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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 -
European Journal of Obstetrics,... Aug 2021To compare the endometrial and vaginal microbiome of women with and without chronic endometritis.
OBJECTIVE
To compare the endometrial and vaginal microbiome of women with and without chronic endometritis.
STUDY DESIGN
A cohort study with 60 patients undergoing assisted reproductive treatment with their own or donated gametes was undertaken. Vaginal and endometrial samples were taken in the cycle prior to embryo transfer. The endometrial and vaginal microbiome was analysed by mass sequencing of the V3V4 region of 16S rRNA gene. Bioinformatics analysis was performed using QIIME2 and MicrobiomeAnalyst packages. Alpha diversity, beta diversity and taxonomic characterization were compared between samples that tested positive and negative for chronic endometritis on CD138 immunohistochemistry.
RESULTS
Different bacterial communities were detected when vaginal and endometrial samples were analysed in patients with and without endometritis diagnosed using CD138 immunohistochemistry. In patients with endometritis, a higher alpha-diversity index was found in vaginal samples (p = 0.15 for the Shannon index) and significant differences were found in endometrial samples (p = 0.01 for the Shannon index). In the beta-diversity analysis, no significant differences were observed between the groups with and without endometritis. Vaginal and endometrial samples from women with endometritis showed a microbiome pattern that was not dominated by Lactobacillus spp. Relative abundance analysis identified Ralstonia and Gardnerella spp. in endometrial samples, and Streptoccoccus and Ureaplasma spp. in vaginal samples of patients diagnosed with chronic endometritis on CD138 immunohistochemistry. When comparing endometrial and vaginal samples diagnosed with endometritis on CD138 immunohistochemistry, both alpha diversity (p = 0.06 for the Shannon index and p = 0.08 for the Simpson index) and beta diversity (p < 0.001) showed significant differences. Lactobacillus spp. (p = 3.76E-4), Ralstonia spp. (p = 8.19E-4), Delftia spp. (p = 0.004) and Anaerobacillus spp. (p = 0.004) were identified in these sample groups.
CONCLUSION
These results demonstrate the existence of a characteristic vaginal and endometrial microbiota in patients with chronic endometritis. Different genera and species were identified in patients with and without chronic endometritis depending on whether the sample was endometrial or vaginal. There is a clear relationship between changes in the vaginal microbiome and chronic endometritis. The microbiota is a continuum throughout the female reproductive tract, so study of the vaginal microbiota could be useful for the diagnosis of diseases of the upper reproductive tract, such as chronic endometritis.
Topics: Cohort Studies; Endometritis; Endometrium; Female; Humans; Microbiota; RNA, Ribosomal, 16S; Vagina
PubMed: 34144490
DOI: 10.1016/j.ejogrb.2021.05.045 -
BMC Genomics Feb 2024Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly...
Shepherd's crook (Geodorum) is a genus of protected orchids that are valuable both medicinally and ornamentally. Geodorum eulophioides (GE) is an endangered and narrowly distributed species, and Geodorum densiflorum (GD) and Geodorum attenuatum (GA) are widespread species. The growth of orchids depend on microorganisms. However, there are few studies on the microbial structure in Geodorum, and little is known about the roles of microorganisms in the endangered mechanism of G. eulophioides. This study analyzed the structure and composition of bacterial and fungal communities in the roots and rhizosphere soil of GE, GD, and GA. The results showed that Delftia, Bordetella and norank_f_Xanthobacteraceae were the dominant bacteria in the roots of Geodorum, while norank_f_Xanthobacteraceae, Gaiella and norank_f_norank_o_Gaiellales were the dominant bacteria in the rhizosphere soil of Geodorum. In the roots, the proportion of Mycobacterium in GD_roadside was higher than that in GD_understory, on the contrary, the proportion of Fusarium, Delftia and Bordetella in GD_roadside was lower than that in GD_understory. Compared with the GD_understory, the roots of GD_roadside had lower microbial diversity. In the endangered species GE, Russula was the primary fungus in the roots and rhizosphere soil, with fungal diversity lower than in the more widespread species. Among the widespread species, the dominant fungal genera in the roots and rhizosphere soil were Neocosmospora, Fusarium and Coprinopsis. This study enhances our understanding of microbial composition and diversity, providing fundamental information for future research on microbial contributions to plant growth and ecosystem function in Geodorum.
Topics: Rhizosphere; Soil; Ecosystem; Fungi; Soil Microbiology; Agaricales; Plant Roots; Bacteria; Fusarium
PubMed: 38418975
DOI: 10.1186/s12864-024-10143-2 -
Bioresources and Bioprocessing Oct 2023Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process....
