretions in female rats. – Àngela Casanova-Martí – Food & Function

Combined Dietary Anthocyanins, Flavonols, and Stilbenoids Alleviate Inflammatory Bowel Disease Symptoms in Mice. – Aurelia Scarano – Frontiers In Nutrition

Ubc9 overexpression and SUMO1 deficiency blunt inflammation after intestinal ischemia/reperfusion. – Jörn Karhausen – Laboratory Investigation; A Journal Of Technical Methods And Pathology

Glucocorticosteroids and ciclosporin do not significantly impact canine cutaneous microbiota. – Giovanni Widmer – Bmc Veterinary Research

The effects of high dose of two manganese supplements (organic and inorganic) on the rumen microbial ecosystem. – Svetlana Kišidayová – Plos One

Hydrogen peroxide production by lactobacilli promotes epithelial restitution during colitis. – Ashish K Singh – Redox Biology

Neuroprotective effects of fecal microbiota transplantation on MPTP-induced Parkinson’s disease mice: gut microbiota, glial reaction and TLR4/TNF-α signaling pathway. – Meng-Fei Sun – Brain, Behavior, And Immunity

Rotenone induces gastrointestinal pathology and microbiota alterations in a rat model of Parkinson’s disease. – Michaela E Johnson – Neurotoxicology

Prenatal Androgen Exposure Causes Hypertension and Gut Microbiota Dysbiosis. – Shermel Sherman – Gut Microbes

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome – Claudia Pogoreutz – Ecology And Evolution

Gut microbiota modulates adoptive cell therapy via CD8α dendritic cells and IL-12. – Mireia Uribe-Herranz – Jci Insight

Animal microbiome
Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract. – Li Zhang – Frontiers In Microbiology

Characterization of gut bacterial flora of Apis mellifera from north-west Pakistan – Syed Ishtiaq Anjum – Saudi Journal Of Biological Sciences

A Member of the Roseobacter Clade, Octadecabacter sp., is the Dominant Symbiont in the Brittle Star Amphipholis squamata. – Kathleen M Morrow – Fems Microbiology Ecology

Alimentary microbes of winter-form Drosophila suzukii. – M T Fountain – Insect Molecular Biology

The development of gut microbiota in ostriches and its association with juvenile growth – Elin Videvall – bioRxiv

Review: Regulation of intestinal health by branched-chain amino acids. – Hua Zhou – Animal Science Journal = Nihon Chikusan Gakkaiho

Book chapter: Termite Gut Microbiome – Navodita Maurice – Sustainability in Plant and Crop Protection

Plant, root, and soil microbiome
Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. – Joseph A Edwards – Plos Biology

Quantitative Genetic Analysis of the Maize Leaf Microbiome – Jason G. Wallace – bioRxiv

 

Variable response of nirK and nirS containing denitrifier communities to long term pH manipulation and cultivation. – Miriam B Herold – Fems Microbiology Letters

Landscape topography structures the soil microbiome in arctic polygonal tundra. – Neslihan Taş – Nature Communications

Effects of soil depth and plant-soil interaction on microbial community in temperate grasslands of northern China. – Xiaodong Yao – The Science Of The Total Environment

Seasonal dynamics in the community structure and trophic structure of testate amoebae inhabiting the Sanjiang peatlands, Northeast China. – Lihong Song – European Journal Of Protistology

Investigation of rhizospheric microbial communities in wheat, barley and two rice varieties at the seedling stage. – Tao Lu – Journal Of Agricultural And Food Chemistry

Increasing N deposition impacts neither diversity nor functions of deadwood-inhabiting fungal communities, but adaptation and functional redundancy warrants ecosystem function. – Witoon Purahong – Environmental Microbiology

Belowground Interactions Impact the Soil Bacterial Community, Soil Fertility, and Crop Yield in Maize/Peanut Intercropping Systems. – Qisong Li – International Journal Of Molecular Sciences

Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. – Liesje Mommer – The New Phytologist

Isolation and characterization of N2 -fixing bacteria from giant reed and switchgrass for plant growth promotion and nutrient uptake – Jia Xu – Journal of Basic Microbiology

