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Chen Q, Huang X, Zhang H, Jiang X, Zeng X, Li W, Su H, Chen Y, Lin F, Li M, Gu X, Jin H, Wang R, Diao D, Wang W, Li J, Wei S, Zhang W, Liu W, Huang Z, Deng Y, Luo W, Liu Z, Zhang B. Characterization of tongue coating microbiome from patients with colorectal cancer. J Oral Microbiol 2024; 16:2344278. [PMID: 38686186 PMCID: PMC11057396 DOI: 10.1080/20002297.2024.2344278] [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: 09/29/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
Background Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue coating microbiome and colorectal cancer (CRC). Methods Metagenomic shotgun sequencing was performed on tongue coating samples collected from 30 patients with CRC, 30 patients with colorectal polyps (CP), and 30 healthy controls (HC). We further validated the potential of the tongue coating microbiota to predict the CRC by a random forest model. Results We found a greater species diversity in CRC samples, and the nucleoside and nucleotide biosynthesis pathway was more apparent in the CRC group. Importantly, various species across participants jointly shaped three distinguishable fur types.The tongue coating microbiome profiling data gave an area under the receiver operating characteristic curve (AUC) of 0.915 in discriminating CRC patients from control participants; species such as Atopobium rimae, Streptococcus sanguinis, and Prevotella oris aided differentiation of CRC patients from healthy participants. Conclusion These results elucidate the use of tongue coating microbiome in CRC patients firstly, and the fur-types observed contribute to a better understanding of the microbial community in human. Furthermore, the tongue coating microbiota-based biomarkers provide a valuable reference for CRC prediction and diagnosis.
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Affiliation(s)
- Qubo Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Biological Resource Center, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
| | - Xiaoting Huang
- Medical Research Center, Huazhong University of Science and Technology Union Shenzhen, Shenzhen, China
| | - Haiyan Zhang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xuanting Jiang
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Xuan Zeng
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Biological Resource Center, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
| | - Wanhua Li
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hairong Su
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ying Chen
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fengye Lin
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Man Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Biological Resource Center, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
| | - Xiangyu Gu
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Huihui Jin
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ruohan Wang
- Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dechang Diao
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Colorectal surgery of Guangdong Provincial Hospital of TCM, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wei Wang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Gastrointestinal Surgery Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jin Li
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Gastrointestinal Surgery Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Sufen Wei
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weizheng Zhang
- Medical Laboratory, Guangzhou Cadre Health Management Center, Guangzhou No.11 People’s Hospital, Guangzhou, China
| | - Wofeng Liu
- Medical Laboratory, Guangzhou Cadre Health Management Center, Guangzhou No.11 People’s Hospital, Guangzhou, China
| | - Zhiping Huang
- Information Department, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yusheng Deng
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Biological Resource Center, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, China
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Wen Luo
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Zuofeng Liu
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Beiping Zhang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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Wang N, Wang H, Bai Y, Zhao Y, Zheng X, Gao X, Zhang Z, Yang L. Metagenomic Analysis Reveals Difference of Gut Microbiota in ADHD. J Atten Disord 2024; 28:872-879. [PMID: 38327077 DOI: 10.1177/10870547231225491] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
OBJECTIVE Although ADHD is highly heritable, some environmental factors contribute to its development. Given the growing evidence that gut microbiota was involved in psychiatric disorders, we aimed to identify the characteristic composition of the gut microbiota in ADHD. METHODS We recruited 47 medication-naive children and adolescents with ADHD, and 60 healthy controls (HCs). We used shotgun metagenomics to measure the structure of the gut microbiota and analyzed the difference in bacterial taxa between ADHD and HCs. RESULTS Significant differences were found between the ADHD and HC groups in both alpha diversity indices (Simpson index, p = .025 and Shannon index, p = .049) and beta diversity indices (Euclidean distance, Bray-Curtis distance, and JSD distance, p < 2.2e-16). Nine representative species best explain the difference. CONCLUSION Patients with ADHD showed significant differences in the composition of the gut microbiota compared with HCs. These results may help identify potential biomarkers of ADHD.
