Comparative genomic analysis between Lactobacillus delbreuckii subsp. lactis and Lactobacillus delbreuckii subsp. bulgaricus of dairy origin

Lactobacillus delbreuckii subsp. lactis and Lactobacillus delbreuckii subsp. bulgaricus are lactic acid bacteria commonly exploited by the dairy industry as starter cultures, mainly for the production of cheese and yogurt. In this work, we present the comparative genomic analysis between the recently sequenced genomes of L. lactis ACA-DC 178 and L. bulgaricus ACA DC 87, isolated from Kasseri cheese and yogurt, respectively. The genome of L. lactis ACA-DC 178 is larger than that of L. bulgaricus ACA-DC 87, containing 2,048 and 1,928 protein coding genes, respectively. Full chromosome alignments revealed strain specific differences, although a high degree of synteny between the two strains was also observed. The core genome of the two stains contained about 1,300 genes while the unique genes of the two strains were als oidentified. The two genomes contained several genomic islands, indicating that a number of genes have been acquired through horizontal gene transfer. We also predicted one confirmed CRISPR system in each genome, three potential antimicrobial peptides in total and also prophage sequences integrated into the genomes of the two strains. Overall,our analysis provides useful insights into the technological potential of the ACA-DC 178 and ACA-DC 87 strains

Characterization of the dairy Streptococcus thermophilus ACA-DC 29 strain through comparative genomics

Background: Although the Streptococcus genus includes mainly pathogenic species, Streptococcus thermophilus is a widely used dairy starter culture of great economic importance for the food industry. S. thermophilus has been adapted to milk probably through a degenerative evolution process that has led to the loss of typical streptococcal pathogenic traits. Objectives: The genome sequence of the yogurt isolate S. thermophilus ACA-DC 29 was analyzed for assessing the technological potential of this strain. Comparative genomics analysis was also performed between the genome of ACA-DC 29 and the existing complete genome sequences of S. thermophilus. Methods:The genome sequence of ACA-DC 29 was annotated using online annotation tools. Full chromosome alignments were calculated with Progressive Mauve. The pangenome, the core genome and the unique genes were predicted with the GView Server. The genomic islands, the CRISPRs and the antimicrobial peptides were predicted with IslandViewer, CRISPRcompar and BAGEL3, respectively. Conclusions:The analysis of the S. thermophilus ACA-DC 29 genome sequence revealed the absence of pathogenic features. Genes related to the adaptation to milk were identified. Full chromosome alignments showed a high degree of synteny among the different strains. The pangenome of the ten strains comprised of approximately 2,300 genes. Concerning the ACA-DC 29 strain, approximately 250 unique genes involved in various biological processes were also identified. Further analysis indicated that several of them may have been acquired through horizontal gene transfer. Five potential antimicrobial peptides and two CRISPR systems, which may confer resistance against phages, were also predicted

Genomics of Streptococcus macedonicus: moving from pathogenicity to adaptation to the dairy environment

Background: Lactic acid bacteria (LAB constitute a significant group of microorganisms found in foods, but also contribute to human health. The Streptococcus bovis/ Streptococcus equinus complex within LAB includes members that have been implicated in human diseases, like endocarditis and colon cancer. Objectives: In this study we compared the three available genome sequences of Streptococcus macedonicus strains isolated from dairy products. Only one strain has its genome complete sequenced and previous analysis showed diminished pathogenic potential and adaptation to the milk environment. Here we present the in silico analysis of these strains, in order to better understand the S. macedonicus species. Methods: Chromosomal maps were constructed using DNA Plotter and whole genome sequence alignments were performed by progressiveMAUVE and Webact in order to visualize conserved genomic regions or chromosomal rearrangements. Genomic islands were identified and visualized by IslandViewer, potential bacteriocins were predicted by BAGEL3 and CRISPRs were analyzed by the tools available in the CRISPRcompar web-service. Conclusions: The analysis revealed that the strains have lost genes involved in the catabolism of complex plant carbohydrates, in the adhesion to the host’s cells and in haemolysis. On the other hand, an extra lactose operon and a proteolytic system characteristic of LAB were identified. Even though our whole genome analysis of S. macedonicus shows adaptation traits to the nutrient-rich dairy environment, analysis of additional S. macedonicus genomes, including non-dairy isolates, may be necessary to clarify its pathogenic potential

Adaptation of Streptococcus macedonicus and Streptococcus thermophilus in milk. Common strategies, distinct ways.

