COVID-19

Modelling donor screening strategies to reduce the risk of SARS-CoV-2 via fecal microbiota transplantation – Olesen et al. – bioRxiv

Oral microbiome

Streptococcus mutans adhesion force sensing in multi-species oral biofilms – Wang et al. – npc Biofilms and Microbiomes

Skin microbiome

HGT in the human and skin commensal Malassezia: A bacterially derived flavohemoglobin is required for NO resistance and host interaction – Ianiri et al. – PNAS

Gut-brain axis

The Serotonin Neurotransmitter Modulates Virulence of Enteric Pathogens – Kumar et al. – Cell Host and Microbe

COVID19
Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography – Kneller et al. – Nature Communications

Pregnancy and early life
Review – Maternal and infant factors that shape neonatal gut colonisation by bacteria – O’Neill et al. – Expert Review of Gastroenterology & Hepatology

Perinatal risk factors for fecal antibiotic resistance gene patterns in pregnant women and their infants – Sosa-Moreno et al. – PLOS One

Human gut microbiome
Microbial and metabolomic profiles in correlation with depression and anxiety co-morbidities in diarrhoea-predominant IBS patients – Liu et al. – BMC Microbiology

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study – Tahseen et al. – Scientific Reports

Animal experiments
Effects of Drinking Water Temperature and Flow Rate during Cold Season on Growth Performance, Nutrient Digestibility and Cecum Microflora of Weaned Piglets – Zhang et al. – Animals

Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs – Lv et al. – PeerJ

Evaluating the association between feed efficiency and the fecal microbiota of early-life Duroc pigs using 16S rRNA sequencing – Si et al. – AMB Express

Establishment and Stability of the Murine Oral Microbiome – Ramos et al. – Journal of Dental Research

Effects of chronic treatment with new strains of Lactobacillus plantarum on cognitive, anxiety- and depressive-like behaviors in male mice – Barros-Santos et al. – PLOS One

Animal microbiome
Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys – Mallott et al. – Scientific Reports

Plant, root, and soil microbiome
Microbial community types and signature-like soil bacterial patterns from fortified prehistoric hills of Thuringia (Germany) – Kohler et al. – Community Ecology

Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality – Zhou et al. – Nature Communications

Prairie plants harbor distinct and beneficial root-endophytic bacterial communities – Adu-Oppong et al. – PLOS One

Water and extremophile microbiome
Surviving marginalized reefs: assessing the implications of the microbiome on coral physiology and survivorship – Roitman et al. – Coral Reefs

Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing – Levican et al. – Animals

Energy-Efficient Single-Stage Nitrite Shunt Denitrification with Saline Sewage through Concise Dissolved Oxygen (DO) Supply: Process Performance and Microbial Communities – Zhuang et al. – Microorganisms

Food microbiology
Dynamics of Microbial Communities, Texture and Flavor in Suan zuo yu during Fermentation – Wang et al. – Food Chemistry

Probiotics / prebiotics
Bifidobacterium bifidum Suppresses Gut Inflammation Caused by Repeated Antibiotic Disturbance Without Recovering Gut Microbiome Diversity in Mice – Ojima et al. – Frontiers in Microbiology

Bacillus subtilis PB6 based probiotic supplementation plays a role in the recovery after the necrotic enteritis challenge – Aljumaah et al. – PLOS One

Bioinformatics
BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline – Shamsaddini et al. – PLOS One

We’ve got a belated post for you today (sorry all!) with a good balance of recent research on plant, animal and free-living microbiomes. Rather than highlight specific pieces of literature, I would encourage any who are interested in the microbiome from an evolutionary perspective to check out the recording of the ERC funded IDEM group’s recent discussion of the Holobiont Concept, featuring some preeminent proponents and critics of this model.