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Affiliation(s)
- Ning Wang
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders, Peking University Sixth Hospital, Beijing, China
- NHC Key Laboratory of Mental Health, Peking University, Beijing, China
| | - Haibin Wang
- Yan'an Third People's Hospital, Shanxi Province, China
| | - Yu Bai
- Yan'an Third People's Hospital, Shanxi Province, China
| | - Yilu Zhao
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders, Peking University Sixth Hospital, Beijing, China
- NHC Key Laboratory of Mental Health, Peking University, Beijing, China
| | - Xiangyu Zheng
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders, Peking University Sixth Hospital, Beijing, China
- NHC Key Laboratory of Mental Health, Peking University, Beijing, China
| | - Xuping Gao
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders, Peking University Sixth Hospital, Beijing, China
- NHC Key Laboratory of Mental Health, Peking University, Beijing, China
| | - Zifeng Zhang
- Yan'an Third People's Hospital, Shanxi Province, China
| | - Li Yang
- Peking University Sixth Hospital, Beijing, China
- Peking University Institute of Mental Health, Beijing, China
- National Clinical Research Center for Mental Disorders, Peking University Sixth Hospital, Beijing, China
- NHC Key Laboratory of Mental Health, Peking University, Beijing, China
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Bommana S, Hu YJ, Kama M, Wang R, Kodimerla R, Jijakli K, Read TD, Dean D. Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji. mBio 2024; 15:e0306323. [PMID: 38117091 PMCID: PMC10790706 DOI: 10.1128/mbio.03063-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Chlamydia trachomatis (Ct) is the most common sexually transmitted bacterium globally. Endocervical and vaginal microbiome interactions are rarely examined within the context of Ct or among vulnerable populations. We evaluated 258 vaginal and 92 paired endocervical samples from Fijian women using metagenomic shotgun sequencing. Over 37% of the microbiomes could not be classified into sub-community state types (subCSTs). We, therefore, developed subCSTs IV-D0, IV-D1, IV-D2, and IV-E-dominated primarily by Gardnerella vaginalis-to improve classification. Among paired microbiomes, the endocervix had a significantly higher alpha diversity and, independently, higher diversity for high-risk human papilloma virus (HPV) genotypes compared to low-risk and no HPV. Ct-infected endocervical networks had smaller clusters without interactions with potentially beneficial Lactobacillus spp. Overall, these data suggest that G. vaginalis may generate polymicrobial biofilms that predispose to and/or promote Ct and possibly HPV persistence and pathogenicity. Our findings expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding Pacific Islanders.
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Affiliation(s)
- Sankhya Bommana
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Yi-Juan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, USA
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Ruohong Wang
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Reshma Kodimerla
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Kenan Jijakli
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Timothy D. Read
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deborah Dean
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Department of Bioengineering, Joint Graduate Program, University of California San Francisco and University of California Berkeley, San Francisco, California, USA
- Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, California, USA
- University of California San Francisco, Benioff Center for Microbiome Medicine, San Francisco, California, USA
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Lin L, Shen K, Xiao L, lin Y, Feng E, Zhang Y. Identification of prosthetic joint infection by Candida using metagenomic shotgun sequencing. Access Microbiol 2023; 5:000425. [PMID: 37970089 PMCID: PMC10634495 DOI: 10.1099/acmi.0.000425] [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: 02/05/2022] [Accepted: 10/03/2023] [Indexed: 11/17/2023] Open
Abstract
Background Periprosthetic joint infection (PJI) is a serious complication after total knee arthroplasty. Fungal infections are prone to biofilm formation, which makes it hard to diagnose and clarify the pathogenic species. Case Presentation This case study provides evidence of a novel PJI pathogen that is otherwise difficult to detect using conventional methods. A patient was reviewed with persistent postoperative pain, swelling and eventually drainage around the left knee after undergoing a bilateral total knee arthroplasty 2 years previously for progressive osteoarthritis. By using metagenomic shotgun sequencing to analyse both bacterial and fungal agent sequences, we were able to identify fungal strains of Candida tropicalis, a rarely reported and difficult-to-culture PJI pathogen. Conclusion Metagenomic shotgun sequencing enables the detection of difficult-to-detect pathogens and the formulation of treatment recommendations for fungal infections with low positive rates based on gene content analysis.
