Hi folks! Another new volunteer poster here up from the ranks of the recently recruited. Today’s post is pre-print and plant/soil heavy. If up until now you’ve focused your reading on animal microbiomes, now’s a great time to check in on our photosynthesizing friends. Lots of great work today on the affect of management strategies on plant-associated and soil microbes. If the transition into the world of the leafy green is too jarring, perhaps try easing yourself in with Marchese et al.’s work on the mycobiome of sea cucumbers – a critter which is plant in common name only.

**************************************

Pregnancy and early life

Review: Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health – Lyons et al. – Nutrients

Human respiratory microbiome

Comment: Microbiota and chronic lung disease in preterm infants. Where is the truth? – Nandakumar and Aly – Journal of Perinatology

Human skin microbiome

The cutaneous microbiome in hospitalized patients with pressure ulcers – de Wert Luuk et al. – Scientific Reports

Human vaginal microbiome

Inflammatory and antimicrobial properties differ between vaginal Lactobacillus isolates from South African women with non-optimal versus optimal microbiota – Manhanzva et al. – Scientific Reports

A meta-analysis of mannose-binding lectin gene polymorphisms with the risk of recurrent vulvovaginal infections – Kalia et al. – Scientific Reports

Human gut microbiome

Review: Gut Microbial Metabolites of Aromatic Amino Acids as Signals in Host–Microbe Interplay – Liu et al. – Trends in Endocrinology & Metabolism

Preprint: Computational Modeling of the Gut Microbiota Predicts Metabolic Mechanisms of Recurrent Clostridioides difficile Infection – Henson – bioRxiv

Preprint: Comparative genomics reveals different population structures associated with host and geographic origin in antimicrobial-resistant Salmonella enterica – Liao et al. – bioRxiv

**************************************

Animal experiments

Preprint: Validating the use of bovine buccal sampling as a proxy for the rumen microbiota using a time course and random forest classification approach – Young et al. – bioRxiv

Animal microbiome

Gut microbial diversity across a contact zone for California voles: implications for lineage divergence of hosts and mito‐nuclear mismatch in the assembly of the mammalian gut microbiome – Lin et al. – Molecular Ecology

Diversity and bioactivity of fungi associated with the marine sea cucumber Holothuria poli: disclosing the strains potential for biomedical applications – Marchese et al. – Journal of Applied Microbiology

Perspective: Microbiome maturation during a unique developmental window – Videvall – Molecular Ecology

Preprint: Microbial interactions in the mosquito gut determine Serratia colonization and blood feeding propensity – Kozlova et al. – bioRxiv

Plant, root, and soil microbiome

Reduced microbial diversity induces larger volatile organic compound emissions from soils – Abis et al. – Scientific Reports

Increased temperatures alter viable microbial biomass, ammonia oxidizing bacteria and extracellular enzymatic activities in Antarctic soils – Barnard et al. – FEMS Microbiology Ecology

One ring to rule them all: an ecosystem engineer fungus fosters plant and microbial diversity in a Mediterranean grassland – Zotti et al. – New Phytologist

Changes in soil fungal communities following anthropogenic disturbance are linked to decreased lodgepole pine seedling performance – Beck et al. – Journal of Applied Ecology

Long-term effects of stump removal and tree species composition on the diversity and structure of soil fungal communities – Modi et al. – FEMS Microbiology Ecology

Effect of treated sewage characteristics on duckweed biomass production and microbial communities – Iwano et al. – Water Science and Technology

Review: Functional roles of microbial symbionts in plant cold tolerance – Acuña‐Rodríguez et al. – Ecology Letters

Preprint: Dryland cropping system, weed communities, and disease status modulate the effect of climate conditions on wheat soil bacterial communities – Ishaq et al. – bioRxiv

Preprint: Cropping systems that improve richness convey greater resistance and resilience to soil fungal, relative to prokaryote, communities – Finn et al. – bioRxiv

Water and extremophile microbiome

Diverse groups of fungi are associated with plastics in the surface waters of the Western South Atlantic and the Antarctic Peninsula – Lacerda et al. – Molecular Ecology

Nitrification kinetics and microbial community dynamics of attached biofilm in wastewater treatment – Skoyles et al. – Water Science and Technology

**************************************

Techniques

Data normalization strategies in metabolomics: Current challenges, approaches, and tools – Misra – European Journal of Mass Spectrometry

**************************************

Microbes on the market

Blog: COVID-19: Impact of Coronavirus Pandemic on Human Microbiome Market 2020. Top Leaders are Dohme Corp, Seres Therapeutics, Synthetic Biologics Inc, Synlogic – Publicist 360

 

 

Hello,

Hope this finds you all well. This is my first post, and hopefully not the last. Here are some interesting articles for you to enjoy today. You may notice that I will end up posting a lot about stress, sleep, and mental illness. I’m pretty diverse and also have a soft spot for nature.

