Stephen D. Kachman

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

In vertebrates, including humans, individuals harbor gut microbial communities whose species composition and relative proportions of dominant microbial groups are tremendously varied. Although external and stochastic factors clearly contribute to the individuality of the microbiota, the fundamental principles dictating how environmental factors and host genetic factors combine to shape this complex ecosystem are largely unknown and require systematic study. Here we examined factors that affect microbiota composition in a large (n = 645) mouse advanced intercross line originating from a cross between C57BL/6J and an ICR-derived outbred line (HR). Quantitative pyrosequencing of the microbiota defined a core measurable microbiota (CMM) of 64 conserved taxonomic groups that varied quantitatively across most animals in the population. Although some of this variation can be explained by litter and cohort effects, individual host genotype had a measurable contribution. Testing of the CMM abundances for cosegregation with 530 fully informative SNP markers identified 18 host quantitative trait loci (QTL) that show significant or suggestive genome-wide linkage with relative abundances of specific microbial taxa. These QTL affect microbiota composition in three ways; some loci control individual microbial species, some control groups of related taxa, and some have putative pleiotropic effects on groups of distantly related organisms. These data provide clear evidence for the importance of host genetic control in shaping individual microbiome diversity in mammals, a key step toward understanding the factors that govern the assemblages of gut microbiota associated with complex diseases.

Murine Gut Microbiota Is Defined by Host Genetics and Modulates Variation of Metabolic Traits

The gastrointestinal tract harbors a complex and diverse microbiota that has an important role in host metabolism. Microbial diversity is influenced by a combination of environmental and host genetic factors and is associated with several polygenic diseases. In this study we combined next-generation sequencing, genetic mapping, and a set of physiological traits of the BXD mouse population to explore genetic factors that explain differences in gut microbiota and its impact on metabolic traits. Molecular profiling of the gut microbiota revealed important quantitative differences in microbial composition among BXD strains. These differences in gut microbial composition are influenced by host-genetics, which is complex and involves many loci. Linkage analysis defined Quantitative Trait Loci (QTLs) restricted to a particular taxon, branch or that influenced the variation of taxa across phyla. Gene expression within the gastrointestinal tract and sequence analysis of the parental genomes in the QTL regions uncovered candidate genes with potential to alter gut immunological profiles and impact the balance between gut microbial communities. A QTL region on Chr 4 that overlaps several interferon genes modulates the population of Bacteroides, and potentially Bacteroidetes and Firmicutes–the predominant BXD gut phyla. Irak4, a signaling molecule in the Toll-like receptor pathways is a candidate for the QTL on Chr15 that modulates Rikenellaceae, whereas Tgfb3, a cytokine modulating the barrier function of the intestine and tolerance to commensal bacteria, overlaps a QTL on Chr 12 that influence Prevotellaceae. Relationships between gut microflora, morphological and metabolic traits were uncovered, some potentially a result of common genetic sources of variation.

CONSTRAINTS OF SEED SIZE ON PLANT DISTRIBUTION AND ABUNDANCE

We examined the correlation between seed size (mass) and spatial and temporal distribution and abundance of plants, using both published data from northern England and 18 years of census data from permanent quadrats in the Chihuahuan Desert, Arizona, USA. In both systems, there were many small-seeded species and few large-seeded ones. Spatial patterns of distribution and abundance were constrained by seed size within triangle envelopes, i.e., small-seeded species had a greater range of abundance and a greater number of sites occupied than did large-seeded species. Temporal patterns of abundance and distribution from the Chihuahuan Desert site were similarly correlated with seed size, i.e., small-seeded species were, in general, more abundant and present in more years than were large-seeded species. These patterns probably result because small-seeded species produce more seeds, are more vagile, and persist longer in seed banks than do large-seeded species. The results are consistent with recent findings from seed bank studies, suggesting the generality of the correlation between seed size and plant abundance and distribution.