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Affiliation(s)
- Liqiong Lin
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
| | - Kaiwei Shen
- Institute for Biochemistry and Molecularbiology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Lili Xiao
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
| | - Yu lin
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
| | - Eryou Feng
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
| | - Yiyuan Zhang
- Department of Orthopedics, Fuzhou Second Hospital, Fuzhou, PR China
- Fujian Provincial Clinical Medical Research Center for First Aid and Rehabilitation in Orthopaedic Trauma, Fuzhou, PR China
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Bajagai YS, Yeoh YK, Li X, Zhang D, Dennis PG, Ouwerkerk D, Dart PJ, Klieve AV, Bryden WL. Enhanced meat chicken productivity in response to the probiotic Bacillus amyloliquefaciens H57 is associated with the enrichment of microbial amino acid and vitamin biosynthesis pathways. J Appl Microbiol 2023; 134:7140527. [PMID: 37096395 DOI: 10.1093/jambio/lxad085] [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: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/21/2023] [Indexed: 04/26/2023]
Abstract
AIMS Sub-therapeutic use of antibiotics as a growth promoter in animal diets has either been banned or voluntarily withdrawn from use in many countries to help curb the emergence of antibiotic-resistant pathogens. Probiotics may be an alternative to antibiotics as a growth promoter. We investigated the effects of a novel probiotic strain Bacillus amyloliquefaciens H57 (H57) on the performance and microbiome-associated metabolic potential. METHODS AND RESULTS Broiler chickens were fed either sorghum- or wheat-based diets supplemented with the probiotic H57. The growth rate, feed intake and feed conversion in supplemented birds were compared with those in non-supplemented control. Caecal microbial metabolic functions were studied with shotgun metagenomic sequencing. H57 supplementation significantly increased the growth rate and daily feed intake of meat chickens relative to the non-supplemented controls without any effect on feed conversion ratio. In addition, relative to the non-supplemented controls, gene-centric metagenomics revealed that H57 significantly altered the functional capacity of the caecal microbiome, with amino acid and vitamin synthesis pathways being positively associated with H57 supplementation. CONCLUSIONS Bacillus amyloliquefaciens H57 improves the performance of meat chickens or broilers and significantly modifies the functional potential of their caecal microbiomes, with enhanced potential capacity for amino acid and vitamin biosynthesis.A feed supplement like H57, with the ability to enhance weight gain through modulation of intestinal microbial functions, has the potential to be an alternative to antibiotic growth promoters and provide substantial benefits to the poultry industry.
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Affiliation(s)
- Yadav Sharma Bajagai
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, Australia
- Central Queensland University, Institute for Future Farming Systems, Rockhampton, Australia
| | - Yun Kit Yeoh
- The University of Queensland, Australian Centre for Ecogenomics, Brisbane, Australia
- Australian Institute of Marine Science, TownsvilleAustralia
| | - Xiuhua Li
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, Australia
| | - Dagong Zhang
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, Australia
| | - Paul G Dennis
- The University of Queensland, School of Earth and Environmental Sciences, Brisbane, Australia
| | - Diane Ouwerkerk
- Department of Agriculture and Fisheries, Brisbane, Australia
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, Australia
| | - Peter J Dart
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, Australia
| | - Athol V Klieve
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, Australia
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, Australia
| | - Wayne L Bryden
- The University of Queensland, School of Agriculture and Food Sciences, Brisbane, Australia
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Brisbane, Australia
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D’aes J, Fraiture MA, Bogaerts B, De Keersmaecker SCJ, Roosens NHCJ, Vanneste K. Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products. Life (Basel) 2022; 12:life12121971. [PMID: 36556336 PMCID: PMC9781105 DOI: 10.3390/life12121971] [Citation(s) in RCA: 2] [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] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Genetically modified microorganisms (GMM) are frequently employed for manufacturing microbial fermentation products such as food enzymes or vitamins. Although the fermentation product is required to be pure, GMM contaminations have repeatedly been reported in numerous commercial microbial fermentation produce types, leading to several rapid alerts at the European level. The aim of this study was to investigate the added value of shotgun metagenomic high-throughput sequencing to confirm and extend the results of classical analysis methods for the genomic characterization of unauthorized GMM. By combining short- and long-read metagenomic sequencing, two transgenic constructs were characterized, with insertions of alpha-amylase genes originating from B. amyloliquefaciens and B. licheniformis, respectively, and a transgenic construct with a protease gene insertion originating from B. velezensis, which were all present in all four investigated samples. Additionally, the samples were contaminated with up to three unculturable Bacillus strains, carrying genetic modifications that may hamper their ability to sporulate. Moreover, several samples contained viable Bacillus strains. Altogether these contaminations constitute a considerable load of antimicrobial resistance genes, that may represent a potential public health risk. In conclusion, our study showcases the added value of metagenomics to investigate the quality and safety of complex commercial microbial fermentation products.