Lactic acid bacteria (LAB) are the most important bacteria in food fermentations. Among the genera included in LAB is the Streptococcus genus, containing a number of species that are commensals and opportunistic pathogens. Up to now only one species in the Streptococcus genus, Streptococcus thermophilus, has been traditionally used as a starter in milk and is considered a domesticated organism. However, Streptococcus macedonicus, belonging to the S. bovis/S. equinus complex (SBSEC), can be also found in milk. In this study, S. macedonicus was fully sequenced and a comparative analysis was performed against all other SBSEC members. According to our analysis, S. macedonicus missed several genes encoding enzymes for the degradation of complex plant carbohydrates typically met in the genome of Streptococcus gallolyticus, indicating a reduced ability to survive in the gastrointestinal tract of herbivores. In addition, two pilus operons necessary for the adhesion of S. gallolyticus to the host and the initiation of infection were absent from the S. macedonicus genome. Adaptation of S. macedonicus to the milk environment was supported by the presence of an extra lactose operon. Finally, the plasmid pSMA198 found in S. macedonicus also provided evidence about the habituation of the species to milk. Our findings support adaptation of S. macedonicus to the rich in nutrients milk environment characterized by diminished biosynthetic capabilities and loss of pathogenicity-related genes in parallel to gene gain events through horizontal gene transfer, similarly to S. thermophilus. Comparative analysis between S. macedonicus and S. thermophilus though revealed numerous species-specific differences at the genomic and proteomic level, suggesting that common strategies can be used by truly divergent organisms during their evolutionary histor

Comparative genomic analysis among three dairy Streptococcus macedonicusstrains

Streptococcus macedonicus and Streptococcus infantarius, two species within the Streptococcus bovis/ Streptococcus equinus complex (SBSEC) are frequently found in spontaneously fermented foods especially of dairy origin. These two species have been suggested to be non-pathogenic and to have been adapted to the dairy environment similarly to Streptococcus thermophilus. Analysis of the first complete genomes of S. macedonicus and S. infantarius indicated that they may be indeed adapted to milk but they also have retained a restricted repertoire of virulence traits when compared to well characterized pathogenic streptococci. In this study we performed comparative genomic analysis among S. macedonicus strains, isolated from Italian, French and Greek dairy products. The contigs of the Italian and French partial genomes were aligned using as a reference the Greek S. macedonicus ACA-DC 198 genome, the only S. macedonicus genome that is completely sequenced to date. Based on these assemblies, we constructed two distinct pseudochromosomes for the French and the Italian strains. Despite the artifactual nature of the two chromosomes, pairwise alignments among the three genomes revealed a high degree of synteny. The genetic information was overall conserved, but strain specific regions also existed. Furthermore, the analysis revealed that the French S. macedonicus strain has lost genes involved in the catabolism of complex plant carbohydrates, in the adhesion to the host’s cells and in haemolysis. On the other hand, an extra lactose operon and a proteolytic system characteristic of lactic acid bacteria were identified, indicating their evolutionary adaptation to the milk environment. Analogous observations could also be made for the Italian strain. Even though our findings further support the adaptation of the S. macedonicus species to milk fermentation, the analysis of the additional S. macedonicus genomes, including non-dairy isolates, may be necessary to clarify its pathogenic potentia

Comparative genomics among dairy strains of Streptococcus thermophilus

Microorganisms like lactic acid bacteria are employed for the biotransformation of raw materials into fermented foods. Fermented foods have increased nutritional value and shelf life as well as improved organoleptic characteristics compared to the raw materials. Interestingly, there are several genera within lactic acid bacteria that are considered to be important for food fermentations including the Streptococcus genus. However, only Streptococcus thermophilus is used as a starter culture. Streptococcus thermophilus has been adapted to milk and dairy products through a reductive evolution process that has led to the loss of typical streptococcal pathogenictraits. In this work we present the comparative genomic analysis among the recently sequenced genome of S. thermophilus ACA-DC 29 is olated from yogurt and the existing seven complete genome sequences of S. thermophilus. Full chromosome alignments revealed a high degree of synteny among the different strains although strain specific differences could also be observed. The pangenome of the eight strains was comprised of approximately 2,300 genes. Concerning the ACA-DC 29 strain, the majority of genes was distributed in the core and the accessory genomes. We also identified a significant percentage of unique genes, i.e. approximately 250, involved in various biological processes. Further analysis of these unique genes revealed that several of them may have been acquired through horizontal gene transfer. We also predicted five potential antimicrobial peptides and two CRISPR systems, which may confer resistance against phages. Overall, our analysis provides useful insights into the technological potential of the ACA-DC 29 strain

