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Applied and Environmental Microbiology Oct 2019and are often predominant in the microbiota of vacuum-packaged (VP) meats after prolonged storage at chiller temperatures, and more so in recent studies. We...
and are often predominant in the microbiota of vacuum-packaged (VP) meats after prolonged storage at chiller temperatures, and more so in recent studies. We investigated the antibacterial activities of and ( = 31) from VP meats by phenotypic characterization and genomic analysis. Five strains showed antibacterial activities against Gram-positive bacteria in a spot-lawn assay, with strains having an intergeneric and strains an intrageneric inhibition spectrum. This inhibitory activity is correlated with the production of predicted bacteriocins, including carnobacteriocin B2 and carnolysin for and divergicin A for The supernatants of both species cultured in meat juice medium under anaerobic conditions retarded the growth of most Gram-positive and Gram-negative bacteria in broth assay in a strain-dependent manner. and produced formate and acetate but not lactate under VP meat-relevant conditions. The relative inhibitory activity by strains was significantly correlated ( < 0.05) to the production of both acids. Genomic analysis revealed the presence of genes required for respiration in both species. In addition, two clusters of have an average nucleotide identity below the cutoff value for species delineation and thus should be considered to be two subspecies. In conclusion, both bacteriocins and organic acids are factors contributing significantly to the antibacterial activity of and under VP meat-relevant conditions. A few strains can be explored as protective cultures to extend the shelf life and improve the safety of VP meats. The results of this study demonstrated that both bacteriocins and organic acids are important factors contributing to the antibacterial activities of from vacuum-packaged (VP) meats. This study demonstrated that formate and acetate are the key organic acids produced by and demonstrated their association with the inhibitory activity of carnobacteria under VP meat-relevant storage conditions. The role of lactate, on the other hand, may not be as important as previously believed in the antimicrobial activities of spp. on chilled VP meats. These findings advance our understanding of the physiology of spp. to better explore their biopreservative properties for chilled VP meats.
Topics: Acetates; Acids; Anti-Bacterial Agents; Bacteriocins; Carnobacterium; Food Microbiology; Food Packaging; Formates; Genome, Bacterial; Gram-Negative Bacteria; Gram-Positive Bacteria; Lactic Acid; Meat; Microbial Sensitivity Tests; Phylogeny; Vacuum
PubMed: 31399404
DOI: 10.1128/AEM.01227-19 -
Caries Research 2010Severe early childhood caries is a microbial infection that severely compromises the dentition of young children. The aim of this study was to characterize the... (Comparative Study)
Comparative Study
BACKGROUND/AIMS
Severe early childhood caries is a microbial infection that severely compromises the dentition of young children. The aim of this study was to characterize the microbiota of severe early childhood caries.
METHODS
Dental plaque samples from 2- to 6-year-old children were analyzed using 16S rRNA gene cloning and sequencing, and by specific PCR amplification for Streptococcus mutans and Bifidobacteriaceae species.
RESULTS
Children with severe caries (n = 39) had more dental plaque and gingival inflammation than caries-free children (n = 41). Analysis of phylotypes from operational taxonomic unit analysis of 16S rRNA clonal metalibraries from severe caries and caries-free children indicated that while libraries differed significantly (p < 0.0001), there was increased diversity than detected in this clonal analysis. Using the Human Oral Microbiome Database, 139 different taxa were identified. Within the limits of this study, caries-associated taxa included Granulicatella elegans (p < 0.01) and Veillonella sp. HOT-780 (p < 0.01). The species associated with caries-free children included Capnocytophaga gingivalis (p < 0.01), Abiotrophia defectiva (p < 0.01), Lachnospiraceae sp. HOT-100 (p < 0.05), Streptococcus sanguinis (p < 0.05) and Streptococcus cristatus (p < 0.05). By specific PCR, S. mutans (p < 0.005) and Bifidobacteriaceae spp. (p < 0.0001) were significantly associated with severe caries.
CONCLUSION
Clonal analysis of 80 children identified a diverse microbiota that differed between severe caries and caries-free children, but the association of S. mutans with caries was from specific PCR analysis, not from clonal analysis, of samples.