Happy reading.

*****************************

• Pregnancy and early life

Review: Maternal Vertical Transmission Affecting Early-life Microbiota Development S. Wang, et al.

• Human skin microbiome

Bacteriophage of the Skin Microbiome in Patients with Psoriasis and Healthy Family Controls H. Wang, et al.

• Human vaginal microbiome

Clinical Research: A 28 Day Clinical Assessment of a Lactic Acid-containing Antimicrobial Intimate Gel Wash Formulation on Skin Tolerance and Impact on the Vulvar Microbiome E. Bruning, et al.

• Human gut microbiome

Altered Fecal Microbiome Years after Traumatic Brain Injury R. J. Urban, et al.

*****************************

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

A Uniquely Altered Oral Microbiome Composition Was Observed in Pregnant Rats With Porphyromonas gingivalis Induced Periodontal Disease M.S. Walkenhorst, et al.

• Animal microbiome (for animals in the wild)

Preprint: Gut microbiome modulates behaviour and life history in two wild rodents J. W. Jameson, et al.

• Plant, root, and soil microbiome

Review: Recent advances in the role of plant metabolites in shaping the root microbiome R.P. Jacoby, et al.

Hi everyone!

In today’s digest there is a range of exciting papers. The first paper looks into using a COVID-19 RBD vaccine on rodents. You will also find a great study on utilising Myxobacterium to fight cucumber wilt – even as an avid cucumber hater I appreciated this one! A third highlight is an exciting clinical study of heat-inactivated Bifidobacterium in reducing patient IBD symptoms.

COVID-19

Preprint: The SARS-CoV-2 receptor-binding domain elicits a potent neutralizing response without antibody-dependent enhancement – Quinlan et al.

Preprint: Comparison of SARS-CoV-2 infections among 3 species of non-human primates – Lu et al.

Preprint: Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence – Leary et al.

Human gut microbiome

Preprint: Short-chain fatty acid production by gut microbiota from children with obesity is linked to bacterial community composition and prebiotic choice – Holmes et al.

Short Review: In sickness and health: Effects of gut microbial metabolites on human physiology – Glowacki & Martens. PLOS Pathogens.

Animal experiments

Evaluation of microbiome-host relationships in the zebrafish
gastrointestinal system reveals adaptive immunity is a target of bis(2-ethylhexyl) phthalate (DEHP) exposure – Adamovsky et al. Environmental Science & Technology.

Abnormal gut microbiota composition is associated with experimental autoimmune prostatitis‐induced depressive‐like behaviors in mice – Du et al. The Prostate.

Plant, root and soil microbiome

Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios – P. Braga et al. Microbiome.

Predatory myxobacterium controls cucumber fusarium wilt by regulating soil microbial community – Ye et al. Microbiome.

Food Microbiology

Green tea polyphenols boost gut-microbiota-dependent mitochondrial TCA and urea cycles in Sprague–Dawley rats – Zhou et al. The Journal of Nutritional Biochemistry.

Probiotics

Heat-inactivated Bifidobacterium bifidum MIMBb75 (SYN-HI-001) in the treatment of irritable bowel syndrome: amulticentre, randomised, double-blind, placebo-controlled clinical trial – Andresen et al. The Lancet Gastroentrology & Hepatology.

¡Buenos dias!

Greetings from Spain as I write my first blog post, I am very excited to have been given this opportunity and I hope I can send a little bit of this enthusiasm to all of you in this sunday morning. In today’s menu we have a really interesting review of Microbiome-Neuronal Signaling along with another of human breast milk with a curius subsection of It’s miRNA composition. All this with many other publications from biorreactors to soil microbiome . I hope you enjoy and forgive my little mistakes.

Hope to see you soon. Adios!