Discovering probiotic microorganisms: invitro, invivo, genetic and omics approaches

Over the past decades the food industry has been revolutionized toward the production of functional foods due to an increasing awareness of the consumers on the positive role of food in wellbeing and health. By definition probiotic foods must contain live microorganisms in adequate amounts so as to be beneficial for the consumer’s health. There are numerous probiotic foods marketed today and many probiotic strains are commercially available. However, the question that arises is how to determine the real probiotic potential of microorganisms. This is becoming increasingly important, as even a superficial search of the relevant literature reveals that the number of proclaimed probiotics is growing fast. While the vast majority of probiotic microorganisms are food-related or commensal bacteria that are often regarded as safe, probiotics from other sources are increasingly being reported raising possible regulatory and safety issues. Potential probiotics are selected after in vitro or in vivo assays by evaluating simple traits such as resistance to the acidic conditions of the stomach or bile resistance, or by assessing their impact on complicated host functions such as immune development, metabolic function or gut–brain interaction. While final human clinical trials are considered mandatory for communicating health benefits, rather few strains with positive studies have been able to convince legal authorities with these health claims. Consequently, concern has been raised about the validity of the workflows currently used to characterize probiotics. In this review we will present an overview of the most common assays employed in screening for probiotics, highlighting the potential strengths and limitations of these approaches. Furthermore, we will focus on how the advent of omics technologies has reshaped our understanding of the biology of probiotics, allowing the exploration of novel routes for screening and studying such microorganisms

Microbiome definition re-visited: old concepts and new challenges

peer-reviewedAbstract The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term “microbiome.” Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstrac

Αλληλούχηση των γονιδιωμάτων lactobacillus zymae, lactobacillus acidipiscis και Lactobacillus rennini: φυσιολογικές, εξελικτικές και τεχνολογικές προεκτάσεις

