Florence Computational Biology Group

Microbiomes and NGS

Bioinformatic analysis of microbiomes


Molecular microbial ecology is massively using next generation sequencing technologies to describe taxonomic composition and infer the functionality of microbial communities. One of the most popular applications based on next generation sequencing technologies is the so-called metagenetic analysis, which relies on the sequencing of the PCR amplicons for single genes of interest, e.g. the 16SrRNA gene for bacteria or 18SrRNA for eukaryotes, having taxonomic or functional value.

The research lines on the anlaysis of microbiomes developed @ Combo rely on two main topics:

1. Development of new algoritms and software for the entire pipeline of analysis (from reads trimming to biostatistical analysis), with the main interest in producing easy-to use software (for instance with GUI), with fast and RAM-saving algorithm, allowing to use the software on standard desktop PC.

2. Analysis of metagenomic and metagenetic data from public databases for important problems in microbial ecology, as antibiotic resistance diffusion and relationships between different biota based on metagenomic functions.

3. Analysis of metagenomic and metagenetic data coming from project dealing with soil bacterial communities functionalities,  coastal ecosystems (microbiomes of sediments and animals' gut), and endophytic microbiomes


Our recent papers on the topic:

Bacci G, Mengoni A, Fiscarelli E, Segata N, Taccetti G, Dolce D, Paganin P, Morelli P, Tuccio V, De Alessandri A, Lucidi V, Bevivino A. A Different Microbiome Gene Repertoire in the Airways of Cystic Fibrosis Patients with Severe Lung Disease. Int J Mol Sci. 2017 Jul 29;18(8). pii: E1654. doi: 10.3390/ijms18081654. PubMed PMID: 28758937; PubMed Central PMCID: PMC5578044.


Checcucci A, Maida I, Bacci G, Ninno C, Bilia AR, Biffi S, Firenzuoli F, Flamini G, Fani R, Mengoni A. Is the plant-associated microbiota of Thymus spp. adapted to plant essential oil? Res Microbiol. 2017 Apr;168(3):276-282. doi: 10.1016/j.resmic.2016.11.004. Epub 2016 Nov 21. PubMed PMID: 27884782.


Abdelrhman KF, Bacci G, Marras B, Nistri A, Schintu M, Ugolini A, Mengoni A. Exploring the bacterial gut microbiota of supralittoral talitrid amphipods. Res Microbiol. 2017 Jan;168(1):74-84. doi: 10.1016/j.resmic.2016.07.009. Epub 2016 Aug 13. PubMed PMID: 27531409.


Abdelrhman KF, Bacci G, Mancusi C, Mengoni A, Serena F, Ugolini A. A First Insight into the Gut Microbiota of the Sea Turtle Caretta caretta. Front Microbiol. 2016 Jul 7;7:1060. doi: 10.3389/fmicb.2016.01060. eCollection 2016. PubMed PMID: 27458451; PubMed Central PMCID: PMC4935691.


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