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Scientific Reports Feb 2020The white leg Litopenaeus vannamei shrimp is of importance to the eastern Pacific fisheries and aquaculture industry but suffer from diseases such as the recently...
The white leg Litopenaeus vannamei shrimp is of importance to the eastern Pacific fisheries and aquaculture industry but suffer from diseases such as the recently emerged early mortality syndrome. Many bacterial pathogens have been identified but the L. vannamei microbiota is still poorly known. Using a next-generation sequencing (NGS) approach, this work evaluated the impact of the inclusion in the diet of mannan oligosaccharide, (MOS, 0.5% w/w), over the L. vannamei microbiota and production behavior of L. vannamei under intensive cultivation in Ecuador. The MOS supplementation lasted for 60 days, after which the shrimp in the ponds were harvested, and the production data were collected. MOS improved productivity outcomes by increasing shrimp survival by 30%. NGS revealed quantitative differences in the shrimp microbiota between MOS and control conditions. In the treatment with inclusion of dietary MOS, the predominant phylum was Actinobacteria (28%); while the control group was dominated by the phylum Proteobacteria (30%). MOS has also been linked to an increased prevalence of Lactococcus- and Verrucomicrobiaceae-like bacteria. Furthermore, under the treatment of MOS, the prevalence of potential opportunistic pathogens, like Vibrio, Aeromonas, Bergeyella and Shewanella, was negligible. This may be attributable to MOS blocking the adhesion of pathogens to the surfaces of the host tissues. Together, these findings point to the fact that the performance (survival) improvements of the dietary MOS may be linked to the impact on the microbiota, since bacterial lines with pathogenic potential towards shrimps were excluded in the gut.
Topics: Actinobacteria; Aeromonas; Animal Feed; Animals; Aquaculture; Bacterial Adhesion; Ecuador; Flavobacteriaceae; Lactococcus; Longevity; Mannans; Microbiota; Oligosaccharides; Penaeidae; Proteobacteria; Seafood; Shewanella; Verrucomicrobia; Vibrio
PubMed: 32066764
DOI: 10.1038/s41598-020-59587-y -
Animals : An Open Access Journal From... Jul 2023The high complexity of the oral microbiota of healthy dogs and the close exposure of humans to companion animals represent a risk of the transmission of potential...
The high complexity of the oral microbiota of healthy dogs and the close exposure of humans to companion animals represent a risk of the transmission of potential zoonotic microorganisms to humans, especially through dog bites, including multidrug-resistant ones. Nonetheless, a limited number of comprehensive studies have focused on the diversity of the microorganisms that inhabit the oral cavities of healthy dogs, particularly based on modern molecular techniques. We investigated bacterial and fungal organisms in the oral cavities of 100 healthy dogs based on a combination of conventional and selective microbiological culture, mass spectrometry (MALDI-TOF MS), and next-generation sequencing. In addition, in vitro antimicrobial susceptibility patterns of isolates and A resistance gene were assessed. A total of 213 bacteria and 20 fungi were isolated. (40/100 = 40%), α-hemolytic (37/100 = 37%), and (22/100 = 22%) were the most prevalent bacteria diagnosed by microbiological culture and MALDI-TOF MS, whereas (10/100 = 10%) was the most common fungi identified. Based on next-generation sequencing of selected 20 sampled dogs, (32.5%), (16.3%), (12.8%), (9.5%), (5%), (3.8%), and (3.4%) genera were prevalent. A high multidrug resistance rate was observed in isolates, particularly to azithromycin (19/19 = 100%), penicillin (15/19 = 78.9%), and sulfamethoxazole/trimethoprim (15/19 = 78.9%). In addition, the A resistance gene was detected in 6.1% (3/49) of coagulase-positive staphylococci. Here, we highlight the microbial complexity of the oral mucosa of healthy dogs, including potential zoonotic microorganisms and multidrug-resistant bacteria, contributing with the investigation of the microbiota and antimicrobial resistance patterns of the microorganisms that inhabit the oral cavity of healthy dogs.
PubMed: 37570276
DOI: 10.3390/ani13152467 -
Scientific Reports Jun 2020Here we report a pilot-sized study to compare the taxonomic composition of sputum microbiome in 17 newly-diagnosed lung cancer (LC) patients and 17 controls. Another...
