Gwi-Deuk Jin

Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens

In the poultry industry, many efforts have been undertaken to further improve the growth performance of broilers and identification and modulation of body weight (BW)-related bacteria could be one of the strategies to improve productivity. However, studies regarding the relationship between microbiota and BW are scarce. The objective of the present study was to investigate the relationship between microbiota and BW in different sections of the gastrointestinal tract (GIT). A total of twenty 18-day-old birds were selected based on the BW, and samples were collected from the three different sections of the GIT, which included the crop, ileum and cecum. Bacterial genomic DNA was extracted from the samples, and the V4 region of 16S rRNA gene were amplified. Amplicons were sequenced on Illumina MiSeq, and microbial communities were analyzed by using QIIME. In principal coordinate analysis, bacterial communities were clustered into three groups, based on the sections of GIT. Several BW-related bacterial groups were identified from linear regression analysis. At the genus level, Streptococcus from the ileum as well as Akkermansia in both ileum and cecum, were negatively related to BW, whereas Bifidobacterium in the ileum and Lactococcus in the cecum showed a positive correlation. The results from the present study showed that particular bacterial communities in the GIT were related to BW, and the study has broadened the understanding of the intestinal microbial ecosystem in broiler chickens.

Age-associated molecular changes are deleterious and may modulate life span through diet

Age-associated molecular changes are deleterious and causally linked with aging and may affect life span through diet. Transition through life span is accompanied by numerous molecular changes, such as dysregulated gene expression, altered metabolite levels, and accumulated molecular damage. These changes are thought to be causal factors in aging; however, because they are numerous and are also influenced by genotype, environment, and other factors in addition to age, it is difficult to characterize the cumulative effect of these molecular changes on longevity. We reasoned that age-associated changes, such as molecular damage and tissue composition, may influence life span when used in the diet of organisms that are closely related to those that serve as a dietary source. To test this possibility, we used species-specific culture media and diets that incorporated molecular extracts of young and old organisms and compared the influence of these diets on the life span of yeast, fruitflies, and mice. In each case, the “old” diet or medium shortened the life span for one or both sexes. These findings suggest that age-associated molecular changes, such as cumulative damage and altered dietary composition, are deleterious and causally linked with aging and may affect life span through diet.

WITHDRAWN: Evaluating the association between body weight and the intestinal microbiota of weaned piglets via 16S rRNA sequencing

This article has been removed: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). The publisher regrets that an error occurred due to a technical issue which led to the premature publication of this paper. This error bears no reflection on the article or its authors. The publisher apologizes to the authors and the readers for this unfortunate error.

Genomic Features and Niche-Adaptation of Enterococcus faecium Strains from Korean Soybean-Fermented Foods.

Certain strains of Enterococcus faecium contribute beneficially to human health and food fermentation. However, other E. faecium strains are opportunistic pathogens due to the acquisition of virulence factors and antibiotic resistance determinants. To characterize E. faecium from soybean fermentation, we sequenced the genomes of 10 E. faecium strains from Korean soybean-fermented foods and analyzed their genomes by comparing them with 51 clinical and 52 non-clinical strains of different origins. Hierarchical clustering based on 13,820 orthologous genes from all E. faecium genomes showed that the 10 strains are distinguished from most of the clinical strains. Like non-clinical strains, their genomes are significantly smaller than clinical strains due to fewer accessory genes associated with antibiotic resistance, virulence, and mobile genetic elements. Moreover, we identified niche-associated gene gain and loss from the soybean strains. Thus, we conclude that soybean E. faecium strains might have evolved to have distinctive genomic features that may contribute to its ability to thrive during soybean fermentation.

Effect of rhubarb (Rheum spp.) root on in vitro and in vivo ruminal methane production and a bacterial community analysis based on 16S rRNA sequence

The objective of this study was to evaluate the anti-methanogenic effect of rhubarb (Rheum spp.) on in vitro, in vivo, and bacterial community composition using Quantitative Insights into Microbial Ecology sequencing. Rhubarb root powder was tested at different concentrations (0, 0.33, 0.67, and 1.33 g/L) in vitro, and all incubations were carried out in triplicate two runs on separate days. Concentrations of 0.67 and 1.33 g/L rhubarb significantly (P < 0.05) reduced methane production and the acetate : propionate ratio compared with those of the Control, without adverse effects on total volatile fatty acids and total gas production. In the second in vivo trial, four Hanwoo (Korean native) steers (live bodyweight, 556 ± 46 kg) with a ruminal cannula were housed individually in metabolic stalls and fed a basal diet twice daily in equal amounts at 0900 hours and 2100 hours. The before rhubarb treatment (before treatment) duration was 24 days for all steers; 14 days were used for diet adaptation and 10 days were used for gas samples collected 1, 2, and 3 h after the morning feeding on Days 3, 5, 7, and 9. We used three syringe needles passed through the ruminal cannula stopper at different time points as a simple and rapid method to sample rumen gas. Thereafter, three mesh bags containing 30 g of sliced rhubarb root each were placed at different depths in the rumen of each steer for 14 days (after treatment), and gas samples were collected on Days 4, 7, 10, 12, and 13. The results showed a significant (P < 0.05) decrease in methane concentration from the rhubarb-treated steers and provide the evidence that this method would be useful for in vivo screening of anti-methanogenic feed additives or plant material. Furthermore, 16s RNA sequencing after treatment showed increases in the numbers of Prevotella, and Lactobacillus, but decreases in Methanobrevibacter. In conclusion, rhubarb had an anti-methanogenic effect in vitro and in vivo, and the increase in the number of Prevotella shifted ruminal fermentation towards propionate production.

