Novel Gut Microbiomes Found in Rural Hondurans Reveal Shocking Links to Genetics and Hidden Microbial Species

Medical News: A groundbreaking new study has uncovered a rich and previously unseen world of microbial life within the guts of people living in rural Honduras, revealing not just new species, but also how human genetics play a surprising role in shaping our internal ecosystems.


Novel Gut Microbiomes Found in Rural Hondurans Reveal Shocking Links to Genetics and
Hidden Microbial Species

Researchers from Yale University and Cornell University conducted the most comprehensive microbiome study to date in Central America, sequencing gut bacteria from 1,889 people living in 18 remote villages in the highlands of western Honduras. This Medical News report details how the study uncovered over 861 new bacterial species, significant genetic links, and a wide range of viruses and parasites previously undocumented in this region.
 
The international research team consisted of scientists from the Human Nature Lab at Yale University, the Meinig School of Biomedical Engineering at Cornell University, and various departments at Yale including Molecular Biophysics and Biochemistry, Biomedical Informatics and Data Science, Computer Science, and Statistics and Data Science.
 
A Unique Gut Ecosystem Unlike Any Other
The researchers found that the gut microbiomes of these Honduran villagers were not only more diverse than those of people in industrialized countries, but also harbored entirely new bacteria. Many of these microbes were adapted to high-fiber diets and traditional lifestyles. The team observed that species from the Prevotella genus dominated the microbiomes, consistent with populations that consume less processed foods and more natural plant-based fibers.
 
One of the most prevalent and interesting species discovered in the study was Lacrimispora amygdalyna, present in 99.5% of individuals. This species, like many others discovered in the study, is not commonly seen in Western populations, further underscoring the uniqueness of this rural microbiome.
 
Thousands of New Microbial Genomes Mapped
Through high-throughput shotgun metagenomic sequencing, researchers assembled over 130,000 microbial genomes, of which 63,459 were classified as high-quality. After filtering and removing duplicates, they documented 2,609 unique species-level genome bins. Astonishingly, 861 of these species had never been seen before and were not present in any global microbiome databases.
 
Many of these bacteria belonged to the Clostridia class, with some capable of producing essential short-chain fatty acids like butyrate and propionate, known for supporting gut health and anti-inflammatory functions. The study also reconstructed protein-coding genes and metabolic pathways, revealing tens of thousands of proteins and genes with no known function.
 
Gut Microbes Reflect Human DNA
To add another layer to their investigation, researchers also sequenced the human genomes of study participants from saliva samples. Using this data, they i dentified strong correlations between individual genetic profiles and their gut microbiome compositions. People who were genetically more similar often had more similar gut bacteria.
 
In some cases, up to 10% of variation in certain bacterial species could be attributed to genetic factors. For instance, specific variants in genes like GABRA4 and COX7B2 were found to influence the presence or abundance of microbes in the gut. These findings support growing evidence that our genes influence which bacteria thrive in our intestines.
 
The Gut Virome and Hidden Parasites
Besides bacteria, the study also looked at viruses and other non-bacterial organisms in the gut. Over 110,000 viral genomes were recovered, including thousands of newly discovered viral species, many of which belong to the Crassvirales family - viruses that infect gut bacteria and may play a role in maintaining microbial balance.
 
Parasitic organisms were also common. More than half of the population carried Blastocystis, a common intestinal protist. Interestingly, those who carried Blastocystis had significantly more diverse gut microbiomes. Other parasites such as Ascaris lumbricoides and Entamoeba histolytica were also found, indicating widespread exposure to soil-transmitted helminths.
 
COVID-19 and Microbiome Instability
Among 301 individuals sampled twice over a two-year period, researchers observed that their gut microbiomes changed significantly over time. There was a decline in bacterial diversity, and for many, the specific bacterial strains changed as well.
 
This temporal instability was more pronounced in individuals who had antibodies to SARS-CoV-2, suggesting that even mild or asymptomatic COVID-19 infections might disrupt gut health. Viral diversity in these individuals increased, while beneficial species like Prevotella decreased.
 
Microbiome Similarity Among Relatives and Friends
Genetic similarity wasn't the only factor influencing microbiome overlap. The study found that people who were socially connected - such as close friends or family members - shared more bacterial strains than unrelated individuals. Even people who were not related but lived in the same household had more similar gut bacteria than those living in different households.
 
This pattern held true even after adjusting for diet and other environmental factors. It indicates that both shared living conditions and social relationships help shape the microbial communities in our guts.
 
Conclusion
The study from rural Honduras is a major leap forward in microbiome science. It not only highlights the vast microbial diversity that exists outside industrialized countries but also uncovers novel bacterial and viral species never before documented. More importantly, it strengthens the evidence that our genes, lifestyle, and social environments all interact to shape the microbiome.
 
By mapping out over 861 new microbial species and showing the deep connection between our genes and gut bacteria, the research underscores the importance of including underrepresented populations in global scientific studies. This knowledge opens up new avenues for microbiome-targeted therapies and personalized medicine based on genetics and microbial profiles.
 
As the researchers emphasize, exploring the microbiomes of traditional communities is not just about discovery - it's about understanding what has been lost in modern societies and how we might restore balance for better health outcomes.
 
The study findings were published on a preprint server and are currently being peer reviewed.
https://www.biorxiv.org/content/10.1101/2025.03.25.645309v1
 
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