Untargeted Fecal Metabolomic Analyses across an Industrialization Gradient Reveal Shared Metabolites and Impact of Industrialization on Fecal Microbiome-Metabolome Interactions.

The metabolome is a central determinant of human phenotypes and includes the plethora of small molecules produced by host and microbiome or taken up from exogenous sources. However, studies of the metabolome have so far focused predominantly on urban, industrialized populations. Through an untargeted metabolomic analysis of 90 fecal samples from human individuals from Africa and the Americas-the birthplace and the last continental expansion of our species, respectively-we characterized a shared human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the shared human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features such as amino acid-conjugated bile acids and urobilin as major metabolic correlates of these behavioral shifts. Additionally, coanalyses with over 5,000 publicly available human fecal samples and cooccurrence probability analyses with the gut microbiome highlight connections between the human fecal metabolome and gut microbiome. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a shared human fecal metabolome. This study represents the first characterization of the shared human fecal metabolome through untargeted analyses of populations along an industrialization gradient. IMPORTANCE As the world becomes increasingly industrialized, understanding the biological consequences of these lifestyle shifts and what it means for past, present, and future human health is critical. Indeed, industrialization is associated with rises in allergic and autoimmune health conditions and reduced microbial diversity. Exploring these health effects on a chemical level requires consideration of human lifestyle diversity, but understanding the significance of any differences also requires knowledge of what molecular components are shared between human groups. Our study reveals the key chemistry of the human gut as defined by varied industrialization-based differences and ubiquitous shared features. Ultimately, these novel findings extend our knowledge of human molecular biology, especially as it is influenced by lifestyle and behavior, and provide steps toward understanding how human biology has changed over our species' history.

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.

Citroniella saccharovorans gen. nov. sp. nov., a member of the family Peptoniphilaceae isolated from a human fecal sample from a coastal traditional community member.

A novel Gram-stain-positive, non-motile, non-spore-forming coccus-shaped obligately anaerobic bacterium was recovered from a fecal sample obtained from an individual from a traditional community located on the southern coast of Peru. The results of analysis based on 16S rRNA gene sequencing indicated the novel bacterium to be phylogenetically distinct from other genera of members of the Peptoniphilaceae family, sharing a loose affinity with the genera Ezakiella, Finegoldia, Gallicola and Parvimonas. The major cellular fatty acids of the novel isolate were determined to be C16:0, C17:1ω8c, and C18:1ω9c. The DNA G+C content was 29.9 mol%. End products of metabolism from peptone yeast glucose broth (PYG) were determined to be acetate and methyl succinate. The diagnostic diamino acid present in the cell wall was lysine. On the basis of the phenotypic, chemotaxonomic and phylogenetic results the organism is a member of a novel genus belonging to the family Peptoniphilaceae for which the name Citroniella saccharovorans gen nov. sp. nov., is proposed. The type strain is M6.X9T (DSM 29873T=CCUG 66799T).

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.

Oral microbiome diversity among Cheyenne and Arapaho individuals from Oklahoma.

OBJECTIVES: There is a major ascertainment bias in microbiome research, with individuals of predominately European ancestry living within metropolitan areas dominating most studies. Here we present a study of the salivary microbiome within a North American Indian community. This research is the culmination of four years of collaboration and community engagement with Cheyenne & Arapaho (C&A) tribal members from western Oklahoma. MATERIALS AND METHODS: Using 16S rRNA gene amplification and next-generation sequencing, we generated microbial taxonomic inventories for 37 individuals representing five towns within the C&A tribes. For comparison, we performed the same laboratory techniques on saliva samples from 20 non-native individuals (NNI) from Norman, Oklahoma. RESULTS: The C&A participants differ from the NNI in having reduced within-individual species richness and higher between-individual variation. Unsupervised clustering analyses reveal that three ecological groupings best fit the data, and while C&A individuals include assignments to all three groups, the NNI individuals are assigned to only one group. One of the ecological groups found exclusively among C&A participants was characterized by high abundance of the oral bacterial genus Prevotella. DISCUSSION: The C&A and NNI participants from Oklahoma have notable differences in their microbiome diversity, with a wider range of variation observed among the C&A individuals, including a higher frequency of bacteria implicated in systemic disorders. Overall, this study highlights the importance of engagement with indigenous communities, and the need for an improved understanding of human microbiome diversity among underrepresented groups and those individuals living outside of metropolitan areas.

