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Ishikawa T, Uejima Y, Okai M, Shiga K, Shoji K, Miyairi I, Kato M, Morooka S, Kubota M, Tagaya T, Tsuji S, Aoki S, Ide K, Niimi H, Uchiyama T, Onodera M, Kawai T. Melting temperature mapping method in children: Rapid identification of pathogenic microbes. J Infect Chemother 2024; 30:475-480. [PMID: 38036030 DOI: 10.1016/j.jiac.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 11/23/2023] [Indexed: 12/02/2023]
Abstract
INTRODUCTION The melting temperature (Tm) mapping method (TM) identifies bacterial species by intrinsic patterns of Tm values in the 16S ribosomal RNA gene (16S rDNA) extracted directly from whole blood. We examined potential clinical application of TM in children with bloodstream infection (BSI). METHODS This was a prospective observational study at a children's hospital in Japan from 2018 to 2021. In patients with diagnosed or suspected BSI, we investigated the match rates of pathogenic bacteria identified by TM and blood culture (BC), the inspection time to identification of TM, and the amount of bacterial DNA in blood samples. RESULTS The median age of 81 patients (93 samples) was 3.6 years. Of 23 samples identified by TM, 11 samples matched the bacterial species with BC (positive-match rate, 48 %). Of 64 TM-negative samples, 62 samples were negative for BC (negative-match rate, 97 %). Six samples, including one containing two pathogenic bacterial species, were not suitable for TM identification. In total, the matched samples were 73 of 93 samples (match rate, 78 %). There were seven samples identified by TM in BC-negative samples from blood collected after antibiotic therapy. Interestingly, the bacteria were matched with BC before antibiotic administration. These TM samples contained as many 16S rDNA copies as the BC-positive samples. The median inspection time to identification using TM was 4.7 h. CONCLUSIONS In children with BSI, TM had high negative-match rates with BC, the potential to identify the pathogenic bacteria even in patients on antibiotic therapy, and more rapid identification compared to BC. REGISTERING CLINICAL TRIALS UMIN000041359https://center6.umin.ac.jp/cgi-open-bin/ctr/ctr_view.cgi?recptno=R000047220.
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Affiliation(s)
- Takashi Ishikawa
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan.
| | - Yoji Uejima
- Division of Infectious Diseases and Immunology, Saitama Children's Medical Center, Saitama, Japan; Department of Clinical Laboratory and Molecular Pathology, Toyama University Hospital, Toyama, Japan
| | - Masashi Okai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Kyoko Shiga
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Kensuke Shoji
- Division of Infectious Diseases, National Center for Child Health and Development, Tokyo, Japan
| | - Isao Miyairi
- Division of Infectious Diseases, National Center for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Department of Pediatric Hematology and Oncology Research, National Center for Child Health and Development, Tokyo, Japan
| | - Shintaro Morooka
- Department of General Pediatrics & Interdisciplinary Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Mitsuru Kubota
- Department of General Pediatrics & Interdisciplinary Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Takashi Tagaya
- Division of Pediatric Emergency and Transport Services, National Center for Child Health and Development, Tokyo, Japan
| | - Satoshi Tsuji
- Division of Pediatric Emergency and Transport Services, National Center for Child Health and Development, Tokyo, Japan
| | - Satoshi Aoki
- Division of Critical Care Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kentaro Ide
- Division of Critical Care Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Hideki Niimi
- Department of Clinical Laboratory and Molecular Pathology, Toyama University Hospital, Toyama, Japan
| | - Toru Uchiyama
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Department of Human Genetics, National Center for Child Health and Development, Tokyo, Japan
| | - Masafumi Onodera
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Gene & Cell Therapy Promotion Center, National Center for Child Health and Development, Tokyo, Japan
| | - Toshinao Kawai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan; Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
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Lei J, Lü W, Wang W, Wang H, Guo X, Cheng P, Gong M, Liu L. [Comparison of the microbiota diversity between autogenous and anautogenous Culex pipiens pallens]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2024; 36:52-58. [PMID: 38604685 DOI: 10.16250/j.32.1374.2023204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
OBJECTIVE To investigate the microbiota composition and diversity between autogenous and anautogenous Culex pipiens pallens, so as to provide insights into unraveling the pathogenesis of autogeny in Cx. pipiens pallens. METHODS Autogenous and anautogenous adult Cx. pipiens pallens samples were collected at 25 ℃, and the hypervariable regions of the microbial 16S ribosomal RNA (16S rRNA) gene was sequenced on the Illumina NovaSeq 6000 sequencing platform. The microbiota abundance and diversity were evaluated using the alpha diversity index, and the difference in the microbiota structure was examined using the beta diversity index. The microbiota with significant differences in the abundance between autogenous and anautogenous adult Cx. pipiens pallens samples was identified using the linear discriminant analysis effect size (LEfSe). RESULTS The microbiota in autogenous and anautogenous Cx. pipiens pallens samples belonged to 18 phyla, 28 classes, 70 orders, 113 families, and 170 genera, and the dominant phyla included Proteobacteria, Bacteroidetes, and so on. At the genus level, Wolbachia was a common dominant genus, and the relative abundance was (77.6 ± 11.3)% in autogenous Cx. pipiens pallens samples and (47.5 ± 8.5)% in anautogenous mosquito samples, while Faecalibaculum (0.4% ± 0.1%), Dubosiella (0.5% ± 0.0%) and Massilia (0.5% ± 0.1%) were specific species in autogenous Cx. pipiens pallens samples. Alpha diversity analysis showed that higher Chao1 index and ACE index in autogenous Cx. pipiens pallens samples than in anautogenous samples (both P values > 0.05), and lower Shannon index (P > 0.05) and Simpson index (P < 0.05) in autogenous Cx. pipiens pallens samples than in anautogenous samples. LEfSe analysis showed a total of 48 significantly different taxa between autogenous and anautogenous Cx. pipiens pallens samples (all P values < 0.05). CONCLUSIONS There is a significant difference in the microbiota diversity between autogenous and anautogenous Cx. pipiens pallens.
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Affiliation(s)
- J Lei
- Shandong Institute of Parasitic Diseases; Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong 272033, China
| | - W Lü
- Shandong Institute of Parasitic Diseases; Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong 272033, China
| | - W Wang
- Shandong Institute of Parasitic Diseases; Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong 272033, China
| | - H Wang
- Shandong Institute of Parasitic Diseases; Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong 272033, China
| | - X Guo
- Shandong Institute of Parasitic Diseases; Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong 272033, China
| | - P Cheng
- Shandong Institute of Parasitic Diseases; Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong 272033, China
| | - M Gong
- Shandong Institute of Parasitic Diseases; Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong 272033, China
| | - L Liu
- Shandong Institute of Parasitic Diseases; Shandong First Medical University & Shandong Academy of Medical Sciences, Jining, Shandong 272033, China
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Narapakdeesakul D, Kaewparuehaschai M, Thongsahuan S, Lekcharoen P, Pengsakul T, Pattaradilokrat S, Kaewthamasorn M. Multi-locus sequence analysis of 'Candidatus Mycoplasma haematomacacae' in free-ranging macaques from Thailand suggestive of a closer relationship to hemotropic mycoplasmas in capuchins and potential origin from bats. Acta Trop 2024; 252:107156. [PMID: 38387771 DOI: 10.1016/j.actatropica.2024.107156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Although 'Candidatus Mycoplasma haematomacacae' (formerly known as 'Candidatus Mycoplasma haemomacaque') has been reported on extensively in macaques from Thailand, the USA, Japan, and Brazil, its genetic characterization has primarily been restricted to the 16S rRNA sequences with no exploration on multi-locus sequence analysis. The primary goal of this study was to characterize 'Ca. M. haematomacacae' among Thai macaques based on multiple genetic markers. Between April 2018 and November 2021, blood samples were taken from 580 free-ranging macaques (560 Macaca fascicularis and 20 Macaca nemestrina) in 15 locations encompassing 10 provinces throughout Thailand. Using the conventional PCR assay targeting the 16S ribosomal RNA (16S rRNA) gene, 338 out of 580 macaques (58.27 %) tested hemoplasma-positive. Of these, 40 positive samples were further subjected to DNA sequencing, and all were identified as 'Ca. M. haematomacacae'. Subsequently, the partial nucleotide sequences of 23S ribosomal RNA (23S rRNA) and RNase P RNA (rnpB) genes of this particular hemoplasma species were amplified through nested PCR assay. The analysis of multi-locus genetic markers revealed that the 23S rRNA and rnpB sequences exhibited higher levels of genetic diversity than the 16S rRNA sequences. Furthermore, the 16S rRNA analyses demonstrated that 'Ca. M. haematomacacae' infecting Old World monkeys (Macaca spp.) was most closely related to hemotropic Mycoplasma spp. in black-capped capuchins (Sapajus apella) and Marcgrave's capuchins (Sapajus flavius) from Brazil, as well as establishing a common ancestor clade with hemotropic Mycoplasma spp. from the Neotropical bats in Belize and Peru and an Old World bat in Spain. The 23S rRNA analyses likewise evidenced that 'Ca. M. haematomacacae' formed a sister clade with hemotropic Mycoplasma spp. in Neotropical bats from Belize and Panama. Thus, the present findings, based on multi-locus sequence analysis, suggest a potential origin of 'Ca. M. haematomacacae' from Neotropical and Old World bats. To the best of the authors' knowledge, this study provided the largest dataset so far of multi-locus genetic sequences of 'Ca. M. haematomacacae' isolated from Thai macaques and enhanced the accuracy of phylogenetic analyses, providing insights into their origins among hemotropic Mycoplasma spp. discovered worldwide.
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Affiliation(s)
- Duriyang Narapakdeesakul
- Veterinary Pathobiology Graduate Program, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand; Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Salintorn Thongsahuan
- Department of National Parks, Wildlife and Plant Conservation, Bangkok 10900, Thailand
| | - Paisin Lekcharoen
- Veterinary Public Health Graduate Program, Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Theerakamol Pengsakul
- Health and Environmental Research Center, Faculty of Environmental Management, Prince of Songkla University, Songkhla 90110, Thailand
| | | | - Morakot Kaewthamasorn
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Cen C, Du Q, Luo B, Wang T, Su J, Qin X, Zhang W, Lu L, Liao Y, Huang Y, Liang Y. Helicobacter pylori causes gastric dysbacteriosis in chronic gastritis patients. Open Life Sci 2024; 19:20220839. [PMID: 38585629 PMCID: PMC10997148 DOI: 10.1515/biol-2022-0839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 01/25/2024] [Accepted: 02/06/2024] [Indexed: 04/09/2024] Open
Abstract
Gastric mucosal samples were procured and underwent the sequencing of 16S ribosomal RNA (16S rRNA) via Illumina high-throughput sequencing technology to explore the impact of Helicobacter pylori (H. pylori) infection on the composition of gastric flora in chronic gastritis (CG) patients. In the results, the operational taxonomic unit (OTU) analysis revealed an overlap of 5706 OTUs shared between the two groups. The top 5 abundance ranking (TOP5) phyla comprised Bacteroidetes, Proteobacteria, Firmicutes, Actinobacteria, and Epsilonbacteraeota, while the TOP5 genus was Lachnospiraceae_NK4A136_group, Helicobacter, Bacteroides, Klebsiella, and Pseudomonas. In the metabolic pathways at the Kyoto Encyclopedia of Genes and Genomes (KEGG)_L3 level, conspicuous variations across seven functions were observed between the H. pylori-positive (HP_Pos) and H. pylori-negative (HP_Neg) groups. Subsequently, functional gene enrichment in KEGG pathways was further validated through animal experimentation. In contrast to the mice in the HP_Neg group, those infected with H. pylori manifested an infiltration of inflammatory cells, an augmentation in gastric acid secretion, and conspicuously elevated scores regarding gastric activity, along with heightened levels of malondialdehyde. In conclusion, CG patients infected with H. pylori displayed a disorder in gastric flora, furnishing a theoretical basis for the prophylaxis of H. pylori infection and its associated pathogenic ramifications.
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Affiliation(s)
- Chao Cen
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Qiuying Du
- Graduate School of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Bin Luo
- Department of Laboratory, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Tonghua Wang
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Jianwei Su
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Xiaoshan Qin
- Department of Gastroenterology, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Wenyan Zhang
- Graduate School of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Lijing Lu
- Graduate School of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Yang Liao
- Graduate School of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Yanqiang Huang
- Department of Pathogen Biology and Immunology, Youjiang Medical University for Nationalities School of Basic Medical Sciences, Baise, Guangxi 533000, China
| | - Yumei Liang
- Department of Neonatology, Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18, Zhongshan Second Road, Youjiang District, Baise, Guangxi 533000, China
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Musilova I, Stranik J, Jacobsson B, Kacerovsky M. Antibiotic treatment reduces the intensity of intraamniotic inflammation in pregnancies with idiopathic vaginal bleeding in the second trimester of pregnancy. Am J Obstet Gynecol 2024; 230:245.e1-245.e14. [PMID: 37516399 DOI: 10.1016/j.ajog.2023.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/23/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND Idiopathic bleeding in the second trimester of pregnancy complicates <1% of all pregnancies. This pregnancy complication can be caused by alterations in local hemostasis in the decidua due to infection/inflammation in the choriodecidual niche. This condition is associated with intraamniotic inflammatory complications. Antibiotic therapy effectively reduces the intensity of intraamniotic inflammation in certain pregnancy pathologies. However, whether antibiotic administration can reduce the intensity of the intraamniotic inflammatory response or eradicate microorganisms in patients with idiopathic bleeding during the second trimester of pregnancy remains unclear. OBJECTIVE This study primarily aimed to determine whether antimicrobial agents can reduce the magnitude of intraamniotic inflammation in patients with idiopathic bleeding in the second trimester of pregnancy by assessing the concentration of interleukin-6 in the amniotic fluid before and after 7 days of antibiotic treatment. The secondary aim was to determine whether treatment with a combination of antibiotics altered the microbial load of Ureaplasma species DNA in amniotic fluid. STUDY DESIGN This retrospective cohort study included singleton-gestation patients with idiopathic bleeding between 15+0 and 27+6 weeks who underwent transabdominal amniocentesis at the time of admission. Follow-up amniocentesis was performed in a subset of patients unless abortion or delivery occurred earlier. Concentrations of interleukin-6 were measured in the amniotic fluid samples, and the presence of microbial invasion of the amniotic cavity was assessed using culture and molecular microbiological methods. Intraamniotic inflammation was defined as an interleukin-6 concentration ≥3000 pg/mL in the amniotic fluid samples. RESULTS A total of 36 patients with idiopathic bleeding in the second trimester of pregnancy were included. All the patients underwent initial amniocentesis. Patients with intraamniotic inflammation (n=25) were treated using a combination of antibiotics consisting of intravenous ceftriaxone, intravenous metronidazole, and peroral clarithromycin. The patients without intraamniotic inflammation (n=11) were treated expectantly. In total, 25 patients delivered 7 days after admission. All patients with intraamniotic inflammation at the initial amniocentesis who delivered after 7 days underwent follow-up amniocentesis. Treatment with antibiotics decreased the interleukin-6 concentration in the amniotic fluid at follow-up amniocentesis compared with that at the initial amniocentesis in patients with intraamniotic inflammation (median [interquartile range]: 3457 pg/mL [2493-13,203] vs 19,812 pg/mL [11,973-34,518]; P=.0001). Amniotic fluid samples with Ureaplasma species DNA had a lower microbial load at the time of follow-up amniocentesis compared with the initial amniocentesis (median [interquartile range]: 1.5×105 copies DNA/mL [1.3×105-1.7×105] vs 8.0×107 copies DNA/mL [6.7×106-1.6×108]; P=.02). CONCLUSION Antibiotic therapy was associated with reduced intraamniotic inflammation in patients with idiopathic bleeding in the second trimester complicated by intraamniotic inflammation. Moreover, antibiotic treatment has been associated with a reduction in the microbial load of Ureaplasma species DNA in the amniotic fluid.