Here we report a pilot-sized study to compare the taxonomic composition of sputum microbiome in 17 newly-diagnosed lung cancer (LC) patients and 17 controls. Another object was to compare the representation of individual bacterial genera and species in sputum with the frequency of chromosomal aberrations in the blood lymphocytes of LC patients and in controls. Both groups were male; average age 56.1 ± 11.5 in patients and 55.7 ± 4.1 in controls. Differences in the species composition of bacterial communities in LC patients and controls were significant (pseudo-F = 1.94; p = 0.005). Increased prevalence in LC patients was detected for the genera Haemophilus and Bergeyella; whereas a decrease was observed for the genera Atopobium, Stomatobaculum, Treponema and Porphyromonas. Donors with high frequencies of chromosomal aberrations had a significant reduction in the microbiome of representatives of the genus Atopobium in the microbiome and a simultaneous increase in representatives of the species Alloprevotella compared to donors with a low level of chromosomal aberrations in lymphocytes. Thus, a comparison of the bacterial composition in the sputum of donors with cytogenetic damages in theirs lymphocytes, warrants further investigations on the potential role of microorganisms in the process of mutagenesis in somatic cells of the host body.
Topics: Aged; Bacteria; Case-Control Studies; Chromosome Aberrations; DNA, Bacterial; DNA, Ribosomal; Female; Humans; Lung Neoplasms; Lymphocytes; Male; Microbiota; Middle Aged; Phylogeny; Pilot Projects; Prevalence; RNA, Ribosomal, 16S; Sequence Analysis, DNA; Sputum
PubMed: 32541778
DOI: 10.1038/s41598-020-66654-x -
Antimicrobial Agents and Chemotherapy Mar 2002BMS-284756, a new des-fluoro(6) quinolone, was very active against 240 aerobic and 180 anaerobic isolates from bite victims. It inhibited 403 of 420 (96%) isolates,...
In vitro activities of the des-fluoro(6) Quinolone BMS-284756 against aerobic and anaerobic pathogens isolated from skin and soft tissue animal and human bite wound infections.
BMS-284756, a new des-fluoro(6) quinolone, was very active against 240 aerobic and 180 anaerobic isolates from bite victims. It inhibited 403 of 420 (96%) isolates, including those of Moraxella spp., CDC group EF-4, and Eikenella corrodens at < or = 2 microg/ml and those of all Pasteurella spp. and Bergeyella zoohelcum at < or = 0.015 microg/ml. Fusobacterium russii and 6 of 11 Fusobacterium nucleatum isolates of animal bite origin were resistant, but isolates of human bite origin were susceptible, which suggests that they were of a different subspecies.
Topics: Animals; Anti-Infective Agents; Bacteria, Aerobic; Bacteria, Anaerobic; Bites and Stings; Cats; Dogs; Fluoroquinolones; Humans; Indoles; Microbial Sensitivity Tests; Quinolones; Skin Diseases, Infectious; Soft Tissue Infections
PubMed: 11850275
DOI: 10.1128/AAC.46.3.866-870.2002 -
Cellular Physiology and Biochemistry :... 2018Periodontitis is a prevalent chronic inflammatory disease caused by enhanced inflammation induced by dysbiotic microbes forming on subgingival tooth sites, which may... (Comparative Study)
Comparative Study
BACKGROUND/AIMS
Periodontitis is a prevalent chronic inflammatory disease caused by enhanced inflammation induced by dysbiotic microbes forming on subgingival tooth sites, which may disturb the balance of the microbial composition in the biofilm and finally result in the progressive destruction of the periodontal ligament and alveolar bone with periodontal pocket formation and/or gingival recession.
METHODS
To elucidate the correlation between subgingival microbiome and IgAN incidence in CP (chronic periodontitis at severe levels) patients, subgingival plaque samples were collected from CP patients without IgAN (Control) and CP patients with IgAN (Disease). 16S rRNA sequencing and comparative analyses of plaque bacterial microbiome between Control and Disease were performed.
RESULTS
Subgingival microbial diversity in Disease was a little higher than that in Control. Besides, significant differences were found in subgingival microbiome between Disease and Control. Compared with that in Control, at phylum level, the abundances of Proteobacteria and Actinobacteria were significantly higher while the abundances of Bacteroidetes, Fusobacteria, Spirochaetae, Synergistetes, and Saccharibacteria were significantly lower in Disease; at class level, the abundances of Betaproteobacteria, Bacilli, Actinobacteria, Flavobacteriia, and Gammaproteobacteria were significantly higher while the abundances of Bacteroidia, Fusobacteriia, Negativicutes, Clostridia, and Spirochaetes were significantly lower in Disease; at genus level, the abundances of Bergeyella, Capnocytophaga, Actinomyces, Corynebacterium, Comamonas, Lautropia, and Streptococcus were significantly higher while the abundances of Treponema and Prevotella were significantly lower in Disease.
