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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 -
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 -
Zhongguo Xue Xi Chong Bing Fang Zhi Za... Nov 2022To investigate the diversity and composition of microflora in laboratory-reared at different developmental stages and larval habitat waters.
OBJECTIVE
To investigate the diversity and composition of microflora in laboratory-reared at different developmental stages and larval habitat waters.
METHODS
The larval habitat waters and different developmental stages of laboratory-reared were collected, and the V3 and V4 regions of the bacterial gene were sequenced using Illumina Miseq next-generation sequencing. The abundance and diversity of the microflora were examined using alpha diversity index in at different developmental stages, and the difference in the microflora compositions was compared in at different developmental stages using principal component analysis (PCA). In addition, the species composition and relative abundance of microflora in A. at different developmental stages were described using histograms and Venn diagrams.
RESULTS
A total of 16 phyla, 30 classes, 72 orders, 129 families and 224 genera of bacteria were detected in larval habitat waters and different developmental stages of The highest bacterial diversity was seen in larval , with Chao index of 125.20 ± 30.48 and Shannon diversity index of 2.04 ± 0.39, which were comparable to those (Chao index of 118.52 ± 15.07 and Shannon diversity index of 2.15 ± 0.30) in larval habitat waters ( = 0.35 and -0.41, both values > 0.05). The bacterial abundance and evenness were significantly greater in female adults than in male adults (Chao index: 42.50 ± 3.54 vs. 18.50 ± 2.13, = 8.23, < 0.05; Shannon diversity index: 1.25 ± 1.67 vs. 0.50 ± 0.05, = 6.00, < 0.05). Proteobacteria, Bacteroidota, Actinobacteriota and Finnicutes were four common phyla of bacteria at each developmental stage of with Proteobacteria dominated at the pupal stage (90.36%), Bacteroidota dominated at the adult stage (46.01% in female adults and 86.11% in male adults), and Actinobacteriota dominated at the larval stage (32.10%). and were common dominant genera of bacteria at each developmental stage of with as the major component at the pupal stage (87.56%), as the main component at the adult stage (46.01% in female adults and 86.11% in male adults, respectively), and as the dominant bacterial genus at the larval stage (12.11%). In addition, , , , , , and were common genera of bacteria at each developmental stage of , with dominated at the larval stage (17.54%) and dominated in larval habitat waters (13.93%).
CONCLUSIONS
There are differences in the composition of symbiotic bacteria at different developmental stages of ; however, similar microflora diversity is maintained at the phylum level. The microflora diversity is comparable in larvae and larval habitat waters of .
Topics: Humans; Adult; Animals; Female; Male; Aedes; Flavobacteriaceae Infections; RNA, Ribosomal, 16S; Microbiota; Larva
PubMed: 36464263
DOI: 10.16250/j.32.1374.2022144 -
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 -
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 -
Microbiome Nov 2022Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of...
BACKGROUND
Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plants and impair the phytoremediation of mine tailings. Nevertheless, pioneer plants can successfully colonize mine tailings and exhibit potential for tailing phytoremediation. Diazotrophs, especially diazotrophic endophytes, can promote the growth of their host plants. This was tested in a mine-tailing habitat by a combination of field sampling, DNA-stable isotope probing (SIP) analysis, and pot experiments.
RESULTS
Bacteria belonging to the genera Herbaspirillum, Rhizobium, Devosia, Pseudomonas, Microbacterium, and Delftia are crucial endophytes for Chinese silvergrass (Miscanthus sinensis) grown in the tailing, the model pioneer plant selected in this study. Further, DNA-SIP using N identified Pseudomonas, Rhizobium, and Exiguobacterium as putative diazotrophic endophytes of M. sinensis. Metagenomic-binning suggested that these bacteria contained essential genes for nitrogen fixation and plant growth promotion. Finally, two diazotrophic endophytes Rhizobium sp. G-14 and Pseudomonas sp. Y-5 were isolated from M. sinensis. Inoculation of another pioneer plant in mine tailings, Bidens pilosa, with diazotrophic endophytes resulted in successful plant colonization, significantly increased nitrogen fixation activity, and promotion of plant growth.
CONCLUSIONS
This study indicated that diazotrophic endophytes have the potential to promote the growth of pioneer plant B. pilosa in mine tailings. Video Abstract.
Topics: Endophytes; Poaceae; Nitrogen Fixation; Bacteria; Plants; Pseudomonas; China; DNA; Plant Roots
PubMed: 36329505
DOI: 10.1186/s40168-022-01379-9 -
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 -
The Science of the Total Environment Mar 2022Strobilurin fungicides are a class of persistent fungicides frequently detected in the environment. Microbes can effectively degrade strobilurins, but the mechanisms are...
