Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle

High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2-5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.

The Global State of the Genetic Counseling Profession

The profession of genetic counseling (also called genetic counselling in many countries) began nearly 50 years ago in the United States, and has grown internationally in the past 30 years. While there have been many papers describing the profession of genetic counseling in individual countries or regions, data remains incomplete and has been published in diverse journals with limited access. As a result of the 2016 Transnational Alliance of Genetic Counseling (TAGC) conference in Barcelona, Spain, and the 2017 World Congress of Genetic Counselling in the UK, we endeavor to describe as fully as possible the global state of genetic counseling as a profession. We estimate that in 2018 there are nearly 7000 genetic counselors with the profession established or developing in no less than 28 countries.

Pathogenic variant in NLRP7 (19q13.42) associated with recurrent gestational trophoblastic disease: Data from early embryo development observed during in vitro fertilization

Objective

To describe in vitro development of human embryos derived from an individual with a homozygous pathogenic variant in NLRP7 (19q13.42) and recurrent hydatidiform mole (HM), an autosomal recessive condition thought to occur secondary to an oocyte defect.

Methods

A patient with five consecutive HM pregnancies was genomically evaluated via next generation sequencing followed by controlled ovarian hyperstimulation, in vitro fertilization (IVF) with intracytoplasmic sperm injection, embryo culture, and preimplantation genetic screening. Findings in NLRP7 were recorded and embryo culture and biopsy data were tabulated as a function of parental origin for any identified ploidy error.

Results

The patient was found to have a pathogenic variant in NLRP7 (c.2810+2T>G) in a homozygous state. Fifteen oocytes were retrieved and 10 embryos were available after fertilization via intracytoplasmic sperm injection. Developmental arrest was noted for all 10 embryos after 144 hours in culture, thus no transfer was possible. These non-viable embryos were evaluated by karyomapping and all were diploid biparental; two were euploid and eight had various aneuploidies all of maternal origin.

Conclusion

This is the first report of early human embryo development from a patient with any NLRP7 mutation. The pathogenic variant identified here resulted in global developmental arrest at or before blastocyst stage. Standard IVF should therefore be discouraged for such patients, who instead need to consider oocyte (or embryo) donation with IVF as preferred clinical methods to treat infertility.

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma

Existing studies characterizing gut microbiome variation in the United States suffer from population ascertainment biases, with individuals of American Indian ancestry being among the most underrepresented. Here, we describe the first gut microbiome diversity study of an American Indian community. We partnered with the Cheyenne and Arapaho (C&A), federally recognized American Indian tribes in Oklahoma, and compared gut microbiome diversity and metabolic function of C&A participants to individuals of non-native ancestry in Oklahoma (NNIs). While the C&A and NNI participants share microbiome features common to industrialized populations, the C&A participants had taxonomic profiles characterized by a reduced abundance of the anti-inflammatory bacterial genus Faecalibacterium, along with a fecal metabolite profile similar to dysbiotic states described for metabolic disorders. American Indians are known to be at elevated risk for metabolic disorders. While many aspects of this health disparity remain poorly understood, our results support the need to further study the microbiome as a contributing factor. As the field of microbiome research transitions to therapeutic interventions, it raises concerns that the continued exclusion and lack of participation of American Indian communities in these studies will further exacerbate health disparities. To increase momentum in fostering these much needed partnerships, it is essential that the scientific community actively engage in and recruit these vulnerable populations in basic research through a strategy that promotes mutual trust and understanding, as outlined in this study.

Abstract 2761: Evaluation of the BOADICEA model for predicting BRCA1 and BRCA2 mutation carrier probabilities in high-risk US Hispanic and Mexican families: A report from the Clinical Cancer Genetics Community Research Network

Background: BRCA1 and BRCA2 (BRCA) mutation prediction models are low cost tools that enable clinicians to target individuals with a higher probability to carry mutations in the BRCA genes. Most of the data used to construct these models were derived from a predominantly non-Hispanic White population. The predictive accuracy of these models in diverse populations is unclear. The Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) was developed using population-based families with multiple affected individuals that were primarily from the UK. The purpose of this study was to investigate and compare the accuracy of BOADICEA for prediction of BRCA mutation status among US Hispanics and a cohort of Mexicans in Guadalajara and Mexico City.

Methods: Hispanic patients undergoing genetic cancer risk assessment (GCRA) were enrolled in an IRB-approved prospective registry from sites within the Clinical Cancer Genetics Community Research Network (CCGCRN), comprised of the City of Hope and 47 collaborating sites representing primarily community-based oncogenetic practices across the US and Latin America, including two cancer institutes in Mexico (University of Guadalajara; Instituto Nacional de Cancerología, Mexico City). Pedigrees were created in Progeny, exported to text files, and then uploaded for probablity calculations according to BOADICEA version 3 guidelines. Accuracy was assessed using an observed versus expected and an area under the receiver operating characteristic (ROC) curve analysis.

Results: Overall, BOADICEA performed better in US Hispanics (area under the curve [AUC] = 0.75) for predicting a BRCA mutation than in the Mexican cohort (AUC = 0.64; p-value = 0.0015). Although BRCA mutations were documented in 238 of 1,247 (19.1%) US Hispanics and 23 of 234 (9.8%) Mexicans, BOADICEA predicted a mean mutation probability of 10.3% and 5.6%, respectively.

Summary: Though generally the best performing model, BOADICEA's ability to predict BRCA mutations has been investigated in previous studies with different populations with varying results. The lower performance of BOADICEA in the Mexican cohort could be a result of the limitations in pedigree data. It's possible that families don't share information about cancer due to cultural norms or fear of stigmitation. It is also possible that the model assumptions about population mutation frequency are inaccurate. The results of this study indicate the need to document the clinical reliability of probability models when evaluating high risk US Hispanics and patients in Mexico.

Citation Format: Jessica Clague, Cynthia Villarreal-Garza, Adrian Daneri Navarro, Alexandra J. Obregon-Tito, Sharon Sand, Tanya A. Chavez, Bita Nehoray, Lacolle Robinson, Lenny Gallardo, Azucena Del Toro, Rosa Alvarez, Kathleen R. Blazer, Blu Yanez, Charité Ricker, Gary W. Unzeitig, Kai Yang, Jeffrey N. Weitzel. Evaluation of the BOADICEA model for predicting BRCA1 and BRCA2 mutation carrier probabilities in high-risk US Hispanic and Mexican families: A report from the Clinical Cancer Genetics Community Research Network. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2761. doi:10.1158/1538-7445.AM2015-2761

Subsistence strategies in traditional societies distinguish gut microbiomes

Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.

Insights from characterizing extinct human gut microbiomes

In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (∼8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.