Opportunistic bacteria confer the ability to ferment prebiotic starch in the adult cystic fibrosis gut

Chronic disruption of the intestinal microbiota in adult cystic fibrosis (CF) patients is associated with local and systemic inflammation, and has been linked to the risk of serious comorbidities. Supplementation with high amylose maize starch (HAMS) might provide clinical benefit by promoting commensal bacteria and the biosynthesis of immunomodulatory metabolites. However, whether the disrupted CF gut microbiota has the capacity to utilise these substrates is not known. We combined metagenomic sequencing, in vitro fermentation, amplicon sequencing, and metabolomics to define the characteristics of the faecal microbiota in adult CF patients and assess HAMS fermentation capacity. Compared to healthy controls, the faecal metagenome of adult CF patients had reduced bacterial diversity and prevalence of commensal fermentative clades. In vitro fermentation models seeded with CF faecal slurries exhibited reduced acetate levels compared to healthy control reactions, but comparable levels of butyrate and propionate. While the commensal genus Faecalibacterium was strongly associated with short chain fatty acid (SCFA) production by healthy microbiota, it was displaced in this role by Clostridium sensu stricto 1 in the microbiota of CF patients. A subset of CF reactions exhibited enterococcal overgrowth, resulting in lactate accumulation and reduced SCFA biosynthesis. The addition of healthy microbiota to CF faecal slurries failed to displace predominant CF taxa, or substantially influence metabolite biosynthesis. Despite significant microbiota disruption, the adult CF gut microbiota retains the capacity to exploit HAMS. Our findings highlight the potential for taxa associated with the altered CF gut microbiotato mediate prebiotic effects in microbial systems subject to ongoing perturbation, irrespective of the depletion of common commensal clades

Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only

Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities (i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community

Pyrosequencing-based characterization of gastrointestinal bacteria of Atlantic salmon (Salmo salar L.) within a commercial mariculture system

AimsThe relationship of Atlantic salmon gastrointestinal (GI) tract bacteria to environmental factors, in particular water temperature within a commercial mariculture system, was investigated.Methods and ResultsSalmon GI tract bacterial communities commercially farmed in south-eastern Tasmania were analysed, over a 13-month period across a standard commercial production farm cycle, using 454 16S rRNA-based pyrosequencing. Faecal bacterial communities were highly dynamic but largely similar between randomly selected fish. In postsmolt, the faecal bacteria population was dominated by Gram-positive fermentative bacteria; however, by midsummer, members of the family Vibrionaceae predominated. As fish progressed towards harvest, a range of different bacterial genera became more prominent corresponding to a decline in Vibrionaceae. The sampled fish were fed two different commercial diet series with slightly different protein, lipid and digestible energy level; however, the effect of these differences was minimal.ConclusionsThe overall data demonstrated dynamic hind gut communities in salmon that were related to season and fish growth phases but were less influenced by differences in commercial diets used routinely within the farm system studied.Significance and Impact of the StudyThis study provides understanding of farmed salmon GI bacterial communities and describes the relative impact of diet, environmental and farm factors

Hydrology is reflected in the functioning and community composition of methanotrophs in the littoral wetland of a boreal lake

In lake ecosystems a major proportion of methane emissions originate from the littoral zone which can have a great spatial variability in hydrology, soil quality and vegetation. Hitherto, spatial heterogeneity and the effects it has on functioning and diversity of methanotrophs in littoral wetlands is poorly understood. A diagnostic microarray based on the particulate methane monooxygenase gene coupled with geostatistics was used to analyze spatial patterns of methanotrophs in the littoral wetland of a eutrophic boreal lake (Lake Kevätön, Eastern Finland). The wetland had a hydrology gradient with mean water table varying from −8 cm to −25 cm. The wettest area comprising the highest methane oxidation, had the highest abundance and species richness of methanotrophs. High water table favoured the occurrence of type Ib methanotrophs whereas type Ia and type II were found under all moisture conditions. Thus the spatial heterogeneity in functioning and diversity of methanotrophs in littoral wetlands is highly dependent on water table which in turn varies spatially in relation to the geomorphology of the wetland. We suggest that changes in water levels resulting from regulation of lakes and/or global change will affect the abundance, activity, diversity of methanotrophs and consequently methane emissions from such systems.

Hydrology is reflected in the functioning and community composition of methanotrophs in the littoral wetland of a boreal lake

In lake ecosystems a major proportion of methane emissions originate from the littoral zone which can have a great spatial variability in hydrology, soil quality and vegetation. Hitherto, spatial heterogeneity and the effects it has on functioning and diversity of methanotrophs in littoral wetlands is poorly understood. A diagnostic microarray based on the particulate methane monooxygenase gene coupled with geostatistics was used to analyze spatial patterns of methanotrophs in the littoral wetland of a eutrophic boreal lake (Lake Kevätön, Eastern Finland). The wetland had a hydrology gradient with mean water table varying from −8 cm to −25 cm. The wettest area comprising the highest methane oxidation, had the highest abundance and species richness of methanotrophs. High water table favoured the occurrence of type Ib methanotrophs whereas type Ia and type II were found under all moisture conditions. Thus the spatial heterogeneity in functioning and diversity of methanotrophs in littoral wetlands is highly dependent on water table which in turn varies spatially in relation to the geomorphology of the wetland. We suggest that changes in water levels resulting from regulation of lakes and/or global change will affect the abundance, activity, diversity of methanotrophs and consequently methane emissions from such systems

The capacity of the fecal microbiota from Malawian infants to ferment resistant starch

© Authors. In Low and Middle-Income Countries (LMIC), weaning is associated with environmentally acquired and inflammation-associated enteric disorders. Dietary intake of high amylose maize starch (HAMS) can promote commensal fermentative bacteria and drive the production of short chain fatty acids (SCFAs). By stabilizing commensal gut microbiology, and stimulating the production of anti-inflammatory metabolites, HAMS supplementation might therefore influence enteric health. However, the extent to which the gut microbiota of LMIC infants are capable of fermenting HAMS is unclear. We assessed the capacity of the fecal microbiota from pre-weaning and weaning Malawian infants to ferment HAMS and produce SCFAs using an in vitro fermentation model. Fecal microbiota from both pre-weaning and weaning infants were able to ferment HAMS, as indicated by an increase in bacterial load and total SCFA concentration, and a reduction in pH. All of these changes were more substantial in the weaning group. Acetate production was observed with both pre-weaning and weaning groups, while propionate production was only observed in the weaning group. HAMS fermentation resulted in significant alterations to the fecal microbial community in the weaning group, with significant increases in levels of Prevotella, Veillonella, and Collinsella associated with propionate production. In conclusion, fecal microbiota from Malawian infants before and during weaning has the capacity to produce acetate through HAMS fermentation, with propionate biosynthetic capability appearing only at weaning. Our results suggest that HAMS supplementation might provide benefit to infants during weaning