Strobilurin fungicides are a class of persistent fungicides frequently detected in the environment. Microbes can effectively degrade strobilurins, but the mechanisms are complex and diverse. Compared with isolated strains, bacterial consortia are more robust in terms of the degradation of multiple pollutants. The enrichment culture XS19 is a group of bacterial strains enriched from soil and degrades six strobilurins at 50 mg/L within 8 d, including azoxystrobin, picoxystrobin, trifloxystrobin, kresoxim-methyl, pyraclostrobin and enestroburin. LC-Q-TOF-MS analysis confirmed that XS19 can demethylate these strobilurins via hydrolysis of the methyl ester group. Analysis of the bacterial communities suggested that Pseudomonas (69.8%), Sphingobacterium (21.2%), Delftia (6.3%), and Achromobacter (1.6%) spp. were highly associated with the removal of strobilurins in the system. Metagenomics-based comprehensive analysis of XS19 suggested that carboxylesterases in Pseudomonas and Sphingobacterium play a central role in the catabolism of strobilurins. Moreover, the carboxylesterase inhibitor bis-p-nitrophenyl phosphate inhibited the degradation activity of strobilurins in XS19. This work proved that XS19 or carboxylesterases can effectively hydrolyze strobilurins, providing a reliable bioremediation paradigm.
Topics: Biodegradation, Environmental; Carboxylic Ester Hydrolases; Fungicides, Industrial; Soil; Strobilurins
PubMed: 34979227
DOI: 10.1016/j.scitotenv.2021.152751 -
3 Biotech May 2021The microbial community structure and succession regularity of six key periods during high-temperature Daqu production were revealed using high-throughput sequencing to...
UNLABELLED
The microbial community structure and succession regularity of six key periods during high-temperature Daqu production were revealed using high-throughput sequencing to explore the factors affecting the flavor formation of Northern Jiang-flavored Baijiu technology. The results showed that among the six Daqu samples, the bacteria mainly included Firmicutes, Actinobacteriota, and Proteobacteria, of which Proteobacteria was the most dominant. The primary fungus was Ascomycota. At the genus level, the primary bacterial groups were , , , , , , , , and . The main fungal groups in the Daqu were , , and . During the initial stage of Daqu production, the dominant bacteria were (20.07%) and (48.30%). As the fermentation temperature of the Daqu increased, , , and became the dominant bacteria during the first Daqu flipping period, the second Daqu flipping period, and the dry-fire period. During these three periods, many bacteria were eliminated, decreasing the bacterial diversity, while a decline in temperature was evident during the Daqu exit period. After adapting to the high-temperature environment, the accumulation of (22.07%), (16.73%), (27.13%), (9.03%) and (6.97%) increased the bacterial diversity during the Daqu exit period. (83.47%) represented the main dominant fungus during the initial production stage but were eliminated with increased temperature. Furthermore, a higher temperature increased the abundance of and , while gradually accumulated in the D, E, and F samples. (79.90%) and (13.83%) became the dominant fungi during the Daqu exit period. In this study, high-throughput sequencing technology was used to reveal the microbial diversity during the high-temperature Daqu production process of Northern Jiang-flavored Baijiu. This provided a scientific basis for improving the production process of this product in the future. Therefore, understanding the formation of the flavor substances and the related microorganisms in Northern Jiang-flavored Baijiu can provide guidance for using them to manipulate the preparation process while implementing microbial control and improving the production procedures.
SUPPLEMENTARY INFORMATION
The online version contains supplementary material available at 10.1007/s13205-021-02779-8.
PubMed: 33968569
DOI: 10.1007/s13205-021-02779-8 -
Pancreas Apr 2022Most previous studies have analyzed bacteria in tumors using resected pancreatic cancer (PC) tissues, because it is difficult to obtain tissue samples from unresectable...
OBJECTIVES
Most previous studies have analyzed bacteria in tumors using resected pancreatic cancer (PC) tissues, because it is difficult to obtain tissue samples from unresectable advanced PC. We aimed to determine whether minimal tissue obtained by endoscopic ultrasound-guided fine-needle aspiration is useful for microbiome analysis.
METHODS
Thirty PC and matched duodenal and stomach tissues (N = 90) were prospectively collected from 30 patients who underwent endoscopic ultrasound-guided fine-needle aspiration. Bacterial DNA was extracted, and 16S rRNA sequencing was performed. The primary outcome was the success rate of bacterial detection in tumors. Bacterial diversity and structure were investigated.
RESULTS
The bacterial detection rates were 80%, 100%, and 97% in PC, gastric, and duodenal samples, respectively. Pancreatic cancer tissues showed a lower α-diversity and a significantly different microbial structure than stomach and duodenal tissues. Proteobacteria were more abundant, whereas Firmicutes, Bacteroidetes, and Fusobacteria were less abundant in PC tissues than in stomach and duodenal tissues. Acinetobacter was more abundant in PC tissues than in stomach and duodenal tissues, and Delftia was more frequently detected in resectable PC.
CONCLUSIONS
Endoscopic ultrasound-guided fine-needle aspiration samples were valuable for PC microbiome analysis, revealing that the bacterial composition of PC is different from that of the stomach and duodenum.
Topics: Endoscopic Ultrasound-Guided Fine Needle Aspiration; Humans; Microbiota; Pancreatic Neoplasms; RNA, Ribosomal, 16S
PubMed: 35695806
DOI: 10.1097/MPA.0000000000002028