Browsing by Subject "16S rRNA"

Now showing 1 - 5 of 5
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    16S rRNA deep sequencing identifies Actinotignum schaalii as the major component of a polymicrobial intra-abdominal infection and implicates a urinary source
    (Microbiology Society, 2017-05-03) Bryan, Andrew; Kirkpatrick, Lindsey M.; Manaloor, John J.; Salipante, Stephen J.; Pediatrics, School of Medicine
    Introduction. It can be difficult to catalogue the individual organisms comprising polymicrobial patient infections, both because conventional clinical microbiological culture does not facilitate the isolation and enumeration of all members of a complex microbial community, and because fastidious organisms may be mixed with organisms that grow rapidly in vitro. Empiric antimicrobial treatment is frequently employed based on the anatomical site and the suspected source of the infection, especially when an appropriately collected surgical specimen is not obtained., Case presentation. We present a case of an intra-abdominal infection in a patient with complex anatomy and recurrent urinary tract infections. Imaging did not reveal a clear source of infection, no growth was obtained from urine cultures and initial abdominal fluid cultures were also negative. In contrast, 16S rRNA deep sequencing of abdominal fluid samples revealed mixed bacterial populations with abundant anaerobes, including Actinotignum schaalii (Actinobaculum schaalii). Ultimately, only Enterobacter cloacae complex and meticillin-resistant Staphylococcus aureus, both of which were identified by sequencing, were recovered by culture., Conclusion. The clinical application of 16S rRNA deep sequencing can more comprehensively and accurately define the organisms present in an individual patient's polymicrobial infection than conventional microbiological culture, detecting species that are not recovered under standard culture conditions or that are otherwise unexpected. These results can facilitate effective antimicrobial stewardship and help elucidate the possible origins of infections.
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    Gut microbiota was modulated by moxibustion stimulation in rats with irritable bowel syndrome
    (Biomed Central, 2018-12-18) Wang, Xiaomei; Qi, Qin; Wang, Yuanyuan; Wu, Huangan; Jin, Xiaoming; Yao, Huan; Jin, Duiyin; Liu, Yanan; Wang, Cun; Anatomy and Cell Biology, IU School of Medicine
    Background: The pathogenesis of irritable bowel syndrome (IBS) is closely related to intestinal dysbacteriosis and can be controlled by moxibustion treatment. However, the mechanism underlying the therapeutic value of moxibustion in IBS treatment remains unknown. Methods: An IBS rat model was established by colorectal distention (CRD) stimulus and mustard oil clyster. Sixty-five male rats were randomly divided into six groups: normal, IBS model, moxibustion, electroacupuncture (EA), Bifid-triple Viable Capsule (BTVC) and Pinaverium Bromide (PB) groups. The moxibustion group was treated with mild moxibustion at the bilateral Tianshu (ST25) and Shangjuxu (ST37) for 10 min/day for 7 days, the EA group was given EA at ST25 and ST37 once daily for 7 days, while the BTVC group and PB groups received Bifid-triple Viable Capsule and Pinaverium Bromide solution (at the proportion of 1:0.018) respectively by gavage once daily for 7 days. After the treatment, abdominal withdrawal reflex (AWR) scores were determined based on CRD stimulus, gut microbiota profiling was conducted by 16S rRNA high-throughput sequencing. Results: Irritable bowel syndrome model rats had significantly increased AWR scores at all intensities (20, 40, 60 and 80 mmHg) compared with the normal group. Moxibustion treatment significantly reduced AWR scores compared with the IBS model group at all intensities. Across all groups the most abundant phyla were Bacteroidetes and Firmicutes followed by Proteobacteria and Candidatus Saccharibacteria. At genus level IBS model rats had a higher abundance of Prevotella, Bacteroides and Clostridium XI and a lower abundance of Lactobacillus and Clostridium XIVa compared with normal rats. These changes in microbiota profiles could however be reversed by moxibustion treatment. Alpha diversity was decreased in IBS model rats compared with normal rats, yet significantly increased in moxibustion- and PB-treated rats compared with IBS rats. Conclusion: Our findings suggest that moxibustion treats IBS by modulating the gut microbiota.
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    Influence of Environmental Factors on the Production of MIB and Geosmin Metabolites by Bacteria in a Eutrophic Reservoir
    (AGU, 2019-07) Clercin, Nicolas A.; Druschel, Gregory K.; Earth Sciences, School of Science
    Occurrences of odorous bacterial metabolites, 2‐methylisoborneol (MIB) and geosmin (GSM), in drinking water supply reservoirs are considered as a nuisance by the water industry and a source of complaints from customers. In Eagle Creek Reservoir, routine monitoring programs of MIB and GSM highlight intense odorous outbreaks during the spring season when high inflow discharges occur. Cyanobacteria have always been assumed to be source of these metabolites even if no known producers are present in raw water. A copper‐based algaecide is often used to terminate the metabolite production and the algal growth in the reservoir. The current study was designed to investigate and identify other biological sources involved in the biosynthesis of MIB and GSM metabolites as well as environmental factors that could be important triggers for the growth of bacterial producers. The community structure of the bacterioplankton was determined using a 16S rRNA gene sequencing technique, which showed that not only Cyanobacteria but Actinobacteria also were involved in the reservoir internal production. Planktothrix species was identified as the main source of GSM (p < 0.001) while Streptomyces (Actinobacteria) was very likely responsible of MIB (p < 0.01). Application of an algaecide disrupted GSM and the growth of Planktothrix but was less effective against MIB and Streptomyces . Statistical analyses revealed that MIB‐ and GSM‐causing bacteria were found abundant when the water was enriched with nitrogen, temperature cooler, and the water column mixed.
