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Background  In order to start to understand the function of individual members of gut microbiota, we cultured, sequenced and analysed bacterial anaerobes from chicken caecum.    Results  Altogether 204 isolates from chicken caecum were obtained in pure cultures using Wilkins-Chalgren anaerobe agar and anaerobic growth conditions. Genomes of all the isolates were determined using the NextSeq platform and subjected to bioinformatic analysis. Among 204 sequenced isolates we identified 133 different strains belonging to seven different phyla -  Firmicutes ,  Bacteroidetes ,  Actinobacteria ,  Proteobacteria ,  Verrucomicrobia ,  Elusimicrobia  and  Synergistetes . Genome sizes ranged from 1.51 Mb in  Elusimicrobium minutum  to 6.70 Mb in  Bacteroides ovatus . Clustering based on the presence of protein coding genes showed that isolates from phyla  Proteobacteria ,  Verrucomicrobia ,  Elusimicrobia  and  Synergistetes  did not cluster with the remaining isolates.  Firmicutes  split into families  Lactobacillaceae ,  Enterococcaceae ,  Veillonellaceae  and order  Clostridiales  from which the  Clostridium perfringens  isolates formed a distinct sub-cluster. All  Bacteroidetes  isolates formed a separate cluster showing similar genetic composition in all isolates but distinct from the rest of the gut anaerobes. The majority of  Actinobacteria  clustered closely together except for the representatives of genus  Gordonibacter  showing that the genome of this genus differs from the rest of  Actinobacteria  sequenced in this study. Representatives of  Bacteroidetes  commonly encoded proteins (collagenase, hemagglutinin, hemolysin, hyaluronidase, heparinases, chondroitinase, mucin-desulfating sulfatase or glutamate decarboxylase) that may enable them to interact with their host. Aerotolerance was recorded in  Akkermansia  and  Cloacibacillus  and was also common among representatives of  Bacteroidetes . On the other hand,  Elusimicrobium  and the majority of  Clostridiales  were highly sensitive to air exposure despite their potential for spore formation.    Conclusions  Major gut microbiota members utilise different strategies for gut colonisation. High oxygen sensitivity of  Firmicutes  may explain their commonly reported decrease after oxidative burst during gut inflammation.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4959-4) contains supplementary material, which is available to authorized users.

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures