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Life (Basel, Switzerland) Aug 2021Emerging evidences link gut microbiota to colorectal cancer (CRC) initiation and development. However, the CRC stage- and spatial-specific bacterial taxa were less...
Emerging evidences link gut microbiota to colorectal cancer (CRC) initiation and development. However, the CRC stage- and spatial-specific bacterial taxa were less investigated, especially in a Chinese cohort, leading to our incomplete understanding of the functional roles of gut microbiota in promoting CRC progression and recurrence. Here, we report the composition and structure of gut microbiota across CRC stages I, II and III, by analyzing the gut mucosal microbiomes of 75 triplet-paired samples collected from on-tumor, adjacent-tumor and off-tumor sites and 26 healthy controls. We observed tumor-specific pattern of mucosal microbiome profiles as CRC progressed and identified ten bacterial taxa with high abundances (>1%) as potential biomarkers for tumor initiation and development. and can serve as biomarkers for CRC stage I. , , , , , and can serve as biomarkers for CRC stage II, while , , , , and can serve as biomarkers for CRC stage III. These biomarkers classified CRC stages I, II and III distinguished from each other with an area under the receiver-operating curve (AUC) > 0.5. Moreover, co-occurrence and co-excluding network analysis of these genera showed strong correlations in CRC stage I, which were subsequently reduced in CRC stages II and III. Our findings provide a reference index for stage-specific CRC diagnosis and suggest stage-specific roles of , , and in driving CRC progression.
PubMed: 34440574
DOI: 10.3390/life11080831 -
Infection and Drug Resistance 2024In recent years, has gained attention for its rare occurrence in patient infections. The literature consists mostly of case reports, necessitating further research to...
BACKGROUND
In recent years, has gained attention for its rare occurrence in patient infections. The literature consists mostly of case reports, necessitating further research to comprehensively understand risk factors, clinical characteristics, and management strategies.
METHODS
We conducted a retrospective cohort study involving patients diagnosed with infection at a tertiary teaching hospital between January 2014 and December 2022. The data included demographic details, comorbidities, bacterial cultures, antibiotic susceptibility, and treatment outcomes.
RESULTS
There were 26 patients diagnosed with infection who were predominantly older with multiple comorbidities. Approximately 76.9% of infection patients had polymicrobial infections. Twenty-one patients had received antibiotics within three months before they developed the infection, and these antibiotics were primarily third-generation cephalosporins, glycopeptides and fluoroquinolones. Antibiotic susceptibility testing showed resistance to aminoglycosides and susceptibility to imipenem, meropenem, ceftazidime, and piperacillin/tazobactam. Treatment outcome showed a mortality rate of 11.5%, mainly in patients with malignancy and advanced age.
CONCLUSION
infections predominantly affect older patients with multiple comorbidities. In terms of antibiotic therapy, carbapenems, cephalosporins, and piperacillin/tazobactam with antipseudomonal activity could all be considered.
PubMed: 38736436
DOI: 10.2147/IDR.S457781 -
Frontiers in Cellular and Infection... 2021has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete...
has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of . TR1180 exhibited resistance to β-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of strains. Comparative genomics analysis of TR1180 with other publicly available genomes of showed diverse genomic features among these strains. TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical , which provide researchers and clinicians with valuable insights into this uncommon species.
Topics: Anti-Bacterial Agents; China; Delftia; Drug Resistance, Bacterial; Female; Genome, Bacterial; Genomics; Humans; Integrons; Phylogeny
PubMed: 34222039
DOI: 10.3389/fcimb.2021.663933 -
Current Microbiology Jun 2024Delftia has been separated from freshwater, sludge, and soil and has emerged as a novel opportunistic pathogen in the female vagina. However, the genomic...
Delftia has been separated from freshwater, sludge, and soil and has emerged as a novel opportunistic pathogen in the female vagina. However, the genomic characteristics, pathogenicity, and biotechnological properties still need to be comprehensively investigated. In this study, a Delftia strain was isolated from the vaginal discharge of a 43-year-old female with histologically confirmed cervical intraepithelial neoplasm (CIN III), followed by whole-genome sequencing. Phylogenetic analysis and average nucleotide identity (ANI) analysis demonstrated that it belongs to Delftia lacustris, named D. lacustris strain LzhVag01. LzhVag01 was sensitive to β-lactams, macrolides, and tetracyclines but exhibited resistance to lincoamines, nitroimidazoles, aminoglycosides, and fluoroquinolones. Its genome is a single, circular chromosome of 6,740,460 bp with an average GC content of 66.59%. Whole-genome analysis identified 16 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, and 11 potential virulence genes. These pathogenic factors may contribute to its colonization in the vaginal environment and its adaptation and accelerate the progression of cervical cancer. This study sequenced and characterized the whole-genome of Delftia lacustris isolated from vaginal discharge, which provides investigators and clinicians with valuable insights into this uncommon species.