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    Moxibustion treatment modulates the gut microbiota and immune function in a dextran sulphate sodium-induced colitis rat model
    (Baishideng Publishing Group, 2018-07-28) Qi, Qin; Liu, Ya-Nan; Jin, Xiao-Ming; Zhang, Lin-Shuang; Wang, Cun; Bao, Chun-Hui; Liu, Hui-Rong; Wu, Huan-Gan; Wang, Xiao-Mei; Anatomy and Cell Biology, School of Medicine
    AIM: To investigate the effect and mechanism of moxibustion in rats with ulcerative colitis. METHODS: A rat colitis model was established by administering 4% dextran sulphate sodium solution. Seventy male rats were randomly divided into seven groups: Healthy controls (HC), ulcerative colitis model group (UC), UC with 7 d of moxibustion (UC-7), UC with 14 d of moxibustion (UC-14), UC with mesalazine gavage (UC-W), HC with 7 d of moxibustion (HC-7), HC with 14 d of moxibustion (HC-14). Moxibustion was applied to the bilateral Tianshu (ST25). Gut microbiome profiling was conducted by 16S rRNA amplicon sequencing, and PCR and ELISA determined the expression of inflammatory cytokines in colon mucosa and serum, respectively. RESULTS: Moxibustion treatment restored the colonic mucosa and decreased submucosal inflammatory cell infiltration in colitis rats. Rats treated with moxibustion and mesalazine had significantly lower levels of the dominant phyla Proteobacteria and the genera Saccharibacteria, Sphingomonas and Barnesiella than colitis rats, and they could restore the microbiome to levels similar to those observed in healthy rats. UC rats had reduced alpha diversity, which could be alleviated by moxibustion therapy, and UC-7 had a higher alpha diversity than UC-14. This finding suggests that short-term (7 d) but no longer term (14 d) moxibustion treatment may significantly affect the gut microbiome. The potential bacterial functions affected by moxibustion may be ascorbate and aldarate metabolism, and amino acid metabolism. Compared with HC group, the levels of the cytokines interleukin-12 (IL-12) (P < 0.05) and IL-6, IL-17, IL-23, interferon-γ, lipopolysaccharide, IgA, tumour necrosis factor-α and its receptors 1 (TNFR1) and TNFR2 (P < 0.01) were all increased, whereas anti-inflammatory cytokine IL-2 and IL-10 (P < 0.01) and transforming growth factor-β (P < 0.05) were decreased in UC rats. These changes were reversed by moxibustion. CONCLUSION: Our findings suggest that moxibustion exerts its therapeutic effect by repairing mucosal tissue damage and modulating the gut microbiome and intestinal mucosal immunity.
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    Specialized pro-resolving mediator lipidome and 16S rRNA bacterial microbiome data associated with human chronic rhinosinusitis
    (Elsevier, 2021-04-01) Vickery, Thad W.; Armstrong, Michael; Kofonow, Jennifer M.; Robertson, Charles E.; Kroehl, Miranda E.; Reisdorph, Nichole A.; Ramakrishnan, Vijay R.; Frank, Daniel N.; Otolaryngology -- Head and Neck Surgery, School of Medicine
    Chronic rhinosinusitis (CRS) is a clinical syndrome defined by symptoms including nasal congestion, facial pain and pressure, anosmia, and rhinorrhea lasting more than 12 weeks. Several mechanistically distinct processes lead to the development of clinical symptoms in CRS including innate immune dysfunction, dysregulated eicosanoid metabolism and perturbations in host-microbiome interactions [1]. We developed a database comprised of patient demographic information, lipid mediator metabolomic profiles, and 16S bacterial rRNA gene sequence data from 66 patients undergoing endoscopic sinus surgery. Briefly, ethmoid sinus tissue and middle meatal swabs were collected from patients, including non-CRS controls, CRS with polyps (CRSwNP), and CRS without polyps (CRSsNP). Lipid mediator pathways from arachidonic acid (AA) and docosahexanoic acid (DHA) were analyzed by liquid chromatography/tandem mass spectrometry. Bacterial taxa were profiled in parallel by 16S rRNA gene sequencing. This database provides a useful compendium of AA/DHA metabolomic profiles and associated bacterial microbiota in patients with varying disease subtypes, demographics, and risk factors/comorbidities.