Regulation of CD4 + CD8 − CD25 + and CD4 + CD8 + CD25 + T cells by gut microbiota in chicken

The gut microbiota in chicken has long been studied, mostly from the perspective of growth performance. However, there are some immunological studies regarding gut homeostasis in chicken. Although CD4+CD25+ T cells are reported to act as regulatory T cells (Tregs) in chicken, there have been no studies showing the relationship between gut microbiota and Tregs. Therefore, we established a model for ‘antibiotics (ABX)-treated chickens’ through administration of an antibiotic cocktail consisting of ampicillin, gentamycin, neomycin, metronidazole, and vancomycin in water for 7 days. CD4+CD8−CD25+ and CD4+CD8+CD25+ T cells in cecal tonsils were significantly decreased in this model. Gram-positive bacteria, especially Clostridia, was responsible for the changes in CD4+CD8−CD25+ or CD4+CD8+CD25+ T cells in cecal tonsils. Feeding ABX-treated chickens with acetate recovered CD4+CD8−CD25+ and CD4+CD8+CD25+ T cells in cecal tonsils. GPR43, a receptor for acetate, was highly expressed in CD4+CD8−CD25+ T cells. In conclusion, our study demonstrated that the gut microbiota can regulate the population of CD4+CD8−CD25+ and CD4+CD8+CD25+ T cells, and that acetate is responsible for the induction of CD4+CD8−CD25+ T cells in cecal tonsils via GPR43.

Complete sequences of eastern water bat, Myotis petax (Chiroptera; Microchiroptera; Vespertilionidae) mitogenome.

Abstract Complete mitochondria genome sequences of myotis petax (Chiroptera; Microchiroptera; Vespertilionidae) were first identified in the present study. The sequences were obtained from the four individuals and composition of nucleotide AT and GC was about 64.58% and 35.42%, respectively. The lengths of mitogenomes were ranged from 17 296 to 17 299 bp. Total 51 variable sites were observed in the four mitogenomes and 38 sites were singleton polymorphic sites. Phylogenic study revealed that the species would have relatively closed evolutionary distance with m. macrodactylus rather than other species in the genus, myotis. Present study will provide important genomic materials supporting confirmation of taxon of species called bats, which is included in one of the largest orders among the mammals.

Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment

The intestinal microbiota affect various physiological traits of host animals such as brain development, obesity, age, and the immune system. In the swine industry, understanding the relationship between intestinal microbiota and growth stage is essential because growth stage is directly related to the feeding system of pigs, thus we studied the intestinal microbiota of 32 healthy pigs across five sows at 10, 21, 63, 93, and 147 d of ages. The intestinal microbiota were altered with growth of pigs and were separated into three distinct clusters. The relative abundance of several phyla and genera were significantly different between growth stages. We observed co-occurrence pattern of the intestinal microbiota at each growth stage. In addition, we predicted the functions of the intestinal microbiota and confirmed that several KEGG pathways were significantly different between growth stages. We also explored the relationship between the intestinal microbiota and innate factors such as the maternal effect and gender. When pigs were young, innate factors affected on construction of intestinal microbiota, however this tendency was disappeared with growth. Our findings broaden the understanding of microbial ecology, and the results will be used as a reference for investigating host-microbe interactions in the swine industry.

Prohibition of antibiotic growth promoters has affected the genomic profiles of Lactobacillus salivarius inhabiting the swine intestine

After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, the feeding environment, including the composition of animal intestinal microbiota, has changed rapidly. We hypothesized that the microbial genomes have also been affected by this legal prohibition, and investigated an important member of the swine gut microbiota, Lactobacillus salivarius, with a pan-genomic approach. Here, we isolated 21 L. salivarius strains composed of 6 strains isolated before the AGP prohibition (SBPs) and 15 strains isolated after the AGP prohibition (SAPs) at an interval of a decade, and the draft genomes were generated de novo. Several genomic differences between SBPs and SAPs were identified, although the number and function of antibiotic resistance genes were not different. SBPs showed larger genome size and a higher number of orthologs, as well as lower genetic diversity, than SAPs. SBPs had genes associated with the utilization of L-rhamnose and D-tagatose for energy production. Because these sugars are also used in exopolysaccharide (EPS) synthesis, we tried to identify differences in biofilm formation-associated genes. The genes for the production of EPSs and extracellular proteins were different in terms of amino acid sequences. Indeed, SAPs formed dense biofilm and survived better than SBPs in the swine intestinal environment. These results suggest that SAPs have evolved and adapted to protect themselves from new selection pressure of the swine intestinal microenvironment by forming dense biofilms, adopting a distinct antibiotic resistance strategy. This finding is particularly important to understand the evolutionary changes in host-microbe interaction and provide detailed insight for the development of effective probiotics for livestock.

Complete genome sequence and SNPs of Raja pulchra (Rajiformes, Rajidae) mitochondria

Abstract Mitochondrial genomes were sequenced from five Raja pulchra individuals, and single-nucleotide polymorphisms (SNPs) were identified by comparing previously announced sequences in this study. Total 117 SNPs were detected and they were present in 2 rRNA genes, 9 tRNA genes, 13 protein coding genes and non-coding region. One deleted polymorphic site, which was located in 16S rRNA gene, was observed in two individuals. Six polymorphic sites were non-synonymous SNPs, which were distributed in ND1, ND2, ATP6 and ND4 gene. Phylogenic analysis validated current taxa. The genome sequences of R. pulchra mitochondria could be comparable information for understanding species divergence and genomic variation among the populations.