Peptoniphilus catoniae sp. nov., isolated from a human faecal sample from a traditional Peruvian coastal community.

A novel Gram-stain-positive, coccus-shaped, obligately anaerobic bacterium was isolated from a faecal sample obtained from an individual in a traditional community located off the southern coast of Peru. Comparative 16S rRNA gene sequence analysis showed the novel bacterium belonged to the genus Peptoniphilus but showed no particular relationship with any species, demonstrating less than 91 % 16S rRNA gene sequence similarity with all members of the genus. The major cellular fatty acids of the novel isolate were determined to be C10 : 0, C14 : 0, C16 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0. The DNA G+C content was 34.4 mol%. End-products of metabolism from peptone-yeast-glucose broth (PYG) were determined to be acetate and butyrate. Based on the phenotypic, chemotaxonomic and phylogenetic results, the organism represents a novel species of the genus Peptoniphilus, for which the name Peptoniphilus catoniae sp. nov. is proposed. The type strain is M6.X2DT ( = DSM 29874T = CCUG 66798T).

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.

Frecuencia de mutación y de variantes de secuencia para los genes BRCA1 y BRCA2 en una muestra de mujeres colombianas con sospecha de síndrome de cáncer de mama hereditario: serie de casos / Frequency of sequence mutations and variants for the BRCA1 and BRCA2 genes in a sample of Colombian women with suspected hereditary breast cancer syndrome: Case series

Describir variantes de secuencia en los genes BRCA1 y BRCA2 en una muestra de pacientes colombianas con historia personal o familiar de cáncer de mama sugestiva de riesgo genético.Materiales y métodos: serie de casos compuesta por 67 pacientes que fueron remitidas para estudio genético por sospecha de síndrome de cáncer de mama y ovario hereditario (HBOC). De los 67 casos, 42 (62,7 %) cumplieron con los criterios de indicación médica de la National Comprehensive Cancer Network (NCCN) del 2013, y en ellos se realizó secuenciación completa de los genes BRCA1 y BRCA2. Se determinó la frecuencia de mutación, variantes de secuencia y significancia clínica de las variantes halladas con base en Breast Cancer Information Core (BIC).Resultados: se identificaron mutaciones para el gen BRCA1 en seis pacientes (14,3 %), no se documentó mutación para el gen BRCA2, además se detectaron 43 variantes genéticas en 27 pacientes (64,2 % de 42 casos). De estas, 21 (48,8 %) fueron identificadas en el gen BRCA1 y 22 (51,2 %) en el gen BRCA2. Dentro de estas variantes, se identificaron 5 mutaciones patogénicas solo en el gen BRCA1, de las cuales solo una había sido reportada previamente en Colombia.Conclusiones: este estudio identifica variantes genéticas patogénicas en el gen BRCA1 no descritas en estudios previos en la población colombiana y otras conocidas en diferentes poblaciones; permitiendo de esta forma ampliar el conocimiento sobre las variantes en población colombiana de los genes BRCA1 y BRCA2. Sin embargo, se requieren más estudios con suficiente poder y calidad metodológica para poder estimar la frecuencia de mutaciones y de variantes de secuencia para estos genes en mujeres colombianas con sospecha de síndrome de cáncer de mama u ovario hereditario...