Relative Importance of Heat-Labile Enterotoxin in the Causation of Severe Diarrheal Disease in the Gnotobiotic Piglet Model by a Strain of Enterotoxigenic Escherichia coli That Produces Multiple Enterotoxins

ABSTRACT Enterotoxigenic Escherichia coli (ETEC) strains that produce multiple enterotoxins are important causes of severe dehydrating diarrhea in human beings and animals, but the relative importance of these enterotoxins in the pathogenesis is poorly understood. Gnotobiotic piglets were used to study the importance of heat-labile enterotoxin (LT) in infection with an ETEC strain that produces multiple enterotoxins. LT− (ΔeltAB) and complemented mutants of an F4+ LT+ STb+ EAST1+ ETEC strain were constructed, and the virulence of these strains was compared in gnotobiotic piglets expressing receptors for F4+ fimbria. Sixty percent of the piglets inoculated with the LT− mutant developed severe dehydrating diarrhea and septicemia compared to 100% of those inoculated with the nalidixic acid-resistant (Nalr) parent and 100% of those inoculated with the complemented mutant strain. Compared to piglets inoculated with the Nalr parent, the mean rate of weight loss (percent per hour) of those inoculated with the LT− mutant was 67% lower (P < 0.05) and that of those inoculated with the complemented strain was 36% higher (P < 0.001). Similarly, piglets inoculated with the LT− mutant had significant reductions in the mean bacterial colony count (CFU per gram) in the ileum; bacterial colonization scores (square millimeters) in the jejunum and ileum; and clinical pathology parameters of dehydration, electrolyte imbalance, and metabolic acidosis (P < 0.05). These results indicate the significance of LT to the development of severe dehydrating diarrhea and postdiarrheal septicemia in ETEC infections of swine and demonstrate that EAST1, LT, and STb may be concurrently expressed by porcine ETEC strains.

Genome Diversification in Phylogenetic Lineages I and II of Listeria monocytogenes: Identification of Segments Unique to Lineage II Populations

Thirteen different serotypes of Listeria monocytogenes can be distinguished on the basis of variation in somatic and flagellar antigens. Although the known virulence genes are present in all serotypes, greater than 90% of human cases of listeriosis are caused by serotypes 1/2a, 1/2b, and 4b and nearly all outbreaks of food-borne listeriosis have been caused by serotype 4b strains. Phylogenetic analysis of these three common clinical serotypes places them into two different lineages, with serotypes 1/2b and 4b belonging to lineage I and 1/2a belonging to lineage II. To begin examining evolution of the genome in these serotypes, DNA microarray analysis was used to identify lineage-specific and serotype-specific differences in genome content. A set of 44 strains representing serotypes 1/2a, 1/2b, and 4b was probed with a shotgun DNA microarray constructed from the serotype 1/2a strain 10403s. Clones spanning 47 different genes in 16 different contiguous segments relative to the lineage II 1/2a genome were found to be absent in all lineage I strains tested (serotype 4b and 1/2b) and an additional nine were altered exclusively in 4b strains. Southern hybridization confirmed that conserved alterations were, in all but two loci, due to absence of the segments from the genome. Genes within these contiguous segments comprise five functional categories, including genes involved in synthesis of cell surface molecules and regulation of virulence gene expression. Phylogenetic reconstruction and examination of compositional bias in the regions of difference are consistent with a model in which the ancestor of the two lineages had the 1/2 somatic serotype and the regions absent in the lineage I genome arose by loss of ancestral sequences.

Nuclear Genes That Encode Mitochondrial Proteins for DNA and RNA Metabolism Are Clustered in the Arabidopsis Genome

The plant mitochondrial genome is complex in structure, owing to a high degree of recombination activity that subdivides the genome and increases genetic variation. The replication activity of various portions of the mitochondrial genome appears to be nonuniform, providing the plant with an ability to modulate its mitochondrial genotype during development. These and other interesting features of the plant mitochondrial genome suggest that adaptive changes have occurred in DNA maintenance and transmission that will provide insight into unique aspects of plant mitochondrial biology and mitochondrial-chloroplast coevolution. A search in the Arabidopsis genome for genes involved in the regulation of mitochondrial DNA metabolism revealed a region of chromosome III that is unusually rich in genes for mitochondrial DNA and RNA maintenance. An apparently similar genetic linkage was observed in the rice genome. Several of the genes identified within the chromosome III interval appear to target the plastid or to be targeted dually to the mitochondria and the plastid, suggesting that the process of endosymbiosis likely is accompanied by an intimate coevolution of these two organelles for their genome maintenance functions.