Lactic acid bacteria (LAB) are one of the most industrially important groups of bacteria. They are used in a variety of ways, including food and feed production, health improvementin humans and animals, and production of macromolecules, enzymes and variousmetabolites. In recent years, the genome sequencing of LAB is booming and the increasedamount of published genomics data brings unprecedented opportunity for us to reveal theimportant traits of LAB. Whole-genome sequences can provide significant informationconcerning the technological and probiotic potential of a strain. Furthermore, genomicanalysis of a strain or comparative genomics among closely related (or not) strains/speciescould deliver important knowledge, such as bacterial diversity and adaptation to diverse ecological niches. In the course of the present thesis, three “wild” LAB strains, namely Lactobacillus zymae ACA-DC 3411, Lactobacillus rennini ACA-DC 565 and Lactobacillus acidipiscis ACA-DC1533, isolated from traditional Greek wheat sourdough, Mana Kopanisti and Kopanisti cheese, respectively, were sequenced by high-throughput sequencing techniques and annotated using a plethora of bioinformatics tools. It is worth noting that these are the first completely sequenced chromosomal assemblies for each of the respective species, since the rest of publicly available genome assemblies are only partially sequenced. Analysis of the L. zymae ACA-DC 3411 chromosomal sequence (2.7 Mbp) identified one type I restriction-modification (RM) system, 19 integrated genomic islands containing a total of 265 genes potentially acquired through horizontal gene transfer, four incomplete and one questionable prophage sequences, as well as six confirmed and six questionable Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems. Furthermore, cluster of orthologous groups (COG) functional classification of the L. zymae protein-coding genes revealed that 1,930 of them (approximately 80%) were assigned to at least one COG category with the most abundant being related to replication, recombination and repair (14%). Analysis of the L. rennini ACA-DC 565 chromosomal sequence (2.4 Mbp) identifiedtoxin-antitoxin proteins, a type II RM system and five CRISPR systems with their associated cas proteins. Furthermore, an incomplete prophage sequence of 17.1 Kbp length containing eight phage-related, seven bacterial and two hypothetical proteins was also identified. According to the COG results, 1,900 protein-coding genes (approximately 87.7%) were assigned to a putative COG category with the most abundant being related to carbohydrate transport and metabolism (9.33%). Compared to the species L. zymae and L. rennini, where only a sole partial genome sequence was available in the beginning of the present thesis (L. zymae DSM 19395T and L.rennini DSM 20253T, respectively) in the National Center for Biotechnology Information database, in the case of L. acidipiscis four partially sequenced genome assemblies were reported, namely KCTC 13900, DSM 15353, JCM 10692T and DSM15836T. It should be noted though, that L. acidipiscis strains KCTC 13900 and DSM 15353 are replicas of the same strainand the same applies for strains JCM 10692T and DSM15836T, as confirmed by an average nucleotide identity heat map. Since the need to identify strain-specific differences has become increasingly vital, comparative genomic analysis among three L. acidipiscis strains (ACA-DC 1533, KCTC 13900 and JCM 10692T) was performed. Based on the results of the pan/coregenome and singleton analysis, L. acidipiscis strains exhibited a high degree of conservation at the genome level. Furthermore, strains ACA-DC 1533 and JCM 10692T, which lack CRISPR arrays, carry two similar prophage sequences although they have been isolated from different ecological niches, i.e. Kopanisti cheese and fermented fish, respectively. On the contrary, strain KCTC 13900 seems to have acquired immunity to these prophages based on the sequences of spacers in its CRISPRs. Nevertheless, a prophage sequence that