Structural diversity across arbuscular mycorrhizal, ectomycorrhizal, and endophytic plant-fungus networks – Hirokazu Toju – bioRxiv

Water and extremophile microbiome
Seasonal variability in the persistence of dissolved environmental DNA (eDNA) in a marine system: The role of microbial nutrient limitation. – Ian Salter – Plos One

Elevated temperature drives kelp microbiome dysbiosis, while elevated carbon dioxide induces water microbiome disruption. – Jeremiah J Minich – Plos One

Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge. – Blake D Ramsby – Molecular Ecology

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems – Navdeep K Dhami – Frontiers In Microbiology

Microbial Community Structure and Function Indicate the Severity of Chromium Contamination of the Yellow River. – Yaxin Pei – Frontiers In Microbiology

Assessing the microbial communities inhabiting drinking water networks and nitrifying enrichments with special respect on nitrifying microorganisms. – Zsuzsanna Nagymáté – Acta Microbiologica Et Immunologica Hungarica

Microbial community composition along a 50,000 year lacustrine sediment sequence. – Aurèle Vuillemin – Fems Microbiology Ecology

Diversity of Rare and Abundant Prokaryotic Phylotypes in the Prony Hydrothermal Field and Comparison with Other Serpentinite-Hosted Ecosystems. – Eléonore Frouin – Frontiers In Microbiology

Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition – Alescia A. Roberto – Water Research

Built environment
Dog introduction alters the home dust microbiota. – Alexandra Sitarik – Indoor Air

Urbanization Reduces Transfer of Diverse Environmental Microbiota Indoors. – Anirudra Parajuli – Frontiers In Microbiology

Removal of artificial sweeteners and their effects on microbial communities in sequencing batch reactors. – Shaoli Li – Scientific Reports

Microbes in space
Soil microbial habitats in an extreme desert Mars-analogue environment – Kimberley Warren-Rhodes – bioRxiv

Food microbiology
** Editorial: Microbiome Yarns: human milk oligosaccharides, Bifidobacterium and immunopowergames. – Kenneth Timmis – Microbial Biotechnology

Detection of Bacterial DNA During the Process of Sake Production Using Sokujo-Moto. – Momoka Terasaki – Current Microbiology

A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial. – Charlotte Bamberger – Nutrients

Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity. – Rocío Escribano-Viana – Frontiers In Microbiology

Review: The Promising Pharmacological Effects and Therapeutic/Medicinal applications of Punica Granatum L. (Pomegranate) as a Functional Food in Humans and Animals. – Kuldeep Dhama – Recent Patents On Inflammation & Allergy Drug Discovery

Probiotics / prebiotics / antibiotics
Bile-Salt-Hydrolases from the Probiotic Strain – Thibault Allain – Frontiers In Microbiology

** A reservoir of ‘historical’ antibiotic resistance genes in remote pristine Antarctic soils. – Marc W Van Goethem – Microbiome

PAHs accelerate the propagation of antibiotic resistance genes in coastal water microbial community. – Jing Wang – Environmental Pollution (Barking, Essex : 1987)

Short-term Oral Antibiotics Treatment Promotes Inflammatory Activation of Colonic Invariant Natural Killer T and Conventional CD4 – Claudia Burrello – Frontiers In Medicine

Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3 – François P. Douillard – Plos One

A probiotic complex, rosavin, zinc, and prebiotics ameliorate intestinal inflammation in an acute colitis mouse model. – Jin-Sil Park – Journal Of Translational Medicine

Phages and viruses
** Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm shift for host-microbe interactions. – Emrah Altindis – Proceedings Of The National Academy Of Sciences Of The United States Of America

Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan. – Mitsuhiro Yoshida – Frontiers In Microbiology

A virus or more in (nearly) every cell: ubiquitous networks of virus-host interactions in extreme environments. – Jacob H Munson-McGee – The Isme Journal

Bioinformatics
MUGAN: Multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment. – Byunghan Lee – Bioinformatics (Oxford, England)

Techniques
Time Radically Alters Ex Situ Evidentiary Soil 16S Bacterial Profiles Produced Via Next-Generation Sequencing – Alyssa J. Badgley – Forensic Sciences