CONCLUSIONS
Our data indicated a correlation between the changes in subgingival microbial structure and IgAN incidence in CP patients, which might be used to predict IgAN incidence in CP patients.
Topics: Adult; Bacteria; Chronic Periodontitis; Female; Gingiva; Glomerulonephritis, IGA; High-Throughput Nucleotide Sequencing; Humans; Male; Microbiota; Phylogeny; Principal Component Analysis; RNA, Ribosomal, 16S; Sequence Analysis, DNA
PubMed: 29807361
DOI: 10.1159/000490029 -
PloS One 2013Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of...
Periodontal disease is the most widespread oral disease in dogs which if left untreated results in significant pain to the pet and loss of dentition. The objective of this study was to identify bacterial species in canine plaque that are significantly associated with health, gingivitis and mild periodontitis (<25% attachment loss). In this survey subgingival plaque samples were collected from 223 dogs with healthy gingiva, gingivitis and mild periodontitis with 72 to 77 samples per health status. DNA was extracted from the plaque samples and subjected to PCR amplification of the V1-V3 region of the 16S rDNA. Pyrosequencing of the PCR amplicons identified a total of 274 operational taxonomic units after bioinformatic and statistical analysis. Porphyromonas was the most abundant genus in all disease stages, particularly in health along with Moraxella and Bergeyella. Peptostreptococcus, Actinomyces, and Peptostreptococcaceae were the most abundant genera in mild periodontitis. Logistic regression analysis identified species from each of these genera that were significantly associated with health, gingivitis or mild periodontitis. Principal component analysis showed distinct community profiles in health and disease. The species identified show some similarities with health and periodontal disease in humans but also major differences. In contrast to human, healthy canine plaque was found to be dominated by Gram negative bacterial species whereas Gram positive anaerobic species predominate in disease. The scale of this study surpasses previously published research and enhances our understanding of the bacterial species present in canine subgingival plaque and their associations with health and early periodontal disease.
Topics: Animals; Bacteria; Cross-Sectional Studies; DNA, Bacterial; DNA, Ribosomal; Dog Diseases; Dogs; Female; Gingiva; Gingivitis; Humans; Male; Periodontitis; RNA, Ribosomal, 16S
PubMed: 24349448
DOI: 10.1371/journal.pone.0083158 -
Veterinary Sciences Jun 2023The pilot study aimed to investigate the effects of GAMS on oral microbiota in healthy dog subjects. Thirty-eight dogs were recruited and randomly allocated to the...
The pilot study aimed to investigate the effects of GAMS on oral microbiota in healthy dog subjects. Thirty-eight dogs were recruited and randomly allocated to the placebo ( = 19) and treatment groups ( = 19). The dogs were treated with mouth spray once daily for 42 days. The changes in the gingival index (GI), plaque index (PI), and calculus index (CI) were measured at baseline (day 0) and end of the study (42nd day). The changes in the oral microbial composition of representative dogs (placebo, = 7; and treatment, = 7) were also evaluated at baseline and end of the study. Oral microbial composition was assessed by sequencing. The sequences were annotated using the QIIME 2.0. The GI, PI, and CI indexes were reduced after the GAMS usage. The abundance of the commensal bacterial phylum Actinobacteria and Chloroflexi, genera , and was improved after six weeks of GAMS usage. GAMS reduced the pathogenic bacterial species, including sp., sp., , and Moreover, some pathogenic bacterial abundances were increased at the end of the study. All the microbial variations were observed within the group. The inter-group analysis revealed that the changes were unrelated to GAMS usage. Further studies need to be carried out using more experimental subjects to confirm the effectiveness of GAMS. More metagenomic data are required to evidence the GMAS impact on the oral microbiome of healthy dogs.
