Validation of a batch cultivation protocol for fecal microbiota of Kenyan infants
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB59472 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:BackgroundThe combination of cultivation studies with molecular analysis approaches allows characterization of the complex human gut microbiota in depth. In vitro cultivation studies of infants living in rural sub-Saharan Africa are scarce. In this study, a batch cultivation protocol for Kenyan infant fecal microbiota was validated.MethodsFresh fecal samples were collected from 10 infants living in a rural area of Kenya. Samples were transported under protective conditions and subsequently prepared for inoculation within less than 30 h for batch cultivation. A diet-adapted cultivation medium was used that mimicked the daily intake of human milk and maize porridge in Kenyan infants during weaning. 16 S rRNA gene amplicon sequencing and HPLC analyses were performed to assess the composition and metabolic activity, respectively, of the fecal microbiota after 24 h of batch cultivation.ResultsHigh abundance of Bifidobacterium (53.4 ± 11.1%) and high proportions of acetate (56 ± 11% of total metabolites) and lactate (24 ± 22% of total metabolites) were detected in the Kenyan infant fecal microbiota. After cultivation started at an initial pH 7.6, the fraction of top bacterial genera (≥ 1% abundant) shared between fermentation and fecal samples was high at 97 ± 5%. However, Escherichia-Shigella, Clostridium sensu stricto 1, Bacteroides and Enterococcus were enriched concomitant with decreased Bifidobacterium abundance. Decreasing the initial pH to 6.9 lead to higher abundance of Bifidobacterium after incubation and increased the compositional similarity of fermentation and fecal samples. Despite similar total metabolite production of all fecal microbiota after cultivation, inter-individual differences in metabolite profiles were apparent.ConclusionsProtected transport and batch cultivation in host and diet adapted conditions allowed regrowth of the top abundant genera and reproduction of the metabolic activity of fresh Kenyan infant fecal microbiota. The validated batch cultivation protocol can be used to study the composition and functional potential of Kenyan infant fecal microbiota in vitro.
| S-EPMC10318780 | biostudies-literature
Project description:Kenyan infant fecal microbiota continuous cultivation
| PRJEB63090 | ENA
Project description:Triple negative breast cancer is an aggressive phenotypic breast cancer characterized by ER negative, PR negative and Her2 negative immunohistochemistry status. We embarked on a study to explore the transcriptome of Kenyan TNBC patients and identify potential biomarkers specific to Kenyan population. The transcriptome sequencing of tumors from Kenyan TNBC patients and comparisons with African American and Caucasian TNBC transcriptomes revealed several interesting targets and dysregulated pathways.
2021-04-28 | GSE142258 | GEO
Project description:Gene expression data from whole-blood collected from Kenyan children with Plasmodium falciparum malaria infection at acute hospital admission (n=15) and at convalescence (n=9). A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Disease State: with Plasmodium falciparum malaria infection at acute hospital admission and at convalescence clinical_history_design
2016-02-15 | E-GEOD-35860 | biostudies-arrayexpress
Project description:Gene expression data from whole-blood collected from Kenyan children with Plasmodium falciparum malaria infection at acute hospital admission (n=15) and at convalescence (n=9). A clinical history design type is where the organisms clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. Disease State: with Plasmodium falciparum malaria infection at acute hospital admission and at convalescence
2016-02-15 | GSE35860 | GEO
Project description:Distinct fiber effect in ex vivo Kenyan infant gut microbiota
| PRJEB67393 | ENA
Project description:We investigated gene expression during the bench-scale batch fermentation phase, glycerol feed phase, glycerol-methanol mixture feed (GM) phase, and at different time points following methanol induction using RNA-Seq. We report that the addition of the GM phase may help to alleviate the adverse effects of methanol addition (alone) on P. pastoris cells. Secondly, enhanced upregulation of the mitogen-activated protein kinase (MAPK) signaling pathway was observed in P. pastoris following methanol induction. The MAPK signaling pathway may be related to P. pastoris cell growth, and may regulate the AOX1 promoter via regulatory factors activated by methanol-mediated stimulation. Thirdly, the unfolded protein response (UPR) and ER-associated degradation (ERAD) pathways were not significantly upregulated during the methanol induction period. These results imply that the presence of unfolded or misfolded phytase protein did not represent a serious problem in our study. Finally, the upregulation of the autophagy pathway during the methanol induction phase may be related to the degradation of damaged peroxisomes but not to the production of phytase. This work describes the metabolic characteristics of P. pastoris during heterologous protein production under high-cell-density fed-batch cultivation. We believe that the results of this study will aid further in-depth studies of P. pastoris protein expression, regulation, and secretory mechanisms.