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Affiliation(s)
- Ivana Musilova
- Biomedical Research Center, University Hospital Hradec Králové, Hradec Králové, Czech Republic; Department of Obstetrics and Gynecology, Hospital Most, Krajská zdravotní a.s., Ústí nad Labem, Czech Republic
| | - Jaroslav Stranik
- Biomedical Research Center, University Hospital Hradec Králové, Hradec Králové, Czech Republic
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Science, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden; Division of Health Data and Digitalisation, Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Marian Kacerovsky
- Biomedical Research Center, University Hospital Hradec Králové, Hradec Králové, Czech Republic; Department of Obstetrics and Gynecology, Hospital Most, Krajská zdravotní a.s., Ústí nad Labem, Czech Republic.
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Lundtorp Olsen C, Massarenti L, Vendius VFD, Gürsoy UK, Van Splunter A, Bikker FJ, Gürsoy M, Damgaard C, Markvart M, Belstrøm D. Probiotics Partly Suppress the Impact of Sugar Stress on the Oral Microbiota-A Randomized, Double-Blinded, Placebo-Controlled Trial. Nutrients 2023; 15:4810. [PMID: 38004205 PMCID: PMC10675525 DOI: 10.3390/nu15224810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The aim was to test if probiotics counteract oral dysbiosis during 14 days of sugar stress and subsequently help restore oral homeostasis. Eighty healthy individuals received either probiotics (n = 40) or placebo lozenges (n = 40) for 28 days and rinsed with a 10% sucrose solution 6-8 times during the initial 14 days of the trial. Saliva and supragingival samples were collected at baseline, day 14, and day 28. Saliva samples were analyzed for levels of pro-inflammatory cytokines, albumin, and salivary enzyme activity. The supragingival microbiota was characterized according to the Human Oral Microbiome Database. After 14 days of sugar stress, the relative abundance of Porphyromonas species was significantly higher (p = 0.03) and remained significantly elevated at day 28 in the probiotic group compared to the placebo group (p = 0.004). At day 28, the relative abundance of Kingella species was significantly higher in the probiotic group (p = 0.03). Streptococcus gordinii and Neisseria elongata were associated with the probiotic group on day 28, while Streptococcus sobrinus was associated with the placebo group on day 14 and day 28. On day 28, the salivary albumin level was significantly lower in the probiotic group. The present study demonstrates a potential stabilizing effect on the supragingival microbiota mediated by consumption of probiotics during short-term sugar stress.
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Affiliation(s)
- Christine Lundtorp Olsen
- Section for Clinical Oral Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (V.F.D.V.); (M.M.); (D.B.)
- ADM Denmark A/S, 3390 Hundested, Denmark
| | - Laura Massarenti
- Section for Oral Biology and Immunopathology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (L.M.); (C.D.)
| | - Vincent Frederik Dahl Vendius
- Section for Clinical Oral Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (V.F.D.V.); (M.M.); (D.B.)
| | - Ulvi Kahraman Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku, 20520 Turku, Finland; (U.K.G.); (M.G.)
| | - Annina Van Splunter
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, 1081 LA Amsterdam, The Netherlands; (A.V.S.); (F.J.B.)
| | - Floris J. Bikker
- Department of Oral Biochemistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, 1081 LA Amsterdam, The Netherlands; (A.V.S.); (F.J.B.)
| | - Mervi Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku, 20520 Turku, Finland; (U.K.G.); (M.G.)
| | - Christian Damgaard
- Section for Oral Biology and Immunopathology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (L.M.); (C.D.)
| | - Merete Markvart
- Section for Clinical Oral Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (V.F.D.V.); (M.M.); (D.B.)
| | - Daniel Belstrøm
- Section for Clinical Oral Microbiology, Department of Odontology, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; (V.F.D.V.); (M.M.); (D.B.)
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Owada M. Radula and Shell Microstructure Variations are Congruent with a Molecular Estimate of Shallow-Water Japanese Chitons. Zoolog Sci 2023; 40:390-403. [PMID: 37818888 DOI: 10.2108/zs220060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 06/29/2023] [Indexed: 10/13/2023]
Abstract
Variations of the radula and shell microstructures in 33 species of Japanese chiton were investigated along with molecular phylogenetic trees. The molecular phylogenetic trees indicated that Chitonida was composed of four clades, of which two clades formed Acanthochitonina and corresponded to Mopalioidea and Cryptoplacoidea, respectively, and the other clades formed Chitonina. In the radula, the shapes of the central and centro-lateral teeth and the petaloid process varied greatly among species or genera and were useful for the identification of particular species or genera. The presence of accessory and petaloid processes and the cusp shape were relatively conserved and useful for recognizing particular genera or even suborders. In the valves, four to six shell layers were found at the section, but the ventral mesostracum was not observed in Acanthochitonina. The shell microstructures in the ventral sublayer of the tegmentum varied at suborder, but those in the other layers were almost constant. The megalaesthete chamber type varied at superfamily and was helpful to identify particular families or superfamilies. The characteristics of the shell layers and shell microstructures appear to be a synapomorphy shared by the members of Acanthochitonina. The classification within Chitonina needs to be reexamined because the variations of the cusp shape and megalaesthete chamber type were relatively large and did not correspond to the current classification. Callochiton formed a sister group with Chitonida and would be equally closely related to Chitonina and Acanthochitonina because of possessing a mosaic of characteristics from both.
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Affiliation(s)
- Masato Owada
- Faculty of Science, Department of Biological Sciences, Kanagawa University, Kanagawa-ku, Yokohama, Kanagawa 221-8686, Japan,
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Liu Y, Liu J, Zhang X, Yun Y. Diversity of Bacteria Associated with Guts and Gonads in Three Spider Species and Potential Transmission Pathways of Microbes within the Same Spider Host. Insects 2023; 14:792. [PMID: 37887804 PMCID: PMC10607309 DOI: 10.3390/insects14100792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023]
Abstract
Microbial symbiosis plays a crucial role in the ecological and evolutionary processes of animals. It is well known that spiders, with their unique and diverse predatory adaptations, assume an indispensable role in maintaining ecological balance and the food chain. However, our current understanding of spider microbiomes remains relatively limited. The gut microbiota and gonad microbiota of spiders can both potentially influence their physiology, ecology, and behavior, including aspects such as digestion, immunity, reproductive health, and reproductive behavior. In the current study, based on high-throughput sequencing of the 16S rRNA V3 and V4 regions, we detected the gut and gonad microbiota communities of three spider species captured from the same habitat, namely, Eriovixia cavaleriei, Larinioides cornutus, and Pardosa pseudoannulata. In these three species, we observed that, at the phylum level classification, the gut and gonad of E. cavaleriei are primarily composed of Proteobacteria, while those of L. cornutus and P. pseudoannulata are primarily composed of Firmicutes. At the genus level of classification, we identified 372 and 360 genera from the gut and gonad bacterial communities. It is noteworthy that the gut and gonad bacterial flora of E. cavaleriei and L. cornutus were dominated by Wolbachia and Spiroplasma. Results show that there were no differences in microbial communities between females and males of the same spider species. Furthermore, there is similarity between the gut and ovary microbial communities of female spiders, implying a potential avenue for microbial transmission between the gut and gonad within female spiders. By comprehensively studying these two microbial communities, we can establish the theoretical foundation for exploring the relationship between gut and gonad microbiota and their host, as well as the mechanisms through which microbes exert their effects.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jia Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaopan Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yueli Yun
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan 430062, China
- Centre for Behavioral Ecology & Evolution, School of Life Sciences, Hubei University, Wuhan 430062, China
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Gamiette G, Ferdinand S, Couvin D, Dard C, Talarmin A. The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses. Parasit Vectors 2023; 16:276. [PMID: 37563598 PMCID: PMC10416417 DOI: 10.1186/s13071-023-05872-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/06/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Angiostrongylus cantonensis (rat lungworm) is the main pathogen responsible for eosinophilic meningitis in humans. One of its intermediate snail hosts, Achatina fulica, was already present in many countries around the world before it appeared in the West Indies in the late 1980s. In the French territories in the Caribbean and northern South America, the first cases of human neuroangiostrongyliasis were reported in Martinique, Guadeloupe and French Guiana in 2002, 2013 and 2017, respectively. In order to better characterize angiostrongyliasis in Guadeloupe, particularly its geographical origin and route of introduction, we undertook molecular characterization of adult worms of Angiostrongylus cantonensis and its intermediate host Achatina fulica. METHODS Genomic DNA of adult Angiostrongylus cantonensis and Achatina fulica was extracted and amplified by polymerase chain reaction (PCR) targeting the mitochondrial genes cytochrome B and C for A. cantonensis and 16S ribosomal RNA for A. fulica. The PCR products were sequenced and studied by phylogenetic analysis. RESULTS Cytochrome B and cytochrome C molecular markers indicate a monophyletic lineage of A. cantonensis adult worms in Guadeloupe. Two sequences of A. fulica were identified. CONCLUSIONS These results confirm the recent introduction of both Angiostrongylus cantonensis and Achatina fulica into Guadeloupe. Achatina fulica in Guadeloupe shares a common origin with those in Barbados and New Caledonia, while Angiostrongylus cantonensis in Guadeloupe shares a common origin with those in Brazil, Hawaii and Japan.
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Affiliation(s)
- Gelixa Gamiette
- Réservoir et Diversité des Pathogènes, Unité Transmission, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France.
| | - Séverine Ferdinand
- Réservoir et Diversité des Pathogènes, Unité Transmission, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France
| | - David Couvin
- Réservoir et Diversité des Pathogènes, Unité Transmission, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France
| | - Céline Dard
- Institute for Advanced Biosciences, Team Host-Pathogen Interactions and Immunity to Infection, INSERM U1209-CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Antoine Talarmin
- Réservoir et Diversité des Pathogènes, Unité Transmission, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, France
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10
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He B, Sheng C, Yu X, Zhang L, Chen F, Han Y. Alterations of gut microbiota are associated with brain structural changes in the spectrum of Alzheimer's disease: the SILCODE study in Hainan cohort. Front Aging Neurosci 2023; 15:1216509. [PMID: 37520126 PMCID: PMC10375500 DOI: 10.3389/fnagi.2023.1216509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/12/2023] [Indexed: 08/01/2023] Open
Abstract
Background The correlation between gut microbiota and Alzheimer's disease (AD) is increasingly being recognized by clinicians. However, knowledge about the gut-brain-cognition interaction remains largely unknown. Methods One hundred and twenty-seven participants, including 35 normal controls (NCs), 62 with subjective cognitive decline (SCD), and 30 with cognitive impairment (CI), were included in this study. The participants underwent neuropsychological assessments and fecal microbiota analysis through 16S ribosomal RNA (rRNA) Illumina Miseq sequencing technique. Structural MRI data were analyzed for cortical anatomical features, including thickness, sulcus depth, fractal dimension, and Toro's gyrification index using the SBM method. The association of altered gut microbiota among the three groups with structural MRI metrics and cognitive function was evaluated. Furthermore, co-expression network analysis was conducted to investigate the gut-brain-cognition interactions. Results The abundance of Lachnospiraceae, Lachnospiracea_incertae_sedis, Fusicatenibacter, and Anaerobutyricum decreased with cognitive ability. Rikenellaceae, Odoribacteraceae, and Alistipes were specifically enriched in the CI group. Mediterraneibacter abundance was correlated with changes in brain gray matter and cerebrospinal fluid volume (p = 0.0214, p = 0.0162) and significantly with changes in cortical structures in brain regions, such as the internal olfactory area and the parahippocampal gyrus. The three colonies enriched in the CI group were positively correlated with cognitive function and significantly associated with changes in cortical structure related to cognitive function, such as the precuneus and syrinx gyrus. Conclusion This study provided evidence that there was an inner relationship among the altered gut microbiota, brain atrophy, and cognitive decline. Targeting the gut microbiota may be a novel therapeutic strategy for early AD.
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Affiliation(s)
- Beiqi He
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Can Sheng
- Department of Neurology, The Affiliated Hospital of Jining Medical University, Jining, China
| | - Xianfeng Yu
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Liang Zhang
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Feng Chen
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Ying Han
- School of Biomedical Engineering, Hainan University, Haikou, China
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
- Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
- National Clinical Research Center for Geriatric Disorders, Beijing, China
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11
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Murugesan S, Al Khodor S. Salivary microbiome and hypertension in the Qatari population. J Transl Med 2023; 21:454. [PMID: 37422685 PMCID: PMC10329805 DOI: 10.1186/s12967-023-04247-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/06/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND The prevalence of hypertension in Qatar is 33 percent of the adult population. It is postulated that the salivary microbiome can regulate blood pressure (BP). However, limited investigations exist to prove this hypothesis. Therefore, we examined the difference in the salivary microbiome composition between hypertensive and normotensive Qatari subjects. METHODS A total of 1190 Qatar Genome Project (QGP) participants (Mean age = 43 years) were included in this study. BP for all participants was classified into Normal (n = 357), Stage1 (n = 336), and Stage2: (n = 161) according to the American Heart Association guidelines. 16S-rRNA libraries were sequenced and analyzed using QIIME-pipeline, and PICRUST was used to predict functional metabolic routes. Machine Learning (ML) strategies were applied to identify salivary microbiome-based predictors of hypertension. RESULTS Differential abundant analysis (DAA) revealed that Bacteroides and Atopobium were the significant members of the hypertensive groups. Alpha and beta diversity indices indicated dysbiosis between the normotensive and hypertensive groups. ML-based prediction models revealed that these markers could predict hypertension with an AUC (Area under the curve) of 0.89. Functional predictive analysis disclosed that Cysteine and Methionine metabolism and the sulphur metabolic pathways involving the renin-angiotensin system were significantly higher in the normotensive group. Therefore, members of Bacteroides and Atopobium can serve as predictors of hypertension. Likewise, Prevotella, Neisseria, and Haemophilus can be the protectors that regulate BP via nitric acid synthesis and regulation of the renin-angiotensin system. CONCLUSION It is one of the first studies to assess salivary microbiome and hypertension as disease models in a large cohort of the Qatari population. Further research is needed to confirm these findings and validate the mechanisms involved.