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data – Jonathan M Palmer – bioRxiv

Genomes
Complete Genome Sequence and Genomic Characterization of – Won-Hyong Chung – Frontiers In Pharmacology

Luteimonas rhizosphaerae sp. nov., isolated from the rhizosphere of Triticum aestivum L. –  Guo-Yan Zhao – International Journal of Systematic and Evolutionary Microbiology

Science, publishing, and career
Testing Hypotheses on Risk Factors for Scientific Misconduct via Matched-Control Analysis of Papers Containing Problematic Image Duplications – Daniele Fanelli – Scientific and Engineering Ethics

Bioscience-scale automated detection of figure element reuse – Daniel E Acuna – bioRxiv

August 3, 2017

The impact of root hairs on rhizosphere soil structure, gut virome dynamics in hematopoietic stem cell transplantation, an art installation made from bacteria found in a 300-year-old copy of Ovid’s Metamorphoses.

Events and jobs

Assistant/Associate Professor of Soil Microbiomes – Colorado State University

Research Lab Tech Intermediate – University of Michigan Center for Microbial Systems Molecular Biology Laboratory

Content, Lead bioRxiv – Cold Spring Harbor Laboratory

General microbiome

Perspective: The evolution of the host microbiome as an ecosystem on a leash – Kevin R Foster – Nature

Animal experiments

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology

Cxcr2 signaling and the microbiome suppress inflammation, bile duct injury, and the phenotype of experimental biliary atresia – Junbae Jee – PLOS ONE

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4 – Kazuaki Nakata – Journal of Biological Chemistry

Early life antibiotic exposure causes intestinal dysbiosis and exacerbates skin and lung pathology in experimental systemic sclerosis – Heena Mehta – Journal of Investigative Dermatology

16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses – Xinxin Ma – Veterinary Microbiology

Plant, root, and soil microbiome

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation – Nicolai Koebernick – New Phytologist

Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides – Markus F F Arnold – mBio

Water and extremophile microbiome

Preprint: Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone” – J Cameron Thrash – bioRxiv

Food microbiology

Fate of Listeria innocua during production and ripening of smeared hard cheese made from raw milk – P Hammer – Journal of Dairy Science

Probiotics/prebiotics

Review: Systematic review: probiotics for functional constipation in children – Katarzyna Wojtyniak – European Journal of Pediatrics

Phages and viruses

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease – Jérôme Legoff – Nature Medicine

Metabolomics

The Opportunities of Metabolomics in Drug Safety Evaluation – Pengcheng Wang – Current Pharmacology Reports

More microbes

SnapShot: Electrochemical Communication in Biofilms – Dong-yeon D Lee – Cell

Microbes in the news

Microbiome: Does it really matter to our health? – Jo Seed – Imperial College London

Lovers Share Colonies of Skin Microbes, Study Finds – Aneri Pattani – New York Times

Scientists map the distribution of antimicrobial resistance across Chinese major cities – EurekAlert

Bacteria could be key to freeing South Pacific of mosquitoes – Emma Maris – Nature

Microbiology: The case of the mysterious messenger – Kaitlin Johnson – Nature

Microbes on the market

World’s First DNA and Microbiome Platform Enters the UK Market – Business Wire

IDbyDNA and ARUP Laboratories Announce Partnership to Develop and Commercialize Novel Infectious Disease Testing Using Metagenomics – PR Newswire

Bacteria art

Bacteria from 300-year-old Ovid poetry volume inspires ‘bio-artist’ – Maev Kennedy – The Guardian

Science, career, and publishing

Preprint: The reproducibility of research and the misinterpretation of P values – David Colquhoun – bioRxiv

Preprint: The GSS is an unreliable indicator of biological sciences postdoc population trends – Christopher L Pickett – bioRxiv

The Plan to End Science’s Sexist #manel Problem – Sarah Scoles – WIRED

  • Featuring Elisabeth Bik!

Non-microbiology picks

Proteins evolve on the edge of supramolecular self-assembly – Hector Garcia-Seisdedos – Nature