Spatial fractionation of phosphorus accumulating biofilm: stratification of polyphosphate accumulation and dissimilatory nitrogen metabolism

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Spatiotemporal succession of phosphorous accumulating biofilms during the first year of establishment

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Pre- and post-race intestinal microbiota in long-distance sled dogs and associations with performance

Although our understanding of the role of the gut microbiota in different diseases is improving, our knowledge regarding how the gut microbiota affects functioning in healthy individuals is still limited. Here, we hypothesize that the gut microbiota could be associated with sled dog endurance-race performance. We investigated the gut microbiota in 166 fecal samples from 96 Alaskan Huskies, representing 16 teams participating in the 2016 Femund Race (400 km) in Norway, relating the microbiota composition to performance and metadata derived from questionnaires. For 16S rRNA gene sequencing-derived compositional data, we found a strong negative association between Enterobacteriaceae (dysbiosis-associated) and Clostridium hiranonis (normobiosis-associated). The teams with the best performances showed both the lowest levels of dysbiosis-associated bacteria prior to the race and the lowest change (decrease) in these bacteria after the race. Taken together, our results support the hypothesis that normobiosis-associated bacteria are involved in resilience mechanisms, potentially preventing growth of Enterobacteriaceae during the race.publishedVersio

Fecal Microbiota Nutrient Utilization Potential Suggests Mucins as Drivers for Initial Gut Colonization of Mother-Child-Shared Bacteria

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Lysates of Methylococcus capsulatus Bath induce a lean-like microbiota, intestinal FoxP3+RORγt+IL-17+ Tregs and improve metabolism

Interactions between host and gut microbial communities are modulated by diets and play pivotal roles in immunological homeostasis and health. We show that exchanging the protein source in a high fat, high sugar, westernized diet from casein to whole-cell lysates of the non-commensal bacterium Methylococcus capsulatus Bath is sufficient to reverse western diet-induced changes in the gut microbiota to a state resembling that of lean, low fat diet-fed mice, both under mild thermal stress (T22 °C) and at thermoneutrality (T30 °C). Concomitant with microbiota changes, mice fed the Methylococcus-based western diet exhibit improved glucose regulation, reduced body and liver fat, and diminished hepatic immune infiltration. Intake of the Methylococcu-based diet markedly boosts Parabacteroides abundances in a manner depending on adaptive immunity, and upregulates triple positive (Foxp3+RORγt+IL-17+) regulatory T cells in the small and large intestine. Collectively, these data point to the potential for leveraging the use of McB lysates to improve immunometabolic homeostasis.publishedVersio

An in vivo study of Gilliamella apicola as a potential vector for tetracycline resistance gene transfer in midgut and hindgut of Apis mellifera

