Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation

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Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background

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Co-infection dynamics of a major food-borne zoonotic pathogen in chicken

A major bottleneck in understanding zoonotic pathogens has been the analysis of pathogen co-infection dynamics. We have addressed this challenge using a novel direct sequencing approach for pathogen quantification in mixed infections. The major zoonotic food-borne pathogen Campylobacter jejuni, with an important reservoir in the gastrointestinal (GI) tract of chickens, was used as a model. We investigated the co-colonisation dynamics of seven C. jejuni strains in a chicken GI infection trial. The seven strains were isolated from an epidemiological study showing multiple strain infections at the farm level. We analysed time-series data, following the Campylobacter colonisation, as well as the dominant background flora of chickens. Data were collected from the infection at day 16 until the last sampling point at day 36. Chickens with two different background floras were studied, mature ( treated with Broilact, which is a product consisting of bacteria from the intestinal flora of healthy hens) and spontaneous. The two treatments resulted in completely different background floras, yet similar Campylobacter colonisation patterns were detected in both groups. This suggests that it is the chicken host and not the background flora that is important in determining the Campylobacter colonisation pattern. Our results showed that mainly two of the seven C. jejuni strains dominated the Campylobacter flora in the chickens, with a shift of the dominating strain during the infection period. We propose a model in which multiple C. jejuni strains can colonise a single host, with the dominant strains being replaced as a consequence of strain-specific immune responses. This model represents a new understanding of C. jejuni epidemiology, with future implications for the development of novel intervention strategies

Surveillance of antimicrobial resistance in the environment - Scientific Opinion of the Panel on Microbial Ecology, Norwegian Scientific Committee for Food and Environment

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Surveillance of antimicrobial resistance in the environment - Scientific Opinion of the Panel on Microbial Ecology, Norwegian Scientific Committee for Food and Environment

Source at https://vkm.no/</a

Surveillance of antimicrobial resistance in the environment - Scientific Opinion of the Panel on Microbial Ecology, Norwegian Scientific Committee for Food and Environment

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Ecology of gut bacteria : Microbial community dynamics investigated using an integrated approach

I dette arbeidet har vi utviklet molekylære metoder for simultant å måle forekomsten av ulike mikrober i komplekse samfunn. Koblet med økologisk analyse gir dette oss helt nye muligheter til å forstå hvordan bakteriesamfunn fungerer, kunnskap av potensielt stor verdi for eksempel i forebygging og behandling av infeksjoner. I sine naturlige miljøer lever bakteriene gjerne i kompliserte samfunn, det være seg i jord, vann eller i menneskekroppen. For eksempel består den normale humane bakterieflora av så mye som 1014 bakterieceller, ca. 100 ganger så mange som det finnes menneskeceller i kroppen. En voksende mengde litteratur dokumenterer en rekke viktige roller disse mikrobene spiller i helse og sykdom, men allikevel er vår viten om deres økologi fortsatt svært ufullkommen. En mye brukt fremgangsmåte i økologiske studier av planter og dyr er analyse av tidsseriedata, en tilnærming som kan gi informasjon om hvilke forhold som styrer utvikingen av økosystemer, for eksempel mekanismer som ligger bak det at populasjoner kollapser og blomstrer. Denne typen analyse er langt mindre brukt til å studere mikrobenes verden, til dels fordi fagdisiplinene generell økologi og mikrobiologi lenge har utviklet seg som separate enheter, men også fordi populasjonsdata på mikrober i komplekse samfunn er vanskelige å oppdrive. Bakterier er i praksis usynlige (utenom i mikroskop), de er ofte vanskelige å skille fra hverandre ut ifra morfologiske kriterier, og de har ekstremt kort generasjonstid (så lite som 10 min. under gunstige forhold). Metodene vi har utviklet gjør det mulig å følge bakteriesamfunn gjennom tid på en relativt hurtig og enkel måte. De er basert på simultan registrering av DNA-molekyler som kan diskriminere mellom de ulike medlemmene av et samfunn, og påfølgende analyse av DNA-signalene v.h.a. regnemetoder som normalt brukes kjemi. Vi har brukt metodene både i infeksjonssituasjoner og laboratoriekulturer, og analyse av de resulterende tidsseriene har gjort oss i stand til å danne hypoteser om hvordan bakteriesamfunn fungerer. Slik informasjon er relevant bl.a. i forhold til sykdommer som oppstår som følge av endringer i kroppens naturlige bakterieflora. Avhandlingen er et resultat av tverrfaglig samarbeid mellom NOFIMA Mat (tidligere Matforsk AS) og Centre for Ecological and Evolutionary Synthesis (CEES, Senter for Fremragende Forskning ved Biologisk Institutt ved UiO)

Promoter elements or RNA transcript stabilizing structures in the 5 UTR of the rbcL gene of Chlamydomonas reinhardtii

The rbcL promoter of C. reinhardtii has been reported to lack a functional -35 consensus motif common to the ó70 type promoters found in prokaryotes and many plastid promoters, while retaining a conserved ó70 like -10 promoter element. Furthermore, sequences located within the first 63 bp of the rbcL 5 UTR were reported to be essential to the rbcL basal promoter (Klein et al., 1994). A similar promoter structure was reported for the atpB gene of C. reinhardtii (Klein et al., 1992), suggesting a separate class of chloroplast promoter in this organism. This study looks at how specific mutations in the 5 UTR region of the rbcL gene affect RNA transcript levels in C. reinhardtii harbouring chimeric gene constructs containing the putative rbcL promoter 5 fused to a GUS reporter gene terminated by a 3 sequence from the C. reinhardtii psbA gene

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

Background Determining ecological roles of community members and the impact of specific taxa on overall biodiversity in the gastrointestinal (GI) microbiota is of fundamental importance. A step towards a systems-level understanding of the GI microbiota is characterization of biotic interactions. Community time series analysis, an approach based on statistical analysis of changing population abundances within a single system over time, is needed in order to say with confidence that one population is affecting the dynamics of another. Results Here, we characterize biotic interaction structures and define ecological roles of major bacterial groups in four healthy individuals by analysing high-resolution, long-term (>180 days) GI bacterial community time series. Actinobacteria fit the description of a keystone taxon since they are relatively rare, but have a high degree of ecological connectedness, and are positively correlated with diversity both within and between individuals. Bacteriodetes were found to be a foundation taxon in that they are numerically dominant and interact extensively, in particular through positive interactions, with other taxa. Although community structure, diversity and biotic interaction patterns were specific to each individual, we observed a strong tendency towards more intense competition within than between phyla. This is in agreement with Darwin’s limiting similarity hypothesis as well as a published biotic interaction model of the GI microbiota based on reverse ecology. Finally, we link temporal enterotype switching to a reciprocal positive interaction between two key genera. Conclusions In this study, we identified ecological roles of key taxa in the human GI microbiota and compared our time series analysis results with those obtained through a reverse ecology approach, providing further evidence in favour of the limiting similarity hypothesis first put forth by Darwin. Larger longitudinal studies are warranted in order to evaluate the generality of basic ecological concepts as applied to the GI microbiota, but our results provide a starting point for achieving a more profound understanding of the GI microbiota as an ecological system