Distributions of model microorganisms along an estuarine gradient

Microbial ecology is the younger sub-discipline of ecology, but its scope is clearly immense. Microorganisms’ specificities represent a major hurdle to the application of traditional ecological approaches. Recently, the opportunity to apply ecological principles to microorganisms was suggested. It is assumed that existing principles might apply, but that they are probably also driven by specific principles. Microorganisms have varying metabolic abilities and are classified as generalists or specialists. We hypothesised that contrasting metabolic properties may drive genotypic distribution. Model generalist and specialist genera were selected and distribution patterns along the salinity gradient of the River Colne estuary studied. Two models were studied in detail, Desulfobulbus a versatile sulphate-reducing bacterial (SRB) genus and Methanosaeta, a strict aceticlastic methanogenic archaea (MA). Isolation of Methanosaeta was attempted in order to link phenotypes to genotypic distribution. Two other models were also studied: Methanosarcina the most versatile MA genus and Desulfobacter a metabolically restricted SRB genus. Denaturing gel gradient electrophoresis (DGGE) and clone libraries analyses were used to determine genotypic distribution patterns. Methanosaeta have proven to be highly recalcitrant to isolation. Adjustments to commonly used anaerobic culturing methods allowed the obtention of Methanosaeta colonies. In contrast to previous studies, colonies were successfully transferred into liquid medium, and growth of pure clonal cultures confirmed. Desulfobulbus genotypic distribution pattern was previously shown to be sequential along the estuary. Contrastingly, Methanosaeta genotypic distribution pattern was found to be monotonic. Furthermore, active genotypes distribution was also found monotonic, with an apparent general increase in activity with decreasing salinity. Distribution patterns of the four different genera confirmed this trend. The generalists were both shown to have sequential distribution patterns. Contrastingly, the specialists were both shown to have monotonic distribution patterns. These results confirm the hypothesis that genotypic distribution patterns microbial communities structure are strongly driven by microorganisms’ metabolic properties and adaptative potential

Distributions of model microorganisms along an estuarine gradient

Microbial ecology is the younger sub-discipline of ecology, but its scope is clearly immense. Microorganisms’ specificities represent a major hurdle to the application of traditional ecological approaches. Recently, the opportunity to apply ecological principles to microorganisms was suggested. It is assumed that existing principles might apply, but that they are probably also driven by specific principles. Microorganisms have varying metabolic abilities and are classified as generalists or specialists. We hypothesised that contrasting metabolic properties may drive genotypic distribution. Model generalist and specialist genera were selected and distribution patterns along the salinity gradient of the River Colne estuary studied. Two models were studied in detail, Desulfobulbus a versatile sulphate-reducing bacterial (SRB) genus and Methanosaeta, a strict aceticlastic methanogenic archaea (MA). Isolation of Methanosaeta was attempted in order to link phenotypes to genotypic distribution. Two other models were also studied: Methanosarcina the most versatile MA genus and Desulfobacter a metabolically restricted SRB genus. Denaturing gel gradient electrophoresis (DGGE) and clone libraries analyses were used to determine genotypic distribution patterns. Methanosaeta have proven to be highly recalcitrant to isolation. Adjustments to commonly used anaerobic culturing methods allowed the obtention of Methanosaeta colonies. In contrast to previous studies, colonies were successfully transferred into liquid medium, and growth of pure clonal cultures confirmed. Desulfobulbus genotypic distribution pattern was previously shown to be sequential along the estuary. Contrastingly, Methanosaeta genotypic distribution pattern was found to be monotonic. Furthermore, active genotypes distribution was also found monotonic, with an apparent general increase in activity with decreasing salinity. Distribution patterns of the four different genera confirmed this trend. The generalists were both shown to have sequential distribution patterns. Contrastingly, the specialists were both shown to have monotonic distribution patterns. These results confirm the hypothesis that genotypic distribution patterns microbial communities structure are strongly driven by microorganisms’ metabolic properties and adaptative potential.EThOS - Electronic Theses Online ServiceEuropean Union (EU) (MEXT-CT-2005-024112)GBUnited Kingdo

Metabolic flexibility as a major predictor of spatial distribution in microbial communities

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology

Isolated Rearing at Lactation Increases Gut Microbial Diversity and Post-weaning Performance in Pigs

