Good Morning! Highlights of today’s digest include a promising probiotic effect of Lactobaccillus helveticus on acute liver failure as shown in an animal model study. Findings from another study about soil sterilization and how it leads to healthier soil microbiome and plant growth by modulating promotion of plant and beneficial microbes associations. Finally, check out an investigation aiming to generate a standardized approach for microbiome profiling by evaluating a series of hypervariable regions of 16S gene and estimating community richness across diverse sample types. Many review articles are also posted. Enjoy!

Pregnancy and early life

Acquisition and Development of the Extremely Preterm Infant Microbiota Across Multiple Anatomical Sites – Young et al. – J of Pediatric Gastroebterology and Nutrition

Multi-site human microbiome

Review: Urobiome: In Sickness and in Health – Wojciuk et al. – Microorganisms

Review: The Skin and Gut Microbiome and Its Role in Common Dermatologic Conditions – Ellis et al. – Microorganisms

Human oral microbiome

Analysis of the human oral microbiome from modern and historical samples with SPARSE and EToKi – Achtman and Zhou – bioRxiv

Human vaginal microbiome

HIV infection is associated with preterm delivery independent of vaginal microbiota in pregnant African women – Gudza-Mugabe et al. – The Journal of Infectious Diseases

Human gut microbiome

Review: Microbial Phenolic Metabolites: Which Molecules Actually Have an Effect on Human Health? – Marhuenda-Munoz et al. – Nutrients

Microbial succession during wheat bran fermentation and colonisation by human faecal microbiota as a result of niche diversification – Paepe et al. – ISME

Bifidogenic and butyrogenic effects of young barely leaf extract in an in vitro human colonic microbiota model – Sasaki et al. – AMB Express

Animal experiments

Dietary energy and protein levels influenced the growth performance, ruminal morphology and fermentation and microbial diversity of lambs – Cui et al. – Scientific Reports

*Lactobacillus helveticus R0052 alleviates liver injury by modulating gut microbiome and metabolome in d-galactosamine-treated rats – Wang et al. – Applied Microbiology and Biotechnology

Plant, root and soil microbiome

Evaluation of the ecological restoration of a coal mine dump by exploring the characteristics of microbial communities – Chen et al. – Applied Soil Ecology

*Soil sterilization leads to re-colonization of a healthier rhizosphere microbiome – Li et al. – Rhizosphere

Water and extremophile microbiome

Microbial composition and variability of natural marine planktonic and biofouling communities from the Bay of Bengal – Angelova et al. – Frontiers in Microbiology

Changes to the microbial communities within groundwater in response to a large crustal earthquake in Kumamoto, southern Japan – Morimura et al. – Journal of Hydrology

Increasing oxygen defciency changes rare and moderately abundant bacterial communities in coastal soft sediments – Sinkko et al. – Scientific Reports Nature Research

Probiotics / peribiotics

Review: Recent systems biology approaches for probiotics use in health aspects: a review – Yadave and Shukla – 3 Biotech

Bioinformatics

A phylogenetic model for the recruitment of species into microbial communities and application to studies of the human microbiome – Darcy et al. – bioRxiv

Developing a Reproducible Microbiome Data Analysis Pipeline Using the Amazon Web Services Cloud for a Cancer Research Group: Proof-of-Concept Study – Bai et al. – JMIR Medical Informatics

Techniques

*Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework – Wasimuddin et al. – bioRxiv

Rapid, selective and single cell electrical detection of antibiotic resistant bacteria – Kumar et al. – bioRxiv

Droplet Digital PCR Technology for Detection of Ilyonectria liriodendri from Grapevine Environmental Samples – Martinez Diz et al. – APS Publications

In today’s digest read about the Million Microbiome of Humans Project, problems in studies of the gut microbiome in Parkinson’s disease, and how bats’ gut bacteria are more closely tied to where bats live. Happy weekend!

Gut microbiome

*Review: Increasing Comparability and Utility of Gut Microbiome Studies in Parkinson’s Disease: A Systematic Review – Jeffrey M. Boertien – Journal of Parkinson’s Disease

Microbiome‐immune‐metabolic axis in the epidemic of childhood obesity: Evidence and opportunities – Halle J. Kincaid – Obesity Reviews

Vaginal microbiome

Cervicovaginal microbiome composition drives metabolic profiles in healthy pregnancy – Andrew Oliver – bioRxiv

Respiratory microbiome

Review: The microbiome of the upper respiratory tract in health and disease – Christina Kumpitsch – BMC Biology

Animal experiments

Lactobacillus helveticus R0052 alleviates liver injury by modulating gut microbiome and metabolome in d-galactosamine-treated rats – Qiangqiang Wang – Applied Microbiology and Biotechnology

Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis – Ariangela J. Kozik – PlosOne

Cranberry extracts promote growth of Bacteroidaceae and decrease abundance of Enterobacteriaceae in a human gut simulator model – Kathleen O’Connor – PlosOne

