March 4, 2021

Happy Thursday from San Francisco! Today’s Microbiome Digest includes: a paper by Marbouty et al. in which a large number of phages and their interacting bacteria were identified in the healthy human gut; a thorough examination by Zhu et al. of the composition and metabolic potential of cave-dwelling bacteria, including sequencing of 14 new bacterial species; and a study by Mu et al. which found that the maternally-derived microbe Lactobacillus reuteri promotes immunoglobulin A production in the neonatal gut.

There is also a study by Serrano-Villar et al. which examined the use of fecal microbiota transplantation (FMTs) in HIV patients. The authors observed that FMT led to engraftment of two bacterial families–Lachnospiraceae and Ruminococcaceae–typically depleted in HIV-infected subjects and decreased levels of a plasma biomarker of intestinal permeability. While the findings are interesting, I remain skeptical of the appropriateness of FMTs in this context. Instead of an FMT–which requires donors and screening of their stool to ensure quality and safety–why not use a probiotic cocktail of Lachnospiraceae and Ruminococcaceae family members and perhaps include prebiotic factors to try to promote engraftment?

Additionally, there is a great article by Ras et al. discussing the results of a pilot study that successfully implemented microbiome-related bioinformatics courses across 11 African countries.

Pregnancy and Early Life
Distinct Changes Occur in the Human Breast Milk Microbiome Between Early and Established Lactation in Breastfeeding Guatemalan Mothers. – Gonzales, E. et al., Frontiers in Microbiology.

Human Skin Microbiome
Spermidine-induced recovery of human dermal structure and barrier function by skin microbiome. – Kim, G. et al. Communications Biology.

Human Vaginal Microbiome
Influence of dapivirine vaginal ring use on cervicovaginal immunity and functional microbiome in adolescent girls. – Farr Zuend, C. et al., AIDS.

Mapping the entire functionally active endometrial microbiota. – Sola-Leyva, A. et al., Human Reproduction.

Genomic relatedness and clinical significance of Streptococcus mitis strains isolated from the urogenital tract of sexual partners. – Mores, C.R. et al., Microbial Genomics.

Human Gut Microbiome
Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome. – Han, Z. et al., Scientific Reports.

Fecal microbiota transplantation in HIV: A pilot placebo-controlled study. – Serrano-Villar, S. et al., Nature Communications.

Gastrointestinal microbiota composition predicts peripheral inflammatory state during treatment of human tuberculosis. – Wipperman, M.F. et al., Nature Communications.

Animal Experiments
Regulation of neonatal IgA production by the maternal microbiota. – Mu, Q. et al., PNAS.

Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism. – Jensen, B.A.H., et al., Nature Communications.

Sex-dependent modulation of immune development by secretory IgA–coated Lactobacillus reuteri isolated from breast milk. – Qi, C. et al., Journal of Dairy Science.

Oral berberine improves brain dopa/dopamine levels to ameliorate Parkinson’s disease by regulating gut microbiota. – Wang, Y. et al., Signal Transduction and Targeted Therapy.

Animal Microbiome
Lactobacillus reuteri-derived extracellular vesicles maintain intestinal immune homeostasis against lipopolysaccharide-induced inflammatory responses in broilers. – Hu, R. et al., Journal of Animal Science and Biotechnology.

Plant, Root, and Soil Microbiome
Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation. – Kaushal, R. et al., Microbiome.

Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations. – Wang, Z. et al., Applied and Environmental Microbiology.

Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt. – Broadbent, A.A.D. et al., ISME Journal.

Water and Extremophile Microbiome
Microbial Community Structure Driven by a Volcanic Gradient in Glaciers of the Antarctic Archipelago South Shetland. – García-Lopez, E. et al., Microorganisms.

Effect of polymer type on the colonization of plastic pellets by marine bacteria. – Hansen, J. et al., FEMS Microbiology Letters.

Lifestyle of sponge symbiont phages by host prediction and correlative microscopy. – Jahn, M.T. et al., ISME Journal.

Bacteria and Metabolic Potential in Karst Caves Revealed by Intensive Bacterial Cultivation and Genome Assembly. – Zhue, H-Z et al., Applied and Environmental Microbiology.

Phages and Viruses
MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut. – Marbouty, M. et al., Elife.

On the evolutionary origins of host–microbe associations. – Sieber, M. et al., PNAS.

Ecology-guided prediction of cross-feeding interactions in the human gut microbiome. – Goyal, A. et al., Nature Communications.

Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa. – Ras, V. et al., PLoS Computational Biology.

Amplicon-based skin microbiome profiles collected by tape stripping with different adhesive film dressings: a comparative study. – Ogai, K. et al., BMC Microbiology.

High-Resolution Differentiation of Enteric Bacteria in Premature Infant Fecal Microbiomes Using a Novel rRNA Amplicon. – Graf, J. et al., mBio.

One thought on “March 4, 2021

  1. >Instead of an FMT–which requires donors and screening of their stool to ensure quality and safety–why not use a probiotic cocktail of Lachnospiraceae and Ruminococcaceae family members and perhaps include prebiotic factors to try to promote engraftment?

    Because the gut microbiome and FMT are far more complex than that. It’ll be decades before we understand the gut microbiome well enough to be able to replace FMT with synthetic versions. A probiotic cocktail of two bacterial families mixed with prebiotics won’t come anywhere near it.

    So far the companies who’ve been attempting to make synthetic versions haven’t been getting good results.

    In my opinion, the primary issue with the HIV study was the same issue with virtually all FMT studies that have been done so far — their donor quality:


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