Topics: Delftia; Genome, Bacterial; Vaginal Discharge; Humans; Female; Adult; Phylogeny; Anti-Bacterial Agents; Drug Resistance, Bacterial; Virulence Factors; Species Specificity
PubMed: 38898312
DOI: 10.1007/s00284-024-03758-x -
PloS One 2021Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage...
Despite the formation of biofilms on catheters for extracorporeal membrane oxygenation (ECMO), some patients do not show bacteremia. To elucidate the specific linkage between biofilms and bacteremia in patients with ECMO, an improved understanding of the microbial community within catheter biofilms is necessary. Hence, we aimed to evaluate the biofilm microbiome of ECMO catheters from adults with (n = 6) and without (n = 15) bacteremia. The microbiomes of the catheter biofilms were evaluated by profiling the V3 and V4 regions of bacterial 16s rRNA genes using the Illumina MiSeq sequencing platform. In total, 2,548,172 reads, with an average of 121,341 reads per sample, were generated. Although alpha diversity was slightly higher in the non-bacteremic group, the difference was not statistically significant. In addition, there was no difference in beta diversity between the two groups. We found 367 different genera, of which 8 were present in all samples regardless of group; Limnohabitans, Flavobacterium, Delftia, Massilia, Bacillus, Candidatus, Xiphinematobacter, and CL0-1 showed an abundance of more than 1% in the sample. In particular, Arthrobacter, SMB53, Neisseria, Ortrobactrum, Candidatus Rhabdochlamydia, Deefgae, Dyella, Paracoccus, and Pedobacter were highly abundant in the bacteremic group. Network analysis indicated that the microbiome of the bacteremic group was more complex than that of the non-bacteremic group. Flavobacterium and CL0.1, which were abundant in the bacteremic group, were considered important genera because they connected different subnetworks. Biofilm characteristics in ECMO catheters varied according to the presence or absence of bacteremia. There were no significant differences in diversity between the two groups, but there were significant differences in the community composition of the biofilms. The biofilm-associated community was dynamic, with the bacteremic group showing very complex network connections within the microbiome.
Topics: Arthrobacter; Bacteremia; Bacteria; Biofilms; Catheter-Related Infections; Extracorporeal Membrane Oxygenation; Female; Humans; Male; Microbiota; Middle Aged; Neisseria; RNA, Ribosomal, 16S; Retrospective Studies
PubMed: 34529734
DOI: 10.1371/journal.pone.0257449 -
Frontiers in Microbiology 2021Microorganisms are ubiquitous in the environment, and the atmosphere is no exception. However, airborne bacterial communities are some of the least studied. Increasing...
Microorganisms are ubiquitous in the environment, and the atmosphere is no exception. However, airborne bacterial communities are some of the least studied. Increasing our knowledge about these communities and how environmental factors shape them is key to understanding disease outbreaks and transmission routes. We describe airborne bacterial communities at two different sites in Tenerife, La Laguna (urban, 600 m.a.s.l.) and Izaña (high mountain, 2,400 m.a.s.l.), and how they change throughout the year. Illumina MiSeq sequencing was used to target 16S rRNA genes in 293 samples. Results indicated a predominance of Proteobacteria at both sites (>65%), followed by Bacteroidetes, Actinobacteria, and Firmicutes. Gammaproteobacteria were the most frequent within the Proteobacteria phylum during spring and winter, while Alphaproteobacteria dominated in the fall and summer. Within the 519 genera identified, was the most frequent during spring (35.75%) and winter (30.73%); (24.49%) and (19.88%) dominated in the summer; and represented 10.26 and 12.41% of fall and winter samples, respectively. was also identified in 17.15% of the fall samples. These five genera were more abundant at the high mountain site, while other common airborne bacteria were more frequent at the urban site (, , , and ). Diversity values showed different patterns for both sites, with higher values during the cooler seasons in Izaña, whereas the opposite was observed in La Laguna. Regarding wind back trajectories, Tropical air masses were significantly different from African ones at both sites, showing the highest diversity and characterized by genera regularly associated with humans (, , and ), as well as others related to extreme conditions () or typically associated with animals (Lachnospiraceae). Marine and African air masses were consistent and very similar in their microbial composition. By contrast, European trajectories were dominated by , , , and . These data contribute to our current state of knowledge in the field of atmospheric microbiology. However, future studies are needed to increase our understanding of the influence of different environmental factors on atmospheric microbial dispersion and the potential impact of airborne microorganisms on ecosystems and public health.
PubMed: 34737729
DOI: 10.3389/fmicb.2021.732961 -
Synthetic and Systems Biotechnology Jun 2022Per- and Polyfluorinated alkyl substances (PFAS) are a broad class of synthetic compounds that have fluorine substituted for hydrogen in several or all locations and are...