COVID-19

Preprint: A virus that has gone viral: Amino acid mutation in S protein of Indian isolate of Coronavirus COVID-19 might impact receptor binding and thus infectivity Priyanka Saha in bioRxiv

Preprint: Potential host range of multiple SARS-like coronaviruses and an improved ACE2-Fc variant that is potent against both SARS-CoV-2 and SARS-CoV-1 Yujun Li et al. in bioRxiv

Preprint: A Highly Scalable and Rapidly Deployable RNA Extraction-Free COVID-19 Assay by Quantitative Sanger Sequencing Devon Chandler-Brown in bioRxiv

Preprint: Nonmedical Masks in Public for Respiratory Pandemics: Droplet Retention by two-layer Textile Barrier Fully Protects Germ-free Mice from Bacteria in Droplets Alexander Rodriguez-Palacios et al. in bioRxiv

General Microbiome

Linoleic acid induces metabolic stress in the intestinal microorganism Bifidobacterium breve DSM 20213 Alice Senizza et al. in Scientific Reports

Human Gut Microbiome

Preprint: Not just ‘immunity’: how the microbiota can reshape our approach to cancer immunotherapy Federico Boem et al. in Immunotherapy

Review: Toward Understanding Microbiome-Neuronal Signaling K. G. Jameson et al. in Molecullar Cell.

Gut microbiota in children with juvenile idiopathic arthritis: characteristics, biomarker identification, and usefulness in clinical prediction Xubo Qian et al. in BMC Genomics

Fecal-associated microbiome differences between traditional Chinese medicine qi-deficiency and balanced constitutions Jianhua Zhen et al. in Journal of Traditional Chinese Medical Sciences

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis Amy I.Yu et al. in Cell Reports

Human Vaginal Microbiome

Review: Recommendations on Screening for Asymptomatic Bacterial Vaginosis in Pregnancy Amanda L. et al. in JAMA

Human nearly-sterile sites

Preprint: Changes to the resistome of Pseudomonas aeruginosa clone ST308 associated with corneal infection over time Mahjabeen Khan et al. in bioRxiv

Pregnancy and early life

Review: Components of human breast milk: from macronutrient to microbiome and microRNA. Su Yeong Kim et al. in Clinical and experimental pediatrics

Animal experiments

The impact of short-term acute heat stress on the rumen microbiome of Hanwoo steers Youl Chang Baek et al. in Journal of Animal Science and Technology (JAST)

Effects of Dietary Microencapsulated Tannic Acid (extracted from Chinese gallnut) Supplementation on the Growth Performance, Intestinal Morphology, and Intestinal Microbiota in Weaning Piglets Meiwei Wang et al. in Journal of Animal Science

Association between oropharyngeal microbiome and weight gain in piglets during pre and post weaning life Andrew Wange Bugenyi et al. in Journal of Animal Science and Technology (JAST)

An early fecal microbiota transfer improves the intestinal conditions on microflora and immunoglobulin and antimicrobial peptides in piglets Teng Teng et al. in Journal of Agricultural and Food Chemistry

Microbial communities and food safety aspects of crickets (Acheta domesticus) reared under controlled conditions X. Fernandez-Cassi et al. in Journal of Insects as Food and Feed

Difference of gut microbiota composition based on the body condition scores in dogs Ju Lan Chun et al. in Journal of Animal Science and Technology (JAST)

Preprint: A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity Jack G Ganley et el. in bioRxiv

Plant, root, and soil microbiome

Geology and climate influence rhizobiome composition of the phenotypically diverse tropical tree Tabebuia heterophylla Yakshi Ortiz et al. in PLOS ONE

Impact of Atrazine Exposure on the Microbial Community Structure in a Brazilian Tropical Latosol Soil Ana Flavia Tonelli Fernandes et al. in Microbes and Environments

Prepint: An intensive multilocation temporal dataset of fungal communities in the root and rhizosphere of Brassica napus NavidBazghaleh in Data et al. in Brief

Comammox bacterial abundance, activity, and contribution in agricultural rhizosphere soils XiaominWang et al. in Science of The Total Environment

Diversity and potential biogeochemical impacts of viruses in bulk and rhizosphere soils Li Bi et al. in Environ Microbiology

Rhizosphere microbiome assemble and its impact on plant growth Qian Qu et al. in Journal of Agricultural and Food Chemistry

