This week in Biofilms and Microbiomes: Monday June 20, 2016

A round-up of what we read last week in the media's coverage of biofilms and microbiomes research.

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Early-life antibiotic exposures, cesarean section, and formula feeding could disrupt microbiome establishment and adversely affect health later in life, reports a new research published in June 15 issue of Science Translational Medicine. The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. To explore this relationship, investigators from Massachusetts General Hospital (MGH) and the Broad Institute, collected stool samples and clinical information (mode of delivery, whether the baby was breast fed, the infant's diet, and antibiotic treatment) from 39 infants over their first three years of life. Each sample was analyzed with a standard, RNA-based sequencing procedure used to identify microbial populations, and more detailed whole-genome sequencing was conducted on about 25 percent of samples to reveal the specific strains of identified microbial species. The investigators noted many interesting observations: first, nearly all infants had high levels of Enterobacteriaceae, Bifidobacteriaceae, and Clostridiaceae at two months of age, but as the infants grew these numbers dropped significantly. Second, the children who were born via C-section had a clear lack of species from the Bacteroides genus, compared to vaginally born children. Surprisingly, seven children who were born vaginally also had this low Bacteroides signature. Third and perhaps the most important was the impact of antibiotics on gut microbiome composition. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, the microbiomes of the kids who had taken antibiotics were less stable than those who had not. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. The second study, led by Nicholas Bokulich and Martin Blaser from New York University, echoed similar conclusions about the impact of antibiotics on infants' gut microbiomes. The team profiled microbial development during the first 2 years of life in a cohort of 43 U.S. infants and identified multiple disturbances associated with antibiotic exposures, cesarean section, and formula feeding. "Mounting evidence associates antibiotic use, cesarean section, and formula feeding with metabolic and immunological disorders later in life, possibly as a consequence of disturbed microbiome development," said the authors. The next step would be to study how these changes in infants' gut microbiomes may or may not be related to health outcomes. Read the press release covered by Science Daily, US News and World Report and Washington Post.

In this press release issued by CosmosID, the genomic data company has announced its partnership with the BioCollective to develop a comprehensive whole-genome shotgun sequencing-based microbiome analysis kit and software that will provide high resolution identification and characterization of microorganisms in the gut. Most microbiome kits offer bacterial analysis based on the DNA sequence of only one or a few genes (i.e. 16S ribosomal RNA), giving a lower-resolution characterization of the microbiome. Now, with The BioCollective's Comprehensive Microbiome Analysis Kit powered by CosmosID, the complete makeup of an individual microbiome can be explored, including species/strain level identification of bacteria, viruses, fungi, parasites and also the characterization of antibiotic resistance and virulence factors. Such in-depth profiling is only possible with the type of service that CosmosID provides - deep sequencing of the entire sample along with accurate analysis employing a highly curated microbial database. The kit is available at the introductory price of $299 (standard price $499), the price includes sample collection, storage, DNA preparation, sequencing, and metagenomic analysis. Additionally, members of The BioCollective will receive a percentage of revenue from microbiome sample sales to scientists for further studies and analysis.

We’d love to hear what you’ve been reading this week. Please comment below.

Richa Dandona

Partnerships and Operations Manager, Nature Partner Journals, Nature Research