Comparative genomics and functional analysis of a highly adhesive dairy Lactobacillus paracasei subsp. paracasei IBB3423 strain

Koryszewska-Bagińska, Anna; Gawor, Jan; Nowak, Adriana; Grynberg, Marcin; Aleksandrzak‐Piekarczyk, Tamara

doi:10.1007/s00253-019-10010-1

Cited by 19 publications

(14 citation statements)

References 92 publications

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“…3a). These data underlined the high number of proteins related to carbohydrate and amino acid transport and metabolism, in accordance with the wide range of sugars metabolized by members of this species (31,62) and with the apparent inability of lactobacilli to synthetize most amino acids (63). Recently, an orthologue of the Escherichia coli glgX gene, which is involved in glycogen metabolism, was identified in L. crispatus genomes (54).…”

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confidence: 53%

Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment

Mancabelli

Mancino

Lugli

et al. 2021

Appl Environ Microbiol

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Vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the vaginal microbiota is dominated by members of the Lactobacillus genus, whose relative abundance and microbial taxa composition are dependent on the healthy status of this human body site. Particularly, among members of this genus, the high prevalence of Lactobacillus crispatus is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 healthy vaginal microbiome samples through shotgun metagenomics analyses. Based on our results we observed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Therefore, we isolated fifteen L. crispatus strains from different environments in which this species is abounding, ranging from vaginal swabs of healthy women to chicken fecal samples. The genomes of these strains were decoded and their genetic content was analyzed and correlated with their physiological features. An extensive comparative genomic analysis encompassing all publicly available genome sequences of L. crispatus and combined with those decoded in this study, revealed a genetic adaptation of strains to their ecological niche. In addition, in vitro growth experiments involving all isolated L. crispatus strains together with a synthetic vaginal microbiota reveal how this species is able to modulate the composition of the vaginal microbial consortia at strain level. Overall, our findings suggest that L. crispatus plays an important ecological role in reducing the complexity of the vaginal microbiota by depleting pathogenic bacteria. Importance The vaginal microbiota is defined as the community of bacteria residing in the human vaginal tract. Recent studies have demonstrated that the high prevalence of Lactobacillus crispatus species is commonly associated with a healthy vaginal environment. In the current study, we assessed the microbial composition of 94 public healthy vaginal samples through shotgun metagenomics analyses. Results showed that L. crispatus was the most representative species and correlated negatively with bacteria involved in vaginal infections. Moreover, we isolated and sequenced the genome of new L. crispatus strains from different environments and the comparative genomics analysis revealed a genetic adaptation of strains to their ecological niche. In addition, in-vitro growth experiments display the capability of this species to modulate the composition of the vaginal microbial consortia. Overall, our findings suggest an ecological role exploited by L. crispatus in reducing the complexity of the vaginal microbiota toward a depletion of pathogenic bacteria.

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Section: Fig 1 Legend (Continued)supporting

confidence: 53%

Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment

Mancabelli

Mancino

Lugli

et al. 2021

Appl Environ Microbiol

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“…A previous study has shown that Bacillus subtilis and Bacillus Coagulans could improve abdominal pain and diarrhea in irritable bowel syndrome (IBS) patients ( Rogha et al, 2014 ). Lactobacillus equigenerosi and Lactobacillus paracasei belonging to the genus Lactobacillus could activate macrophages to suppress inflammation in IBS patients ( Koryszewska-Baginska et al, 2019 ). Lactococcus lactis ssp.…”

Section: Discussionmentioning

confidence: 99%

A Metagenomic Insight Into the Hindgut Microbiota and Their Metabolites for Dairy Goats Fed Different Rumen Degradable Starch

Han

Xuexin

et al. 2021

Front. Microbiol.

