A diet change from dry food to beef induces reversible changes on the faecal microbiota in healthy, adult client-owned dogs.

BACKGROUND: Diet has a major influence on the composition of the gut microbiota, whose importance for gut health and overall well-being is increasingly recognized. Knowledge is limited regarding health implications, including effects on the faecal microbiota, of feeding a diet with high content of red meat to dogs, despite some owners' apparent preference to do so. The aim of this study was to evaluate how a diet change from commercial dry food to one with a high content of boiled minced beef and vice versa influenced the faecal microbiota, and short chain fatty acid profile in healthy, adult, client-owned dogs. RESULTS: The diet change influenced the faecal microbiota composition and diversity (Shannon diversity index). The most abundant OTUs in samples of dogs fed the dry food and high minced beef were affiliated with the species Faecalibacterium prausnitzii and Clostridia hiranonis respectively. The high minced beef diet apparently also influenced the short chain fatty acid profile, with increased isovaleric acid, as well as an increase in faecal pH. These effects were reversed when the commercial dry food was reintroduced in weeks 6 and 7. CONCLUSIONS: Results of this study can aid in the understanding of how diet changes influence the faecal microbiota and metabolite content on a short-term basis. Long-term studies are required to investigate potential implications for canine gut and general health.

Does Maternal Perinatal Probiotic Supplementation Alter the Intestinal Microbiota of Mother and Child?

OBJECTIVES: Maternal probiotic supplementation has been shown to prevent the development of atopic dermatitis in the offspring. We aimed to investigate whether probiotics in pregnant and breast-feeding mothers altered the colonization pattern and the diversity of the mothers' and children's intestinal microbiota. METHODS: In a randomized, double-blind trial, women received probiotic milk or placebo from 36 weeks of gestation up to 3 months postnatally while breast-feeding. The probiotic milk contained Lactobacillus rhamnosus GG, L acidophilus La-5, and Bifidobacterium animalis subsp. lactis Bb-12. Stool samples were collected from the mothers at 30 to 36 weeks of gestation and 3 months after birth, and from the child at age 10 days, 3 months, 1 year, and 2 years, and bacteria were analyzed by quantitative polymerase chain reaction. Additionally, stool samples from 3-month-old and 2-year-old children were characterized using 16S ribosomal RNA gene deep sequencing to estimate the bacterial classes and genera, and the α- and ß-diversity. RESULTS: Three months after birth, both the prevalence and the relative abundance of the administered probiotic bacteria were significantly increased among the mothers in the probiotic group compared with among those in the placebo group. Only the Lactobacillus rhamnosus GG bacteria colonized the children at 10 days and at 3 months of age. There were no significant differences in the abundance of the administered probiotic bacteria between the groups at 1 and 2 years of age. For the bacterial classes and genera, and α- and ß-diversity, there were no significant differences between the groups. CONCLUSIONS: Different probiotic bacteria seem to have different ability to transfer from the mother to the child. We found no evidence that the probiotics altered the microbial composition or α- and ß-diversity of the children.

Chrom3D: three-dimensional genome modeling from Hi-C and nuclear lamin-genome contacts.

Current three-dimensional (3D) genome modeling platforms are limited by their inability to account for radial placement of loci in the nucleus. We present Chrom3D, a user-friendly whole-genome 3D computational modeling framework that simulates positions of topologically-associated domains (TADs) relative to each other and to the nuclear periphery. Chrom3D integrates chromosome conformation capture (Hi-C) and lamin-associated domain (LAD) datasets to generate structure ensembles that recapitulate radial distributions of TADs detected in single cells. Chrom3D reveals unexpected spatial features of LAD regulation in cells from patients with a laminopathy-causing lamin mutation. Chrom3D is freely available on github.

4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?

Genome-wide sequencing technologies enable investigations of the structural properties of the genome in various spatial dimensions. Here, we review computational techniques developed to model the three-dimensional genome in single cells versus ensembles of cells and assess their underlying assumptions. We further address approaches to study the spatio-temporal aspects of genome organization from single-cell data.

