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The microbiota world seen with the eyes of metaproteomics

20 Nov 2020 1:04 PM | Anonymous member (Administrator)

Bruno Tilocca and Paola Roncada, HUPO B/D-HPP Food and Nutrition Team, University Magna Græcia of Catanzaro, Catanzaro, Italy

The animal gastrointestinal tract provides the perfect milieu for hosting the heterogeneous ensemble of microorganisms (bacteria, virus, fungi and protozoa) that are commonly harbored in the intestine. Here, microbiota members establish a complex and intricate network of interconnections among each other and the hosting organism. Recent investigations unveiled the importance of understanding the synergistic interactions between the host and its microbiota, enlightening how the fine orchestration of the gut microbiota composition and activity impact a variety of biochemical and physiological processes that are, in turn, responsible for both beneficial and detrimental health conditions in humans and animals. In this context, Dr. Bruno Tilocca along with the other researchers of the “Feed-gut-microbiota” group of the University of Hohenheim employed a microbial community fingerprint through 16S rRNA gene sequencing and metaproteomics to study the active bacterial fraction inhabiting the diverse sections of the chicken and pig gastrointestinal tract. Investigating the microbiota by the sole genome-targeting approaches enables a comprehensive depiction of the microbial consortia architecture and its potential functions as assessed through the functional prediction of the sequenced genetic elements. Nevertheless, structural composition assessed by microbial community fingerprint has been leveraged by Dr. Tilocca and colleagues while optimizing a metaproteomic workflow aimed at the effective functional featuring of the microbial community harbouring the diverse intestine sections. Specifically, the bacterial families identified by the 16S rRNA gene sequencing are employed for the construction of a single non-redundant in-house database. The database dependent searches performed by the custom databases resulted in a higher protein identification rate as compared with the conventional metaproteomics workflow expecting bioinformatic searches against publicly available databases. Also, the use of DNA-driven custom database enabled a statistically confident identification of the protein dataset and its successive functional classification. Through metaproteomics Dr. Tilocca and colleagues gained a fair depiction of the metabolically active bacterial fraction, allowing for the elucidation of the core microbiota composition along with the major biochemical pathways the gut microbiota members of the diverse gastrointestinal tract sections are involved in. Marked differences were observed in the microbial communities of the diverse gastrointestinal tract sections in both structural and functional terms. Both chicken and porcine animal model reported increased microbial diversity when moving toward the caudal direction. Interestingly, discrepancies were observed when comparing the microbiota architecture assessed by the DNA-based method and the metaproteomics. The higher bacteria heterogeneity highlighted by the metaproteomics has been attributed to the changing microbiota dynamics and the fact that changes in protein abundance occur earlier than changes of DNA copy numbers. This observation provides support in the identification of metaproteomics as a suitable discipline for the investigation of the microbial community composition in dynamic contexts, representing a valuable tool to highlight the microbial specimens driving the changes required to the achievement of a novel homeostatic balance. Besides, functional featuring of the microbiota in the diverse gastrointestinal sections through metaproteomics enabled deciphering biochemical involvement of the bacterial families in the diverse sections other than clarify the contribution of the microbiota in the animal physiological processes and the response to external stimuli such as the reaction to environmental stressors

More recently, research interests of the Dr. Tilocca are extended to the study of the microbial communities inhabiting “abiotic” ecological niches such as the milk and its by-product. In this view, Dr. Tilocca along with the Prof. Paola Roncada, at the Department of Health Science of the University “Magna Graecia” of Catanzaro, are running an articulated research project aimed at featuring the Nicastrese raw milk, and cheese. Here, metaproteomics is the method of choice as it enables the demonstration the microbiological signature (i.e. the active bacterial fraction) of the raw milk of this typical Calabrian goat bred and describes the structural and functional shaping of the microbiota throughout the diverse cheese-making steps. Besides, metaproteomics allows for detailing the biochemical role of the microbiota in ensuring both biosafety and the development of the unique gustatory and olfactory essences of this traditional product. In this view, researchers are confident that employing such innovative approach might open new avenues for the fair valorization of this and other ancient and typical products with unevaluable benefits for the social and economic reality at a local level other than delighting the palate of the consumers, worldwide.

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