was absent from strains ACA-DC 1533 and JCM 10692T was identified in strain KCTC 13900. Interestingly, these results suggest a potential existence of lineages within the species. Based on the above mentioned presence/absence patterns of these genomic traits, strains ACA-DC 1533 and JCM 10692T appeared to be quite related despite the different isolation source. Since L. acidipiscis belongs to the Lactobacillus salivarius clade, which is mainly consistsof commensal isolates, comparative genomics among representative strains in the clade was performed to investigate the level of their genomic diversity. Thus, comparative genomic analysis among L. acidipiscis ACA-DC 1533, L. salivarius UCC118 and Lactobacillus ruminis ATCC 27782 revealed significant differences in the number of glycobiome-related proteins,proteolytic enzymes, transporters, insertion sequences and regulatory proteins. Additionally, the probiotic potential of L. acidipiscis ACA-DC 1533 was investigated and compared to the extensively studied probiotic L. salivarius UCC118 strain; however, no obvious genomic traits supporting a probiotic potential of ACA-DC 1533 strain were found. Furthermore, the detection of glycine-betaine transporters in the ACA-DC 1533 chromosome may explain theability of the strain/species to grow in fermented foods with high salt concentrations. Finally, in silico analysis of the ACA-DC 1533 chromosome identified genes encoding key enzymes involved in metabolic pathways (mainly during the amino acids catabolism) that could underpin the production of major volatile compounds, thus contributing to the distinctpiquant flavor of Kopanisti cheese.Τα οξυγαλακτικά βακτήρια είναι μία από τις πιο σημαντικές ομάδες βακτηρίων για τη βιομηχανία. Τα βακτήρια αυτά χρησιμοποιούνται στην παραγωγή τροφίμων και ζωοτροφών,στη βελτίωση της υγείας του ανθρώπου και των ζώων, στην παραγωγή μακρομορίων,ενζύμων και διαφόρων μεταβολιτών. Τα τελευταία χρόνια, η αλληλούχιση όλο και περισσότερων οξυγαλακτικών βακτηρίων καθώς και η ανάλυσή τους με εργαλεία βιοπληροφορικής μας έχει προσφέρει πρωτοφανείς ευκαιρίες για να ανακαλύψουμε σημαντικά χαρακτηριστικά των βακτηρίων αυτών. Η αλληλούχιση ολόκληρων γονιδιωμάτων μπορούν να παρέχουν σημαντικές πληροφορίες σχετικά με το τεχνολογικό και το προβιοτικό δυναμικό ενός στελέχους. Επιπλέον, η γονιδιωματική ανάλυση ενός στελέχους ή η συγκριτική γονιδιωματική ανάλυση μεταξύ φυλογενετικά κοντινών (ή μη) στελεχών/ειδών μπορεί να προσφέρει σημαντικές γνώσεις, όπως η βακτηριακή ποικιλομορφία και η προσαρμογή σε ποικίλους οικολογικούς θώκους. Στα πλαίσια της παρούσας διδακτορικής διατριβής, τρία "άγρια" στελέχη οξυγαλακτικών βακτηρίων, ο Lactobacillus zymae ACA-DC 3411, ο Lactobacillus rennini ACADC 565 και ο Lactobacillus acidipiscis ACA-DC 1533, τα οποία έχουν απομονωθεί από παραδοσιακά Ελληνικά προϊόντα ζύμωσης και συγκεκριμένα από προζύμι, Μάνα Κοπανιστή και Κοπανιστή, αντιστοίχως, αλληλουχήθηκαν με τεχνικές υψηλής απόδοσης και τα γονιδιώματά τους σχολιάστηκαν χρησιμοποιώντας πληθώρα σύγχρονων εργαλείων βιοπληροφορικής. Αξίζει να σημειωθεί ότι αυτές είναι τα πρώτες ολόκληρες χρωμοσωμικές αλληλουχίες για κάθε ένα από τα αντίστοιχα είδη, καθώς οι υπόλοιπες αλληλουχίες που βρίσκονται στις διάφορες βάσεις δεδομένων είναι μερικώς αλληλουχιμένες. Η ανάλυση της χρωμοσωμικής αλληλουχίας του στελέχους L. zymae ACA-DC 3411 μεγέθους 2,7 Mbp αναγνώρισε ένα σύστημα περιορισμού-τροποποίησης (RM) τύπου Ι, 19 γονιδιωματικές νήσους που περιείχαν συνολικά 265 γονίδια τα οποία πιθανότατα να προήλθαν από οριζόντια μεταφορά, τέσσερις ημιτελείς και μία υπο αμφισβήτηση αλληλουχίες προφάγων και έξι επιβεβαιωμένα και έξι υπο αμφισβήτηση συστήματα που ονομάζονται συγκεντρωμένες τακτικές παρεμβαλλόμενες σύντομες παλινδρομικές επαναλήψεις (CRISPR). Επιπλέον, η λειτουργική ταξινόμηση των γονιδίων που κωδικοποιούν πρωτεΐνες στις διάφορες ορθόλογες ομάδες γονιδίων (COG) έδειξε ότι 1.930 γονίδια(περίπου 80%) εντοπίστηκαν σε τουλάχιστον μία κατηγορία COG. Η κατηγορία COG με τα περισσότερα γονίδια (14%) σχετίζεται