Mapping gastrointestinal gene expression patterns in wild primates and humans via fecal RNA-seq

Heritable oral microbes and their importance in microbiome research for public health

In 2016, I made part of an effort to characterize oral microbial communities in twins with dental caries. Here, I revisit the results published by me and my colleagues in Cell Host & Microbe in 2017, which shed light on plaque biofilm bacteria influenced by host genotype and their role in oral disease.

The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing

BACKGROUND

The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the L. rosalia mitogenome from feces, a sample which can be collected non-invasively.

RESULTS

Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the L. rosalia mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin (Saguinus imperator) and the mitogenome of the closely related black lion tamarin (Leontopithecus chrysopygus). The L. rosalia mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the L. chrysopygus mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3' side of several coding regions.

CONCLUSIONS

Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.

The Diversity of Primates: From Biomedicine to Conservation Genomics

Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.

Short communication: Molecular markers for epithelial cells across gastrointestinal tissues and fecal RNA in preweaning dairy calves

The objective of this study was to compare the transcription of gene markers for gastrointestinal (GI) epithelial cells, including fatty acid binding protein 2 (FABP2) and cytokeratin 8 (KRT8), and tight junction complex genes (TJP1, CLDN1, CLDN4) in fecal RNA against several GI tract tissue sections in dairy calves. Eight healthy Jersey calves were euthanized at 5 wk of age, and postmortem samples were collected from rumen, duodenum, jejunum, ileum, large intestine, cecum, and feces for total RNA isolation. Tissues and fecal samples were immediately frozen in liquid nitrogen until RNA isolation. A real-time quantitative PCR analysis was performed using a single standard curve composited of equal amounts of all samples, including cDNA from fecal and GI tract tissues. The mRNA expression of the tight junctions TJP1, CLDN1, and CLDN4 was greater in fecal RNA compared with lower GI tract tissues (i.e., duodenum, jejunum, ileum, large intestine, and cecum). Similar to fecal RNA, rumen tissue had greater expression of tight junctions CLDN1 and CLDN4 than lower GI tract tissues. Similarly, rumen tissue had greater expression of TPJ1 than all lower GI tract tissues except duodenum. The expression of TJP1 and CLDN4 was greater in fecal RNA than in rumen tissue; in contrast, CLDN1 mRNA expression was greater in rumen tissue than in the fecal RNA. The expression of FABP2 was greater in duodenum in comparison to all tissue except ileum. The mRNA expression of FABP2 in fecal samples was similar to jejunum and ileum. The expression of KRT8 in fecal samples was similar to duodenum, large intestine, and cecum. The fecal RNA had a greater expression of KRT8 in comparison to jejunum and ileum. The rumen tissue had the lowest mRNA expression of KRT8. The expression levels of FABP2, KRT8, and tight junction genes observed in fecal transcripts suggest that a considerable amount of RNA derived from GI tract epithelial cells can be detected in fecal RNA, which is in agreement with previous data in neonatal dairy calves and other biological models including humans, rodents, and primates. The greater expression of tight junctions in fecal RNA in comparison to sections of the low GI remains to be understood, and due to the importance of tight junctions in GI physiology, further clarification of this effect is warranted. The similarities in mRNA expression of FABP2 and KRT8 between fecal RNA and intestinal sections add up to the accumulating evidence that fecal RNA can be used to investigate molecular alterations in the GI tract of neonatal dairy calves. Further research in this area should include high-throughput transcriptomic analysis via RNA-seq to uncover novel molecular markers for specific sections of the GI tract of neonates.

Gut health, stress, and immunity in neonatal dairy calves: the host side of host-pathogen interactions

The cumulative evidence that perinatal events have long-lasting ripple effects through the life of livestock animals should impact future nutritional and management recommendations at the farm level. The implications of fetal programming due to malnutrition, including neonatal survival and lower birth weights, have been characterized, particularly during early and mid-gestation, when placental and early fetal stages are being developed. The accelerated fetal growth during late pregnancy has been known for some time, while the impact of maternal stressors during this time on fetal development and by extent its postnatal repercussions on health and performance are still being defined. Maternal stressors during late pregnancy cannot only influence colostrogenesis but also compromise adequate intestinal development in the fetus, thus, that further limits the newborn's ability to absorb nutrients, bioactive compounds, and immunity (i.e., immunoglobulins, cytokines, and immune cells) from colostrum. These negative effects set the newborn calf to a challenging start in life by compromising passive immunity and intestinal maturation needed to establish a mature postnatal mucosal immune system while needing to digest and absorb nutrients in milk or milk replacer. Besides the dense-nutrient content and immunity in colostrum, it contains bioactive compounds such as growth factors, hormones, and cholesterol as well as molecular signals or instructions [e.g., microRNAs (miRNAs) and long non-coding RNAs (lncRNAs)] transferred from mother to offspring with the aim to influence postnatal gut maturation. The recent change in paradigm regarding prenatal materno-fetal microbiota inoculation and likely the presence of microbiota in the developing fetus intestine needs to be addressed in future research in ruminants. There still much to know on what prenatal or postnatal factors may predispose neonates to become susceptible to enteropathogens (e.g., enterotoxigenic Escherichia coli), causing diarrhea. From the host-side of this host-pathogen interaction, molecular data such as fecal RNA could, over time, help fill those gaps in knowledge. In addition, merging this novel fecal RNA approach with more established microbiome techniques can provide a more holistic picture of an enteropathogenesis and potentially uncover control points that can be addressed through management or nutrition at the farm level to minimize preweaning morbidity and mortality.

Prime time for primate functional genomics

Functional genomics research is continually improving our understanding of genotype-phenotype relationships in humans, and comparative genomics perspectives can provide additional insight into the evolutionary histories of such relationships. To specifically identify conservation or species-specific divergence in humans, we must look to our closest extant evolutionary relatives. Primate functional genomics research has been steadily advancing and expanding, in spite of several limitations and challenges that this field faces. New technologies and cheaper sequencing provide a unique opportunity to enhance and expand primate comparative studies, and we outline possible paths going forward. The potential human-specific insights that can be gained from primate functional genomics research are substantial, and we propose that now is a prime time to expand such endeavors.