The 6th Congress of the International Human Microbiome Consortium took place on November 9-11, 2016 in Houston, TX. This first IHMC congress to be held in the USA attracted a wide international audience with attendees from Africa, Asia, Latin America, Australia, Europe, and the United States. This unique community of scientists came together to discuss a wide range of topics in the field of human microbiome science, including crosstalk of environmental microbes with the human microbiome, the importance of microbial communities outside the gut, the role of maternal-infant interactions in the early establishment of the microbiome, and the importance of microbiome science in global health. In this post, we highlight a few key topics that generated significant discussion at the conference.
Sequencing the microbiome: 16S or WGS – or both?
On the first day of the conference, an important question was posed to the audience which generated significant debate thereafter: as the field of microbiome science moves forward, what is the relative utility of 16S rRNA (16S) sequencing versus Whole Genome Shotgun (WGS) sequencing? When evaluating the impact of microbiota in disease, should we rely on the relatively crude taxonomic and inferred metagenomic calls made from 16S data? Is the deep functional data elucidated by WGS sequencing required to discover meaningful insights in host-microbial biology? Overall, lower sequencing cost and reduced computational requirements have made 16S sequencing the preferred choice by most investigators. However, as demonstrated by numerous talks given throughout the conference, 16S data alone may miss many subtleties in a given microbial community. For instance, Dr. Dusko Ehrlich, a major contributor to the MetaHIT project and a vocal advocate for WGS sequencing, demonstrated how WGS sequencing allowed his group to identify individuals who harbored specific bacterial strains that appeared to be resistant to antibiotic treatment. Furthermore, Dr. Owen White demonstrated that specific strains of the same bacterial species were differentially confined to various areas in the body, indicating microbial adaptations to a given niche at the strain level. Importantly, these findings would be nearly impossible to discover with the use of 16S data, demonstrating the importance of WGS sequencing in strain level analysis. Throughout the conference, most agreed that 16S data was useful, particularly as a rapid and cost effective means to assess microbial communities. However, WGS sequencing is keenly desired by many investigators, but will only become widespread when sequencing cost decreases and more advanced bioinformatics tools become widely available.
Where do our microbiomes come from?
In a session devoted to Women and Infant Health, Dr. Maria Collado discussed how a mother’s microbiome influences her baby’s developing microbiome. Numerous studies have indicated that the fetal environment is not sterile, suggesting that influences during gestation such as maternal diet may play a key role in defining the offspring microbiome. Furthermore, the intimate contact between the mother and infant microbiomes does not cease at birth, as, for example, breast milk contains numerous bioactive components—such as human milk oligosaccharides (HMO) and the milk microbiome—with the potential to influence the infant microbiome. Specifically, Dr. Collado discussed how infants of mothers who are nonsecretors (they do not carry an active copy of the FUT2 gene, preventing the synthesis of specific HMOs) have delayed establishment of Bifidobacterium in their gut, suggesting that the altered HMO composition in the milk of these mothers influences colonization of the infant gut microbiome. Given that early microbial colonization runs in parallel with maturation of the infant immune system, broadening our understanding of the maternal and environmental influences on the infant microbiome during this critical period in early life represents an important area for further investigation.
Does the host drive the microbiome?
A final set of talks sought to identify factors that alter our microbiota and dissect the potential outcomes for human health. Of note, Dr. Jack Gilbert of the University of Chicago proposed that our skin is not the outer limit of our microbiota. His work demonstrated that transient environmental microbes can have dramatic and lasting effects on health. He presented compelling data regarding the environmental microbiomes of Amish and Hutterite homes along with the relative rates of asthma in these populations. The Amish and the Hutterites are of similar genetic ancestry and both practice traditional communal lifestyles. However, they differ in their farming practices: the Amish use only man and animal power, while the Hutterites have embraced industrial farming techniques. Amish children work on family farms from a young age and have no incidence of asthma. Hutterite children, however, do not work outside the home until later in life and have nearly four times the incidence of asthma. Dr. Gilbert found that microbe-containing dust from both Amish and Hutterite barns is protective against lung inflammation, and thus he posits that early life exposures in the Amish population shape the development of the innate immune system leading to protection against asthma. Overall this work highlights the important role of the microbiota in driving homeostasis and promoting health. By gaining insight into these important interactions, in the future we may be able to generate targeted therapies by harnessing the power of microbes.
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