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Affiliation(s)
- Selvasankar Murugesan
- Maternal and Child Health Division, Research Department, Sidra Medicine, 26999, Doha, Qatar
| | - Souhaila Al Khodor
- Maternal and Child Health Division, Research Department, Sidra Medicine, 26999, Doha, Qatar.
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12
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Fan KC, Lin CC, Liu YC, Chao YP, Lai YJ, Chiu YL, Chuang YF. Altered gut microbiota in older adults with mild cognitive impairment: a case-control study. Front Aging Neurosci 2023; 15:1162057. [PMID: 37346147 PMCID: PMC10281289 DOI: 10.3389/fnagi.2023.1162057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/02/2023] [Indexed: 06/23/2023] Open
Abstract
Introduction The microbiota-gut-brain axis is implicated in Alzheimer's disease. Gut microbiota alterations in mild cognitive impairment (MCI) are inconsistent and remain to be understood. This study aims to investigate the gut microbial composition associated with MCI, cognitive functions, and structural brain differences. Methods A nested case-control study was conducted in a community-based prospective cohort where detailed cognitive functions and structural brain images were collected. Thirty-one individuals with MCI were matched to sixty-five cognitively normal controls by age strata, gender, and urban/rural area. Fecal samples were examined using 16S ribosomal RNA (rRNA) V3-V4 sequencing. Compositional differences between the two groups were identified and correlated with the cognitive functions and volumes/thickness of brain structures. Results There was no significant difference in alpha and beta diversity between MCIs and cognitively normal older adults. However, the abundance of the genus Ruminococcus, Butyricimonas, and Oxalobacter decreased in MCI patients, while an increased abundance of nine other genera, such as Flavonifractor, were found in MCIs. Altered genera discriminated MCI patients well from controls (AUC = 84.0%) and were associated with attention and executive function. Conclusion This study provides insights into the role of gut microbiota in the neurodegenerative process.
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Affiliation(s)
- Kang-Chen Fan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yi-Chien Liu
- Department of Neurology, Cardinal Tien Hospital, New Taipei, Taiwan
| | - Yi-Ping Chao
- Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yen-Jun Lai
- Division of Medical Imaging, Department of Radiology, Far Eastern Memorial Hospital, New Taipei, Taiwan
| | - Yen-Ling Chiu
- Department of Medical Research, Far Eastern Memorial Hospital, Taipei, Taiwan
- Graduate Program in Biomedical Informatics and Graduate Institute of Medicine, Yuan Ze University, Taoyuan, Taiwan
- Graduate Institute of Clinical Medicine, National Taiwan University, Taipei, Taiwan
| | - Yi-Fang Chuang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Public Health, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Psychiatry, Far Eastern Memorial Hospital, New Taipei, Taiwan
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Li X, Tian Z, Cui R, Lv J, Yang X, Qin L, Liu Z, Zhang C, Jin C, Xu Y, Chen ZJ, Zhao H, Zhao S. Association between Pregestational Vaginal Dysbiosis and Incident Hypertensive Disorders of Pregnancy Risk: a Nested Case-Control Study. mSphere 2023:e0009623. [PMID: 37017519 DOI: 10.1128/msphere.00096-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
A balanced vaginal microbiome dominated by Lactobacillus can help promote women's reproductive health, with Lactobacillus crispatus showing the most beneficial effect. However, the potential role of vaginal microbiomes in hypertensive disorders of pregnancy (HDP) development is not thoroughly explored. In this nested case-control study based on an assisted reproductive technology follow-up cohort, we prospectively assessed the association between pregestational vaginal microbiomes with HDP by collecting vaginal swabs from 75 HDP cases (HDP group) and 150 controls (NP group) and using 16S amplicon sequencing for bacterial identification. The vaginal microbial composition of the HDP group significantly differed from that of the NP group. The abundance of L. crispatus was significantly lower, and the abundances of Gardnerella vaginalis was significantly higher, in the HDP group than in the NP group. Of note, L. crispatus-dominated vaginal community state type was associated with a decreased risk for HDP (odds ratio = 0.436; 95% confidence interval, 0.229 to 0.831) compared with others. Additionally, network analysis revealed different bacterial interactions with 61 and 57 exclusive edges in the NP and HDP groups, respectively. Compared with the HDP group, the NP group showed a higher weighted degree and closeness centrality. Several taxa, including G. vaginalis, L. iners, and bacterial vaginosis-associated bacteria (Prevotella, Megasphaera, Finegoldia, and Porphyromonas), were identified as "drivers" for network rewiring. Notable alterations of predicted pathways involved in amino acid, cofactor, and vitamin metabolism; membrane transport; and bacterial toxins were observed in the HDP group. IMPORTANCE The etiology of HDP remains unclear to date. Effective methods for the individualized prediction and prevention are lacking. Pregestational vaginal dysbiosis precedes the diagnosis of HDP, providing a novel perspective on the etiology of HDP. Early pregnancy is the critical period of placental development, and abnormal placentation initiates HDP development. Thus, disease prevention should be considered before pregnancy. Vaginal microbiome characterization and probiotic interventions before pregnancy are preferred because of their safety and potential for early prevention. This study is the first to prospectively assess associations between pregestational vaginal microbiome and HDP. L. crispatus-dominated vaginal community state type is linked to a reduced risk for HDP. These findings suggest that vaginal microbiome characterization may help identify individuals at high risk for HDP and offer potential targets for the development of novel pregestational intervention methods.
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Affiliation(s)
- Xiao Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Zhaomei Tian
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Ran Cui
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Jiale Lv
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Xin Yang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Reproductive Medicine Center of Zibo Maternal and Child Health Care Hospital, Zibo, Shandong, China
| | - Lang Qin
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Zheng Liu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Changlong Zhang
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Congcong Jin
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Reproductive Medicine Center of The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yanqi Xu
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Linyi People's Hospital, Linyi, Shandong, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences, China
| | - Han Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Shandong First Medical University, Jinan, Shandong, China
| | - Shigang Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong, China
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Liu C, Liu C, Gao F, Wang A, Wang H, Yang Y, He L. Composition of Particulate Matter and Bacterial Community in Gut Contents and Surrounding Sediments of Three Sipunculan Species ( Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus). Int J Mol Sci 2023; 24:ijms24066001. [PMID: 36983074 PMCID: PMC10054262 DOI: 10.3390/ijms24066001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus are three important sipunculan species in tropical intertidal zones. In this study, the particle size, organic matter content, and bacterial community composition in the gut contents of three different sipunculans and their surrounding sediments were analyzed. The grain size fractions of sipunculans' guts were significantly different from those of their surrounding sediments; particle size fractions < 500 μm were favored by the sipunculans. As for the total organic matter (TOM), higher contents of organic matter were observed in the guts than in the surrounding sediments in all three sipunculan species. The bacterial community composition of all the samples was investigated by 16S rRNA gene sequencing, in which a total of 8974 OTUs were obtained from 24 samples based on a 97% threshold. The predominant phylum identified from the gut contents of three sipunculans was Planctomycetota, while the predominant phylum in their surrounding sediments was Proteobacteria. At the genus level, the most abundant genus was Sulfurovum (average 4.36%) in the surrounding sediments, while the most abundant genus was Gplla (average 12.76%) in the gut contents. The UPGMA tree showed that the samples from the guts of three different sipunculans and their surrounding sediments were clustered separately into two groups, which showed that these three sipunculans had a different bacterial community composition with their surrounding sediments. The grain size and total organic matter (TOM) had the greatest impacts on the bacterial community composition at both the phylum and genus levels. In conclusion, the differences in particle size fractions, organic matter content, and bacterial community composition between the gut contents and surrounding sediments in these three sipunculan species might be caused by their selective ingestion.
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Affiliation(s)
- Chunsheng Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Chuang Liu
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Fei Gao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Haiqing Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Yumei Yang
- College of Marine Science, Hainan University, Haikou 570228, China
| | - Linwen He
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou 570228, China
- College of Marine Science, Hainan University, Haikou 570228, China
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Kunimitsu M, Nakagami G, Kitamura A, Minematsu T, Koudounas S, Ogai K, Sugama J, Takada C, Yeo S, Sanada H. Relationship between healing status and microbial dissimilarity in wound and peri-wound skin in pressure injuries. J Tissue Viability 2023; 32:144-150. [PMID: 36344337 DOI: 10.1016/j.jtv.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 10/02/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
AIM Wound infection is the most serious cause of delayed healing for patients with pressure injuries. The wound microbiota, which plays a crucial role in delayed healing, forms by bacterial dissemination from the peri-wound skin. To manage the bioburden, wound and peri-wound skin care has been implemented; however, how the microbiota at these sites contribute to delayed healing is unclear. Therefore, we investigated the relationship between healing status and microbial dissimilarity in wound and peri-wound skin. METHODS A prospective cohort study was conducted at a long-term care hospital. The outcome was healing status assessed using the DESIGN-R® tool, a wound assessment tool to monitor the wound healing process. Bacterial DNA was extracted from the wound and peri-wound swabs, and microbiota composition was analyzed using 16S rRNA gene analysis. To evaluate microbial similarity, the weighted UniFrac dissimilarity index between wound and peri-wound microbiota was calculated. RESULTS Twenty-two pressure injuries (7 deep and 15 superficial wounds) were included in the study. For deep wounds, the predominant bacteria in wound and peri-wound skin were the same in the healing wounds, whereas they were different in all cases of hard-to-heal wounds. Analysis based on the weighted UniFrac dissimilarity index, there was no significant difference for healing wounds (p = 0.639), while a significant difference was found for hard-to-heal wounds (p = 0.047). CONCLUSIONS Delayed healing is possibly associated with formation of wound microbiota that is different in composition from that of the skin commensal microbiota. This study provides a new perspective for assessing wound bioburden.
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Affiliation(s)
- Mao Kunimitsu
- Department of Gerontological Nursing/Wound Care Management, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Japan Society for the Promotion of Science, Tokyo, Japan
| | - Gojiro Nakagami
- Department of Gerontological Nursing/Wound Care Management, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Global Nursing Research Center, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Aya Kitamura
- Department of Gerontological Nursing/Wound Care Management, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeo Minematsu
- Global Nursing Research Center, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Skincare Science, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Sofoklis Koudounas
- Department of Skincare Science, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Ogai
- AI Hospital/Macro Signal Dynamics Research and Development Center, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Ishikawa, Japan
| | - Junko Sugama
- Research Center for Implementation Nursing Science Initiative, School of Health Sciences, Fujita Health University, Aichi, Japan
| | - Chika Takada
- Department of Nursing, Sengi Hospital, Ishikawa, Japan
| | - SeonAe Yeo
- School of Nursing, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hiromi Sanada
- Department of Gerontological Nursing/Wound Care Management, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Global Nursing Research Center, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Elfiky SA, Mahmoud Ahmed S, Elmenshawy AM, Sultan GM, Asser SL. Study of the gut microbiome as a novel target for prevention of hospital-associated infections in intensive care unit patients. Acute Crit Care 2023; 38:76-85. [PMID: 36935537 PMCID: PMC10030239 DOI: 10.4266/acc.2022.01116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/23/2022] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Hospital-acquired infections (HAIs) are increasing due to the spread of multi-drugresistant organisms. Gut dysbiosis in an intensive care unit (ICU) patients at admission showed an altered abundance of some bacterial genera associated with the occurrence of HAIs and mortality. In the present study, we investigated the pattern of the gut microbiome in ICU patients at admission to correlate it with the development of HAIs during ICU stay. METHODS Twenty patients admitted to an ICU with a cross-matched control group of 30 healthy subjects of matched age and sex. Quantitative SYBR green real-time polymerase chain reaction was done for the identification and quantitation of selected bacteria. RESULTS Out of those twenty patients, 35% developed ventilator-associated pneumonia during their ICU stay. Gut microbiome analysis showed a significant decrease in Firmicutes and Firmicutes to Bacteroidetes ratio in ICU patients in comparison to the control and in patients who developed HAIs in comparison to the control group and patients who did not develop HAIs. There was a statistically significant increase in Bacteroides in comparison to the control group. There was a statistically significant decrease in Bifidobacterium and Faecalibacterium prausnitzii and an increase in Lactobacilli in comparison to the control group with a negative correlation between Acute Physiology and Chronic Health Evaluation (APACHE) II score and Firmicutes to Bacteroidetes and Prevotella to Bacteroides ratios. CONCLUSIONS Gut dysbiosis of patients at the time of admission highlights the importance of identification of the microbiome of patients admitted to the ICU as a target for preventing of HAIs.
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Affiliation(s)
- Suzan Ahmed Elfiky
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Alexandria University, Alexandria Governorate, Egypt
| | - Shwikar Mahmoud Ahmed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Alexandria University, Alexandria Governorate, Egypt
| | - Ahmed Mostafa Elmenshawy
- Department of Critical Care Medicine, Faculty of Medicine, Alexandria University, Alexandria Governorate, Egypt
| | - Gehad Mahmoud Sultan
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Alexandria University, Alexandria Governorate, Egypt
| | - Sara Lotfy Asser
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Alexandria University, Alexandria Governorate, Egypt
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Iwami N, Kawamata M, Ozawa N, Yamamoto T, Watanabe E, Mizuuchi M, Moriwaka O, Kamiya H. Therapeutic intervention based on gene sequencing analysis of microbial 16S ribosomal RNA of the intrauterine microbiome improves pregnancy outcomes in IVF patients: a prospective cohort study. J Assist Reprod Genet 2023; 40:125-135. [PMID: 36534230 PMCID: PMC9840729 DOI: 10.1007/s10815-022-02688-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
PURPOSE A Lactobacillus-dominated microbiota in the endometrium was reported to be associated with favorable reproductive outcomes. We investigated in this study whether 16S ribosomal RNA (rRNA) gene sequencing analysis of the uterine microbiome improves pregnancy outcomes. METHODS This prospective cohort study recruited a total of 195 women with recurrent implantation failure (RIF) between March 2019 and April 2021 in our fertility center. Analysis of the endometrial microbiota by 16S rRNA gene sequencing was suggested for all patients who had three or more failed embryo transfers (ETs). One hundred and thirty-one patients underwent microbial 16S rRNA gene sequencing (study group) before additional transfers, while 64 patients proceeded to ET without that analysis (control group). The primary outcome was to compare the cumulative clinical pregnancy rate of two additional ETs. MAIN RESULTS An endometrial microbiota considered abnormal was detected in 30 patients (22.9%). All but one of these 30 patients received antibiotics according to the bacterial genus detected in their sample, followed by treatment with probiotics. As a result, the cumulative clinical pregnancy rate (study group: 64.5% vs. control group: 33.3%, p = 0.005) and the ongoing pregnancy rate (study group: 48.9% vs. control group: 32.8%, p = 0.028) were significantly increased in the study group compared to the control group. CONCLUSION Personalized treatment recommendations based on the microbial 16S rRNA gene sequencing of the uterine microbiota can improve IVF outcomes of patients with RIF. TRIAL REGISTRATION The University Hospital Medical Information Network (UMIN) Clinical Trial Registry: UMIN000036050 (date of registration: March 1, 2019).