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High starch diets have been proven to increase the risk of hindgut acidosis in high-yielding dairy animals. As an effective measurement of dietary carbohydrate for ruminants, studies on rumen degradable starch (RDS) and the effects on the gut microbiota diversity of carbohydrate-active enzymes (CAZymes), and Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology functional categories are helpful to understand the mechanisms between gut microbiota and carbohydrate metabolism in dairy goats. A total of 18 lactating goats (45.8 ± 1.54 kg) were randomly divided equally into three dietary treatments with low dietary RDS concentrations of 20.52% (LRDS), medium RDS of 22.15% (MRDS), and high RDS of 24.88% (HRDS) on a DM basis for 5 weeks. Compared with the LRDS and MRDS groups, HRDS increased acetate molar proportion in the cecum. For the HRDS group, the abundance of family Ruminococcaceae and genus Ruminococcaceae UCG-010 were significantly increased in the cecum. For the LRDS group, the butyrate molar proportion and the abundance of butyrate producer family Bacteroidale_S24-7, family Lachnospiraceae, and genus Bacteroidale_S24-7_group were significantly increased in the cecum. Based on the BugBase phenotypic prediction, the microbial oxidative stress tolerant and decreased potentially pathogenic in the LRDS group were increased in the cecum compared with the HRDS group. A metagenomic study on cecal bacteria revealed that dietary RDS level could affect carbohydrate metabolism by increasing the glycoside hydrolase 95 (GH95) family and cellulase enzyme (EC 3.2.1.4) in the HRDS group; increasing the GH13_20 family and isoamylase enzyme (EC 3.2.1.68) in the LRDS group. PROBIO probiotics database showed the relative gene abundance of cecal probiotics significantly decreased in the HRDS group. Furthermore, goats fed the HRDS diet had a lower protein expression of Muc2, and greater expression RNA of interleukin-1β and secretory immunoglobulin A in cecal mucosa than did goats fed the LRDS diet. Combined with the information from previous results from rumen, dietary RDS level altered the degradation position of carbohydrates in the gastrointestinal (GI) tract and increased the relative abundance of gene encoded enzymes degrading cellulose in the HRDS group in the cecum of dairy goats. This study revealed that the HRDS diet could bring disturbances to the microbial communities network containing taxa of the Lachnospiraceae and Ruminococcaceae and damage the mucus layer and inflammation in the cecum of dairy goats.

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“…We further identified this isolate as a novel strain L. paracasei LP10266 based on Vitek MS, 16S rRNA polymerase chain reaction (PCR), and biochemical tests. High-throughput sequencing technology [ 16 ] was used to predict the tissue invasion and identify biomarkers implicated in the pathogenicity of lactobacilli [ 17 ]. Our results have demonstrated that L. paracasei LP10266 has shown shared pathogenic properties with other pathogenic bacteria and evolved multiple mechanisms to adapt and survive in human body.…”

Section: Introductionmentioning

confidence: 99%

Characterization of a bacterial strain Lactobacillus paracasei LP10266 recovered from an endocarditis patient in Shandong, China

et al. 2021

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Background Lactobacilli are often recognized as beneficial partners in human microbial environments. However, lactobacilli also cause diseases in human, e.g. infective endocarditis (IE), septicaemia, rheumatic vascular disease, and dental caries. Therefore, the identification of potential pathogenic traits associated with lactobacilli will facilitate the prevention and treatment of the diseases caused by lactobacilli. Herein, we investigated the genomic traits and pathogenic potential of a novel bacterial strain Lactobacillus paracasei LP10266 which has caused a case of IE. We isolated L. paracasei LP10266 from an IE patient’s blood to perform high-throughput sequencing and compared the genome of strain LP10266 with those of closely related lactobacilli to determine genes associated with its infectivity. We performed the antimicrobial susceptibility testing on strain LP10266. We assessed its virulence by mouse lethality and serum bactericidal assays as well as its serum complement- and platelet-activating ability. The biofilm formation and adherence of strain LP10266 were also studied. Results Phylogenetic analysis revealed that strain LP10266 was allied with L. casei and L. paracasei. Genomic studies revealed two spaCBA pilus clusters and one novel exopolysaccharides (EPS) cluster in strain LP10266, which was sensitive to ampicillin, penicillin, levofloxacin, and imipenem, but resistant to cefuroxime, cefazolin, cefotaxime, meropenem, and vancomycin. Strain LP10266 was nonfatal and sensitive to serum, capable of activating complement 3a and terminal complement complex C5b-9 (TCC). Strain LP10266 could not induce platelet aggregation but displayed a stronger biofilm formation ability and adherence to human vascular endothelial cells (HUVECs) compared to the standard control strain L. paracasei ATCC25302. Conclusion The genome of a novel bacterial strain L. paracasei LP10266 was sequenced. Our results based on various types of assays consistently revealed that L. paracasei LP10266 was a potential pathogen to patients with a history of cardiac disease and inguinal hernia repair. Strain LP10266 showed strong biofilm formation ability and adherence, enhancing the awareness of L. paracasei infections.

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Comparative genomics and functional analysis of a highly adhesive dairy Lactobacillus paracasei subsp. paracasei IBB3423 strain

Cited by 19 publications

References 92 publications

Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment

Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment

A Metagenomic Insight Into the Hindgut Microbiota and Their Metabolites for Dairy Goats Fed Different Rumen Degradable Starch

Characterization of a bacterial strain Lactobacillus paracasei LP10266 recovered from an endocarditis patient in Shandong, China

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