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Bommana S, Richards G, Kama M, Kodimerla R, Jijakli K, Read TD, Dean D. Metagenomic Shotgun Sequencing of Endocervical, Vaginal, and Rectal Samples among Fijian Women with and without Chlamydia trachomatis Reveals Disparate Microbial Populations and Function across Anatomic Sites: a Pilot Study. Microbiol Spectr 2022; 10:e0010522. [PMID: 35579443 PMCID: PMC9241848 DOI: 10.1128/spectrum.00105-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 01/30/2022] [Accepted: 04/20/2022] [Indexed: 11/20/2022] Open
Abstract
Chlamydia trachomatis is a sexually transmitted pathogen and a global public health concern. Little is known about the microbial composition and function across endocervical, vaginal, and rectal microbiomes in the context of C. trachomatis infection. We evaluated the microbiomes of 10 age-matched high-risk Fijian women with and without C. trachomatis using metagenomic shotgun sequencing (MSS). Lactobacillus iners and Lactobacillus crispatus dominated the vagina and endocervix of uninfected women. Species often found in higher relative abundance in bacterial vaginosis (BV)-Mageeibacillus indolicus, Prevotella spp., Sneathia spp., Gardnerella vaginalis, and Veillonellaceae spp.-were dominant in C. trachomatis-infected women. This combination of BV pathogens was unique to Pacific Islanders compared to previously studied groups. The C. trachomatis-infected endocervix had a higher diversity of microbiota and microbial profiles that were somewhat different from those of the vagina. However, community state type III (CST-III) and CST-IV predominated, reflecting pathogenic microbiota regardless of C. trachomatis infection status. Rectal microbiomes were dominated by Prevotella and Bacteroides, although four women had unique microbiomes with Gardnerella, Akkermansia, Bifidobacterium, and Brachyspira. A high level of microbial similarity across microbiomes in two C. trachomatis-infected women suggested intragenitorectal transmission. A number of metabolic pathways in the endocervix, driven by BV pathogens and C. trachomatis to meet nutritional requirements for survival/growth, 5-fold higher than that in the vagina indicated that endocervical microbial functions are likely more diverse and complex than those in the vagina. Our novel findings provide the impetus for larger prospective studies to interrogate microbial/microbiome interactions that promote C. trachomatis infection and better define the unique genitorectal microbiomes of Pacific Islanders. IMPORTANCE Chlamydia trachomatis is the primary cause of bacterial sexually transmitted infections worldwide, with a disturbing increase in annual rates. While there is a plethora of data on healthy and pathogenic vaginal microbiomes-defining microbial profiles and associations with sexually transmitted infections (STIs)-far fewer studies have similarly examined the endocervix or rectum. Further, vulnerable populations, such as Pacific Islanders, remain underrepresented in research. We investigated the microbial composition, structure, and function of these anatomic microbiomes using metagenomic shotgun sequencing among a Fijian cohort. We found, primarily among C. trachomatis-infected women, unique microbial profiles in endocervical, vaginal, and rectal microbiomes with an increased diversity and more complex microbial pathways in endocervical than vaginal microbiomes. Similarities in microbiome composition across sites for some women suggested intragenitorectal transmission. These novel insights into genitorectal microbiomes and their purported function require prospective studies to better define Pacific Islander microbiomes and microbial/microbiome interactions that promote C. trachomatis infection.
