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Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate.

ABSTRACT: Background: Nutrient and energy metabolism in human colon depends on bacterial growth rate that is determined by the colonic transit rate. Objective: A novel approach, De-stat culture was used to distinguish the fast and slow growing sub-populations from fecal microbiota. Design: The enrichment and metabolism of bacteria from pooled fecal cultures of children was studied at dilution rates D = 0.2-0.0 1/h in mucin-supplemented media containing either arabinogalactan or apple pectin. Results: The study revealed clear differentiation of the fecal microbiota at higher (above 0.1 1/h) and lower (below 0.1 1/h) dilution rates, along with metabolic changes. Similarity of the fast and slow growing bacteria was observed in two different fecal pools and on both substrates, suggesting the dilution rate as the main triggering parameter for selection of bacteria. At high dilution rates, the species Collinsella aerofaciens, Dorea longicatena, Escherichia coli, Lachnoclostridium torques, and different Bacteroides (B. caccae, B. fragilis, B. ovatus, B. thetaiotaomicron, B. vulgatus) were dominant in both media variants. At low dilution rates, Akkermansia muciniphila, Eisenbergiella tayi, Negativicoccus succinivorans, and a group of Ruminococcaceae became dominant in both media and in both fecal pools. This change in bacterial population accompanied by the increased production of propionic and butyric acids as well as higher consumption of alanine and branched chain amino acids at low dilution rates. Conclusions: The study suggests that specific growth rate has important effect on the dynamics of colon microbiota. Manipulation of the proportions of fast and slow growing gut bacteria through modulation of the transit rate could be a target in human nutrition studies. The De-stat study would enable to predict changes in microbiota composition associated with the decrease or increase of the colonic transit rate.

SUBMITTER: Adamberg K

PROVIDER: S-EPMC6282430 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

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Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate.

Adamberg K K Adamberg S S

Microbial ecology in health and disease 20181130 1

Background: Nutrient and energy metabolism in human colon depends on bacterial growth rate that is determined by the colonic transit rate. Objective: A novel approach, De-stat culture was used to distinguish the fast and slow growing sub-populations from fecal microbiota. Design: The enrichment and metabolism of bacteria from pooled fecal cultures of children was studied at dilution rates D = 0.2-0.0 1/h in mucin-supplemented media containing either arabinogalactan or ...[more]

PMID: 30532686

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Project description:Chicken growth traits are important in poultry production, however, little is known for its regulatory mechanism at epigenetic level. Therefore, this study aims to compare DNA methylation profiles between fast- and slow-growing broilers in order to identify candidate genes underlying chicken growth. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation pattern in high and low tails of Recessive White Rock (WRRh, WRRl) and that of Xinhua Chickens (XHh, XHl). The results showed that the average of methylation density was the lowest in CGIs followed by promoters. Within the gene body, the methylation density of introns was higher than UTRs and exons. Moreover, different methylation levels were observed in different repeat types with the highest in LINE/CR1. Methylated CGIs were prominently distributed in the intergenic regions and were enriched in the size range of 200-300 bp. In total 13,294 methylated genes were found in four samples, including 4,085 differentially methylated genes between WRRh and WRRl, 5,599 between XHh and XHl, 4,204 between WRRh and XHh, as well as 7,301 between WRRl and XHl. Moreover, 132 differentially methylated genes related to growth and metabolism were observed in both inner contrasts (WRRh Vs. WRRl and XHh Vs. XHl), whereas 129 differentially methylated genes related to growth and metabolism were found in both across-breed contrasts (WRRh Vs. XHh and WRRl Vs. XHl). Further analysis showed that overall 75 genes exhibited altered DNA methylation in all four contrasts, which included some well-known growth factors of IGF1R, FGF12, FGF14, FGF18, FGFR2, and FGFR3. In addition, we further validate the MeDIP-seq results by bisulfite sequencing in some regions. 12 Breast muscle samples were collected from two breeds of different growth rate, Recessive White Rock (WRR) and Xinhua Chickens (XH). Each breed included low and high-weight groups and 3 samples from each group were pooled equally for methylated DNA immunoprecipitation-sequencing (MeDIP-seq).

Project description:Endogenously determined inter-individual differences in growth rate of bivalve molluscs have been widely analyzed at different organizational levels. Most studies have focused on the characterization of the physiological differences between fast (F) and slow (S) growing individuals. Although several genes have been described to be up regulated on fast growing individuals, the molecular basis underlying the mechanisms at the origin of growth variation is still poorly understood. In the present study we reared mussel spat of the species Mytilus galloprovincialis under diets below the pseudofaeces threshold (BP) and above the pseudofaeces threshold (AP). After 3 months, F and S mussels on each condition were selected, so that 4 experimental groups were obtained: FBP, SBP, FAP and SAP. We hypothesized that nurturing conditions during their growing period would modify the molecular basis of growth rate differences. However, results of feeding experiments showed that F mussels displayed higher clearance and ingestion rates and higher efficiencies of food selection prior to ingestion, as well as higher gill surface areas, irrespective of the rearing nutritional environment. To decipher molecular mechanism at the origin of growth variation, gills of the 4 mussel groups were dissected, and used for transcriptome analysis with a custom Agilent single channel microarray. Gene expression analysis revealed i) a low number (12) of genes differentially expressed associated to maintenance condition differences and ii) 117 genes differentially expressed when comparing fast and slow growing mussels (FBP + FAP vs. SBP + SAP). We further investigated this comparison: GO terms and KEGG pathway association of the differentially expressed genes allowed us to analyze the functions involved on the differentially expressed encoding. Transcriptomic differences between F and S mussels were mainly based on the up-regulation of response to stimulus, growth and cell activity Biological Process GO terms. Regarding the KEGG terms, carbohydrate metabolism and Krebs cycle were found to be up-regulated in F mussels whereas biosynthetic processes were up-regulated in S mussels. Among the differentially expressed genes that are annotated, the following ones were found to be up regulated in F mussels: i) Mucin, related to mucus secretion, known to be crucial in food acquisition and pre-ingestive selection processes in bivalves, ii) genes related to growth such as Myostatin or Insulin-like growth factor, iii) genes involved in feeding activity, such as Fibrocystin or Dynein and iv) genes involved in the energetic metabolism; Citrate synthase. S mussels mainly over-expressed genes related to immune system and defence (Leucine-rich repeat-containing protein, Metalloendopeptidase, Small heat shock protein 24, Multidrug resistance,…).The present results suggest that differences in feeding activity and in the allocation of metabolic energy between growth groups could account for the differences in growth rate in spat of Mytilus galloprovincialis. In accordance with their higher feeding rates and growth, fast growing mussels were found to mainly over-express genes involved in the development and maintenance of such activities, however, slow growing mussels needed to expend energy in immune and defence processes to ensure survival at the expense of growth rate.

Dataset Information

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate.

Publications

Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate.

Similar Datasets

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