Per- and Polyfluorinated alkyl substances (PFAS) are a broad class of synthetic compounds that have fluorine substituted for hydrogen in several or all locations and are globally categorized as PFCs (perfluorochemicals; commonly called fluorinated chemicals). These compounds have unique chemical and physical properties that enable their use in non-stick surfaces, fire-fighting efforts, and as slick coatings. However, recent concerns over the health effects of such compounds, specifically perfluorooctanoic acid and perfluorooctane sulfonic acid (PFOA, PFOS; PFOA/S), have led to increased attention and research by the global community into degradation methods. In this study, soil samples from PFAS-contamination sites were cultured and screened for microbes with PFOA/S degradation potential, which led to the identification of It was found that isolated from PFAS-contaminated soils was capable of growth in minimal media with PFOA as a sole carbon resource, and an observable fluoride concentration increase was observed when cells were exposed to PFOA. This suggests potential activity of a dehalogenase enzyme that may be of use in PFOA or PFAS microbial remediation efforts. Several associated haloacid dehalogenases have been identified in the genome and have been engineered for expression in for rapid production and purification. These enzymes have shown potential for enzymatic defluorination, a significant step in biological degradation and removal of PFOA/S from the environment. We hypothesize that bioremediation of PFAS using naturally occurring microbial degradation pathways may represent a novel approach to remove PFAS contamination.
PubMed: 35224235
DOI: 10.1016/j.synbio.2022.02.005 -
Frontiers in Cellular and Infection... 2023Over the last few decades, a growing body of evidence has suggested a role for various infectious agents in Alzheimer's disease (AD) pathogenesis. Despite diverse...
BACKGROUND
Over the last few decades, a growing body of evidence has suggested a role for various infectious agents in Alzheimer's disease (AD) pathogenesis. Despite diverse pathogens (virus, bacteria, fungi) being detected in AD subjects' brains, research has focused on individual pathogens and only a few studies investigated the hypothesis of a bacterial brain microbiome. We profiled the bacterial communities present in non-demented controls and AD subjects' brains.
RESULTS
We obtained postmortem samples from the brains of 32 individual subjects, comprising 16 AD and 16 control age-matched subjects with a total of 130 samples from the frontal and temporal lobes and the entorhinal cortex. We used full-length 16S rRNA gene amplification with Pacific Biosciences sequencing technology to identify bacteria. We detected bacteria in the brains of both cohorts with the principal bacteria comprising (formerly ) and two species each of and genera. We used a hierarchical Bayesian method to detect differences in relative abundance among AD and control groups. Because of large abundance variances, we also employed a new analysis approach based on the Latent Dirichlet Allocation algorithm, used in computational linguistics. This allowed us to identify five sample classes, each revealing a different microbiota. Assuming that samples represented infections that began at different times, we ordered these classes in time, finding that the last class exclusively explained the existence or non-existence of AD.
CONCLUSIONS
The AD-related pathogenicity of the brain microbiome seems to be based on a complex polymicrobial dynamic. The time ordering revealed a rise and fall of the abundance of with pathogenicity occurring for an off-peak abundance level in association with at least one other bacterium from a set of genera that included , , , , and . may also be involved with outcompeting the species, which were strongly associated with non-demented brain microbiota, whose early destruction could be the first stage of disease. Our results are also consistent with a leaky blood-brain barrier or lymphatic network that allows bacteria, viruses, fungi, or other pathogens to enter the brain.
Topics: Humans; Alzheimer Disease; RNA, Ribosomal, 16S; Bayes Theorem; Microbiota; Bacteria; Propionibacterium acnes; Brain; Acne Vulgaris
PubMed: 37780846
DOI: 10.3389/fcimb.2023.1123228 -
PeerJ 2020Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and...
Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of presence and prevalence and is adaptable to different campuses and experimental questions.
PubMed: 32322441
DOI: 10.7717/peerj.8925 -
Insects Jan 2022Silkworm, L., research involves studies on improving strains for enhanced sustainability of high-quality silk production. Several of these have investigated the factors...
Silkworm, L., research involves studies on improving strains for enhanced sustainability of high-quality silk production. Several of these have investigated the factors affecting growth and development of silkworm larvae and cocoon characteristics that subsequently affect the yield and quality of silk. The gut microbiota has been reported to impact growth and development of silkworms and has been linked, in particular, with absorption and utilization of nutrients and immunity to diseases. The silkworm strains maintained in the Philippines lack sufficient biological data for use in strain improvement. This prompted efforts to augment the data by profiling bacterial communities through high-throughput 16S rRNA gene amplicon sequencing and analysis in four of the local silkworm strains that are bred and maintained in the country. Results of the study showed that the four silkworm strains are abundant in bacteria that belong to the genera , , , and . Results also showed that bacterial diversity and evenness increase as larvae mature, which can be correlated to larval development and shifts in the amount and age of mulberry leaves the larvae consume.
PubMed: 35055946
DOI: 10.3390/insects13010100