PubMed: 37505829
DOI: 10.3390/vetsci10070424 -
Journal of Clinical Microbiology Jan 2009Intra-amniotic infection and inflammation are major causes of preterm birth (PTB). However, intra-amniotic inflammation is often detected in the absence of infection.... (Comparative Study)
Comparative Study
Intra-amniotic infection and inflammation are major causes of preterm birth (PTB). However, intra-amniotic inflammation is often detected in the absence of infection. This may partly be due to the culturing methods employed in hospital laboratories, which are unable to detect the uncultivated species. In this study, intra-amniotic microbial infections associated with PTB were examined by both culture and 16S rRNA-based culture-independent methods and were corroborated by the presence of intra-amniotic inflammation. Amniotic fluid (AF) specimens from 46 pregnancies complicated by PTB and 16 asymptomatic women were analyzed. No bacterial DNA was amplified in AF collected from the asymptomatic women. Among the 46 samples associated with PTB, bacterial DNA was amplified from all (16/16) of the culture-positive samples and 17% (5/30) of the culture-negative samples. In the culture-positive group, additional species were detected in more than half (9/16) of the cases by PCR and clone analysis. Altogether, approximately two- thirds of the species detected by the culture-independent methods were not isolated by culture. They included both uncultivated and difficult-to-cultivate species, such as Fusobacterium nucleatum, Leptotrichia (Sneathia) spp., a Bergeyella sp., a Peptostreptococcus sp., Bacteroides spp., and a species of the order Clostridiales. To examine intra-amniotic inflammation, an AF proteomic fingerprint (mass-restricted score) was determined by surface-enhanced laser desorption ionization-time-of-flight mass spectrometry. Inflammation was detected in all five samples which were culture negative but PCR positive. Women who were PCR positive more often had elevated interleukin-6 levels in their AF, histological chorioamnionitis, and funisitis and delivered neonates with early-onset neonatal sepsis. Previously unrecognized, uncultivated, or difficult-to-cultivate species may play a key role in the initiation of PTB.
Topics: Adult; Amnion; Amniotic Fluid; Bacteria; Bacterial Infections; Cloning, Molecular; DNA, Bacterial; DNA, Ribosomal; Female; Humans; Infant, Newborn; Mass Spectrometry; Polymerase Chain Reaction; Pregnancy; Pregnancy Complications, Infectious; Premature Birth; Proteome; RNA, Ribosomal, 16S
PubMed: 18971361
DOI: 10.1128/JCM.01206-08 -
Journal of Infection in Developing... Mar 2012Misidentification of Brucella species from clinical specimens using commercial bacterial identification systems is a recurring problem. An isolate from a bacterimic...
Misidentification of Brucella species from clinical specimens using commercial bacterial identification systems is a recurring problem. An isolate from a bacterimic patient was identified as Bergeyella zoohelcum by MicroScan Walk-Away (Siemens Healthcare Diagnostics Inc., West Sacramento, CA, USA) and as Brucella melitensis by Vitek 2 system (bioMérieux Inc., Durham, NC, USA). Because of this identification ambiguity by the two automated bacterial identification systems we performed 16S rRNA sequencing and serotyping of the isolate and confirmed it as a Brucella spp. Combining the sequence data with the Vitek 2 system data we conclude that the infection was caused by B. melitensis.
Topics: Adult; Automation; Bacteremia; Bacterial Typing Techniques; Brucella melitensis; Brucellosis; DNA, Bacterial; Diagnostic Errors; Flavobacteriaceae; Flavobacteriaceae Infections; Genes, rRNA; Humans; Male; RNA, Ribosomal, 16S; Reagent Kits, Diagnostic; Sequence Analysis, DNA; Serotyping
PubMed: 22421611
DOI: 10.3855/jidc.2252 -
Microbiology and Immunology Mar 2019Two gram-negative, catalase-negative, oxidase-positive strains (PAGU 1467 and PAGU 1468) isolated from patients with infective endocarditis were investigated to...
Two gram-negative, catalase-negative, oxidase-positive strains (PAGU 1467 and PAGU 1468) isolated from patients with infective endocarditis were investigated to determine their taxonomic status. 16S rRNA gene sequence analysis indicated that the two strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. Strains PAGU 1467 and PAGU 1468 were highly related to each other (98.8% 16S rRNA gene sequence similarity). Phylogenetically closely-related species to PAGU 1467 comprised Bergeyella zoohelcum (95.0% 16S rRNA gene sequence similarity), Riemerella anatipestifer (94.3%) and Cloacibacterium normanense (94.3%). The major fatty acids of the two isolates were iso-C , iso-C 3-OH and iso-C 3-OH. The presence of C 3-OH and iso-C 2-OH allowed these isolates to be distinguished from B. zoohelcum. Menaquinone MK-6 was the only respiratory quinone in these organisms; this is a consistent characteristic of the family Flavobacteriaceae. The guanine-plus-cytosine content of the genomic DNA was 42.0%, which is higher than that of other close phylogenetic relatives. On the basis of their phenotypic properties and genetic distinctiveness, isolates PAGU 1467 and PAGU 1468 were classified within the novel genus Spodiobacter, as Spodiobacter cordis gen. nov., sp. nov., which is also the type species. The type strain of S. cordis is PAGU 1467 ( = CCUG 65564 = NBRC 109998 ).
Topics: Bacterial Typing Techniques; Base Composition; DNA, Bacterial; Endocarditis; Fatty Acids; Flavobacteriaceae; Humans; Phylogeny; RNA, Ribosomal, 16S
PubMed: 30817020
DOI: 10.1111/1348-0421.12673