Topics: Abiotrophia; Actinobacteria; Bacteria; Bifidobacterium; Capnocytophaga; Carnobacteriaceae; Child; Child, Preschool; Clone Cells; Cloning, Molecular; Dental Caries; Dental Enamel; Dental Plaque; Dental Plaque Index; Dental Pulp Exposure; Dentin; Female; Gingivitis; Gram-Positive Bacteria; Humans; Male; Metagenome; Periodontal Index; RNA, Ribosomal, 16S; Streptococcus; Streptococcus mutans; Veillonella
PubMed: 20861633
DOI: 10.1159/000320158 -
World Journal of Gastroenterology Sep 2017To investigate the intestinal luminal microbiota (LM) and mucosa-associated microbiota (MAM) in Chinese patients with functional gastrointestinal disorders (FGIDs) and...
AIM
To investigate the intestinal luminal microbiota (LM) and mucosa-associated microbiota (MAM) in Chinese patients with functional gastrointestinal disorders (FGIDs) and examine the association between these communities and the expression of toll-like receptor (TLR) 2 and TLR4.
METHODS
Thirty-two Chinese subjects who suffered from symptoms of FGIDs, as confirmed by gastroenterologists, were enrolled in this study. Fresh faecal samples and descending colonic mucosal biopsies were collected from the subjects before (faecal) and during (mucosal) flexible colonoscopy. For analysis of the samples, we performed high-throughput sequencing of the V3-V4 region of the gene and reverse transcription (RT)-PCR to detect the expression of colonic TLR2 and TLR4. Differences in the stool and mucosal microbiota were examined and a correlation network analysis was performed.
RESULTS
The microbiota of faecal samples was significantly more diverse and richer than that of the mucosal samples, and the LM and MAM populations differed significantly. TLR2 expression showed a significant positive correlation with TLR4 expression. In the MAM samples, the genera and , which belong to the family Ruminococcaceae, were inversely correlated with TLR4 expression ( = -0.45817, = 0.0083 and = -0.5306, = 0.0018, respectively). , which belongs to Carnobacteriaceae, and , which belongs to Streptococcaceae, were inversely correlated with TLR2 expression ( = -0.5573, = 0.0010 and = -0.5435, = 0.0013, respectively). In the LM samples, examination at phylum, class, or order level revealed no correlation with TLR4 expression. , which belongs to Ruminococcaceae, and , which belongs to Streptococcaceae, were inversely correlated with TLR2 expression ( = -0.5743, = 0.0058 and = -0.3905, = 0.0271, respectively).
CONCLUSION
Microbial compositions of LM and MAM in Chinese patients with FGIDs are different. Expression of TLRs may be affected by the type of bacteria that are present in the gut.
Topics: Adult; Bacteria; Biopsy; Colon; Colonoscopy; Computational Biology; Feces; Female; Gastrointestinal Diseases; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; Humans; Intestinal Mucosa; Male; Middle Aged; Phylogeny; RNA, Bacterial; RNA, Ribosomal, 16S; Reverse Transcriptase Polymerase Chain Reaction; Toll-Like Receptor 2; Toll-Like Receptor 4; Young Adult
PubMed: 29085211
DOI: 10.3748/wjg.v23.i36.6665 -
PLoS Pathogens Feb 2024
Topics: Gram-Positive Cocci; Carnobacteriaceae
PubMed: 38300905
DOI: 10.1371/journal.ppat.1011955 -
Frontiers in Microbiology 2022Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using...
Taxonomic and functional microbial communities may respond differently to anthropogenic coastal impacts, but ecological quality monitoring assessments using environmental DNA and RNA (eDNA/eRNA) in response to pollution are poorly understood. In the present study, we investigated the utility of the co-occurrence network approach's to comprehensively explore both structure and potential functions of benthic marine microbial communities and their responses to Cu and Fe fractioning from two sediment deposition coastal zones of northern Chile 16S rRNA gene metabarcoding. The results revealed substantial differences in the microbial communities, with the predominance of two distinct module hubs based on study zone. This indicates that habitat influences microbial co-occurrence networks. Indeed, the discriminant analysis allowed us to identify keystone taxa with significant differences in eDNA and eRNA comparison between sampled zones, revealing that , , and were the primary representatives from Off Loa, whereas , , , and were the families responsible for the observed changes in Mejillones Bay. The quantitative evidence from the multivariate analyses supports that the benthic microbial assemblages' features were linked to specific environments associated with Cu and Fe fractions, mainly in the Bay. Furthermore, the predicted functional microbial structure suggested that transporters and DNA repair allow the communities to respond to metals and endure the interacting variable environmental factors like dissolved oxygen, temperature, and salinity. Moreover, some active taxa recovered are associated with anthropogenic impact, potentially harboring antibiotic resistance and other threats in the coastal zone. Overall, the method of scoping eRNA in parallel with eDNA applied here has the capacity to significantly enhance the spatial and functional understanding of real-time microbial assemblages and, in turn, would have the potential to increase the acuity of biomonitoring programs key to responding to immediate management needs for the marine environment.