Animal microbiome

*Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome – Holly L. Lutz – mSystems

High-throughput sequencing reveals the core gut microbiota of the mud crab (Scylla paramamosain) in different coastal regions of southern China – Hongling Wei – BMC Genomics

Probiotics

Production of multiple bacteriocins, including the novel bacteriocin gassericin M, by Lactobacillus gasseri LM19, a strain isolated from human milk – Enriqueta Garcia-Gutierrez – bioRxiv

Infected chronic ischemic wound topically treated with a multi-strain probiotic formulation: a novel tailored treatment strategy – Salvatore Venosi – Journal of Translational Medicine

Genomic and epidemiological evidence of bacterial transmission from probiotic capsule to blood in ICU patients – Idan Yelin – Nature Medicine

Water microbiome

Species-level microbiome composition of activated sludge – introducing the MiDAS 3 ecosystem-specific reference database and taxonomy – Marta Nierychlo – bioRxiv

Comparative microbial diversity across temperature gradients in hot springs from Yellowstone and Iceland – Peter T Podar – bioRxiv

Niche partitioning of microbial communities in riverine floodplains – Marc Peipoch – Scientific Reports

Biodegradability of wastewater determines microbial assembly mechanisms in full-scale wastewater treatment plants – Bing Zhang – Water Research

Techniques

Microfluidic cultivation and analysis tools for interaction studies of microbial co-cultures – Alina Burmeister and Alexander Grünberger – Current Opinion in Biotechnology

Selective culture enrichment and sequencing of feces to enhance detection of antimicrobial resistance genes in third-generation cephalosporin resistant Enterobacteriaceae – Leon Peto – PlosOne

Microbiome in News

*Million Microbiome of Humans Project – PRNewswire
Scientists from China, Sweden, Denmark, France, Latvia and other countries will cooperate in microbial metagenomic research, aiming to analyze one million microbial samples and build the world’s largest database of human microbiome.

Increased risk of childhood asthma development associated with specific infant airway microbiota ¹. 

By: Puck deRoos

According to the CDC the prevalence of childhood asthma has dramatically increased within the past decade, rising to become the top reason for missed school days and affecting over 6 million children in the United States alone². 

Researchers at the University of Copenhagen have found an association between an infant’s airway microbiota at one month old and the development of childhood asthma by age six. 

Previously, another factor associated with an increased risk of developing childhood asthma was delivery via cesarean section³, while living with farm animals, an older sibling, or attending day care decreased the risk of developing childhood asthma ^4,5. 

In this new study, scientists have specifically found a correlation between the presence of Veillonella (importance 28.1%), Prevotella (23.7%), and Gemella (importance 16.3%) bacteria in the airway at age one month with an increased risk of asthma development before age six. Furthermore, they analyzed the topical airway immune profile from the mucosal lining and discovered an independent correlation between the previously mentioned bacteria and the development of childhood asthma. 

At age one month, researchers found that children who developed asthma had a higher diversity of microbes, but also have an increased ratio of high-risk bacteria Vallonella and Prevotella. They found no association between specific taxa of microbes and asthma development by 6 years at ages 1 week or 3 months old. 

A larger proportion of high-risk bacteria in a critical period of airway immune development poses a major threat to normal development. The children who developed asthma early in life showed a reduction in tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β), which are secreted by the bodies immune cells to fight inflammation and infections. They convergently showed an increase in Chemokine (C-C motif) ligand 2 (CCL2) and CCL17 levels in the topical immune profile. 

The airway microbiota samples were taken during the first three months of life from 700 children monitored for the development of asthma using 16S ribosomal RNA gene amplicon sequencing from the population based Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC 2010). The use of this cohort strengthened the results of the study because all children were sampled during infancy before the development of any symptoms, and were uniformly monitored for the development of any asthmatic symptoms through childhood. 

The findings of this study suggest that the development of childhood asthma may be connected to the interactions between early-life airway microbiota and the developing immune system. Because different areas of the human body have different microbial compositions which are considered healthy, determining specific microbes increasing the risk for childhood asthma may provide tools to prevent the disease’s spread.

1. Thorsen, J., Rasmussen, M.A., Waage, J. et al. Infant airway microbiota and topical immune perturbations in the origins of childhood asthma. Nat Commun 10, 5001 (2019) doi:10.1038/s41467-019-12989-7
2. The Centers for Disease Control and Prevention (CDC, 2019).
3. Thavagnanam, S., Fleming, J., Bromley, A., Shields, M. D. & Cardwell, C. R. A meta-analysis of the association between Caesarean section and childhood asthma. Clin. Exp. Allergy38, 629–633 (2008).
4. Illi, S. et al. Protection from childhood asthma and allergy in Alpine farm environments—the GABRIEL advanced studies. J. Allergy Clin. Immunol. 129, 1470–1477.e6 (2012).
5. Ball, T. M. et al. Siblings, day-care attendance, and the risk of asthma and wheezing during childhood. N. Engl. J. Med.343, 538–543 (2000).