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Affiliation(s)
- Sankhya Bommana
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Gracie Richards
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Reshma Kodimerla
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Kenan Jijakli
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Timothy D. Read
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Deborah Dean
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
- Department of Bioengineering, Joint Graduate Program, University of California San Francisco and University of California Berkeley, San Francisco, California, USA
- Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, California, USA
- Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, California, USA
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Liang Q, Li J, Zou Y, Hu X, Deng X, Zou B, Liu Y, Wei L, Liang L, Wen X. Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease. Front Cell Dev Biol 2021; 9:731867. [PMID: 34900990 PMCID: PMC8657412 DOI: 10.3389/fcell.2021.731867] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 06/28/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022] Open
Abstract
Background: Dry eye disease (DED) is a multifactorial inflammatory disease of the ocular surface. It is hypothesized that dysbiosis of the conjunctival microbiota contributes to the development of DED. However, species-level compositions of the conjunctival microbiota in DED and the potential dysbiosis involving microorganisms other than bacteria remain largely uncharacterized. Methods: We collected conjunctival impression samples from a cohort of 95 individuals, including 47 patients with DED and 48 healthy subjects. We examined the conjunctival microbiota of these samples using shotgun metagenomic sequencing and analyzed microbial dysbiosis in DED at the species level. Results: The conjunctival microbiota in DED exhibited a decreased α-diversity and an increased inter-individual variation. The α-diversity of female patients with DED was higher than that of male patients. Despite a decreased prevalence in DED, 23 microbial species were identified to show abnormally high abundance in DED samples positive for the species. Among these species, a fungal species Malassezia globosa was enriched female patients. In addition, distinct patterns of associations with disease status were observed for different species of the same genus. For DED subtypes, Staphylococcus aureus and S. capitis were associated with meibomian gland dysfunction (MGD), whereas S. hominis was enriched in patients solely with aqueous tear deficiency (ATD). The microbiota of patients with a mixed type of diagnosis was more similar to MGD patients than ATD patients. Conclusion: We demonstrated that the conjunctival microbiota dysbiosis in DED is characterized by significant heterogeneity. Microbial signatures may offer novel insights into the complicated etiology of DED and potentially promote the development of personalized treatment for DED in the future.
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Affiliation(s)
- Qiaoxing Liang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jing Li
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanli Zou
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, Foshan Hospital Affiliated to Southern Medical University, Foshan, China
| | - Xiao Hu
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiuli Deng
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yu Liu
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lingyi Liang
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Wen
- State Key Laboratory of Ophthalmology, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Schott C, Weigt SS, Turturice BA, Metwally A, Belperio J, Finn PW, Perkins DL. Bronchiolitis obliterans syndrome susceptibility and the pulmonary microbiome. J Heart Lung Transplant 2018; 37:1131-1140. [PMID: 29929823 DOI: 10.1016/j.healun.2018.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 10/19/2017] [Revised: 03/30/2018] [Accepted: 04/18/2018] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Lung transplantation outcomes remain complicated by bronchiolitis obliterans syndrome (BOS), a major cause of mortality and retransplantation for patients. A variety of factors linking inflammation and BOS have emerged, meriting further exploration of the microbiome as a source of inflammation. In this analysis, we determined features of the pulmonary microbiome associated with BOS susceptibility. METHODS Bronchoalveolar lavage (BAL) samples were collected from 25 patients during standard of care bronchoscopies before BOS onset. Microbial DNA was isolated from BAL fluid and prepared for metagenomics shotgun sequencing. Patient microbiomes were phenotyped using k-means clustering and compared to determine effects on BOS-free survival. RESULTS Clustering identified 3 microbiome phenotypes: Actinobacteria dominant (AD), mixed, and Proteobacteria dominant. AD microbiomes, distinguished by enrichment with Gram-positive organisms, conferred reduced odds and risks for patients to develop acute rejection and BOS compared with non-AD microbiomes. These findings were independent of treatment models. Microbiome findings were correlated with BAL cell counts and polymorphonuclear cell percentages. CONCLUSIONS In some populations, features of the microbiome may be used to assess BOS susceptibility. Namely, a Gram-positive enriched pulmonary microbiome may predict resilience to BOS.
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Affiliation(s)
- Cody Schott
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois
| | - S Samuel Weigt
- Division of Pulmonary, Critical Care Medicine, Allergy, and Clinical Immunology, Department of Internal Medicine, University of California at Los Angeles, Los Angeles, California
| | - Benjamin A Turturice
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois
| | - Ahmed Metwally
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - John Belperio
- Division of Pulmonary, Critical Care Medicine, Allergy, and Clinical Immunology, Department of Internal Medicine, University of California at Los Angeles, Los Angeles, California
| | - Patricia W Finn
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois
| | - David L Perkins
- Division of Nephrology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois; Department of Surgery, University of Illinois at Chicago, Chicago, Illinois.
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