με την αντιγραφή, τον ανασυνδυασμό και την επιδιόρθωση του DNA.H ανάλυση της χρωμοσωμικής αλληλουχίας του L. rennini ACA-DC 565 μεγέθους 2,4Mbp αναγνώρισε αρκετές πρωτεΐνες τοξίνης-αντιτοξίνης, ένα σύστημα RM τύπου II και πέντε συστήματα CRISPR με τις σχετικές πρωτεΐνες cas. Επιπλέον, προσδιορίστηκε μια ημιτελής αλληλουχία προφάγου μήκους 17,1 Kbp που περιείχε οκτώ γονίδια φάγων, επτά γονίδια βακτηρίων και δύο γονίδια με υποθετική λειτουργία. Σύμφωνα με τα αποτελέσματα της κατανομής των γονιδίων στις διάφορες λειτουργικές κατηγορίες COG, 1.900 γονίδια (περίπου87,7%) κατατάχθηκαν κάποια κατηγορία COG, ενώ η κατηγορία COG με τα περισσότερα γονίδια (9,33%) σχετίζεται με τη μεταφορά και το μεταβολισμό των υδατανθράκων.Ενώ για τα είδη L. zymae και L. rennini, υπήρχε μόνο ένα γονιδίωμα μερικώς αλληλουχημένο στο Εθνικό Κέντρο Βιοτεχνολογικών Πληροφοριών ο L. zymae DSM 19395Tκαι ο L. rennini DSM 20253T, αντίστοιχα, στην περίπτωση του L. acidipiscis υπήρχαν τέσσερα γονιδιώματα μερικώς αλληλουχημένα για τα στελέχη KCTC 13900, DSM 15353, JCM 10692Tκαι DSM 15836T. Παρόλα αυτά πρέπει να σημειωθεί ότι τα στελέχη KCTC 13900 και DSM 15353 είναι κλώνοι, όπως συμβαίνει και με τα στελέχη στελέχη JCM 10692T και DSM15836T το οποίο φάνηκε σε θερμικό χάρτη που υπολογίζει το ποσοστό ομοιότητας μεταξύ 2 αλληλουχιών. Λόγω του ότι η ανάγκη για την εύρεση διαφορών μεταξύ στελεχών γίνεται όλο και πιο απαραίτητη, κάναμε συγκριτική γονιδιωματική ανάλυση μεταξύ των τριών στελεχών του L. acidipiscis (ACA-DC 1533, KCTC 13900 και JCM 10692T). Με βάση τα αποτελέσματα της ανάλυσης του παν-γονιδιώματος, του κοινού γονιδιώματος μεταξύ των στελεχών, αλλά και των μοναδικών γονιδίων κάθε στελέχους, τα τρία στελέχη του L. acidipiscis παρουσίασαν υψηλό βαθμό συντήρησης σε επίπεδο γονιδιώματος. Επιπλέον, φάνηκε ότι τα στελέχη ACADC1533 και JCM 10692T δεν διαθέτουν συστήματα CRISPR αλλά έχουν δύο παρόμοιες περιοχές προφάγων στα γονιδιώματά τους παρόλο που έχουν απομονωθεί από διαφορετικά οικοσυστήματα, τα οποία είναι η Κοπανιστή και ζυμούμενο ψάρι, αντίστοιχα. Αντίθετα, η ανάλυση των συστημάτων CRISPR του στελέχους KCTC 13900 έδειξε ότι το βακτήριο έχει αποκτήσει ανοσία προφάγους που βρέθηκαν στα άλλα δύο στελέχη του L. acidipiscis. Παρόλα αυτά, μια αλληλουχία προφάγου που δεν βρέθηκε στα στελέχη ACA-DC 1533 και JCM10692T βρέθηκε στο στέλεχος KCTC 13900. Τα ευρήματα αυτά υποδηλώνουν την ύπαρξη γενεαλογικού χαρακτήρα εντός του είδους. Από τα παραπάνω μοτίβα παρουσίας/απουσίας γενετικών χαρακτηριστικών στα τρία γονιδιώματα, φαίνεται ότι τα στελέχη ACA-DC 1533 καιJCM 10692T είναι περισσότερο κοντά παρόλο που έχουν απομονωθεί από διαφορετικάοικοσυστήματα.Δεδομένου ότι ο L. acidipiscis ανήκει στον κλάδο του Lactobacillus salivarius, ο οποίος αποτελείται κυρίως από συμβιωτικά είδη, πραγματοποιήθηκε συγκριτική γονιδιωματική ανάλυση μεταξύ επιλεγμένων στελεχών του κλάδου για να διερευνηθεί το επίπεδο ποικιλομορφίας μεταξύ των γονιδιωμάτων. Η συγκριτική γονιδιωματική ανάλυση μεταξύ τωνL. acidipiscis ACA-DC 1533, L. salivarius UCC118 και Lactobacillus ruminis ATCC 27782 αποκάλυψε σημαντικές διαφορές στον αριθμό των πρωτεϊνών που σχετίζονται με μεταβολισμό των υδατανθράκων, των πρωτεολυτικών ενζύμων, των μεταφορέων, των αλληλουχιών εισαγωγής και των ρυθμιστικών πρωτεινών. Στη συνέχεια διερευνήθηκε το προβιοτικό δυναμικό του L. acidipiscis ACA-DC 1533 σε σύγκριση με τον προβιοτικό L.salivarius UCC118, ωστόσο δεν βρέθηκαν προφανή γονιδιωματικά χαρακτηριστικά που να υποστηρίζουν ένα προβιοτικό δυναμικό για το στέλεχος ACA-DC 1533. Επιπλέον, η εύρεση μεταφορέων γλυκίνης- βεταΐνης στο χρωμόσωμα του ACA-DC 1533 θα μπορούσε να εξηγήσει την ικανότητα του στελέχους / είδους να αναπτυχθεί σε ζυμούμενα τρόφιμα με υψηλές συγκεντρώσεις άλατος. Τέλος, εντοπίστηκαν αρκετά γονίδια στο γονιδίωμα του ACA-DC 1533 που κωδικοποιούν ένζυμα κλειδιά τα οποία εμπλέκονται σε μεταβολικά μονοπάτια (κυρίως κατά τον καταβολισμό των αμινοξέων) από τα οποία παράγονται πτητικές ενώσεις,συμβάλλοντας με αυτόν το τρόπο στην ιδιαίτερη πικάντικη γεύση της Κοπανιστής