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Affiliation(s)
- Nanako Iwami
- Department of Reproductive Health, Iryo Hojin Shadan Kamiya Ladies Clinic, Nittsu Bldg 2nd floor 2-1, Nishi 2-Chome, Kita 3-Jo, Chuo-Ku, Sapporo, Hokkaido, 060-0003, Japan.
| | - Miho Kawamata
- Department of Reproductive Health, Iryo Hojin Shadan Kamiya Ladies Clinic, Nittsu Bldg 2nd floor 2-1, Nishi 2-Chome, Kita 3-Jo, Chuo-Ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Naoko Ozawa
- Department of Reproductive Health, Iryo Hojin Shadan Kamiya Ladies Clinic, Nittsu Bldg 2nd floor 2-1, Nishi 2-Chome, Kita 3-Jo, Chuo-Ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Takahiro Yamamoto
- Department of Reproductive Health, Iryo Hojin Shadan Kamiya Ladies Clinic, Nittsu Bldg 2nd floor 2-1, Nishi 2-Chome, Kita 3-Jo, Chuo-Ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Eri Watanabe
- Department of Reproductive Health, Iryo Hojin Shadan Kamiya Ladies Clinic, Nittsu Bldg 2nd floor 2-1, Nishi 2-Chome, Kita 3-Jo, Chuo-Ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Masahito Mizuuchi
- Department of Reproductive Health, Iryo Hojin Shadan Kamiya Ladies Clinic, Nittsu Bldg 2nd floor 2-1, Nishi 2-Chome, Kita 3-Jo, Chuo-Ku, Sapporo, Hokkaido, 060-0003, Japan
- Department of Reproductive Health, Iryo Hojin Shadan Mizuuchi Women's Clinic, 2-5 Toyooka 4Jo 3Chome, Asahikawa, Hokkaido, 078-8234, Japan
| | - Osamu Moriwaka
- Department of Reproductive Health, Iryo Hojin Shadan Kamiya Ladies Clinic, Nittsu Bldg 2nd floor 2-1, Nishi 2-Chome, Kita 3-Jo, Chuo-Ku, Sapporo, Hokkaido, 060-0003, Japan
| | - Hirobumi Kamiya
- Department of Reproductive Health, Iryo Hojin Shadan Kamiya Ladies Clinic, Nittsu Bldg 2nd floor 2-1, Nishi 2-Chome, Kita 3-Jo, Chuo-Ku, Sapporo, Hokkaido, 060-0003, Japan
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Zhang X, Li X, Xu H, Fu Z, Wang F, Huang W, Wu K, Li C, Liu Y, Zou J, Zhu H, Yi H, Kaiming S, Gu M, Guan J, Yin S. Changes in the oral and nasal microbiota in pediatric obstructive sleep apnea. J Oral Microbiol 2023; 15:2182571. [PMID: 36875426 PMCID: PMC9980019 DOI: 10.1080/20002297.2023.2182571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023] Open
Abstract
Background Several clinical studies have demonstrated that pediatric obstructive sleep apnea (OSA) is associated with dysbiosis of airway mucosal microbiota. However, how oral and nasal microbial diversity, composition, and structure are altered in pediatric OSA has not been systemically explored. Methods 30 polysomnography-confirmed OSA patients with adenoid hypertrophy, and 30 controls who did not have adenoid hypertrophy, were enrolled. Swabs from four surface oral tissue sites (tongue base, soft palate, both palatine tonsils, and adenoid) and one nasal swab from both anterior nares were collected. The 16S ribosomal RNA (rRNA) V3-V4 region was sequenced to identify the microbial communities. Results The beta diversity and microbial profiles were significantly different between pediatric OSA patients and controls at the five upper airway sites. The abundances of Haemophilus, Fusobacterium, and Porphyromonas were higher at adenoid and tonsils sites of pediatric patients with OSA. Functional analysis revealed that the differential pathway between the pediatric OSA patients and controls involved glycerophospholipids and amino acid metabolism. Conclusions In this study, the oral and nasal microbiome of pediatric OSA patients exhibited certain differences in composition compared with the controls. However, the microbiota data could be useful as a reference for studies on the upper airway microbiome.
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Affiliation(s)
- Xiaoman Zhang
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinyi Li
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huajun Xu
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhihui Fu
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fan Wang
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weijun Huang
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kejia Wu
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenyang Li
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yupu Liu
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianyin Zou
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaming Zhu
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongliang Yi
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Su Kaiming
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meizhen Gu
- Department of Otorhinolaryngology-Head and Neck Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jian Guan
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shankai Yin
- Department of Otolaryngology Head and Neck Surgery & Shanghai Key Laboratory of Sleep Disordered Breathing & Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Jan HE, Tsai CS, Lee NY, Tsai PF, Wang LR, Chen PL, Ko WC. The first case of Francisella novicida infection in Taiwan: bacteraemic pneumonia in a haemodialysis adult. Emerg Microbes Infect 2022; 11:310-313. [PMID: 34986740 PMCID: PMC8786238 DOI: 10.1080/22221751.2022.2026199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/03/2022] [Indexed: 11/19/2022]
Abstract
Tularaemia is a zoonotic disease caused by Francisella tularensis (F. tularensis). Human infection is rare and can be life-threatening. F. tularensis subsp. novicida used to be a subspecies of F. tularensis, is now considered a different species, F. novicida. Though less virulent, F. novicida can cause morbidity and mortality among debilitated or immunocompromised patients. We reported that an adult with end-stage renal disease undergoing haemodialysis and a history of melioidotic aortic aneurysm developed F. novicida bacteraemic pneumonia, which was uneventfully treated by antimicrobial therapy. The microbiological confirmation of F. novicida infection relies on 16S rRNA sequencing. It is the first case of F. novicida infection in Taiwan.
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Affiliation(s)
- Hao-En Jan
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chin-Shiang Tsai
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Internal Medicine, National Cheng Kung University Hospital, Dou-Liou Branch, College of Medicine, National Cheng Kung University, Yunlin, Taiwan
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nan-Yao Lee
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Fang Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Li-Rong Wang
- Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Lin Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center for Infection Control, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Zhao J, Bai M, Ning X, Qin Y, Wang Y, Yu Z, Dong R, Zhang Y, Sun S. Expansion of Escherichia-Shigella in Gut Is Associated with the Onset and Response to Immunosuppressive Therapy of IgA Nephropathy. J Am Soc Nephrol 2022; 33:2276-2292. [PMID: 36041791 PMCID: PMC9731625 DOI: 10.1681/asn.2022020189] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/25/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Gut dysbiosis is postulated to participate in the pathogenesis of IgA nephropathy (IgAN). However, the key bacterial taxa closely associated with IgAN onset and treatment response have not been identified. METHODS We recruited 127 patients with IgAN who were treatment naive and 127 matched healthy controls (HCs) who were randomly divided into discovery and validation cohorts to investigate the characteristics of their gut microbiota and establish a bacterial diagnosis model for IgAN. A separate cohort of 56 patients and HCs was investigated to assess crossregional validation. A further 40 patients with primary membranous nephropathy (MN) were enrolled to probe disease-specific validation. A subgroup of 77 patients was prospectively followed to further dissect the association between alterations in gut microbiota and treatment response after 6 months of immunosuppressive therapy. Fecal microbiota samples were collected from all participants and analyzed using 16S ribosomal RNA sequencing. RESULTS Decreased α-diversity (Shannon, P=0.03), altered microbial composition (Adonis, P=0.0001), and a striking expansion of the taxonomic chain Proteobacteria-Gammaproteobacteria-Enterobacteriales-Enterobacteriaceae-Escherichia-Shigella (all P<0.001) were observed in patients with IgAN who were treatment naive, which reversed only in patients who achieved clinical remission after 6 months of immunosuppressive therapy. Importantly, seven operational taxa units, of which Escherichia-Shigella contributed the most, were determined to be the optimal bacterial classifier of IgAN (AUC=0.8635, 0.8551, 0.8026 in discovery, validation, and cross-regional validation sets, respectively), but did not effectively distinguish patients with IgAN versus those with MN (AUC=0.6183). Bacterial function prediction further verified enrichment of the shigellosis infection pathway in IgAN. CONCLUSION Gut dysbiosis, characterized by a striking expansion of genus Escherichia-Shigella, is a hallmark of patients with IgAN and may serve as a promising diagnostic biomarker and therapeutic target for IgAN. Further studies are warranted to investigate the potential contribution of Escherichia-Shigella in IgAN pathogenesis.
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Affiliation(s)
- Jin Zhao
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Ming Bai
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Xiaoxuan Ning
- Department of Geriatrics, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yunlong Qin
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yuwei Wang
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Zixian Yu
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Ruijuan Dong
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Yumeng Zhang
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Shiren Sun
- Department of Nephrology, Xijing Hospital, Fourth Military Medical University, Xi’an, China
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Zhou XQ, Ma J, Wang RY, Wang RH, Wu YQ, Yang XY, Chen YJ, Tang XN, Sun ET. [Bacterial community diversity in Dermatophagoides farinae using high-throughput sequencing]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2022; 34:630-634. [PMID: 36642905 DOI: 10.16250/j.32.1374.2022105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
OBJECTIVE To investigate the bacterial community diversity in Dermatophagoides farinae. METHODS Laboratory-cultured D. farinae was collected, and the composition of microbial communities was determined by sequence analyses of the V4 region in the bacterial 16S ribosomal RNA (16S rRNA) gene on an Illumina PE250 high-throughput sequencing platform. Following quality control and filtering of the raw sequence files, valid reads were obtained and subjected to operational taxonomic units (OTU) clustering and analysis of the composition of microbial communities and alpha diversity index using the Usearch software, Silva database, and Mothur software. RESULTS A total of 187 616 valid reads were obtained, and 469 OTUs were clustered based on a sequence similarity of more than 97%. OTU annotation showed that the bacteria in D. farinae belonged to 26 phyla, 43 classes, 100 orders, 167 families and 284 genera. The bacteria in D. farinae were mainly annotated to five phyla of Proteobacteria, Firmicutes, Bacteroidota, Actinobacteriota, and Acidobacteriota, with Proteobacteria as the dominant phylum, and mainly annotated to five dominant genera of Ralstonia, norank-f-Mitochondria, Staphylococcus and Sphingomonas, with Wolbachia identified in the non-dominant genus. CONCLUSIONS A high diversity is identified in the composition of the bacterial community in D. farinae, and there are differences in bacterial community diversity and abundance among D. farinae.
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Affiliation(s)
- X Q Zhou
- Department of Medical Parasitology, Wannan Medical College, Wuhu, Anhui 241002, China
| | - J Ma
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, Anhui 241002, China
| | - R Y Wang
- Department of Environmental Hygiene and Occupational Health, School of Public Health, Wannan Medical College, China
| | - R H Wang
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Y Q Wu
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, Anhui 241002, China
| | - X Y Yang
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, Anhui 241002, China
| | - Y J Chen
- Department of Environmental Hygiene and Occupational Health, School of Public Health, Wannan Medical College, China
| | - X N Tang
- Department of Medical Parasitology, Wannan Medical College, Wuhu, Anhui 241002, China
| | - E T Sun
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, Anhui 241002, China
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Zhao YQ, Xia A, Zhang MH, Li JL, Zhu GD, Tang JX. [Microbiota structure and diversity in Aedes albopictus at different developmental stages]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2022; 34:475-483. [PMID: 36464263 DOI: 10.16250/j.32.1374.2022144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
OBJECTIVE To investigate the diversity and composition of microflora in laboratory-reared Aedes albopictus at different developmental stages and larval habitat waters. METHODS The larval habitat waters and different developmental stages of laboratory-reared A. albopictus were collected, and the V3 and V4 regions of the bacterial 16S rRNA gene were sequenced using Illumina Miseq next-generation sequencing. The abundance and diversity of the microflora were examined using alpha diversity index in A. albopictus at different developmental stages, and the difference in the microflora compositions was compared in A. albopictus at different developmental stages using principal component analysis (PCA). In addition, the species composition and relative abundance of microflora in A. albopictus 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 A. albopictus. The highest bacterial diversity was seen in larval A. albopictus, 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 (t = 0.35 and -0.41, both P 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, t = 8.23, P < 0.05; Shannon diversity index: 1.25 ± 1.67 vs. 0.50 ± 0.05, t = 6.00, P < 0.05). Proteobacteria, Bacteroidota, Actinobacteriota and Finnicutes were four common phyla of bacteria at each developmental stage of A. albopictus, 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%). Elizabethkingia and Rahnella 1 were common dominant genera of bacteria at each developmental stage of A. albopictus, with Rahnellal as the major component at the pupal stage (87.56%), Elizabethkingia as the main component at the adult stage (46.01% in female adults and 86.11% in male adults, respectively), and Microbacteria as the dominant bacterial genus at the larval stage (12.11%). In addition, Delftia, Elizabethkingia, Romboutsia, Serratia, Rahnella 1, Enterococcus and Microbacterium were common genera of bacteria at each developmental stage of A. albopictus, with Edaphobaculum dominated at the larval stage (17.54%) and Sphingobacterium dominated in larval habitat waters (13.93%). CONCLUSIONS There are differences in the composition of symbiotic bacteria at different developmental stages of A. albopictus; however, similar microflora diversity is maintained at the phylum level. The microflora diversity is comparable in larvae and larval habitat waters of A. albopictus.
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Affiliation(s)
- Y Q Zhao
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, China
| | - A Xia
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, China
| | - M H Zhang
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, China
| | - J L Li
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, China
| | - G D Zhu
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, China
| | - J X Tang
- School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
- Key Laboratory of National Health Commission on Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu 214064, China
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Wu Y, Sun J, Yu P, Zhang W, Lin Y, Ma D. The rhizosphere bacterial community contributes to the nutritional competitive advantage of weedy rice over cultivated rice in paddy soil. BMC Microbiol 2022; 22:232. [PMID: 36180838 PMCID: PMC9523940 DOI: 10.1186/s12866-022-02648-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/22/2022] [Indexed: 11/18/2022] Open
Abstract
Background Weedy rice competes for nutrients and living space with cultivated rice, which results in serious reductions in rice production. The rhizosphere bacterial community plays an important role in nutrient competition between species. It is therefore important to clarify the differences in the diversities of the inter rhizosphere bacterial community between cultivated rice and weedy rice. The differences in compositions and co-occurrence networks of the rhizosphere bacterial community of cultivated rice and weedy rice are largely unknown and thus the aim of our study. Results In our study, the different rhizosphere bacterial community structures in weedy rice (AW), cultivated rice (AY) and cultivated rice surrounded by weedy rice (WY) were determined based on 16S rRNA gene sequencing. The majority of the WY rhizosphere was enriched with unique types of microorganisms belonging to Burkholderia. The rhizosphere bacterial community showed differences in relative abundance among the three groups. Network analysis revealed a more complex co-occurrence network structure in the rhizosphere bacterial community of AW than in those of AY and WY due to a higher degree of Microbacteriaceae and Micrococcaceae in the network. Both network analysis and functional predictions reveal that weedy rice contamination dramatically impacts the iron respiration of the rhizosphere bacterial community of cultivated rice. Conclusions Our study shows that there are many differences in the rhizosphere bacterial community of weedy rice and cultivated rice. When cultivated rice was disturbed by weedy rice, the rhizosphere bacterial community and co-occurrence network also changed. The above differences tend to lead to a nutritional competitive advantage for weedy rice in paddy soils. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02648-1.
