Bacterial Community Structure at the Microscale in Two Different Soils.

The spatial distributions of bacteria in the soil matrix have a role in ecosystem function, for example, at the small scale, through gene transfer or xenobiotic degradation. Soil bacterial biogeography has been evidenced at the large scale, but data are scarce at the small scale. The objective of this work was to determine the spatial pattern of bacterial diversity, in spatially referenced microsamples, in order to define bacterial community spatial traits.

OligoSpecificitySystem: global matching efficiency calculation of oligonucleotide sets taking into account degeneracy and mismatch possibilities.

Oligonucleotide sets are widely used in molecular biology to target a group of nucleic acid sequences using Polymerase Chain Reaction (PCR)-based technologies. Currently, the global matching efficiency of an oligonucleotide set is considered to be equal to the lower matching efficiency calculated for each oligonucleotide. However, sequences matching the limiting oligonucleotide did not always match the other oligonucleotide of the set, resulting in a biased evaluation of the matching efficiency.

Rapid adaptation of the bacterial community in the growing rabbit caecum after a change in dietary fibre supply.

This work aimed to study the response of the growing rabbit caecal ecosystem (bacterial community and caecal environmental parameters) after a switch from a control to a low-fibre diet (LFD). A group of 160 rabbits were fed ad libitum a control diet (ADF: 20.4%) from weaning (36 days).

Chikungunya virus impacts the diversity of symbiotic bacteria in mosquito vector.

Mosquitoes transmit numerous arboviruses including dengue and chikungunya virus (CHIKV). In recent years, mosquito species Aedes albopictus has expanded in the Indian Ocean region and was the principal vector of chikungunya outbreaks in La Reunion and neighbouring islands in 2005 and 2006. Vector-associated bacteria have recently been found to interact with transmitted pathogens.

Study of an aquifer contaminated by ethyl tert-butyl ether (ETBE): site characterization and on-site bioremediation.

Ethyl tert-butyl ether (ETBE) was detected at high concentration (300mgL(-1)) in the groundwater below a gas-station. No significant carbon neither hydrogen isotopic fractionation of ETBE was detected along the plume. ETBE and BTEX biodegradation capacities of the indigenous microflora Pz1-ETBE and of a culture (MC-IFP) composed of Rhodococcus wratislaviensis IFP 2016, Rhodococcus aetherivorans IFP 2017 and Aquincola tertiaricarbonis IFP 2003 showed that ETBE and BTEX degradation rates were in the same range (ETBE: 0.

Changes over time in the bacterial communities associated with fluid and food particles and the ruminal parameters in the bovine rumen before and after a dietary change.

This work aimed to study the changes over time in the bacterial communities associated with the fluid and food particle fractions of the cow rumen following a change in diet. Four cannulated cows were fed a hay-based diet for 21 days and were then switched to a corn-silage-based diet for 33 days. The bacterial communities were regularly characterized by capillary electrophoresis - single-strand conformation polymorphism (CE-SSCP) and qPCR, and the main ruminal parameters were determined.

Postnatal development of the rabbit caecal microbiota composition and activity.

This study describes the development of the rabbit caecum microbiota and its metabolic activities from the neonatal (day 2) until the subadult period (day 70). The caecal microbiota was analysed using 16S rRNA gene approaches coupled with capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) and qPCR. At day 2, rabbits harboured population levels up to 8.

Comparison of the archaeal community in the fermentative compartment and faeces of the cow and the rabbit.

The archaeal community in the fermentative compartment and faeces of the cow and the rabbit were compared by analysis capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) profiles of 16S rRNA genes. Ruminal and faecal contents were sampled in five cows for three weeks. Hard and soft faeces were collected in 14 rabbits for three consecutive weeks and caecal contents were sampled in the third week.

StatFingerprints: a friendly graphical interface program for processing and analysis of microbial fingerprint profiles.

Molecular fingerprint methods are widely used to compare microbial communities in various habitats. The free program StatFingerprints can import, process, and display fingerprint profiles and perform numerous statistical analyses on them, and also estimate diversity indexes. StatFingerprints works with the free program R, providing an environment for statistical computing and graphics.

Molecular analysis of the bacterial community in digestive tract of rabbit.

This work aimed to study the stability over time of the bacterial community in caecum and faeces of the rabbit (diversity index and structure) without experimental disturbance and to evaluate its relationships with environmental parameters. Soft and hard faeces of 14 rabbits were sampled for 5 weeks while caecal content was sampled on the 3rd week (by surgery) and the 5th week (at slaughter). Bacterial communities were assessed by studying CE-SSCP profiles of 16S rRNA genes fragments.

Spatial and temporal variations of the bacterial community in the bovine digestive tract.

Aims: Improved knowledge of the bacterial community of the digestive tract is required to enhance the efficiency of digestion in herbivores. This work aimed to study spatial and temporal variations of the bacterial communities in the bovine digestive tract and their correlation with gut environmental parameters.

Methods And Results: Rumen content and faeces of five cows were sampled for 3 weeks.