To describe sequence variants in the BRCA1 and BRCA2 genes in a sample of Colombian patients with a personal or family history of breast cancer suggestive of genetic risk.Materials and methods: Case series consisting of 67 patients referred for genetic testing because of suspected hereditary breast and ovarian cancer syndrome (HBOC). Of the 67 cases, 42 (62.7%) met the medical indication criteria of the 2013 National Comprehensive Cancer Network (NCCN) and they were subjected to the entire sequencing of the BRCA1 and BRCA2 genes. A determination was made of the frequency of sequence mutation, variants, and of the clinical significance of the variants found based on the Breast Cancer Information Core (BIC).Results: Mutations were identified for the BRCA 1 gene in six patients (14.3%), no mutation was documented for the BRCA 2 gene, and 43 genetic variants were found in 27 patients (64.2% of 42 cases). Of these, 21 (48.8%) were identified in the BRCA1 gene and 22 (51.2%) in the BRCA 2 gene. Among these variants, 5 pathogenic mutations were found only in the BRCA1 gene and, of those, only 1 had been reported previously in Colombia.Conclusions: This study identifies pathogenic genetic variants in the BRCA1 gene not described previously in the Colombian population, as well as others known in different populations. Therefore, it helps expand knowledge regarding the variants of the BRCA1 and BRCA2 genes in the Colombian population. However, additional studies are required with sufficient power and methodological quality to estimate the frequency of sequence mutations and variants for the BRCA1 and BRCA2 genes in Colombian women suspected of having the hereditary breast or ovarian cancer syndrome...

Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru.

A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08V(T), was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth with PYG were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08V(T) (DSM 23598(T) = CCUG 59712(T)).

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.

Ezakiella peruensis gen. nov., sp. nov. isolated from human fecal sample from a coastal traditional community in Peru.

A novel Gram-stain positive, non-motile, non-sporeforming coccus-shaped, obligately anaerobic bacterium was isolated from a fecal sample of an individual residing in a traditional Peruvian community. The organism was characterized using biochemical, chemotaxonomic and phylogenetic methods. Comparative 16S rRNA gene sequence analyses and phenotypic characteristics demonstrated that the organism was biochemically and phenotypically related, but distinct, from a group of organisms referred to as the Gram-stain positive anaerobic cocci (GPAC). The major cellular fatty acids of the novel isolate were determined to be C16:0 (18.3%), C18:1ω9c (39.8%), C18:2ω6,9c/C18:0 ANTE (13.2%). Fermentation end products from PYG are acetate and formate. Cell-wall peptidoglycan was found to be A4α (L-Lys-L-Ala-L-Glu) and the G + C content was determined to be 38.4 mol%. Based on the phenotypic, chemotaxonomic, and phylogenetic results, Ezakiella peruensis gen. nov., sp. nov., is now proposed. The type strain is M6.X2(T) (DSM 27367(T) = NBRC 109957 (T) = CCUG 64571(T)).

Possible positive selection for an arsenic-protective haplotype in humans.

BACKGROUND: Arsenic in drinking water causes severe health effects. Indigenous people in the South American Andes have likely lived with arsenic-contaminated drinking water for thousands of years. Inhabitants of San Antonio de los Cobres (SAC) in the Argentinean highlands generally carry an AS3MT (the major arsenic-metabolizing gene) haplotype associated with reduced health risks due to rapid arsenic excretion and lower urinary fraction of the monomethylated metabolite. OBJECTIVES: We hypothesized an adaptation to high-arsenic living conditions via a possible positive selection for protective AS3MT variants and compared AS3MT haplotype frequencies among different indigenous groups. METHODS: Indigenous groups we evaluated were a) inhabitants of SAC and villages near Salta in northern Argentina (n = 346), b) three Native American populations from the Human Genome Diversity Project (HGDP; n = 25), and c) five Peruvian populations (n = 97). The last two groups have presumably lower historical exposure to arsenic. RESULTS: We found a significantly higher frequency of the protective AS3MT haplotype in the SAC population (68.7%) compared with the HGDP (14.3%, p < 0.001, Fisher exact test) and Peruvian (50.5%, p < 0.001) populations. Genome-wide microsatellite (n = 671) analysis showed no detectable level of population structure between SAC and Peruvian populations (measure of population differentiation FST = 0.006) and low levels of structure between SAC and HGDP populations (FST < 0.055 for all pairs of populations compared). CONCLUSIONS: Because population stratification seems unlikely to explain the differences in AS3MT haplotype frequencies, our data raise the possibility that, during a few thousand years, natural selection for tolerance to the environmental stressor arsenic may have increased the frequency of protective variants of AS3MT. Further studies are needed to investigate this hypothesis.

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.