Water and extremophile microbiome

Patterns in extracellular enzyme activity and microbial diversity in deep-sea Mediterranean sediments NagissaMahmoudi et al. in Deep Sea Research

Preprint: Towards a probiotic approach for building plumbing – Nutrient-based selection during biofilm formation on flexible polymeric materials Lisa Neu in bioRxiv

Built environment

The biogeography and assembly of microbial communities in wastewater treatment plants in China Bing Zhang et al. in Environmental Science & Technology

Aerobic biodegradation of p-nitrophenol in a nitrifying sludge bioreactor: System performance, sludge property and microbial community shift MingrunLi et al. in Journal of Environmental Management

Microbes on the market

Blog: Microbiome Therapeutics Market 2020 Latest Trends, Technology Studies, Substantial Growth, Key Developments and Future Analysis till 2025 Anita in Science In Me

Blog: Microbiome Sequencing Services Market: Opportunities and Forecast Assessment, 2019-2025 supriya in Curius Desk

Techniques

preprint: Combining light sheet microscopy and expansion microscopy for fast 3D imaging of virus-infected cells with super-resolution Luca Mascheroni et al. in bioRxiv

Good morning. This is my first contribution to the Microbiome Digest. It is an interesting opportunity to survey some of the current literature and areas of research, and I hope that the literature summarized below will be of interest to readers. Today’s digest also includes articles on covid-19. There are two publications on metabolomic and/or proteomic profiling of covid-19 patients, and one which analyzes genetic variants of the ACE-2 protein across a database taken from the Italian population. A topic of personal interest to me is how and whether the level of glycosylation and sialylation on the ACE-2 protein and on the coronavirus spike protein may influence binding and covid-19 infectivity. However, this is not covered in the publication.

The two papers in the pregnancy and early life section discuss the development of the infant microbiome, with regard to dysbiosis in preterm infants and with regard to the contribution of maternal milk-derived microbes.

The extremophile paper by Roy et al. looks at the microbial population in boron-rich extremophile environments. Alkyl borates are known to form boronate complexes with saccharides and it would be interesting to profile the enzymatic functions of these strains for potential borate-metabolizing capability.

The techniques paper by Fergusson et al. describes the building of a mass spectral database by which Burkholderia and related bacterial strains can be identified from their MALDI-TOF metabolite profile, using the Bruker Biotyper platform. Both nucleic acid sequencing and metaproteomic tools were invoked by An et al., in their Ecotoxicology paper investigating the mechanism of microbial metabolism of toxic dye molecules in the environment.

Several papers discuss correlations between microbial populations and disease states. For example, Tengeler’s paper describes the use of MRI to to study the effects on the brains of germ-free mouse brains, following transplantation of gut bacteria from humans with and without ADHD, while Zheng et al. describe microbiome signatures which correlate with lung cancer.

Under the Market Analysis section, a $38M deal between Second Genome and Gilead has been announced.

Covid-19
Preprint:
The relationship of COVID-19 severity with cardiovascular disease and its traditional risk factors: A systematic review and meta-analysis
Matsushita, K. et al.

Preprint:
Repurposing Therapeutics for COVID-19: Rapid Prediction of Commercially available drugs through Machine Learning and Docking
Mahapatra, S. et al.

Preprint:
Proteomic and Metabolomic Characterization of COVID-19 Patient Sera
Bo Shen et al.

Preprint:
Plasma Metabolomic and Lipidomic Alterations Associated with COVID-19
Wu, D. et al.

Preprint:
Estimating false-negative detection rate of SARS-CoV-2 by RT-PCR
Wikramaratna, P. et al.

Preprint:
ACE2 variants underlie interindividual variability and susceptibility to COVID-19 in Italian population
Renieri, A. et al.

General Microbiome

MP10-18 FUNCTIONAL ANALYSIS OF THE URINARY TRACT MICROBIOME OF CALCIUM OXALATE STONE FORMERS
N Kachroo et al,
The Journal of Urology, 2020

Microbial Engineering Community (mce): Selecting Key Players in Microbiomes
CEG Camacho et al.
Chemical Engineering Transactions, 2020

Pregnancy and early life

Contributors to Dysbiosis in Very-Low-Birth-Weight Infants
MW Groer et al.
Journal of Obstetric, Gynecologic, & Neonatal Nursing, 2020

A cross-sectional pilot study of birth mode and vaginal microbiota in reproductive-age women
CA Stennett et al.
PLOS one, 2020