PubMed: 36726571
DOI: 10.3389/fmicb.2022.1020491 -
BMC Infectious Diseases May 2021Carnobacterium species are lactic acid-producing Gram-positive bacteria that have been approved by the US Food and Drug Administration and Health Canada for use as a... (Review)
Review
BACKGROUND
Carnobacterium species are lactic acid-producing Gram-positive bacteria that have been approved by the US Food and Drug Administration and Health Canada for use as a food bio-preservative. The use of live bacteria as a food additive and its potential risk of infections in immunocompromised patients are not well understood.
CASE PRESENTATION
An 81-year-old male with a history of metastatic prostate cancer on androgen deprivation therapy and chronic steroids presented to our hospital with a 2-week history of productive cough, dyspnea, altered mentation, and fever. Extensive computed tomography imaging revealed multifocal pneumonia without other foci of infection. He was diagnosed with pneumonia and empirically treated with ceftriaxone and vancomycin. Blood cultures from admission later returned positive for Carnobacterium inhibens. He achieved clinical recovery with step-down to oral amoxicillin/clavulanic acid for a total 7-day course of antibiotics.
CONCLUSIONS
This is the fourth reported case of bacteremia with Carnobacterium spp. isolated from humans. This case highlights the need to better understand the pathogenicity and disease spectrum of bacteria used in the food industry for bio-preservation, especially in immunocompromised patients.
Topics: Aged, 80 and over; Amoxicillin-Potassium Clavulanate Combination; Androgen Antagonists; Anti-Bacterial Agents; Bacteremia; Blood Culture; Canada; Carnobacterium; Ceftriaxone; Food Microbiology; Gram-Positive Bacterial Infections; Humans; Immunocompromised Host; Male; Pneumonia, Bacterial; Prostatic Neoplasms; Vancomycin
PubMed: 33933029
DOI: 10.1186/s12879-021-06095-7 -
Oral microbiota distinguishes acute lymphoblastic leukemia pediatric hosts from healthy populations.PloS One 2014In leukemia, oral manifestations indicate aberrations in oral microbiota. Microbiota structure is determined by both host and environmental factors. In human hosts, how...
In leukemia, oral manifestations indicate aberrations in oral microbiota. Microbiota structure is determined by both host and environmental factors. In human hosts, how health status shapes the composition of oral microbiota is largely unknown. Taking advantage of advances in high-throughput sequencing, we compared the composition of supragingival plaque microbiota of acute lymphoblastic leukemia (ALL) pediatric patients with healthy controls. The oral microbiota of leukemia patients had lower richness and less diversity compared to healthy controls. Microbial samples clustered into two major groups, one of ALL patients and another of healthy children, with different structure and composition. Abundance changes of certain taxa including the Phylum Firmicutes, the Class Bacilli, the Order Lactobacillales, the Family Aerococcaceae and Carnobacteriaceae, as well as the Genus Abiotrophia and Granulicatella were associated with leukemia status. ALL patients demonstrated a structural imbalance of the oral microbiota, characterized by reduced diversity and abundance alterations, possibly involved in systemic infections, indicating the importance of immune status in shaping the structure of oral microbiota.
Topics: Biodiversity; Case-Control Studies; Child; Child, Preschool; Cluster Analysis; Female; Healthy Volunteers; Humans; Male; Metagenome; Microbiota; Mouth; Precursor Cell Lymphoblastic Leukemia-Lymphoma; Risk Factors
PubMed: 25025462
DOI: 10.1371/journal.pone.0102116 -
Journal of Dairy Science May 2023A multicenter observational study to evaluate genome-wide association was conducted in early-lactation Holstein cows (n = 293) from 36 herds in Canada, the USA, and...