Shifts in the Midgut/Pyloric Microbiota Composition within a Honey Bee Apiary throughout a Season.

Honey bees (Apis mellifera) are prominent crop pollinators and are, thus, important for effective food production. The honey bee gut microbiota is mainly host specific, with only a few species being shared with other insects. It currently remains unclear how environmental/dietary conditions affect the microbiota within a honey bee population over time. Therefore, the aim of the present study was to characterize the composition of the midgut/pyloric microbiota of a honey bee apiary throughout a season. The rationale for investigating the midgut/pyloric microbiota is its dynamic nature. Monthly sampling of a demographic homogenous population of bees was performed between May and October, with concordant recording of the honey bee diet. Mixed Sanger-and Illumina 16S rRNA gene sequencing in combination with a quantitative PCR analysis were used to determine the bacterial composition. A marked increase in α-diversity was detected between May and June. Furthermore, we found that four distinct phylotypes belonging to the Proteobacteria dominated the microbiota, and these displayed major shifts throughout the season. Gilliamella apicola dominated the composition early on, and Snodgrassella alvi began to dominate when the other bacteria declined to an absolute low in October. In vitro co-culturing revealed that G. apicola suppressed S. alvi. No shift was detected in the composition of the microbiota under stable environment/dietary conditions between November and February. Therefore, environmental/dietary changes may trigger the shifts observed in the honey bee midgut/pyloric microbiota throughout a season.

High or low correlation between co-occuring gene clusters and 16S rRNA gene phylogeny.

Ribosomal RNA (rRNA) genes are universal for all living organisms. Yet, the correspondence between genome composition and rRNA phylogeny remains poorly known. The aim of this study was to use the information from genome sequence databases to address the correlation between rRNA gene phylogeny and total gene composition in bacteria. This was done by analysing 327 genomes with TIGRFAM functional gene annotations. Our approach consisted of two steps. First, we searched for discriminatory clusters of co-occurring genes. Using a multivariate statistical approach, we identified 11 such clusters which contain genes that were co-occurring only in a subset of genomes and contributed to explain the gene content differences between genome subsets. Second, we mapped the discovered clusters to 16S rRNA-based phylogeny and calculated the correlation between co-occuring genes and phylogeny. Six of the 11 clusters exhibited significant correlation with 16S rRNA gene phylogeny. The most distinct phylogenetic finding was a high correlation between iron-sulfur oxidoreductases in combination with carbon nitrogen ligases and Chlorobium. The other correlations identified covered relatively large phylogroups: Actinobacteria were positively associated with kinases, while Gammaproteobacteria were positively associated with methylases and acyltransferases. The suggested functional differences between higher phylogroups, however, need experimental verification.

An eight-year investigation of bovine livestock fecal microbiota.

Cattle represent a major source of fecal contamination worldwide. Understanding the natural variation of the bovine livestock fecal microbiota is therefore important. For this reason we addressed the yearly differences of the fecal microbiota for bovine livestock reared in the same geographical region from 1999 to 2007 - analyzing a total of 300 samples representing a range of experimental regimes. The aim of our work was to determine the effect of year visa experimental regime of the bovine livestock fecal microbiota. We used a newly developed high-throughput 16S rRNA sequencing approach (a single mixed Sanger sequence was generated per sample) in combination with deep pyrosequencing. We found that similar feeding and treatment regimes for different years showed major differences in the fecal microbiota, suggesting other factors important for shaping the fecal microbiota than those experimentally controlled. Ruminococcaeae, Peptostreptococcaceae, Acinetobacter, Escherichia/Shigella, Lachnospiraceae and Lactobacillales were the main taxa associated with the yearly fluctuations. Furthermore, we found that fecal samples with high levels of Lactobacillales, Ruminococcaea and Lachnospiraceae had the most even species distributions. The Peptostreptococcaceae and Acinetobacter dominated samples, on the other hand, showed a few highly dominant taxa. Testing of neutrality showed that the evenly distributed samples were explained by a neutral mode (that the assembly of the microbiota was random), while for the other samples there were overrepresentation of the dominant species (indicating bacterial-bacterial nice competition). We therefore propose that there are natural yearly fluctuations of the bovine livestock microbiota - both with respect to ecology and composition. This knowledge will have impact on our management of fecal bacteria in the environment, since it is very difficult to predict risk based on historical data.