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Affiliation(s)
- Yue Wu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Pengcheng Yu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Weiliang Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Youze Lin
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
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Zhu Z, Ma X, Wu J, Xiao Z, Wu W, Ding S, Zheng L, Liang X, Luo J, Ding D, Zhao Q. Altered Gut Microbiota and Its Clinical Relevance in Mild Cognitive Impairment and Alzheimer's Disease: Shanghai Aging Study and Shanghai Memory Study. Nutrients 2022; 14:nu14193959. [PMID: 36235612 PMCID: PMC9570603 DOI: 10.3390/nu14193959] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/14/2022] [Accepted: 09/17/2022] [Indexed: 11/25/2022] Open
Abstract
Altered gut microbiota has been reported in individuals with mild cognitive impairment (MCI) and Alzheimer’s disease (AD). Previous research has suggested that specific bacterial species might be associated with the decline of cognitive function. However, the evidence was insufficient, and the results were inconsistent. To determine whether there is an alteration of gut microbiota in patients with MCI and AD and to investigate its correlation with clinical characteristics, the fecal samples from 94 cognitively normal controls (NC), 125 participants with MCI, and 83 patients with AD were collected and analyzed by 16S ribosomal RNA sequencing. The overall microbial compositions and specific taxa were compared. The clinical relevance was analyzed. There was no significant overall difference in the alpha and beta diversity among the three groups. Patients with AD or MCI had increased bacterial taxa including Erysipelatoclostridiaceae, Erysipelotrichales, Patescibacteria, Saccharimonadales, and Saccharimonadia, compared with NC group (p < 0.05), which were positively correlated with APOE 4 carrier status and Clinical Dementia Rating (correlation coefficient: 0.11~0.31, p < 0.05), and negatively associated with memory (correlation coefficient: −0.19~−0.16, p < 0.01). Our results supported the hypothesis that intestinal microorganisms change in MCI and AD. The alteration in specific taxa correlated closely with clinical manifestations, indicating the potential role in AD pathogenesis.
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Affiliation(s)
- Zheng Zhu
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaoxi Ma
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jie Wu
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhenxu Xiao
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Wanqing Wu
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Saineng Ding
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Li Zheng
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Xiaoniu Liang
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Jianfeng Luo
- Department of Biostatistics, School of Public Health, Fudan University, Shanghai 200032, China
| | - Ding Ding
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Qianhua Zhao
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
- National Center for Neurological Disorders, Huashan Hospital, Fudan University, Shanghai 200040, China
- MOE Frontiers Center for Brain Science, Fudan University, Shanghai 200040, China
- State Key Laboratory of Medical Neurobiology, Institute of Brain Science, Fudan University, Shanghai 200040, China
- Correspondence:
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Rajkumari J, Katiyar P, Dheeman S, Pandey P, Maheshwari DK. The changing paradigm of rhizobial taxonomy and its systematic growth upto postgenomic technologies. World J Microbiol Biotechnol 2022; 38:206. [PMID: 36008736 DOI: 10.1007/s11274-022-03370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 07/28/2022] [Indexed: 11/29/2022]
Abstract
Rhizobia are a diazotrophic group of bacteria that are usually isolated form the nodules in roots, stem of leguminous plants and are able to form nodules in the host plant owing to the presence of symbiotic genes. The rhizobial community is highly diverse, and therefore, the taxonomy and genera-wise classification of rhizobia has been constantly changing since the last three decades. This is mainly due to technical advancements, and shifts in definitions, resulting in a changing paradigm of rhizobia taxonomy. Initially, the taxonomic definitions at the species and sub species level were based on phylogenetic analysis of 16S rRNA sequence, followed by polyphasic approach to have phenotypic, biochemical, and genetic analysis including multilocus sequence analysis. Rhizobia mainly belonging to α- and β-proteobacteria, and recently new additions from γ-proteobacteria had been classified. Nowadays rhizobial taxonomy has been replaced by genome-based taxonomy that allows gaining more insights of genomic characteristics. These omics-technologies provide genome specific information that considers nodulation and symbiotic genes, along with molecular markers as taxonomic traits. Taxonomy based on complete genome sequence (genotaxonomy), average nucleotide identity, is now being considered as primary approach, resulting in an ongoing paradigm shift in rhizobial taxonomy. Also, pairwise whole-genome comparisons, phylogenomic analyses offer correlations between DNA and DNA re-association values that have delineated biologically important species. This review elaborates the present classification and taxonomy of rhizobia, vis-a-vis development of technical advancements, parameters and controversies associated with it, and describe the updated information on evolutionary lineages of rhizobia.
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Affiliation(s)
- Jina Rajkumari
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India
| | - Prashant Katiyar
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India
| | - Shrivardhan Dheeman
- Department of Microbiology, Sardar Bhagwan Singh University, Dehra Dun, Uttarakhand, 248161, India
| | - Piyush Pandey
- Department of Microbiology, Assam University, Silchar, Assam, 788011, India.
| | - Dinesh Kumar Maheshwari
- Department of Botany and Microbiology, Gurukula Kangri Vishwavidyalaya, Haridwar, 249-404, India.
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Kunimitsu M, Nakagami G, Minematsu T, Koudounas S, Sanada H. An in vivo critically colonised wound model with dysbiotic wound microbiota. Int Wound J 2022; 20:648-658. [PMID: 35932181 PMCID: PMC9927901 DOI: 10.1111/iwj.13906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 11/28/2022] Open
Abstract
In critically colonised wounds, many of the signs of infection are often absent, and delayed healing may be the only clinical sign. The prevention of critical colonisation is important, but its pathophysiology has not yet been elucidated. We have previously reported that dysbiotic microbiota dissimilar to the peri-wound skin microbiota may develop in critically colonised wounds. To investigate the role of dysbiotic microbiota, this study aimed to develop a critically colonised wound model by transplantation of dysbiotic microbiota. To transplant microbiota, a bacterial solution (dysbiosis group) or with Luria-Bertani medium (commensal group) was inoculated to full-thickness wounds of rats. The bacterial solution was prepared by anaerobically culturing bacteria from donor rats on an artificial dermis in Luria-Bertani medium for 72 hours. As a result, the degree of the change in the microbial similarity between pre- and post-transplantation of microbiota was significantly higher in the dysbiosis group (P < .001). No signs of infection were observed in any rat in either group. The wound area in the dysbiosis group was significantly larger (P < .001), and there was a significant infiltration of neutrophils (P < .001). All rats of the dysbiosis group represented the clinical features of critically colonised wounds. Furthermore, there were significantly fewer regulatory T cells in the wounds of the dysbiosis group. This is the first study to develop a novel animal model that represents the clinical features of critically colonised wounds and will be useful in investigating the pathogenesis of critical colonisation via regulatory T cells.
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Affiliation(s)
- Mao Kunimitsu
- Department of Gerontological Nursing/Wound Care ManagementGraduate School of Medicine, The University of TokyoTokyoJapan,Japan Society for the Promotion of ScienceTokyoJapan
| | - Gojiro Nakagami
- Department of Gerontological Nursing/Wound Care ManagementGraduate School of Medicine, The University of TokyoTokyoJapan,Global Nursing Research Center, Graduate School of Medicine, The University of TokyoTokyoJapan
| | - Takeo Minematsu
- Global Nursing Research Center, Graduate School of Medicine, The University of TokyoTokyoJapan,Department of Skincare ScienceGraduate School of Medicine, The University of TokyoTokyoJapan,Ishikawa Prefectural Nursing UniversityIshikawaJapan
| | - Sofoklis Koudounas
- Department of Skincare ScienceGraduate School of Medicine, The University of TokyoTokyoJapan
| | - Hiromi Sanada
- Department of Gerontological Nursing/Wound Care ManagementGraduate School of Medicine, The University of TokyoTokyoJapan,Global Nursing Research Center, Graduate School of Medicine, The University of TokyoTokyoJapan,Ishikawa Prefectural Nursing UniversityIshikawaJapan
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Zhou F, Su Z, Li Q, Wang R, Liao Y, Zhang M, Li J. Characterization of Bacterial Differences Induced by Cleft-Palate-Related Spatial Heterogeneity. Pathogens 2022; 11. [PMID: 35890015 DOI: 10.3390/pathogens11070771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/10/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Cleft palate (CP) patients have a higher prevalence of oral and respiratory tract bacterial infections than the general population. Nevertheless, characteristics of bacterial differences induced by CP-related anatomical heterogeneity are unknown. Methods: In this study, we systematically described the characteristics of bacteria in the oral and nasal niches in healthy children, CP children, healthy adolescents, CP adolescents, and postoperative adolescents by 454-pyrosequencing technology (V3−V6) to determine bacterial differences induced by CP. Results: Due to the CP-induced variations in spatial structure, the early establishment of microecology in CP children was different from that in healthy children. Nasal bacterial composition showed greater changes than in the saliva. Moreover, such discrepancy also appeared in CP and postoperative adolescents who had even undergone surgery > 10 years previously. Interestingly, we found by Lefse analysis that part of bacterial biomarkers in the nasal cavity of CP subjects was common oral flora, suggesting bacterial translocation between the oral and nasal niches. Therefore, we defined the oral−nasal translocation bacteria as O-N bac. By comparing multiple groups, we took the intersection sets of O-N bacs selected from CP children, CP adolescents, and postoperative adolescents as TS O-N bacs with time−character, including Streptococcus, Gemella, Alloprevotella, Neisseria, Rothia, Actinomyces, and Veillonella. These bacteria were at the core of the nasal bacterial network in CP subjects, and some were related to infectious diseases. Conclusions: CP would lead to significant and long-term differences in oral and nasal flora. TS O-N bacs migrating from the oral to the nasal might be the key stone causing nasal flora dysbiosis in the CP patients.
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Nguyen HB, Nguyen TKL, Ung TT, Mai TTN, Tran TNH, Ngo VQT, Le VA. Case of misdiagnosed melioidosis from Hue city, Vietnam. Iran J Microbiol 2022; 14:430-433. [PMID: 37124859 PMCID: PMC10132338 DOI: 10.18502/ijm.v14i3.9796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Melioidosis is an emerging infection, a potentially fatal tropical disease caused by Burkholderia pseudomallei in humans and animals, endemic in Southeast Asia and northern Australia. Diagnosis remains problematic due to its similarity to many other infections. The lack of clinical awareness and correct microbiological diagnosis contributes to the misidentification of melioidosis. We present a melioidosis case, which was misdiagnosed with pneumonia and septicemia due to Aeromonas salmonicida, leading to ineffective prolonged-course antibiotic treatment for the patient.
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Affiliation(s)
- Hoang Bach Nguyen
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
- Corresponding author: Hoang Bach Nguyen, Ph.D, Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam. Tel: +84-983303187 Fax: +84-2343826269
| | - Thi Khanh Linh Nguyen
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Thi Thuy Ung
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Thi Thao Nhi Mai
- Department of Basic Internal Medicine, Phan Chau Trinh University, Quang Nam, Vietnam
| | - Thi Nhu Hoa Tran
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Viet Quynh Tram Ngo
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
| | - Van An Le
- Department of Microbiology, Hue University of Medicine and Pharmacy, Hue University, Hue, Vietnam
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Silvestre AM, Pinto ACJ, Schleifer WF, Miranda LS, Silva LAF, Casali DM, Souza KLR, Gasparini VGL, Cruz GD, Suen G, Millen DD. Relationships of the Microbial Communities with Rumen Epithelium Development of Nellore Cattle Finished in Feedlot Differing in Phenotypic Residual Feed Intake. Animals (Basel) 2022; 12. [PMID: 35405810 DOI: 10.3390/ani12070820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/14/2022] [Accepted: 02/28/2022] [Indexed: 01/27/2023] Open
Abstract
The objective of this study was to examine the relationships among ruminal microbial community, rumen morphometrics, feeding behavior, feedlot performance, and carcass characteristics of Nellore cattle, classified by residual feed intake (RFI). Twenty-seven Nellore yearling bulls with an initial body weight (BW) of 423.84 ± 21.81 kg were fed in feedlot for 107 d in individual pens to determine the RFI phenotype. Bulls were categorized as high RFI (>0.5 SD above the mean, n = 8), medium RFI (±0.5 SD from the mean, n = 9), and low RFI (<0.5 SD below the mean, n = 10). At harvest, whole rumen content samples were collected from each bull to evaluate ruminal microbial community, including bacteria and protozoa. The carcass characteristics were determined by ultrasonography at the beginning and at the end of the experimental period, and behavior data were collected on d 88. As a result of ranking Nellore bulls by RFI, cattle from low-RFI group presented lesser daily dry matter intake (DMI), either in kilograms (p < 0.01) or as percentage of BW (p < 0.01) than high-RFI yearling bulls, resulting in improved gain:feed (G:F). However, variables, such as average daily gain (ADG), final BW, hot carcass weight (HCW) and other carcass characteristics did not differ (p > 0.05) across RFI groups. The eating rate of either dry matter (DM )(p = 0.04) or neutral detergent fiber (NDF) (p < 0.01) was slower in medium-RFI yearling bulls. For ruminal morphometrics an RFI effect was observed only on keratinized layer thickness, in which a thinner layer (p = 0.04) was observed in low-RFI Nellore yearling bulls. Likewise, Nellore yearling bulls classified by the RFI did not differ in terms of Shannon’s diversity (p = 0.57) and Chao richness (p = 0.98). Our results suggest that the differences in feed efficiency of Nellore bulls differing in phenotypic RFI should be attributed to metabolic variables other than ruminal microorganisms and epithelium, and deserves further investigation.
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Choi JH, Yoon YM, Kim YJ, Han KH. Role of 16S Ribosomal RNA Analysis in Identification of Microorganisms in Febrile Urinary Tract Infection of Infants. Indian J Pediatr 2022:10.1007/s12098-022-04121-3. [PMID: 35286567 DOI: 10.1007/s12098-022-04121-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 11/21/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVES To assess the role of 16S ribosomal RNA analysis in microbial identification in febrile infants under six months of age diagnosed with UTI, and compare it with the conventional culture results. METHODS Young infants under 6 mo of age who were suspected UTI from May 2018 to April 2019 had been enrolled. Uropathogens were analyzed by the traditional microbiologic culture system and the 16S rRNA analysis. The 16S rRNA analysis included 16S rRNA amplicon band confirmation and bacterial identification through the sequencing analysis. RESULTS A total of 57 infants with the febrile UTI were enrolled, and the median age was 3 mo. Uropathogens were identified in 43 patients (75.4%) in a conventional culture method: Escherichia coli in 38 patients (88.4%), Klebsiella pneumoniae in 3 (7.0%), Enterobacter cloacae in 1 (2.3%), and Pseudomonas aeruginosa in 1 (2.3%). Fifty urine samples (87.8%) had positive 16S rRNA amplicon band on electrophoresis. Among the 16S rRNA-positive urines, 40 samples were available for the sequence analysis of 16S rRNA, and the identification of bacteria were as follows: E. fergusonii in 36, K. pneumoniae in 3, and Shigella flexneri in 1. The sensitivity of 16S rRNA sequencing was 81.4% [95% confidence interval (CI), 67.4-90.3%] and the specificity was 64.3% (95% CI, 38.8-83.7%). CONCLUSION Uropathogen identification using 16S rRNA analysis could be applied to manage the febrile UTI in young infants clinically in combination with the conventional culture.