Honey bees, along with other wild type bees such as bumble bees, are the world’s most important pollinators. Their existence provide humans and animals important food supply, and also contribute to maintenance of the ecological biodiversity. By their pollination services they cover large spatial areas and their high interaction with the environments lead to spread of bacteria, thus also, presumably gene fragments, between them and the environment. The merging spread of antibiotic resistance is of major concern, and the environment play an important role, were spread of such genes, are being exchanged and transferred between and within different habitats. The role insects play in such spread of resistance is not well studied, and this thesis direct focus on potential role of the commensal bacteria Gilliamella apicola in the gastro intestinal tract of the honey bee Apis mellifera, as vectors for transfer of the antibiotic resistance gene tetB. In addition we aimed to look at bacterial compositions of the honey bee gut, after exposure to the broad-spectrum antibiotic tetracycline, and compare the microbiota of the two different gut compartments midgut and hindgut. By in vivo study, using 1080 caged honeybees, feeding trials were performed, by providing the honeybees sugar solutions with supplements in the form of tetracycline, and/or bacterial cultures of G. apicola. Methods used in the study involved both qualitative and quantitative PCR, 16S rRNA metagenome sequencing, and Sanger sequencing. A total of 267 midgut and 267 hindgut samples were analyzed. Our findings show high prevalence of tetB in Norwegian honeybees, with presence of the gene in 44% of the honeybees. No effects on abundance of the gene was observed with treatment with tetracycline, however a significant effect of treatment with G. apicola, and presence of the gene was observed, although evidence for gene transfer could not be confirmed. Bacterial composition comparison showed an increased abundance of Lactobacillus spp., associated to tetracycline treatment. In addition, differences in bacterial compositions in the midgut and hindguts were observed, where midgut microbiota showed to harbor a more unstable microbiota, compared to hindgut microbiota. Big differences were also observed in the midgut microbiota of bees from the colony versus caged bees.Honningbier, sammen med andre villtype bier som humler, er verdens viktigste pollinatorer. Deres eksistens gir mennesker og dyr viktig matforsyning, og de bidrar også til vedlikehold av økologisk biologisk mangfold. Med deres pollineringstjenester, dekker de store områder og ved å interagere med omgivelsene i stor grad, bidrar de muligens til spredning av bakterier, derav også trolig gen-fragmenter, mellom dem og miljøet. Den økende forekomsten av spredning av antibiotika resistens er av stor bekymring, og miljøet spiller trolig en viktig rolle i forbindelse med slik spredning. Hvilken rolle insekter spiller i spredning av resistens er ikke kjent, og denne oppgaven retter fokus mot Gilliamella apicola, en tarmbakterie funnet i honningbien Apis mellifera, som potensiell vektor i forbindelse med overføring av antibiotika resistensgenet tetB. I tillegg var det ønskelig å undersøke bakterie komposisjonen i tarmen hos bie, etter eksponering for det bredspektrede antibiotikumet tetrasyklin, samt sammenligne bakterieflora i midtmage og endetarm. I et in vivo forsøk, med 1080 honningbier i bur, ble det utført fôringsforsøk ved å gi sukkerløsninger med supplementer i form av tetrasyklin, og/eller bakteriekulturer med G. apicola. Metoder som ble brukt i forbindelse med studien involverte både kvalitativ og kvantitativ PCR, 16S rRNA metagenomsekvensering, og Sanger-sekvensering. Totalt ble 267 midtmage og 267 endetarms prøver analysert. Våre funn viser høy forekomst av tetB i norske honningbier, med tilstedeværelse av genet i 44% av biene. Behandling med tetrasyklin ga ingen effekt på antall bier positive for tetB, men derimot ble det observert effekt av behandling med G. apicola, selv om det ikke ble funnet noen bevis for genoverføring. Ved behandling med tetrasyklin, økte mengden av arter tilhørende Lactobacillus. I tillegg ble det observer forskjeller i bakteriesammensetninger i midtmage og endetarm, hvor mikrobiotaen i midtmage viste seg å være mer ustabil, enn mikrobiota i endetarm. Det ble også observert store forskjeller I midtmage mikrobiota mellom bier i kube og bier i bur.M-M

Reduced metagenome sequencing for strain-resolution taxonomic profiles

Background Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. Results We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. Conclusion We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS

Atlantic salmon raised with diets low in long-chain polyunsaturated n-3 fatty acids in freshwater have a Mycoplasma-dominated gut microbiota at sea

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Ecological Processes Affecting Long-Term Eukaryote and Prokaryote Biofilm Persistence in Nitrogen Removal from Sewage

The factors affecting long-term biofilm stability in sewage treatment remain largely unexplored. We therefore analyzed moving bed bioreactors (MBBRs) biofilm composition and function two years apart from four reactors in a nitrogen-removal sewage treatment plant. Multivariate ANOVA revealed a similar prokaryote microbiota composition on biofilm carriers from the same reactors, where reactor explained 84.6% of the variance, and year only explained 1.5%. Eukaryotes showed a less similar composition with reactor explaining 56.8% of the variance and year 9.4%. Downstream effects were also more pronounced for eukaryotes than prokaryotes. For prokaryotes, carbon source emerged as a potential factor for deterministic assembly. In the two reactors with methanol as a carbon source, the bacterial genus Methylotenera dominated, with M. versatilis as the most abundant species. M. versatilis showed large lineage diversity. The lineages mainly differed with respect to potential terminal electron acceptor usage (nitrogen oxides and oxygen). Searches in the Sequence Read Archive (SRA) database indicate a global distribution of the M. versatilis strains, with methane-containing sediments as the main habitat. Taken together, our results support long-term prokaryote biofilm persistence, while eukaryotes were less persistent