A multicenter observational study to evaluate genome-wide association was conducted in early-lactation Holstein cows (n = 293) from 36 herds in Canada, the USA, and Australia. Phenotypic observations included rumen metabolome, acidosis risk, ruminal bacterial taxa, and milk composition and yield measures. Diets ranged from pasture supplemented with concentrates to total mixed rations (nonfiber carbohydrates = 17 to 47, and neutral detergent fiber = 27 to 58% of dry matter). Rumen samples were collected <3 h after feeding and analyzed for pH, ammonia, d- and l-lactate, volatile fatty acid (VFA) concentrations, and abundance of bacterial phyla and families. Eigenvectors were produced using cluster and discriminant analyses from a combination of pH and ammonia, d-lactate, and VFA concentrations, and were used to estimate the probability of the risk of ruminal acidosis based on proximity to the centroid of 3 clusters, termed high (24.0% of cows), medium (24.2%), and low risk (51.8%) for acidosis. DNA of sufficient quality was successfully extracted from whole blood (218 cows) or hair (65 cows) collected simultaneously with the rumen samples and sequenced using the Geneseek Genomic Profiler Bovine 150K Illumina SNPchip. Genome-wide association used an additive model and linear regression with principal component analysis (PCA) population stratification and a Bonferroni correction for multiple comparisons. Population structure was visualized using PCA plots. Single genomic markers were associated with milk protein percent and the center logged ratio abundance of the phyla Chloroflexi, SR1, and Spirochaetes, and tended to be associated with milk fat yield, rumen acetate, butyrate, and isovalerate concentrations and with the probability of being in the low-risk acidosis group. More than one genomic marker was associated or tended to be associated with rumen isobutyrate and caproate concentrations, and the center log ratio of the phyla Bacteroidetes and Firmicutes and center log ratio of the families Prevotellaceae, BS11, S24-7, Acidaminococcaceae, Carnobacteriaceae, Lactobacillaceae, Leuconostocaceae, and Streptococcaceae. The provisional NTN4 gene, involved in several functions, had pleiotropy with 10 bacterial families, the phyla Bacteroidetes and Firmicutes, and butyrate. The ATP2CA1 gene, involved in the ATPase secretory pathway for Ca transport, overlapped for the families Prevotellaceae, S24-7, and Streptococcaceae, the phylum Bacteroidetes, and isobutyrate. No genomic markers were associated with milk yield, fat percentage, protein yield, total solids, energy-corrected milk, somatic cell count, rumen pH, ammonia, propionate, valerate, total VFA, and d-, l-, or total lactate concentrations, or probability of being in the high- or medium-risk acidosis groups. Genome-wide associations with the rumen metabolome, microbial taxa, and milk composition were present across a wide geographical and management range of herds, suggesting the existence of markers for the rumen environment but not for acidosis susceptibility. The variation in pathogenesis of ruminal acidosis in the small population of cattle in the high risk for acidosis group and the dynamic nature of the rumen as cows cycle through a bout of acidosis may have precluded the identification of markers for acidosis susceptibility. Despite a limited sample size, this study provides evidence of interactions between the mammalian genome, the rumen metabolome, ruminal bacteria, and milk protein percentage.
Topics: Female; Animals; Cattle; Rumen; Ammonia; Genome-Wide Association Study; Isobutyrates; Lactation; Fatty Acids, Volatile; Milk Proteins; Butyrates; Diet; Bacteria; Lactates; Acidosis; Hydrogen-Ion Concentration; Fermentation; Mammals; Cattle Diseases
PubMed: 36894426
DOI: 10.3168/jds.2022-22573 -
MBio 2012The distribution, genome location, and evolution of the four paralogous zinc metalloproteases, IgA1 protease, ZmpB, ZmpC, and ZmpD, in Streptococcus pneumoniae and...