Milk Microbiome and Neonatal Colonization: Overview.
S Rautava
Nestle Nutrition Institute workshop series, 2020

Oral Microbiome

Single-Cell Genomics and the Oral Microbiome
M Podar et al.
Journal of Dental Research, 2020

Dysbiosis of saliva microbiome in patients with oral lichen planus
Fei Yan Yu et al. BMC Microbiology, 2020

Gut Microbiome

Specific gut microbiome signature predicts the early-stage lung cancer
Yajuan Zheng et al.
Gut Microbes, 2020

Complex influences of gut microbiome metabolism on various drug responses
Sihyun Chae et al.
Translational and Clinical Pharmacology, 2020

Gut Microbiota, Its Role in Induction of Alzheimer’s Disease Pathology, and Possible Therapeutic Interventions: Special Focus on Anthocyanins
MS Khan et al.
Cells, 2020

Faecal microbiota transplantation: indications, evidence and safety
WT Soo et al.
Australian Prescriber, 2020

PhD Thesis:
The effect of faecal microbiota transplantation in irritable bowel syndrome. A double blind, randomized placebo controlled single centre study
Peter Johnsen

Animal Experiments
Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice
Anouk C. Tengeler et al.
Microbiome 2020

Aberrant gut microbiota alters host metabolome and impacts renal failure in humans and rodents
Xifan Wang et al.
Gut, 2020

Animal Microbiome
The microbiota of dairy milk: a review
Eugenio Parente
International Dairy Journal, 2020

Plant, root and soil Microbiome
Comparative analysis of the total and active bacterial communities in the surface sediment of Lake Taihu
T Liu et al.
FEMS Microbiology Ecology, 2020

Recovery of fen peatland microbiomes and predicted functional profiles after rewetting
WJ Emsens et al.
The ISME Journal, 2020

Microbial assemblages associated with the rhizosphere and endosphere of an herbage, Leymus chinensis.
J Chen et al.
Microbial biotechnology, 2020

Insights into the earthworm gut multi-kingdom microbial communities
R Sapkota et al.
Science of the Total Environment, 2020

Prevalent root-derived phenolics drive shifts in microbial community composition and prime decomposition in forest soil
MJ Zwetsloot et al.
Soil Biology and Biochemistry, 2020

Extremophile Microbiomes
Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica
EM Bottos et al.
FEMS Microbiology Ecology, 2020

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics
Weipeng Zhang et al.
Microbiome 2020

Integrated metagenomic and metaproteomic analyses reveal potential degradation mechanism of azo dye-Direct Black G by thermophilic microflora
X An et al.
Ecotoxicology and Environmental Safety, 2020

Microbiome and ecology of a hot spring-microbialite system on the Trans-Himalayan Plateau
C Roy et al.
Scientific Reports, 2020

Microbes in Built Environments

An in-depth survey of the microbial landscape of the walls of a neonatal operating room
D Derilus et al.
PLOS ONE, 2020

Phages and Viruses

Preprint:
Infection with novel Bacteroides phage BV01 alters host transcriptome and bile acid metabolism in a common human gut microbe
DE Campbell et al.

Bioinformatics and Techniques

Development of a Custom MALDI-TOF Mass Spectrometric Database for Identification of Environmental Burkholderia and Related Genera.
CH Fergusson et al.
Environmental Microbiology, 2020

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics
Eli Levy Karin et al.
Microbiome 2020

Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories
Shan Sun et al.
Microbiome 2020

Preprint:
DNA Thermo-Protection Facilitates Whole Genome Sequencing of Mycobacteria Direct from Clinical Samples by the Nanopore Platform
Sophie George et al.

Preprint:
Seeker: Alignment-free identification of bacteriophage genomes by deep learning
Noam Auslander et al.

Multiview learning for understanding functional multiomics
ND Nguyen et al.
PLOS Computational Biology, 2020

Microbes on the Market

News Article:
Gilead agrees microbiome deal with Second Genome
Ben Hargreaves, Biopharma Reporter

Market Report:
Human Microbiome Market Future Outlook 2020-2026. Major Players are Dohme Corp, Seres …
Science In Me

Market Report:
Europe Human Microbiome Market to Offer Increased Growth Prospects for Manufacturers up to 2025
Sameer Joshi, Curious Desk (blog)