Unveiling an abundant core microbiota in the human adult colon by a phylogroup-independent searching approach.

The potential presence of widespread and stable bacterial core phylogroups in the human colon has promoted considerable attention. Despite major efforts, no such phylogroups have yet been identified. Therefore, using a novel phylogroup- and tree-independent approach, we present a reanalysis of 1,114,722 V2 region and 71,550 near full-length 16S rRNA sequences from a total of 210 human beings, with widespread geographic origin, ethnic background and diet, in addition to a wide range of other mammals. We found two highly prevalent core phylogroups (cores 1 and 2), belonging to the clostridial family Lachnospiraceae. These core phylogroups showed a log-normal distribution among human individuals, while non-core phylogroups showed more skewed distributions towards individuals with low levels compared with the log-normal distribution. Molecular clock analyses suggest that core 2 co-evolved with the radiation of vertebrates, while core 1 co-evolved with the mammals. Taken together, the stability, prevalence and potential functionality support the fact that the identified core phylogroups are pivotal in maintaining gut homeostasis and health.

Temporal development of the infant gut microbiota in immunoglobulin E-sensitized and nonsensitized children determined by the GA-map infant array.

At birth, the human infant gut is sterile, but it becomes fully colonized within a few days. This initial colonization process has a major impact on immune development. Our knowledge about the correlations between aberrant colonization patterns and immunological diseases, however, is limited. The aim of the present work was to develop the GA-map (Genetic Analysis microbiota array platform) infant array and to use this array to compare the temporal development of the gut microbiota in IgE-sensitized and nonsensitized children during the first 2 years of life. The GA-map infant array is composed of highly specific 16S rRNA gene-targeted single nucleotide primer extension (SNuPE) probes, which were designed based on extensive infant 16S rRNA gene sequence libraries. For the clinical screening, we analyzed 216 fecal samples collected from a cohort of 47 infants (16 sensitized and 31 nonsensitized) from 1 day to 2 years of age. The results showed that at a high taxonomic level, Actinobacteria was significantly overrepresented at 4 months while Firmicutes was significantly overrepresented at 1 year for the sensitized children. At a lower taxonomic level, for the sensitized group, we found that Bifidobacterium longum was significantly overrepresented at the age of 1 year and Enterococcus at the age of 4 months. For most phyla, however, there were consistent differences in composition between age groups, irrespective of the sensitization state. The main age patterns were a rapid decrease in staphylococci from 10 days to 4 months and a peak of bifidobacteria and bacteroides at 4 months. In conclusion, our analyses showed consistent microbiota colonization and IgE sensitization patterns that can be important for understanding both normal and diseased immunological development in infants.

Development of gut microbiota in infants not exposed to medical interventions.

Knowledge of the composition of a normal healthy gut microbiota during infancy is important for understanding the role of gut microbiota in disease. A limitation of previous studies is that they are based on infants who have been subject to factors, which can have a profound disruptive effect on the natural colonization process. We describe the colonization process, during the first 4 months after birth, in 85 infants who have experienced no major medical or dietary interventions. They were all vaginally delivered, healthy, term infants, who were not exposed to antibiotics, exclusively breastfed during their first month of life and at least partially breastfed up to 4 months. Selected microbial groups were identified by targeting small subunit microbial ribosomal RNA genes. In contrast to more recent studies, but in agreement with older studies, almost all our infants harbored γ-Proteobacteria and Bifidobacterium. Yet undefined non-cultivable species belonging to Bacteroides, as well as microbes identified as Lachnospiraceae 2, were common. Strong associations were observed between some specific constituents of microbiota at day 4 and the concentration of specific microbial groups at day 120, indicating that early gut microbiota may influence later microbiota. Novel information of the undisturbed composition of early gut microbiota in babies is presented.