UNLABELLED
The distribution, genome location, and evolution of the four paralogous zinc metalloproteases, IgA1 protease, ZmpB, ZmpC, and ZmpD, in Streptococcus pneumoniae and related commensal species were studied by in silico analysis of whole genomes and by activity screening of 154 representatives of 20 species. ZmpB was ubiquitous in the Mitis and Salivarius groups of the genus Streptococcus and in the genera Gemella and Granulicatella, with the exception of a fragmented gene in Streptococcus thermophilus, the only species with a nonhuman habitat. IgA1 protease activity was observed in all members of S. pneumoniae, S. pseudopneumoniae, S. oralis, S. sanguinis, and Gemella haemolysans, was variably present in S. mitis and S. infantis, and absent in S. gordonii, S. parasanguinis, S. cristatus, S. oligofermentans, S. australis, S. peroris, and S. suis. Phylogenetic analysis of 297 zmp sequences and representative housekeeping genes provided evidence for an unprecedented selection for genetic diversification of the iga, zmpB, and zmpD genes in S. pneumoniae and evidence of very frequent intraspecies transfer of entire genes and combination of genes. Presumably due to their adaptation to a commensal lifestyle, largely unaffected by adaptive mucosal immune factors, the corresponding genes in commensal streptococci have remained conserved. The widespread distribution and significant sequence diversity indicate an ancient origin of the zinc metalloproteases predating the emergence of the humanoid species. zmpB, which appears to be the ancestral gene, subsequently duplicated and successfully diversified into distinct functions, is likely to serve an important but yet unknown housekeeping function associated with the human host.
IMPORTANCE
The paralogous zinc metalloproteases IgA1 protease, ZmpB, ZmpC, and ZmpD have been identified as crucial for virulence of the human pathogen Streptococcus pneumoniae. This study maps the presence of the corresponding genes and enzyme activities in S. pneumoniae and in related commensal species of the genera Streptococcus, Gemella, and Granulicatella. The distribution, genome location, and sequence diversification indicate that zmpB is the ancestral gene predating the evolution of today's humanoid species. The ZmpB protease may play an important but yet unidentified role in the association of streptococci of the Mitis and Salivarius groups with their human host, as it is ubiquitous in these two groups, except for a fragmented gene in Streptococcus thermophilus, the only species not associated with humans. The relative sequence diversification of the IgA1 protease, ZmpB, and ZmpD is striking evidence of differences in selection for diversification of these surface-exposed proteins in the pathogen S. pneumoniae compared to the closely related commensal streptococci.
Topics: Adaptation, Biological; Carnobacteriaceae; Cluster Analysis; Computational Biology; Evolution, Molecular; Gemella; Genome, Bacterial; Humans; Metalloproteases; Phylogeny; Sequence Homology; Streptococcus
PubMed: 23033471
DOI: 10.1128/mBio.00303-12 -
Genome Biology Dec 2020Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of...
BACKGROUND
Staphylococcus aureus is a leading cause of healthcare- and community-associated infections and can be difficult to treat due to antimicrobial resistance. About 30% of individuals carry S. aureus asymptomatically in their nares, a risk factor for later infection, and interactions with other species in the nasal microbiome likely modulate its carriage. It is thus important to identify ecological or functional genetic elements within the maternal or infant nasal microbiomes that influence S. aureus acquisition and retention in early life.
RESULTS
We recruited 36 mother-infant pairs and profiled a subset of monthly longitudinal nasal samples from the first year after birth using shotgun metagenomic sequencing. The infant nasal microbiome is highly variable, particularly within the first 2 months. It is weakly influenced by maternal nasal microbiome composition, but primarily shaped by developmental and external factors, such as daycare. Infants display distinctive patterns of S. aureus carriage, positively associated with Acinetobacter species, Streptococcus parasanguinis, Streptococcus salivarius, and Veillonella species and inversely associated with maternal Dolosigranulum pigrum. Furthermore, we identify a gene family, likely acting as a taxonomic marker for an unclassified species, that is significantly anti-correlated with S. aureus in infants and mothers. In gene content-based strain profiling, infant S. aureus strains are more similar to maternal strains.
CONCLUSIONS
This improved understanding of S. aureus colonization is an important first step toward the development of novel, ecological therapies for controlling S. aureus carriage.
Topics: Carnobacteriaceae; Female; Humans; Infant; Metagenomics; Microbiota; Mothers; Nose; RNA, Ribosomal, 16S; Staphylococcal Infections; Staphylococcus aureus; Streptococcus
PubMed: 33308267
DOI: 10.1186/s13059-020-02209-7