2019-12-20 | GSE142326 | GEO
Project description:A time series of whole-genome transcription profiling of E. coli K-12 W3110 was performed to study the dynamic physiological response of E. coli K-12 W3110 to limited carbon conditions. cDNA from eight time intervals after glucose limitation, representing different stages of glucose depletion, along with cDNA of an unrestricted growth were hybridized to whole-genome microarrays of E. coli K-12. Glucose concentrations were gradually reduced in a fed-batch cultivation process with constant feeding rate in a bioreactor. Major focus was put on the dynamic changes in the transcription level of genes involved in the central carbon metabolism (glycolysis, pentose phosphate pathway, TCA cycle and glyoxylate shunt), high-affinity glucose transport systems, movement, growth, and stress response. In total, 40 microarrays were hybridized. The data were statistically analysed using the software R (R, 2005) and the Limma package included (Smyth, 2005). The data were normalized â??print-tip-loessâ??. â??Multiple hypothesis testingâ?? correction was performed with the method of Benjamini and Hochberg (Benjamini and Hochberg, 1995), which controls the â??false discovery rateâ?? (fdr). Genes were regarded as differentially expressed when the â??adjusted p valuesâ?? were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The reproducibility of dye swap experiments as well as biological replicates was estimated by calculating â??Pearsonâ??s correlation coefficientsâ??. A high correlation was observed for the dye swap pairs (with averaged Pearsonâ??s correlation coefficients of 0.89 ± 0.06 for the reference samples and of 0.87 ± 0.08 for the different points of time) as well as for biological replicates (with averaged Pearsonâ??s correlation coefficients of 0.86 ± 0.04 for the red channel (Cy5) and 0.80 ± 0.09 for the green channel (Cy3)). Benjamini, Y., and Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 57, 289-300. Smyth, G.K. (2005). Limma: Linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, R. Gentleman, Carrey, V., Dudoit, S., Irizzary, I., Huber, W., ed. (New York, Springer), pp. 397-420. R (2005). R: A language and environment for statistical computing. (R Development Core Team). Supplementary files: Data_table_A: TabelleA_Signifikante.txt Description: Data table with coefficients of the linear model for every gene which was differentially expressed for at least one point in time according to the reference sample. The statistical analysis was performed as described in Series section (GSE10307) based on the normalized log2(test/ref) ratios in the Sample records' VALUE columns. Data_table_B1: Tabelle_B1; /E. coli/, unlimited growth via glucose limitation (glucose concentration < 0.05 gL-1) Data_table_B2: Tabelle_B2; /E. coli/, unlimited growth via glucose limitation, acetate concentration = 0.35 gL-1 Data_table_B3: Tabelle_B3; /E. coli/, unlimited growth via glucose limitation, 30 min after depletion of extracellular acetate Data_table_B4: Tabelle_B4; /E. coli/, unlimited growth via glucose limitation, 50 min after depletion of extracellular acetate Data_table_B5: Tabelle_B5; /E. coli/, unlimited growth via glucose limitation, 110 min after depletion of extracellular acetate Data_table_B6: Tabelle_B6; /E. coli/, unlimited growth via glucose limitation, 170 min after depletion of extracellular acetate Data_table_B7: Tabelle_B7; /E. coli/, unlimited growth via glucose limitation, 230 min after depletion of extracellular acetate Data_table_B8: Tabelle_B8; /E. coli/, unlimited growth via glucose limitation, 350 min after depletion of extracellular acetate Description: Data_tables_B1-B8 report statistical values (A: average intensity value (1/2log2(test*ref)); M: average expression value (log2(test/ref)), t and P.value ('adjusted P.value')) for every point in time (studied conditions are described above for the corresponding table). Every differentially expressed gene of the corresponding point in time according to the reference sample is listed. Genes were regarded as differentially expressed when their 'adjusted P.values' were < 0.05, therefore nominally controlling the expected fdr to less than 0.05. The data are based on maximal three biological replicates (three independent fed-batch cultivations). RT-PCR_results_7genes.txt and RT-PCR_protocol.PDF Keywords: Time course, stress response Hybridization involved the hybridization of a common reference (unlimited growth, batch phase) on all arrays together with each sample of interest. This allowed the direct comparison of the transcripts of a time series taken during fed-batch cultivation with the unlimited reference sample. All samples were taken in duplicates and the experiments were performed as dye swap experiments. The first four samples of the time series (T1 - T4) were taken from three individual fed-batch cultivations (three biological replicates), the subsequent four samples (T5 - T8) were taken only from two individual fed-batch cultivations. On each array, the genes were spotted in duplicates. Therefore, twelve replicates (duplicates on dye swaps for three cultivations) were analyzed for T1 â?? T4 and eight replicates (duplicates on dye swaps for two cultivations) were analyzed for T5 â?? T8.
2010-05-19 | E-GEOD-10307 | biostudies-arrayexpress
Project description:The effect of respiration (aerobic cultivation in the presence of heme and vitamin K2) was compared with unsupplemented aerobic cultivation with Lactobacillus plantarum.
2010-01-01 | GSE18432 | GEO
Project description:Genome wide DNA methylation profiling of isolated monocyte samples from healthy Kenyan children, the same children during an episode of acute malaria, healthy Kenyan adults, and healthy adults from the United States. The Illumina Infinium MethylationEPIC BeadChip microarray was used to obtain DNA methylation profiles across approximately 860,000 CpGs in negatively selected monocyte samples. Samples included monocytes from 8 children from western Kenya obtained while healthy and matching samples from the same 8 Kenyan children obtained during an episode of acute uncomplicated Plasmodium falciparum malaria, 8 healthy malaria-immune adults from western Kenya, and 8 healthy malaria-naive adults from the US. Abstract -- Background: Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profiles in monocytes from young adults and children from western Kenya. Results: We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles. Conclusions: These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.
2021-03-11 | GSE157611 | GEO