Thermoregulatory profile of a newer genetic line of pigs

Researchers and producers alike have noted the increased susceptibility to heat stress exhibited by the newer genetic lines of pigs. A study was conducted to gather baseline information on the effects of acute heat stress on total heat production (THP), respiratory quotient (RQ), respiration rate (RR), and rectal temperature (Trectal) and to investigate the dynamic interaction of these parameters in growing–finishing barrows. Sixteen moderate–lean growth barrows were randomly assigned to a set of treatments as dictated by a repeated 4×4 Latin square crossover design. Pigs were moved from an individual pen to an indirect calorimeter where one of four environmental treatments (18, 24, 28, 32°C) were applied for 20 h. During the treatment exposure RR, THP, RQ and Trectal were measured. For the 2-week period between treatments, pigs were housed at thermoneutral (22°C). THP was found to be 17–20% higher than the published standards but comparable with other contemporary studies. Respiration rate was found to be a leading indicator of stress.

Transcriptional profiling of the sperm storage organs of Drosophila melanogaster.

The occurrence of female sperm storage across taxa indicates the importance of this complex and dynamic process. Organs responsible for sperm storage (SSOs) and proteins expressed therein, are important in fundamental aspects of reproduction and could play a major role in evolutionary processes such as post‐mating sexual selection. Given the essential role of SSOs, it is surprising that the process of sperm storage is so poorly understood. This study investigated the transcriptome of female Drosophila melanogaster SSOs (seminal receptacle and spermathecae). Spermathecae were enriched for proteases and metabolic enzymes while the seminal receptacle was enriched for genes involved in localization, signaling and ion transport. Differences in functional gene categories indicate that these organs play unique roles in sperm storage.

LABORATORY AND FIELD TESTING OF SEED SPACING UNIFORMITY FOR SUGARBEET PLANTERS

Five planter configurations were evaluated for seed spacing uniformity at three field speeds using a seed location method in the field and a laboratory method involving an opto-electronic sensor system. Planter seed spacing uniformity was described using the Coefficient of Precision (CP3) measure. Results showed that CP3 measures determined using the laboratory test method were significantly different from those determined using the field test method. This indicated the laboratory test method cannot be used to predict planter seed spacing uniformity in the field. Seed spacing uniformity determined in laboratory tests was higher than, or equal to, seed spacing uniformity determined in field tests. This indicated the laboratory test method may be useful to screen out planters or planter units with poor uniformity of seed metering. Field testing of the planters that perform well in laboratory tests must be conducted to adequately determine the seed spacing uniformity of those planters in the field. Results from laboratory and field tests could be useful in determining areas for improvement of planters or planter units.

Comparison of the Contributions of Heat-Labile Enterotoxin and Heat-Stable Enterotoxin b to the Virulence of Enterotoxigenic Escherichia coli in F4ac Receptor-Positive Young Pigs

ABSTRACT In swine, the most common and severe enterotoxigenic Escherichia coli (ETEC) infections are caused by strains that express K88 (F4)+ fimbriae, heat-labile enterotoxin (LT), heat-stable enterotoxin b (STb), and enteroaggregative E. coli heat-stable toxin 1. Previous studies based on a design that involved enterotoxin genes cloned into a nontoxigenic fimbriated strain have suggested that LT but not STb plays an important role in dehydrating diarrheal disease in piglets <1 week old and also enhances bacterial colonization of the intestine. In the present study, we compared these two toxins in terms of importance for piglets >1 week old with a study design that involved construction of isogenic single- and double-deletion mutants and inoculation of 9-day-old F4ac receptor-positive gnotobiotic piglets. Based on the postinoculation percent weight change per h and serum bicarbonate concentrations, the virulence of the STb− mutant (ΔestB) did not significantly differ from that of the parent. However, deletion of the LT genes (ΔeltAB) in the STb− mutant resulted in a complete abrogation of weight loss, dehydration, and metabolic acidosis in inoculated pigs, and LT complementation restored the virulence of this strain. These results support the hypothesis that LT is a more significant contributor than STb to the virulence of F4+ ETEC infections in young F4ac receptor-positive pigs less than 2 weeks old. However, in contrast to previous studies with gnotobiotic piglets, there was no evidence that the expression of LT enhanced the ability of the F4+ ETEC strain to colonize the small intestine.