Environment and diet are two major factors affecting the human gut microbiome. In this study, we used a pig model to determine the impact of these two factors during lactation on the gut microbiome, immune system, and growth performance. We assigned 80 4-day-old pigs from 20 sows to two rearing strategies at lactation: conventional rearing on sow’s milk (SR) or isolated rearing on milk replacer supplemented with solid feed starting on day 10 (IR). At weaning (day 21), SR and IR piglets were co-mingled (10 pens of 4 piglets/pen) and fed the same corn-soybean meal-dried distiller grain with solubles- and antibiotic-free diets for eight feeding phase regimes. Fecal samples were collected on day 21, 62, and 78 for next-generation sequencing of the V4 hypervariable region of the bacterial 16S rRNA gene. Results indicate that IR significantly increased swine microbial diversity and changed the microbiome structure at day 21. Such changes diminished after the two piglet groups were co-mingled and fed the same diet. Post-weaning growth performance also improved in IR piglets. Toward the end of the nursery period (NP), IR piglets had greater average daily gain (0.49 vs. 0.41 kg/d; P < 0.01) and average daily feed intake (0.61 vs. 0.59 kg/d; P < 0.01) but lower feed efficiency (0.64 vs. 0.68; P = 0.05). Consequently, IR piglets were heavier by 2.9 kg (P < 0.01) at the end of NP, and by 4.1 kg (P = 0.08) at market age compared to SR piglets. Interestingly, pigs from the two groups had similar lean tissue percentage. Random forest analysis showed that members of Leuconostoc and Lactococcus best differentiated the IR and SR piglets at weaning (day 21), were negatively correlated with levels of Foxp3 regulatory T cell populations on day 20, and positively correlated with post-weaning growth performance. Our results suggest that rearing strategies may be managed so as to accelerate early-life establishment of the swine gut microbiome to enhance growth performance in piglets

On the Relationship between Sialomucin and Sulfomucin Expression and Hydrogenotrophic Microbes in the Human Colonic Mucosa

The colonic mucus layer is comprised primarily of acidomucins, which provide viscous properties and can be broadly classified into sialomucins or sulfomucins based on the presence of terminating sialic acid or sulfate groups. Differences in acidomucin chemotypes have been observed in diseases such as colorectal cancer and inflammatory bowel disease, and variation in sialo- and sulfomucin content may influence microbial colonization. For example, sulfate derived from sulfomucin degradation may promote the colonization of sulfate-reducing bacteria (SRB), which through sulfate respiration generate the genotoxic gas hydrogen sulfide. Here, paired biopsies from right colon, left colon, and rectum of 20 subjects undergoing routine screening colonoscopies were collected to enable parallel histochemical and microbiological studies. Goblet cell sialo- and sulfomucins in each biopsy were distinguished histochemically and quantified. Quantitative PCR and multivariate analyses were used to examine the abundance of hydrogenotrophic microbial groups and SRB genera relative to acidomucin profiles. Regional variation was observed in sialomucins and sulfomucins with the greatest abundance of each found in the rectum. Mucin composition did not appear to influence the abundance of SRB or other hydrogenotrophic microbiota but correlated with the composition of different SRB genera. A higher sulfomucin proportion correlated with higher quantities of Desulfobacter, Desulfobulbus and Desulfotomaculum, relative to the predominant Desulfovibrio genus. Thus, acidomucin composition may influence bacterial sulfate respiration in the human colon, which may in turn impact mucosal homeostasis. These results stress the need to consider mucus characteristics in the context of studies of the microbiome that target intestinal diseases

Fat, fibre and cancer risk in African Americans and rural Africans

Rates of colon cancer are much higher in African Americans (65: 100,000) than in rural South Africans (Peer reviewe

Fat, fibre and cancer risk in African Americans and rural Africans

Rates of colon cancer are much higher in African Americans (65: 100,000) than in rural South Africans (Peer reviewe

Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints

The gut microbiome of primates, including humans, is reported to closely follow host evolutionary history, with gut microbiome composition being specific to the genetic background of its primate host. However, the comparative models used to date have mainly included a limited set of closely related primates. To further understand the forces that shape the primate gut microbiome, with reference to human populations, we expanded the comparative analysis of variation among gut microbiome compositions and their primate hosts, including 9 different primate species and 4 human groups characterized by a diverse set of subsistence patterns (n = 448 samples). The results show that the taxonomic composition of the human gut microbiome, at the genus level, exhibits increased compositional plasticity. Specifically, we show unexpected similarities between African Old World monkeys that rely on eclectic foraging and human populations engaging in nonindustrial subsistence patterns; these similarities transcend host phylogenetic constraints. Thus, instead of following evolutionary trends that would make their microbiomes more similar to that of conspecifics or more phylogenetically similar apes, gut microbiome composition in humans from nonindustrial populations resembles that of generalist cercopithecine monkeys. We also document that wild cercopithecine monkeys with eclectic diets and humans following nonindustrial subsistence patterns harbor high gut microbiome diversity that is not only higher than that seen in humans engaging in industrialized lifestyles but also higher compared to wild primates that typically consume fiber-rich diets