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Affiliation(s)
- Jae Hong Choi
- Department of Pediatrics, College of Medicine, Jeju National University, Jeju, 23241, Korea
| | - Young Mi Yoon
- Department of Pediatrics, Jeju National University Hospital, Jeju, Korea
| | - Yoon-Joo Kim
- Department of Pediatrics, College of Medicine, Jeju National University, Jeju, 23241, Korea
| | - Kyoung Hee Han
- Department of Pediatrics, College of Medicine, Jeju National University, Jeju, 23241, Korea.
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Jiang H, Lv L, Ahmed T, Jin S, Shahid M, Noman M, Osman HEH, Wang Y, Sun G, Li X, Li B. Effect of the Nanoparticle Exposures on the Tomato Bacterial Wilt Disease Control by Modulating the Rhizosphere Bacterial Community. Int J Mol Sci 2021; 23:414. [PMID: 35008839 PMCID: PMC8745216 DOI: 10.3390/ijms23010414] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 01/04/2023] Open
Abstract
Ralstonia Solanacearum is one of the most infectious soil-borne bacterial plant pathogens, causing tomato bacterial wilt (TBW). Nanotechnology is an emerging area of research, particularly the application of nanoparticles (NPs) as nanopesticides to manage plant disease is gaining attention nowadays. However, the interaction between NPs and rhizosphere bacterial communities remains largely elusive. This study indicated that metal NPs (CuO, ZnO, and FeO) reduced the incidence of bacterial wilt to varying degrees and affected the composition and structure of the rhizosphere bacterial community. The results revealed that the application of metal oxide NPs can improve the morphological and physiological parameters of TBW infected tomato plants. Among all, CuONPs amendments significantly increase the Chao1 and Shannon index. In the early stage (the second week), it significantly reduces the relative abundance of pathogens. However, the relative abundance of beneficial Streptomyces bacteria increased significantly, negatively correlated with the relative abundance of pathogenic bacteria. In addition, the nano-treatment group will enrich some potential beneficial bacteria such as species from Sphingomonadaceae, Rhizobiaceae, etc. In general, our research provides evidence and strategies for preventing and controlling soil-borne disease tomato bacterial wilt with metal oxide NPs.
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Affiliation(s)
- Hubiao Jiang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | - Luqiong Lv
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | - Shaomin Jin
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | - Muhammad Shahid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan;
| | - Muhammad Noman
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
| | | | - Yanli Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.W.); (G.S.)
| | - Guochang Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.W.); (G.S.)
| | - Xuqing Li
- Hangzhou Academy of Agricultural Science, Hangzhou 310024, China
| | - Bin Li
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; (H.J.); (L.L.); (T.A.); (S.J.); (M.N.)
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Chen L, Yan S, Yang M, Yu F, Wang J, Wang X, Xu H, Shi J, Pan L, Zeng Y, Li S, Li L, You L, Peng Y. The gut microbiome is associated with bone turnover markers in postmenopausal women. Am J Transl Res 2021; 13:12601-12613. [PMID: 34956476 PMCID: PMC8661154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/05/2021] [Indexed: 06/14/2023]
Abstract
OBJECTIVE The association of the gut microbiome with bone turnover markers (BTMs) in postmenopausal women is poorly understood. METHODS Fecal samples were collected from 97 Chinese postmenopausal women, and the serum CTX and P1NP were determined. Individuals with serum CTX lower or higher than the median value were divided into LCTX and P1NP groups; and individuals with serum P1NP lower or higher than the median value were grouped into LP1NP and HP1NP groups. Microbiota profiles were determined by high-throughput 16S rRNA gene sequencing. RESULTS In postmenopausal women, only Faecalibacterium showed significant alteration in the HCTX group compared with the LCTX group (P=0.004, q=0.143). Linear discriminant analysis effect size (LEfSe) analysis revealed that Clostridiaceae (P=0.015, LDA=2.89), Faecalibacterium (P=0.017, LDA=4.60), Prevotella (P=0.040, LDA=3.61) and Clostridium (P=0.007, LDA=2.79) were abundant in the LCTX group, and Facklamia (P=0.044, LDA=3.10) was enriched in the HCTX group. Peptostreptococcaceae (P=0.048, LDA=2.83) and the SMB53 (P=0.028, LDA=2.05) genus were enriched in the LPINP group, and Veillonellaceae (P=0.025, LDA=4.43) and the S24_7 (P=0.023, LDA=3.08) family were enriched in the HPINP group. Six taxa correlated with BTMs in all subjects, including Clostridium (Clostridiaceae) that was negatively correlated with serum CTX amounts significantly (r=-0.34, P<0.001). CONCLUSION This study identified taxa-specific differences in the intestinal microflora associated with BTMs, notably CTX. These findings may help in uncovering the roles of gut microbiota on bone metabolism.
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Affiliation(s)
- Lin Chen
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Shuai Yan
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Ming Yang
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Fudong Yu
- Basic Reproduction Laboratory, Shanghai Institute of Planned Parenthood Research, Fudan UniversityShanghai 200032, China
| | - Jingjing Wang
- Shanghai Key Laboratory for Pancreatic Diseases, Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Xiaoxin Wang
- Shanghai Key Laboratory for Pancreatic Diseases, Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Huanbai Xu
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Jianxia Shi
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Ling Pan
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Yuexi Zeng
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Siyu Li
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Li Li
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Li You
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
| | - Yongde Peng
- Department of Endocrinology and Metabolism, Shanghai General Hospital, Shanghai Jiao Tong University School of MedicineShanghai 200080, China
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Xu L, Sun X, Wan X, Li K, Jian F, Li W, Jiang R, Han R, Li H, Kang X, Wang Y. Dietary supplementation with Clostridium butyricum improves growth performance of broilers by regulating intestinal microbiota and mucosal epithelial cells. ACTA ACUST UNITED AC 2021; 7:1105-1114. [PMID: 34738041 PMCID: PMC8551407 DOI: 10.1016/j.aninu.2021.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/11/2021] [Accepted: 01/17/2021] [Indexed: 12/14/2022]
Abstract
Clostridium butyricum has been widely considered an antibiotic substitute in recent years. It can promote growth performance, improve the immune response and enhance the intestinal barrier function of the host. In the present study, 1-d-old Arbor Acres (AA) broilers were fed C. butyricum (1 × 109 cfu/kg) for 28 d. The transcriptomic characteristics of epithelial cells of the cecal mucosa were determined by RNA-sequence, and the cecal microbiota composition was explored by 16S ribosomal RNA gene sequencing. The changes in the intestinal mucosa of broilers were then analyzed by tissue staining. Gene Ontology (GO) annotations identified substance transport and processes and pathways that might participate in intestinal development and cell viability. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the differentially expressed genes are involved in numerous pathways related to amino acid and vitamin metabolism and antioxidant and defensive functions, among others. The relative expression of some genes associated with intestinal barrier function (claudins 2, 15, 19, and 23, tight junction proteins 1, 2, and 3 and mucin 1) was significantly increased in the treatment group (P < 0.05 or P < 0.01). Moreover, the proportion of Firmicutes was higher in the C. butyricum-treated group, whereas the proportion of Proteobacteria was higher in the control group. At the genus level, the relative abundances of Butyricicoccus and Lactobacillus, among other bacteria, were increased after C. butyricum supplementation. The tissue staining analysis showed that the cecal mucosa of broilers was significantly ameliorated after the addition of C. butyricum (P < 0.05 or P < 0.01). These results showed that dietary supplementation with C. butyricum can enhance the antioxidant capacity, mucosal barrier function, and stabilize the cecal microbiota, resulting in improving the growth performance.
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Affiliation(s)
- Laipeng Xu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiangli Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xianhua Wan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Keke Li
- Henan Jinbaihe Biotechnology Co., Ltd, Anyang, 455000, China
| | - Fuchun Jian
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
| | - Yanbin Wang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Research Center of Germplasm Resources for Poultry, Zhengzhou, 450046, China
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Colgan DJ, Ahyong ST, Mardon K, Brereton IM. Rare specimen identification in an un-integrated taxonomy: implications of DNA sequences from a Taiwanese Philine (Mollusca, Philinidae). Zookeys 2021; 1060:93-110. [PMID: 34616205 PMCID: PMC8463522 DOI: 10.3897/zookeys.1060.28809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 08/24/2021] [Indexed: 11/12/2022] Open
Abstract
Many species of the gastropod genus Philine have been named from northeastern Asia but scanty descriptions based predominantly on shells make it difficult to determine which are valid. This, plus the sporadic anatomical and genetic information available for many of these species has led to what may be described as an un-integrated taxonomy. In this situation, it is generally preferable to postpone dissection of rare and unusual specimens until relevant diagnostic characters can be established in broader studies. Micro-CT scanning and DNA sequencing were used to examine such a specimen collected recently from deep waters off northeastern Taiwan. Micro-CT examination of the morphology of the internal shell and gizzard plates suggested that, among named species, the sequenced specimen is most similar to P.otukai. It cannot, however, be definitively referred to P.otukai as that species lacks adequate anatomical description or known DNA sequences. Phylogenetic analyses of newly collected DNA sequences show the specimen to be most closely related to, but distinct from the northern Atlantic Ocean and Mediterranean species, Philinequadripartita. The sequences also confirm genetically that five or more species of Philine occur in northeast Asia, including at least three subject to considerable taxonomic uncertainty.
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Affiliation(s)
- Donald J Colgan
- Australian Museum Research Institute, 1 William St., Sydney 2010 Australia Australian Museum Research Institute Sydney Australia
| | - Shane T Ahyong
- Australian Museum Research Institute, 1 William St., Sydney 2010 Australia Australian Museum Research Institute Sydney Australia.,School of Biological, Earth & Environmental Sciences, University of New South Wales, Kensington, NSW 2052, Australia University of New South Wales Kensington Australia
| | - Karine Mardon
- Centre for Advanced Imaging/National Imaging Facility, University of Queensland, Brisbane 4072, Australia University of Queensland Brisbane Australia
| | - Ian M Brereton
- Centre for Advanced Imaging/National Imaging Facility, University of Queensland, Brisbane 4072, Australia University of Queensland Brisbane Australia
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Stotz MK, Henry DD, Crossland WL. Characterization of bacterial DNA identified in abscessed and non-abscessed bovine hepatic tissue at the time of harvest. J Anim Sci 2021; 99:6381665. [PMID: 34610106 PMCID: PMC8525596 DOI: 10.1093/jas/skab280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022] Open
Abstract
Bacteriological characterization of bovine liver abscesses has been accomplished by cultural methods but DNA methods are still needed, as many bacteria are not conducive to laboratory culture. In addition to this gap in research, there have been no studies which identify the bacterial presence within healthy, non-abscessed liver tissue. The objective of this study was to compare the bacteriome of both abscessed and non-abscessed bovine livers in an observational case-control study design. Fifty-six livers, obtained from Holstein steers, were scored according to a modified Elanco liver abscess score description where A- was partitioned into active abscesses or scarred where only scars were present. Parenchyma tissue was collected from non-abscessed livers (n = 22) and scarred livers (n = 7), and purulent material was collected from abscessed livers (n = 24), and DNA was extracted for 16s rRNA gene sequence-based bacterial analysis. Across liver samples, 21 total phyla were identified with a mean of 14. Predominant phyla, accounting for >98% of reads, were Fusobacteria (51.7%), Bacteroidetes (26.9%), Proteobacteria (8.03%), Firmicutes (5.39%), Cyanobacteria (3.85%), and Actinobacteria (2.21%). Proteobacteria, Cyanobacteria, and Firmicutes were greater in non-abscessed and scarred livers, whereas Fusobacteria and Bacteroidetes prevailed in abscessed livers. Non-abscessed livers shared 3,059 operational taxonomic units (OTU) with abscessed livers (total OTU of all livers = 4,167), but non-abscessed livers had greater richness and evenness, whereas abscessed livers had greater dominance (P ≤ 0.0014). Liver score affected the relative abundance of OTU (R = 0.463; P = 0.001) but abscessed livers shared ≥ 40% similarity and were not different from each other (P ≥ 0.370). Of the predominant OTU (top 10 as a % of reads), three OTU (Fusobacteria necrophorum, Bacteroides spp., and Trueperella pyogenes) were shared across both abscessed and non-abscessed livers. Fusobacterium necrophorum was the dominant OTU regardless of liver score, and the single most abundant OTU, even among non-abscessed livers. We describe bacterial DNA detected in non-abscessed bovine liver tissue for the first time, which indicates possible presence of viable bacteria with pathogenic potential in apparently healthy liver tissue.
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Affiliation(s)
- Miranda K Stotz
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, USA
| | - Darren D Henry
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, USA
| | - Whitney L Crossland
- Department of Animal and Food Sciences, Texas Tech University, Lubbock, TX, USA
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Yang M, Li F, Zhang R, Wu Y, Yang Q, Wang F, Yu Z, Liu J, Cha B, Gong Q, Yang B, Sun B, Ding H. Alteration of the Intestinal Microbial Flora and the Serum IL-17 Level in Patients with Graves' Disease Complicated with Vitamin D Deficiency. Int Arch Allergy Immunol 2021; 183:225-234. [PMID: 34544076 DOI: 10.1159/000518949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/06/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Intestinal flora is associated with Graves' disease (GD). This study explored the association of serum 25(OH)D with the diversity of the intestinal flora and serum IL-17 in GD patients. METHODS Patients newly diagnosed with GD at 2 centers between 2018 and 2021 were consecutively included. According to their 25(OH)D levels, they were divided into the deficiency group, the insufficiency group, and the sufficiency group. Some patients with vitamin D deficiency or insufficiency were randomly selected and were matched with healthy volunteers (normal control [NC]) in terms of sex, age, and case number. The diversity and differential species of the intestinal flora and serum IL-17 levels were compared. RESULTS Serum 25(OH)D negatively correlated with serum IL-17, the platelet/lymphocyte ratio, and TSH receptor antibody. The diversity of the intestinal flora decreased in the GD group, with noticeable differences in the composition of the intestinal flora when compared with the NC group. At the phylum level, the GD group exhibited a significantly lower abundance of Firmicutes but a higher abundance of Actinobacteria. At the genus level, the GD group exhibited higher relative abundances of Bifidobacterium, Collinsella, and Pediococcus but lower abundances of Roseburia and Dialister. CONCLUSIONS The changes in the vitamin D level and the composition of the intestinal flora may partially contribute to the development of GD.
