Microbial Ecology in Health and Disease最新文献

Background: The availability of fresh stool samples is a prerequisite in most gut microbiota functional studies. Objective: Strategies for amplification and long-term gut microbiota preservation from fecal samples would favor sample sharing, help comparisons and reproducibility over time and between laboratories, and improve the safety and ethical issues surrounding fecal microbiota transplantations. Design: Taking advantage of in vitro gut-simulating systems, we amplified the microbial repertoire of a fresh fecal sample and assessed the viability and resuscitation of microbes after preservation with some common intracellular and extracellular acting cryoprotective agents (CPAs), alone and in different combinations. Preservation efficiencies were determined after 3 and 6 months and compared with the fresh initial microbiota diversity and metabolic activity, using the chemostat-based Environmental Control System for Intestinal Microbiota (ECSIM) in vitro model of the gut environment. Microbial populations were tested for fermentation gas, short-chain fatty acids, and composition of amplified and resuscitated microbiota, encompassing methanogenic archaea. Results: Amplification of the microbial repertoire from a fresh fecal sample was achieved with high fidelity. Dimethylsulfoxide, alone or mixed with other CPAs, showed the best efficiency for functional preservation, and the duration of preservation had little effect. Conclusions: The amplification and resuscitation of fecal microbiota can be performed using specialized in vitro gut models. Correct amplification of the initial microbes should ease the sharing of clinical samples and improve the safety of fecal microbiota transplantation. Abbreviations: CDI, Clostridium difficile infection; CPA, cryoprotective agent; D, DMSO, dimethylsulfoxide; FMT, fecal microbiota transplantation; G, glycerol; IBD, inflammatory bowel disease; P, PEG-4000, polyethylene glycol 4000 g.mol^-1; SCFA, short-chain fatty acid; SNR, signal-to-noise ratio.

Objective: Alterations of gut microbiota composition or function may participate in the pathophysiology of several diseases. We aimed to explore the effect of chronic alcohol overconsumption on gut microbial metabolism, as assessed by evaluating ¹³C-D-xylose breath test results. Materials and methods: We investigated all ¹³C-D-xylose breath tests performed at Lovisenberg Diaconal Hospital during the years 2005 to 2011, using patient files for diagnosing the patients into one of three patient categories: alcohol overconsumption, coeliac disease and functional bowel disorder. In addition, a group of healthy controls was included. The time curves of ¹³CO₂ excretion in breath samples were divided into two phases, evaluating small intestinal absorption (0-60 min) and colonic microbial metabolism (90-240 min), respectively. Results: A total of 719 patients underwent ¹³C-D-xylose breath testing during the inclusion period. Thirty-five had a history of alcohol overconsumption, 66 had coeliac disease, and 216 had a functional bowel disorder, while 44 healthy controls were included for comparison. The alcohol overconsumption group had similar small intestinal phase results as the group of patients with untreated coeliac disease. During the colonic phase, the group of patients with alcohol overconsumption differed from all the other groups in terms of ¹³C-xylose recovery, with significantly less ¹³CO₂ excretion compared to the other groups. Conclusion: The results suggest that patients with a history of alcohol overconsumption suffer from both small intestinal malabsorption and impaired colonic microbial metabolism. The role of gut microbiota in chronic alcohol overconsumption should be investigated further.

​Background: Consumption of Lactobacillus paracasei Lpc-37 or Bifidobacterium lactis HN019 by 2-5-year-old children was found to reduce risk for diarrhoea and fever during the rainy season. Objective: Can changes in faecal short chain fatty acids (SCFAs) or branched chain fatty acids (BCFAs) explain the observed positive influence of probiotics and their role on nutritional status and diarrhoea risk? Design: Faecal samples were analysed for SCFAs and BCFAs and correlated to Bifidobacterium and Lactobacillus levels; both at the start and after nine months' consumption of either of the two probiotic strains, or placebo. Results: No differences in SCFAs, BCFAs, Lactobacillus or Bifidobacterium levels were found between boys and girls. Severely underweight children were observed to have the highest Lactobacillus levels. Probiotic intervention was found to be associated with higher levels of selected SCFAs and BCFAs in subjects who had experienced diarrhoea. Treatment with either of the probiotics led to changes in SCFAs and BCFAs. SCFAs, acetate, propionate and butyrate, were found to correlate with each other. Likewise, BCFAs isobutyrate, 2-methylbutyrate and isovalerate correlated with each other. After the intervention, L. paracasei Lpc-37 correlated positively with total Bifidobacterium counts and isovalerate levels. B. lactis HN019 counts were found to correlate positively with total bacterial counts and negatively with propionate levels. Conclusions: ​Nutritional status was associated with higher levels of faecal lactobacilli; the meaning of this requires further investigation. The intervention with the two probiotics was observed to influence the levels of faecal SCFAs and BCFAs and there is a differential response in those who developed diarrhoea and those who did not. It is, however, not clear to what extent this is a mechanism that explains the earlier observed effect the strains had on diarrhoea risk.

Background: Colorectal cancer (CRC) is one of the most common cancer types worldwide. The role of the intestinal microbiota in CRC, however, is not well established. In particular, the co-variation between age, tumor progression and microbiota remains largely unknown. Objective and design: We therefore used a recently developed A/J Min/+ mouse model resembling human CRC to investigate how microbial composition in cecum correlates with tumor progression, butyrate and age. Results: We found that the association between the gut microbiota and tumor load was stronger, by far, than the association with both butyrate and age. The strongest direct tumor association was found for mucosal bacteria, with nearly 60% of the significantly correlating operational taxonomic units being correlated with CRC tumor load alone. Conclusion: We favor a systemic association between tumor load and microbiota, since the correlations are associated with tumor load in gut segments other than the cecum (both small and large intestine).

The gut microbiota is considered an organ that co-develops with the host throughout its life. The composition and metabolic activities of the gut microbiota are subject to a complex interplay between the host genetics and environmental factors, such as lifestyle, diet, stress and antimicrobials. It is evident that certain prebiotics, and antimicrobials produced by lactic acid bacteria (LAB), can shape the composition of the gut microbiota and its metabolic activities to promote host health and/or prevent diseases. In this review, we aim to give an overview of the impact of prebiotic fibres, and bacteriocins from LAB, on the gut microbiota and its activities, which affect the physiology and health of the host. These represent two different mechanisms in modulating the gut microbiota, the first involving exploitative competition by which the growth of beneficial bacteria is promoted and the latter involving interference competition by which the growth of pathogens and other unwanted bacteria is prevented. For interference competition in the gut, bacteriocins offer special advantages over traditional antibiotics, in that they can be designed to act towards specific unwanted bacteria and other pathogens, without any remarkable collateral effects on beneficial microbes sharing the same niche.

Background: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years. Objective: To cultivate bacterial strains from permafrost. Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40-60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences. Results: Genomic sequence analysis revealed the close relation of the isolated ancient bacteria to the modern bacteria of this species. Moreover, several genes associated with resistance to different groups of antibiotics were found in the S. hominis MMP2 genome. Conclusions: These findings supports a hypothesis that antibiotic resistance has an ancient origin. The enrichment of cultivated bacterial communities with ancient permafrost strains is essential for the analysis of bacterial evolution and antibiotic resistance.