Surprising species-level diversity in our gut bacteria
Research continues to focus on the microbiome and its key role in human health and disease. Among the most important findings is that our personal colonies of bacterial, fungal and viral species that we carry in and on our bodies every day prevents new bacteria, including harmful species, from taking up residence. This phenomenon, known as colonization resistance, protects us both directly and indirectly.
Commensals, our usual bacteria, can out-compete disease-causing pathogenic bacteria for specific locations, preventing their colonization. More directly, commensal metabolism products and inhibitory agents, such as bacterially derived peptide antibiotics (known as lantibiotics), inhibit the ability of harmful species from colonizing healthy individuals. Importantly, disruptions in our commensal flora, such as the use of antibiotics, can open the door for harmful pathogens. Antibiotics non-specifically kill both bad and good bacteria, thereby disrupting colonization resistance. Because antibiotic usage is prevalent in hospitals, their use can leave patients susceptible to infection with antibiotic-resistant, harmful bacteria. Therefore, the characterization of a specific commensal population that can be given to patients as a probiotic, similar to yogurt, in order to reconstitute the helpful microbes lost during antibiotic use would have potential therapeutic benefits.
Investigating bacterial diversity
A University of Chicago laboratory, led by Eric Pamer, MD, Donald F. Steiner Professor of Medicine and Microbiology and director of The University of Chicago Duchossois Family Institute, recently published an investigation in Cell Host & Microbe describing inter- and intra-species diversity within the Lachnospiraceae bacteria family. This family, a term describing a broader classification of organisms than a genus or a species, is highly abundant in the adult human microbiome. Lachnospiraceae provide a variety of benefits to the host, including mechanisms supporting colonization resistance, such as lantibiotic production, short-chain fatty acid production for immune stimulation, and intestinal acidification. Therefore, disruptions in the Lachnospiraceae population could adversely impact the host, making them a noteworthy family for researchers.
The team in the Pamer lab, led by postdoctoral fellow Matthew Sorbara, PhD, and bioinformatician Eric Littmann, sought to better understand the members of the Lachnospiraceae family, particularly its diversity. Whole-genome sequencing and gene annotation are techniques used to identify an organism’s complete DNA repertoire, as well as what the genes coded in that DNA do, respectively. The authors applied these techniques to fecal samples collected from 20 human donors. They identified a total of 273 bacterial isolates representing 27 gut species by 16S rRNA sequence analysis. Members of the same bacterial family share a core genome; however, the Pamer lab found that the genome shared between Lachnospiraceae isolates was surprisingly small, with only 397 protein-encoding genes. What was most shocking is that isolates of the same species averaged only 62.6% of the same genes, and that an individual could be co-colonized by these genetically distinct members of the same species.
What’s contributing to this surprising level of observed diversity? “We think a lot of this has to do with the donor that the bugs are derived from,” Littmann hypothesized. “So when we collect Ruminococcus gnavus from multiple donors, we see signatures that are donor-specific for those bugs.”
“You do have a strong donor impact, for sure,” added Sorbara, but cautioned that colonization networks are complex. “We have examples where there are multiple types of strains of particular members of the family from a single donor, so they can coexist in an individual, as well.”
The Pamer lab continues to add to their biobank of whole-genome-sequenced strains. In addition to Lachnospiraceae, the biobank currently contains close to 1000 diverse whole-genome-sequenced microbiota isolates, and work is underway to collect and characterize additional whole-genome-sequenced isolates. This biobank is available upon request to academic researchers and promises to be an incredible resource for the scientific community moving forward.
The Lachnospiraceae family of commensals are capable of promoting colonization resistance through the production of short-chain fatty acids and acidification of the intestinal lumen. Therefore, the Lachnospiraceae family is particularly interesting when selecting bacterial consortia for the restoration of gut homeostasis following environmental disruption, such as after antibiotic usage. With this in mind, the authors assessed differences in isolate ability to produce the short-chain fatty acid butyrate, with only 90 out of 273 isolates having complete pathways for the production of butyrate from acetyl CoA. This again demonstrated the surprising genetic variability between members of the same family.
The authors also reported profound intra-species diversity by UMAP analysis, a tool for simplified visualization of large datasets, such as datasets generated from genomic sequencing. In this analysis, DNA sequences from species clustered distinctly from one another, suggesting that there is diversity at the species level in the Lachnospiraceae family. The genetic variations between members of the same species were further analyzed for representative clusters, showing variability in carbohydrate utilization and the production of antimicrobial peptides between members of the same species. These data supported a previous publication from the Pamer lab describing varied lantibiotic production by Blautia isolates1.
The big picture
These findings enhance our knowledge of the inter- and intra-species diversity found within the Lachnospiraceae family, especially diversity in clinically-relevant pathways, such as colonization resistance, regulation of the host’s immune system and proinflammatory pathways. Understanding this diversity is critical for future therapeutics promoting Lachnospiraceae colonization. According to Littmann, “As the [Duchossois Family Institute] moves forward with adult consortia to treat infections or increase short-chain fatty acid absorption in the colon after someone gets antibiotics, just knowing that you’re putting a Ruminococcus gnavus in your consortia might be insufficient. You need to look at the whole genome, because some gnavus will be able to make some metabolites whereas others will not. That’s a problem, I think, in the literature in general.” As a direct follow up to this work, the Pamer lab has begun to ask how the genomic diversity demonstrated in this paper could affect metabolite production by different isolates.
“We’ve actively done metabolic screening on over 250 of the Lachnospiraceae and see changes in terms of what metabolites they’re making,” said Sorbara. This genomic and metabolic profiling can then be applied to inform the design of small bacterial consortia with specific goals, such as maximal short-chain fatty acid production or colonization resistance to harmful strains. Sorbara explained, “We can use either antibiotic-treated or germ-free mouse models to test those predictions.”
Littmann agreed, saying, “It’ll be fun to start problem-solving and engineering how you could make a productive community with the fewest number of isolates.” While specific consortia are not yet available, this and ongoing research by the Pamer lab promises to provide critical insights into the development of such therapeutic probiotics.
The study, “Functional and genomic variation between human-derived isolates of Lachnospiraceae reveals inter- and intra-species diversity,” was published July 2020 in Cell Host & Microbe. Additional authors include Emily Fontana, Thomas U. Moody, Mergim Gjonbalaj, Vincent Eaton, and Ruth Seok from Memorial Sloan Kettering Cancer Center; Ingrid M. Leiner and Claire E. Kohout from the University of Chicago.