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Affiliation(s)
- Mengxue Yang
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Fei Li
- Department of Endocrinology, Zunyi Medical University, Zunyi, China
| | - Rui Zhang
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Yueyue Wu
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Qian Yang
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Fang Wang
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Zhiyan Yu
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Jun Liu
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Bingbing Cha
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Qihai Gong
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, China
| | - Bo Yang
- Department of Endocrinology, Zunyi Medical University, Zunyi, China
| | - Bowen Sun
- Department of Endocrinology, Zunyi Medical University, Zunyi, China
| | - Heyuan Ding
- Department of Endocrinology, Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
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Selvakumar DR, Krishnamoorthy S, Venkatesan K, Ramanathan A, Abbott PV, Angambakkam Rajasekaran P. Active Bacteria in Carious Dentin of Mandibular Molars with Different Pulp Conditions: An In Vivo Study. J Endod 2021; 47:1883-1889. [PMID: 34534554 DOI: 10.1016/j.joen.2021.08.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION This study evaluated the relative abundance and ribosomal activity of selected bacteria in carious dentin of teeth with different pulp conditions. METHODS Thirty healthy patients with class I occlusal caries in molars were categorized into 3 groups based on the pulp diagnosis: normal pulp (NP, n = 10) with caries extending less than half the thickness of dentin (as assessed radiographically), reversible pulpitis (n = 10), and symptomatic irreversible pulpitis (n = 10) with caries extending more than two thirds of the thickness of dentin. Carious dentin samples were collected from the deepest part of the cavity and stored in RNAlater solution (Ambion Inc, Austin, TX). Eight bacterial taxa were evaluated from the samples: Streptococcus mutans, Lactobacillus fermentum, Veillonella, Actinomyces, Rothia dentocariosa, Olsenella profusa, Prevotella intermedia, and Bifidobacterium dentium. The 16S ribosomal RNA (rRNA) gene and 16S rRNA were quantified by real-time polymerase chain reaction and used to calculate the relative genome abundance and relative ribosomal abundance. The Fisher exact test was used to compare proportions between groups. The mean rank difference between the various groups was assessed using the Kruskal-Wallis test with the Bonferroni-Holm correction. RESULTS The reversible pulpitis group had significantly higher 16S rRNA gene and rRNA counts of Actinomyces (P < .001 and P = .002) and B. dentium (P = .005 and P = .007) relative to the NP group. The symptomatic irreversible pulpitis group had significantly higher 16S rRNA gene and rRNA counts of L. fermentum (P < .001 and P < .001), Actinomyces (P < .001 and P < .001), O. profusa (P < .001 and P < .001), P. intermedia (P = .001 and P = .002), and Bifidobacterium (P < .001 and P < .001) relative to the NP group. CONCLUSIONS Specific bacterial activity varies in carious dentin of teeth with different pulp conditions.
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Affiliation(s)
- Deepan Raj Selvakumar
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamilnadu, India
| | - Sridevi Krishnamoorthy
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamilnadu, India
| | - Keerthi Venkatesan
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamilnadu, India
| | | | - Paul Vincent Abbott
- UWA Dental School, The University of Western Australia, Nedlands, Western Australia, Australia
| | - PradeepKumar Angambakkam Rajasekaran
- Department of Conservative Dentistry and Endodontics, Thai Moogambigai Dental College and Hospital, Dr. MGR Educational and Research Institute, Chennai, Tamilnadu, India.
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Khasapane NG, Nkhebenyane JS, Kwenda S, Khumalo ZTH, Mtshali PS, Taioe MO, Thekisoe OMM. Application of culture, PCR, and PacBio sequencing for determination of microbial composition of milk from subclinical mastitis dairy cows of smallholder farms. Open Life Sci 2021; 16:800-808. [PMID: 34458582 PMCID: PMC8374232 DOI: 10.1515/biol-2021-0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/31/2021] [Accepted: 06/21/2021] [Indexed: 01/04/2023] Open
Abstract
Mastitis is a cow disease usually signalized by irritation, swelling, and soreness of the udder. It is characterized by physical, chemical, and biological changes in the udder and milk. The aim of this study was to detect and characterize pathogens causing subclinical mastitis (SCM) from the milk of dairy cows of small-scale farmers through culture and molecular techniques. Milk was collected from 32 cows belonging to 8 small-scale farmers around Harrismith District, South Africa. The results showed that screening of SCM by California mastitis test and somatic cell counts (SCC) was 21.87 and 25%, respectively. Culture methods revealed the presence of Staphylococcus aureus at 93% followed by Streptococci spp. and Escherichia coli at 36.4 and 13.3%, respectively. The PCR could only detect E. coli, while single-molecule real-time sequencing showed a total of 2 phyla, 5 families, 7 genera, and 131 species. Clostridiaceae was the most abundant family, while Romboutsia was the most abundant genus followed by Turicibacter spp. The present study has documented the occurrence of SCM causing pathogens in milk collected from cows of small-scale farmers in Harrismith, indicating that SCM may be present at higher levels than expected.
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Affiliation(s)
- Ntelekwane G Khasapane
- Department of Life Sciences, Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein, 9300, South Africa
| | - Jane S Nkhebenyane
- Department of Life Sciences, Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein, 9300, South Africa
| | - Stanford Kwenda
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Zamantungwa T H Khumalo
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa.,Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Private Bag X04, Onderstepoort, 0110, South Africa
| | - Phillip S Mtshali
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Moeti O Taioe
- Epidemiology, Parasites and Vectors, Agricultural Research Council - Onderstepoort Veterinary Research (ARC-OVR), Onderstepoort 0110, South Africa
| | - Oriel M M Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, 2531, South Africa
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Yj OK, Hee Lee S, Sang You H, Ju Lee Y, Sun Kang S, Hee Hyun S. Estimation of Personal Environment Via Fingertip Microbiome and Mobile Phone Surfaces. Iran J Biotechnol 2021; 19:e2696. [PMID: 34435058 PMCID: PMC8358174 DOI: 10.30498/ijb.2021.2696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background: Fingerprints can serve to identify individuals, but fingerprint quality may be deteriorated, even to the point of eliminating fingerprints, due to the external environment. Objective: Poor fingerprint quality cannot be effectively used to identify individuals; hence, the need for other methods. Materials and Methods: We investigated the utility of bacterial communities and the only microorganisms present in the sample to identify internal and external factors in individuals.
Samples included eight participants’ fingerprints and their mobile phone surfaces. Bacterial DNA in the samples was sequenced using next-generation sequencing to target the
V3–V4 region in the 16S ribosomal RNA gene. The QIIME program was used to perform a taxonomic assignment and alpha diversity and beta diversity analyses based on the sequence data. Results: Until now, personal identification has only relied on microbial communities. However, this study identified microbial differences according to Korean mobile phones, fingertips,
or gender, and confirmed the possibility of characterization of samples when it was difficult to identify individuals by the microbial community. The biodiversity and composition
of individual bacterial communities were affected by internal and external environments. Bacteria from individuals and mobile phones were shared due to contact between mobile
phone surfaces and fingertips. Of the eight Koreans, six of the fingertips and mobile phone samples matched each other for personal identification. Conclusions: This study confirmed that the bacteria from an individual could be matched with the contact object and could be used as forensic evidence. Such bacterial profiling of
individuals may confer forensic evidence and serve as a basis for improving the accuracy of forensic verification.
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Affiliation(s)
- O K Yj
- Department of Biomedical Laboratory Science, Eulji University, 77, Gyeryong-ro, 771 beon-gil, Jung-gu, Daejeon, 34824, Republic of Korea
| | - Song Hee Lee
- Department of Senior Healthcare, BK21 plus program, Graduate School, Eulji University, 77, Gyeryong-ro, 771 beon-gil, Jung-gu, Daejeon, 34824, Republic of Korea
| | - Hee Sang You
- Department of Senior Healthcare, BK21 plus program, Graduate School, Eulji University, 77, Gyeryong-ro, 771 beon-gil, Jung-gu, Daejeon, 34824, Republic of Korea
| | - Young Ju Lee
- Department of Biomedical Laboratory Science, Eulji University, 77, Gyeryong-ro, 771 beon-gil, Jung-gu, Daejeon, 34824, Republic of Korea
| | - Sang Sun Kang
- Department of Biology Education, Chungbuk National University, 1, Chundae-ro, Seowon-gu, Cheongju, Chungbuk, 28644, Republic of Korea
| | - Sung Hee Hyun
- Department of Biomedical Laboratory Science, Eulji University, 77, Gyeryong-ro, 771 beon-gil, Jung-gu, Daejeon, 34824, Republic of Korea.,Department of Senior Healthcare, BK21 plus program, Graduate School, Eulji University, 77, Gyeryong-ro, 771 beon-gil, Jung-gu, Daejeon, 34824, Republic of Korea
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Yatera K, Noguchi S, Mukae H. Perspective on the clone library method for infectious diseases. Respir Investig 2021:S2212-5345(21)00123-4. [PMID: 34400128 DOI: 10.1016/j.resinv.2021.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/23/2021] [Accepted: 07/04/2021] [Indexed: 01/27/2023]
Abstract
Recently, culture-independent molecular methods, such as DNA sequencing techniques targeting the 16S-ribosomal RNA (rRNA) gene and/or other housekeeping genes with Sanger method-based technologies, next generation sequencing (NGS), and metagenomic analysis, have been developed for detecting microorganisms in the human body; these can provide information on microbiomes of samples from individuals with or without infectious diseases. Determining the bacterial species is crucial in identifying causative bacteria of upper and lower respiratory tract infections, especially for Streptococcus species, but NGS analysis is often not precise enough to identify bacteria at the species level. This review briefly introduces previous observations of the microbiome of samples from various respiratory and other infections assessed using the clone library method with Sanger sequencing of the 16S-rRNA gene. On analysis of 16S-rRNA gene-sequence data of bronchoalveolar lavage fluid obtained from pneumonia lesions in patients with bacterial pneumonia and lung abscess, anaerobes are often detected in non-elderly patients with pneumonia, and the detection rate of Staphylococcus aureus in patients with hospital-acquired pneumonia is lower than that previously reported. Analysis of pleural effusion samples from patients with pleurisy indicated a more important role of anaerobes than previous believed. The other topics reviewed include microbiomes of nontuberculous mycobacteriosis and lower respiratory tract infections in children with permanent tracheostomy due to neuromuscular disorders, in nasal discharge, in bacterial vaginosis, in the intracystic fluid of postoperative maxillary cyst, and in bacterial conjunctivitis; urine microbiota in urethritis; fecal microbiota; and newly detected infectious organisms in the human respiratory tract.
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Sánchez-Pellicer P, Navarro-López V, González-Tamayo R, Llopis-Ruiz C, Núñez-Delegido E, Ruzafa-Costas B, Navarro-Moratalla L, Agüera-Santos J. Descriptive Study of Gut Microbiota in Infected and Colonized Subjects by Clostridiodes difficile. Microorganisms 2021; 9:microorganisms9081727. [PMID: 34442805 PMCID: PMC8401824 DOI: 10.3390/microorganisms9081727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 11/17/2022] Open
Abstract
Clostridiodes difficile can lead to a range of situations from the absence of symptoms (colonization) to severe diarrhea (infection). Disruption of gut microbiota provides an ideal environment for infection to occur. Comparison of gut microbiota of infected and colonized subjects could provide relevant information on susceptible groups or protectors to the development of infection, since the presence of certain genera could be related to the inhibition of transition from a state of colonization to infection. Through high-throughput sequencing of 16S rDNA gene, we performed alpha and beta diversity and composition studies on 15 infected patients (Group CDI), 15 colonized subjects (Group P), and 15 healthy controls (Group CTLR). A loss of alpha diversity and richness and a different structure have been evidenced in the CDI and P groups with respect to the CTRL group, but without significant differences between the first two. In CDI and P groups, there was a strong decrease in phylum Firmicutes and an expansion of potential pathogens. Likewise, there was a loss of inhibitory genus of C. difficile germination in infected patients that were partially conserved in colonized subjects. Therefore, infected and colonized subjects presented a gut microbiota that was completely different from that of healthy controls, although similar to each other. It is in composition where we found that colonized subjects, especially in minority genera, presented differences with respect to those infected.
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Affiliation(s)
- Pedro Sánchez-Pellicer
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
- Correspondence: (P.S.-P.); (V.N.-L.)
| | - Vicente Navarro-López
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
- Infectious Diseases Unit, University Hospital of Vinalopó, Carrer Tonico Sansano Mora, 14, 03293 Elche, Spain
- Correspondence: (P.S.-P.); (V.N.-L.)
| | - Ruth González-Tamayo
- Biochemistry Laboratory, Vega Baja Hospital, Carretera Orihuela-Almoradí s/n, 03314 San Bartolomé, Spain;
| | - Coral Llopis-Ruiz
- Microbiology Laboratory, University Hospital of Vinalopó, Carrer Tonico Sansano Mora, 14, 03293 Elche, Spain;
| | - Eva Núñez-Delegido
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Beatriz Ruzafa-Costas
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Laura Navarro-Moratalla
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
| | - Juan Agüera-Santos
- MiBioPath Group, Health and Science Faculty, Catholic University of Murcia, Campus de los Jerónimos, 135, 30107 Murcia, Spain; (E.N.-D.); (B.R.-C.); (L.N.-M.); (J.A.-S.)
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Tiimub BM, Zhou ZC, Zhu L, Liu Y, Shuai XY, Xu L, Niyungeko C, Meng LX, Sun YJ, Chen H. Characteristics of bacterial community and ARGs profile in engineered goldfish tanks with stresses of sulfanilamide and copper. Environ Sci Pollut Res Int 2021; 28:38706-38717. [PMID: 33742379 DOI: 10.1007/s11356-021-13239-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
Abuse of antibiotics in aquaculture have been alarming and might aggravate spread of resistance genes in the environment. Holistic ARGs proliferation checks require deeper analyses of coupled absolute abundances in 16S rRNA bacteria communities at the phylum level to detect biomarkers. Sulfanilamide (sul) and copper II sulfate (CuSO4 II) were, therefore, designed and added as separate or combined treatments in 9 replicate engineered goldfish tanks comprising 3 individual sul, 3 CuSO4 II, 3 (sul + CuSO4 II) combinations, and 3 controls within 180 days. The DNA from water and fish guts was sequenced under qPCR to determine 16S rRNA bacteria biomarkers co-occurring with the correspondent ARGs. Combined chemical addition at 0.8-1.5 mg sul + 0.5-1.0 mg CuSO4 II/3 L of tank waters reduced sequenced 16S rRNA bacteria absolute abundances in fish gut and water samples while portraying the biomarkers. Absolute abundances of the entire 16S rRNA bacteria was higher in fish guts (3.4 × 1014-4.9 × 108 copies/g) than water samples (1.5 × 109-2.6 × 1015 copies/L), respectively. Much as sul 1(log) were dominant over intl 1(log) genes, and their fundamental profiles were also higher in the fish guts than water samples; the Spearman's correlation analyses revealed positive relationship (p < 0.01 and r = 0.873) among the biomarkers of both ARG pairs at the phylum level and the physicochemical parameters. In the fish gut and water samples ratios, Bacteroidetes (10-85:12-85%) > Proteobacteria (10-50:15-65%) > Planktomycetes (10-52:8-25%) featured prominently based on LEfSe use as the hot-spotted biomarkers, hence justifying its higher prospects towards innovative environmental microbiological and biotechnological studies.