Seminar Recordings

ERC IDEM Group Holobiont Discussion – Dr. Scott Gilbert (7:17), Dr. Joan Roughgarden (1:05:03), Dr. Ford Doolittle (2:04:42)

General microbiome

Intestinal fermentation in vitro models to study food- induced gut microbiota shift: an updated review – Nissen et al. – FEMS Microbiology Letters

Human gut microbiome

Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions – Baldini et al. – BMC Biology

High Oscillospira abundance indicates constipation and low BMI in the Guangdong Gut Microbiome Project – Chen et al. – Scientific Reports

Animal microbiome

Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice – Belheouane et al. – The ISME Journal

Competitive traits of coral symbionts may alter the structure and function of the microbiome – McIlroy et al. – The ISME Journal

Evolutionary development and co‐phylogeny of primate‐associated bifidobacteria – Lugli et al. – Environmental Microbiology

Plant, root, and soil microbiome

Microbial functional traits in phyllosphere are more sensitive to anthropogenic disturbance than in soil – Xiang et al. – Environmental Pollution

Water and extremophile microbiome

Eutrophication as a driver of microbial community structure in lake sediments – Han et al. – Environmental Microbiology

Techniques

MetaFS: Performance assessment of biomarker discovery in metaproteomics – Tang et al. – Briefings in Bioinformatics

Microbes on the market

(Radio) Using our Microbiome to Change the Way We Live – KPCW https://www.kpcw.org/post/using-our-microbiome-change-way-we-live#stream/0

Greetings from Western New York! This is my first post to Microbiome Digest and I hope it turns out well as I have been busy trying to learn the nuances of publishing on WordPress over the past few months. As a retired Ophthalmologist with a Laboratory Medicine background and research studies in Microbiology I have a distinct affinity for microbiome-related research as it pertains to dysbiosis and pathogenesis. I have included some interesting articles on the association of the microbiome in gallstone disease, gastric and esophageal cancers as well as in HPV cancers. There is also a brief news article pertaining to handwashing of significance in the COVID-19 world we are currently living in. Stay safe and enjoy!

COVID-19

Novel Coronavirus disease 2019 (COVID-19): new challenges and new responsibilities in developing countries. FR Anjum, et al.- Human Vaccines & Immunotherapeutics

APPLIED MICROBIOLOGY

Microplastics provide new microbial niches in aquatic environments. Y Yang, et al.- Applied Microbiology and Biotechnology

GENERAL MICROBIOME

Gallstone Disease and Microbiome. IN Grigor’eva, et al.- Microorganisms

PREGNANCY AND EARLY LIFE

Bacterial Peptidoglycans from Microbiota in Neurodevelopment and Behavior. A Gonzalez-Santana,et al.- Trends in Molecular Medicine

HUMAN SKIN MICROBIOME

News Article: You Need To Use Soap & Sanitizer — But You Also Need To Tend To Your Microbiome

HUMAN GUT MICROBIOME

Comparison of the gut microbiome composition among individuals with acute or long-standing spinal cord injury vs. able-bodied controls. J Li, W Van Der Pol, et al. – The Journal of Spinal Cord …

Influence of microbiota on immunity and immunotherapy for gastric and esophageal cancers. X Zhang, et al.- Gastroenterology Report

ANIMAL MICROBIOME

Exposure of CuO nanoparticles and their metal counterpart leads to change in the gut microbiota and resistome of collembolans. J Ding, et al.- Chemosphere

PLANT, ROOT AND SOIL MICROBIOME

Soil Bacterial Diversity and Potential Functions Are Regulated by Long-Term Conservation Tillage and Straw Mulching. C Liu, et al- Microorganisms

WATER AND EXTREMOPHILE MICROBIOME

Patterns of environmental variability influence coral‐associated bacterial and algal communities on the Mesoamerican Barrier Reef. L Speare, et al.- Molecular Ecology

PROBIOTICS / PREBIOTICS

Saccharomyces boulardii: What Makes It Tick as Successful Probiotic?. P Pais, et al. – Journal of Fungi

PHAGES AND VIRUSES

Expression and functional study of VpV262 Pol, a moderately halophilic DNA polymerase from the Vibrio parahaemolyticus phage VpV262. Y Gao, et al.- Enzyme and Microbial Technology

Microbiome factors in HPV-driven carcinogenesis and cancers. D Lin, et al.- Plos Pathogens

BIOINFORMATICS

Gut–Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization. B Tilocca, et al.- Int. J. Mol. Sci