Additional file 5: of Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization

Table S3. Abundance of the genes tested by real time PCR expressed as threshold cycle value. (PDF 83 kb

Additional file 4: of Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization

Fig. S1. Metagenomic fragment recruitment of V.limneticus sp. nov. concatenated genome on Amazon lake metagenomic datasets. A) Recruitment plot on Lake Ananå. B) Recruitment plot on Mancapuru Great lake. LPS biosynthesis and nif operon genomic islands are highlighted in red. (PDF 1778 kb

Data ms Di Cesare et al to Mol Ecol

Data ms Di Cesare et al to Mol Eco

Resistance genes detected before and after sediment incubation in antibiotic-supplemented BHI broth.

*<p>detected both in sediment and in broth.</p

Location of the fish farm and of the sampling stations.

<p>The map is from <a href="http://earthobservatory.nasa.gov/" target="_blank">http://earthobservatory.nasa.gov/</a>, image courtesy Jesse Allen.</p

Control strains used in PCR assays.

a<p>American Type Culture Collection.</p

Abundance of benthic enterococci.

<p>Enterococcal abundance in the farm sediments and at the control site was determined by qPCR before and after incubation with antibiotic-supplemented BHI broth. A, St. 1; B, St. 2 and C, St. 3. *Not detectable i.e.</p

Primer pairs used to detect resistance genes in PCR assays.

<p>Primer pairs used to detect resistance genes in PCR assays.</p

Table_1.docx

<p>Diet and lifestyle have a strong influence on gut microbiota, which in turn has important implications on a variety of health-related aspects. Despite great advances in the field, it remains unclear to which extent the composition of the gut microbiota is modulated by the intake of animal derived products, compared to a vegetable based diet. Here the specific impact of vegan, vegetarian, and omnivore feeding type on the composition of gut microbiota of 101 adults was investigated among groups homogeneous for variables known to have a role in modulating gut microbial composition such as age, anthropometric variables, ethnicity, and geographic area. The results displayed a picture where the three different dietetic profiles could be well distinguished on the basis of participant’s dietetic regimen. Regarding the gut microbiota; vegetarians had a significantly greater richness compared to omnivorous. Moreover, counts of Bacteroidetes related operational taxonomic units (OTUs) were greater in vegans and vegetarians compared to omnivores. Interestingly considering the whole bacterial community composition the three cohorts were unexpectedly similar, which is probably due to their common intake in terms of nutrients rather than food, e.g., high fat content and reduced protein and carbohydrate intake. This finding suggests that fundamental nutritional choices such as vegan, vegetarian, or omnivore do influence the microbiota but do not allow to infer conclusions on gut microbial composition, and suggested the possibility for a preferential impact of other variables, probably related to the general life style on shaping human gut microbial community in spite of dietary influence. Consequently, research were individuals are categorized on the basis of their claimed feeding types is of limited use for scientific studies, since it appears to be oversimplified.</p

Data_Sheet_1.xlsx

<p>Diet and lifestyle have a strong influence on gut microbiota, which in turn has important implications on a variety of health-related aspects. Despite great advances in the field, it remains unclear to which extent the composition of the gut microbiota is modulated by the intake of animal derived products, compared to a vegetable based diet. Here the specific impact of vegan, vegetarian, and omnivore feeding type on the composition of gut microbiota of 101 adults was investigated among groups homogeneous for variables known to have a role in modulating gut microbial composition such as age, anthropometric variables, ethnicity, and geographic area. The results displayed a picture where the three different dietetic profiles could be well distinguished on the basis of participant’s dietetic regimen. Regarding the gut microbiota; vegetarians had a significantly greater richness compared to omnivorous. Moreover, counts of Bacteroidetes related operational taxonomic units (OTUs) were greater in vegans and vegetarians compared to omnivores. Interestingly considering the whole bacterial community composition the three cohorts were unexpectedly similar, which is probably due to their common intake in terms of nutrients rather than food, e.g., high fat content and reduced protein and carbohydrate intake. This finding suggests that fundamental nutritional choices such as vegan, vegetarian, or omnivore do influence the microbiota but do not allow to infer conclusions on gut microbial composition, and suggested the possibility for a preferential impact of other variables, probably related to the general life style on shaping human gut microbial community in spite of dietary influence. Consequently, research were individuals are categorized on the basis of their claimed feeding types is of limited use for scientific studies, since it appears to be oversimplified.</p