Fermentation is the key process required for developing the characteristic properties of cigar tobacco leaves, complex microorganisms are involved in this process. However, the microbial fermentation mechanisms during the fermentation process have not been well-characterized. This study investigated the dynamic changes in conventional chemical composition, flavor compounds, and bacterial community during the fermentation of cigar tobacco leaves from Hainan and Sichuan provinces in China, as well as the potential roles of bacteria. Fermentation resulted in a reduction of conventional chemical components in tobacco leaves, with the exception of a noteworthy increase in insoluble protein content. Furthermore, the levels of 10 organic acids and 19 amino acids showed a significant decrease, whereas the concentration of 30 aromatic substances exhibited a unimodal trend. Before fermentation, the bacterial community structures and dominant bacteria in Hainan and Sichuan tobacco leaves differed significantly. As fermentation progressed, the community structures in the two regions became relatively similar, with Delftia, Ochrobactrum, Rhodococcus, and Stenotrophomonas being dominant. Furthermore, a total of 12 functional bacterial genera were identified in Hainan and Sichuan tobacco leaves using bidirectional orthogonal partial least squares (O2PLS) analysis. Delftia, Ochrobactrum, and Rhodococcus demonstrated a significant negative correlation with oleic acid and linoleic acid, while Stenotrophomonas and Delftia showed a significant negative correlation with undesirable amino acids, such as Ala and Glu. In addition, Bacillus showed a positive correlation with benzaldehyde, while Kocuria displayed a positive correlation with 2-acetylfuran, isophorone, 2, 6-nonadienal, and β-damascenone. The co-occurrence network analysis of microorganisms revealed a prevalence of positive correlations within the bacterial network, with non-abundant bacteria potentially contributing to the stabilization of the bacterial community. These findings can improve the overall tobacco quality and provide a novel perspective on the utilization of microorganisms in the fermentation of cigar tobacco leaves.
PubMed: 38647588
DOI: 10.1186/s40643-023-00694-9 -
The ISME Journal Nov 2023Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms...
Metabolic cross-feeding is a pervasive microbial interaction type that affects community stability and functioning and directs carbon and energy flows. The mechanisms that underlie these interactions and their association with metal/metalloid biogeochemistry, however, remain poorly understood. Here, we identified two soil bacteria, Bacillus sp. BP-3 and Delftia sp. DT-2, that engage in a two-tiered mutualism. Strain BP-3 has low utilization ability of pyruvic acid while strain DT-2 lacks hexokinase, lacks a phosphotransferase system, and is defective in glucose utilization. When strain BP-3 is grown in isolation with glucose, it releases pyruvic acid to the environment resulting in acidification and eventual self-killing. However, when strain BP-3 is grown together with strain DT-2, strain DT-2 utilizes the released pyruvic acid to meet its energy requirements, consequently rescuing strain BP-3 from pyruvic acid-induced growth inhibition. The two bacteria further enhance their collective competitiveness against other microbes by using arsenic as a weapon. Strain DT-2 reduces relatively non-toxic methylarsenate [MAs(V)] to highly toxic methylarsenite [MAs(III)], which kills or suppresses competitors, while strain BP-3 detoxifies MAs(III) by methylation to non-toxic dimethylarsenate [DMAs(V)]. These two arsenic transformations are enhanced when strains DT-2 and BP-3 are grown together. The two strains, along with their close relatives, widely co-occur in soils and their abundances increase with the soil arsenic concentration. Our results reveal that these bacterial types employ a two-tiered mutualism to ensure their collective metabolic activity and maintain their ecological competitive against other soil microbes. These findings shed light on the intricateness of bacterial interactions and their roles in ecosystem functioning.
Topics: Arsenic; Soil; Symbiosis; Ecosystem; Pyruvic Acid; Bacteria; Glucose
PubMed: 37737252
DOI: 10.1038/s41396-023-01519-5 -
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 -
Animals : An Open Access Journal From... Dec 2023The present study was carried out to determine the seminal microbiota of boars and their correlation with sperm quality. A total of 17 ejaculates were collected from 17...
The present study was carried out to determine the seminal microbiota of boars and their correlation with sperm quality. A total of 17 ejaculates were collected from 17 Duroc boars and were classified according to sperm quality into two groups: low-quality ( = 8) and high-quality ( = 9). Each ejaculate was subjected to (i) semen evaluation, (ii) bacterial culture and MALDI-TOF identification, and (iii) 16S rRNA gene sequencing and bioinformatic analyses. No difference in the total bacterial count, alpha diversity, and beta diversity between the high-quality group and the low-quality group was detected ( > 0.05). While was negatively correlated with sperm quality ( < 0.05), was positively correlated with sperm quality ( < 0.05). Lactobacillales (25.2%; LB) and Enterobacterales (10.3%; EB) were the most dominant bacteria and negatively correlated: EB = 507.3 - 0.5 × LB, R = 0.24, < 0.001. Moreover, the abundance of was negatively correlated with LB (r = -0.754, < 0.001) and positively correlated with (r = 0.533, < 0.05). was positively correlated with (r = 0.485, < 0.05), (r = 0.622, < 0.01), and (r = 0.489, < 0.05). In conclusion, seminal microbiota is significantly associated with boar semen qualities. The distributions of the most dominant bacterial genera, the differences in the abundance of small subset microbes, and their correlation appear to have far more impact than the overall seminal bacterial content (e.g., total bacterial count, alpha diversity, and beta diversity) on sperm quality.
PubMed: 38136874
DOI: 10.3390/ani13243837