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Affiliation(s)
- Benjamin Makimilua Tiimub
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Zhen-Chao Zhou
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Lin Zhu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Yang Liu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Xin-Yi Shuai
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Lan Xu
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Christophe' Niyungeko
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Ling-Xuan Meng
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Yu-Jie Sun
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China
| | - Hong Chen
- Department of Environmental Engineering, College of Environmental and Resource Sciences, Zhejiang University, 310058, Hangzhou, People's Republic of China.
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Kamel O, Van Noten H, Argudín MA, Martiny D. Butyricimonas faecihominis and Eubacterium callanderi mixed bloodstream infection after appendicular peritonitis. Anaerobe 2021; 71:102419. [PMID: 34311107 DOI: 10.1016/j.anaerobe.2021.102419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/25/2021] [Accepted: 07/22/2021] [Indexed: 11/19/2022]
Affiliation(s)
- Omar Kamel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium.
| | - Héloïse Van Noten
- Infectious Diseases Department, CHU Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Maria A Argudín
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), Brussels, Belgium; Faculty of Medicine and Franco, University of Mons (UMONS), Mons, Belgium
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44
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Kim HJ, Han J, Kim BJ, Lee KW, Hyeong K, Choi YU. New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes. Mol Biol Rep 2021; 48:5795-5801. [PMID: 34292472 DOI: 10.1007/s11033-021-06559-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 07/08/2021] [Indexed: 11/27/2022]
Abstract
BACKGROUND Two deep-sea eels collected from the Western Pacific Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae. METHODS AND RESULTS To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S ribosomal RNA [16S rRNA]). Through molecular phylogenetic analysis based on mtDNA COI and 16S rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the Western Pacific Ocean, respectively. CONCLUSIONS This is the first study to report new records of the genera Bassozetus and Synaphobranchus from the Western Pacific Ocean based on COI and 16S rRNA genes.
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Affiliation(s)
- Han-Jun Kim
- Marine Bio-Resources Research Unit, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Jeonghoon Han
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Byung-Jik Kim
- Animal Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Kyun-Woo Lee
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Kiseong Hyeong
- Global Ocean Research Center, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea
| | - Young-Ung Choi
- Marine Bio-Resources Research Unit, Korea Institute of Ocean Science and Technology (KIOST), Busan, 49111, Republic of Korea.
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Abstract
BACKGROUND Subjective cognitive decline (SCD) is the earliest symptomatic manifestation of preclinical Alzheimer's disease (AD). Gut microbiota may serve as a susceptibility factor for AD. Altered gut microbiota has been reported in patients with mild cognitive impairment (MCI) and AD dementia. However, whether gut microbial compositions changed in SCD remains largely unknown. OBJECTIVE To characterize the gut microbiota in SCD. METHODS In this study, a total of 105 participants including 38 normal controls (NC), 53 individuals with SCD, and 14 patients with cognitive impairment (CI) were recruited. Gut microbiota of all participants isolated from fecal samples were investigated using 16S ribosomal RNA (rRNA) Illumina Miseq sequencing technique. The gut microbial compositions were compared among the three groups, and the association between altered gut microbiota and cognitive performance was analyzed. To validate the alteration of gut microbiota in SCD, we conducted amyloid positron emission tomography (PET) in selected participants and further compared the gut microbiota among subgroups. RESULTS The abundance of phylum Firmicutes, class Clostridia, order Clostridiales, family Ruminococcaceae, and genus Faecalibacterium showed a trend toward a progressive decline from NC to SCD and CI. Specifically, the abundance of the anti-inflammatory genus Faecalibacterium was significantly decreased in SCD compared with NC. In addition, altered bacterial taxa among the three groups were associated with cognitive performance. The findings were validated in SCD participants with positive amyloid evidence. CONCLUSION The composition of gut microbiota is altered in individuals with SCD. This preliminary study will provide novel insights into the pathophysiological mechanism of AD.
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Affiliation(s)
- Can Sheng
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Li Lin
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Hua Lin
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Xiaoni Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Ying Han
- Department of Neurology, Xuanwu Hospital of Capital Medical University, Beijing, China.,School of Biomedical Engineering, Hainan University, Haikou, China.,Center of Alzheimer's Disease, Beijing Institute for Brain Disorders, Beijing, China
| | - Shu-Lin Liu
- Genomics Research Center, State-Province Key Laboratories of Biomedicine Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China.,HMU-UCCSM Centre for Infection and Genomics, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China.,Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
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46
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Lim S, Rajagopal S, Jeong YR, Nzegwu D, Wright ML. Group B Streptococcus and the vaginal microbiome among pregnant women: a systematic review. PeerJ 2021; 9:e11437. [PMID: 34046261 PMCID: PMC8136278 DOI: 10.7717/peerj.11437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/20/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Vaginal microbiome studies frequently report diversity metrics and communities of microbiomes associated with reproductive health outcomes. Reports of Streptococcus agalactiae (also known as Group B Streptococcus or GBS), the leading cause of neonatal infectious morbidity and mortality, are notably lacking from the studies of the vaginal microbiome, despite being a known contributor to preterm birth and other complications. Therefore, the purpose of this systematic review was to explore the frequency of GBS reporting in vaginal microbiome literature pertaining to pregnancy and to examine methodological bias that contributes to differences in species and genus-level microbiome reporting. Lack of identification of GBS via sequencing-based approaches due to methodologic or reporting bias may result incomplete understanding of bacterial composition during pregnancy and subsequent birth outcomes. METHODOLOGY A systematic review was conducted following the PRISMA guideline. Three databases (PubMed, CINAHL, and Web of Science) were used to identify papers for review based on the search terms "vaginal microbiome", "pregnancy", and "16S rRNA sequencing". Articles were evaluated for methods of DNA extraction and sequencing, 16S region, taxonomy classification database, number of participants or vaginal specimens, and pregnancy trimester. RESULTS Forty-five research articles reported employing a metagenomic approach or 16S approach for vaginal microbiome analysis during pregnancy that explicitly reported taxonomic composition and were included in this review. Less than 30% of articles reported the presence of GBS (N = 13). No significant differences in methodology were identified between articles that reported versus did not report GBS. However, there was large variability across research methods used for vaginal microbiome analysis and species-level bacterial community reporting. CONCLUSION Considerable differences in study design and data formatting methods may contribute to underrepresentation of GBS, and other known pathogens, in existing vaginal microbiome literature. Previous studies have identified considerable variation in methodology across vaginal microbiome studies. This study adds to this body of work because in addition to laboratory or statistical methods, how results and data are shared (e.g., only analyzing genus level data or 20 most abundant microbes), may hinder reproducibility and limit our understanding of the influence of less abundant microbes. Sharing detailed methods, analysis code, and raw data may improve reproducibility and ability to more accurately compare microbial communities across studies.
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Affiliation(s)
- Sungju Lim
- School of Nursing, The University of Texas at Austin, Austin, TX, United States of America
| | - Shilpa Rajagopal
- College of Natural Sciences, Biology Instructional Office, The University of Texas at Austin, Austin, TX, United States of America
| | - Ye Ryn Jeong
- School of Nursing, The University of Texas at Austin, Austin, TX, United States of America
| | - Dumebi Nzegwu
- College of Liberal Arts, Department of Health and Society, The University of Texas at Austin, Austin, TX, United States of America
| | - Michelle L. Wright
- School of Nursing, The University of Texas at Austin, Austin, TX, United States of America
- Dell Medical School, Department of Women’s Health, University of Texas at Austin, Austin, TX, United States of America
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47
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Baruch Z, Liddicoat C, Cando-Dumancela C, Laws M, Morelli H, Weinstein P, Young JM, Breed MF. Increased plant species richness associates with greater soil bacterial diversity in urban green spaces. Environ Res 2021; 196:110425. [PMID: 33157108 DOI: 10.1016/j.envres.2020.110425] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
The vegetation and soil microbiome within urban green spaces is increasingly managed to help conserve biodiversity and improve human health concurrently. However, the effects of green space management on urban soil ecosystems is poorly understood, despite their importance. Across 40 urban green spaces in metropolitan Adelaide, South Australia, we show that soil bacterial communities are strongly affected by urban green space type (incl. sport fields, community gardens, parklands and revegetated areas), and that plant species richness is positively associated with soil bacterial diversity. Importantly, these microbiome trends were not affected by geographic proximity of sample sites. Our results provide early evidence that urban green space management can have predictable effects on the soil microbiome, at least from a diversity perspective, which could prove important to inform policy development if urban green spaces are to be managed to optimise population health benefits.
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Affiliation(s)
- Zdravko Baruch
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Craig Liddicoat
- School of Public Health, University of Adelaide, Adelaide, SA, 5005, Australia; College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia
| | | | - Mark Laws
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Hamish Morelli
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Philip Weinstein
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia; School of Public Health, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jennifer M Young
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Adelaide, SA, 5042 Australia.
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48
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Amachawadi RG, Tom WA, Hays MP, Fernando SC, Hardwidge PR, Nagaraja TG. Bacterial community analysis of purulent material from liver abscesses of crossbred cattle and Holstein steers fed finishing diets with or without tylosin. J Anim Sci 2021; 99:skab076. [PMID: 33693672 PMCID: PMC8075120 DOI: 10.1093/jas/skab076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/04/2021] [Indexed: 01/04/2023] Open
Abstract
Liver abscesses in feedlot cattle are polymicrobial infections. Culture-based studies have identified Fusobacterium necrophorum as the primary causative agent, but a number of other bacterial species are frequently isolated. The incidence of liver abscesses is highly variable and is affected by a number of factors, including cattle type. Holstein steers raised for beef production have a higher incidence than crossbred feedlot cattle. Tylosin is the commonly used antimicrobial feed additive to reduce the incidence of liver abscesses. The objective of this study was to utilize 16S ribosomal RNA amplicon sequence analyses to analyze the bacterial community composition of purulent material of liver abscesses of crossbred cattle (n = 24) and Holstein steers (n = 24), each fed finishing diet with or without tylosin. DNA was extracted and the V3 and V4 regions of the 16S rRNA gene were amplified, sequenced, and analyzed. The minimum, mean, and maximum sequence reads per sample were 996, 177,070, and 877,770, respectively, across all the liver abscess samples. Sequence analyses identified 5 phyla, 14 families, 98 genera, and 102 amplicon sequence variants (ASV) in the 4 treatment groups. The dominant phyla identified were Fusobacteria (52% of total reads) and Proteobacteria (33%). Of the top 25 genera identified, 17 genera were Gram negative and 8 were Gram positive. The top 3 genera, which accounted for 75% of the total reads, in the order of abundance, were Fusobacterium, Pseudomonas, and Bacteroides. The relative abundance, expressed as percent of total reads, of phyla, family, and genera did not differ (P > 0.05) between the 4 treatment groups. Generic richness and evenness, determined by Shannon-Weiner and Simpson's diversity indices, respectively, did not differ between the groups. The UniFrac distance matrices data revealed no clustering of the ASV indicating variance between the samples within each treatment group. Co-occurrence network analysis at the genus level indicated a strong association of Fusobacterium with 15 other genera, and not all of them have been previously isolated from liver abscesses. In conclusion, the culture-independent method identified the bacterial composition of liver abscesses as predominantly Gram negative and Fusobacterium as the dominant genus, followed by Pseudomonas. The bacterial community composition did not differ between crossbred and Holstein steers fed finishing diets with or without tylosin.
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Affiliation(s)
| | - Wesley A Tom
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Michael P Hays
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - Samodha C Fernando
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Philip R Hardwidge
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
| | - T G Nagaraja
- Department of Diagnostic Medicine/Pathobiology, Kansas State University, Manhattan, KS 66506, USA
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49
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Abstract
Growth temperature is one of the most representative biological parameters for characterizing living organisms. Prokaryotes have been isolated from various temperature environments and show wide diversity in their growth temperatures. We herein constructed a database of growth TEMPeratures of Usual and RAre prokaryotes (TEMPURA, http://togodb.org/db/tempura), which contains the minimum, optimum, and maximum growth temperatures of 8,639 prokaryotic strains. Growth temperature information is linked with taxonomy IDs, phylogenies, and genomic information. TEMPURA provides useful information to researchers working on biotechnological applications of extremophiles and their biomolecules as well as those performing fundamental studies on the physiological diversity of prokaryotes.
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Affiliation(s)
- Yu Sato
- International Center for Biotechnology, Osaka University
| | - Kenji Okano
- International Center for Biotechnology, Osaka University
| | - Hiroyuki Kimura
- Research Institute of Green Science and Technology, Shizuoka University.,Department of Geosciences, Faculty of Science, Shizuoka University
| | - Kohsuke Honda
- International Center for Biotechnology, Osaka University
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50
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Saito S, Aoki Y, Tamahara T, Goto M, Matsui H, Kawashima J, Danjoh I, Hozawa A, Kuriyama S, Suzuki Y, Fuse N, Kure S, Yamashita R, Tanabe O, Minegishi N, Kinoshita K, Tsuboi A, Shimizu R, Yamamoto M. Oral Microbiome Analysis in Prospective Genome Cohort Studies of the Tohoku Medical Megabank Project. Front Cell Infect Microbiol 2021; 10:604596. [PMID: 33585276 PMCID: PMC7878372 DOI: 10.3389/fcimb.2020.604596] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/07/2020] [Indexed: 12/26/2022] Open
Abstract
A baseline oral microbiome study of the Tohoku Medical Megabank Organization (TMM) was planned to characterize the profile of the oral microbiome in the Japanese population. The study also aimed to clarify risk factors for multifactorial diseases by integrated analysis of the oral microbiome and host genome/omics information. From 2013 to 2016, we collected three types of oral biospecimens, saliva, supragingival plaque, and tongue swab, from a total of 25,101 participants who had a dental examination in TMM. In this study, we used two independent cohorts; the Community-Based Cohort and Birth and Three-Generation Cohort as discovery and validation cohorts, respectively, and we selected participants examined by a single dentist. We found through the 16S ribosomal RNA gene sequencing analysis of 834 participants of the Community-Based Cohort Study that there are differences in the microbial composition and community structure between saliva and plaque. The species diversities in both saliva and plaque were increased in correlation with the severity of periodontal disease. These results were nicely reproduced in the analysis of 455 participants of the Birth and Three-Generation Cohort Study. In addition, strong positive and negative associations of microbial taxa in both plaque and saliva with periodontitis-associated biofilm formation were detected by co-occurrence network analysis. The classes Actinobacteria and Bacilli, including oral health-associated bacterial species, showed a positive correlation in saliva. These results revealed differences in microbial composition and community structure between saliva and plaque and a correlation between microbial species and the severity of periodontal disease. We expect that the large database of the oral microbiome in the TMM biobank will help in the discovery of novel targets for the treatment and prevention of oral diseases, as well as for the discovery of therapeutic and/or preventive targets of systemic diseases.
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Affiliation(s)
- Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Toru Tamahara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Maki Goto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroyuki Matsui
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Clinical Genetics, Ageo Central General Hospital, Ageo, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Riu Yamashita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Biosample Research Center, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
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