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Liu F, Wei R, Xu X, Lan M, Tao B, Liang Z, Zeng J. Alterations of gut microbiota in infants with biliary atresia identified by 16S rRNA-sequencing. BMC Pediatr 2024; 24:117. [PMID: 38355416 PMCID: PMC10865691 DOI: 10.1186/s12887-024-04582-9] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 01/21/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Biliary atresia (BA) is a severe neonatal disease with progressive intra- and extra-hepatic bile ducts inflammation and hepatic fibrosis. Characterization of gut microbiome profiles in infants with biliary atresia can provide valuable information and potential disease biomarkers. Our study aims to explore the relationship between gut microbiota and biliary atresia. METHODS 16 S ribosomal RNA (rRNA) gene sequencing was carried out to identify the differences in composition and diversity of gut microbiota between infants with BA and healthy subjects. A total of 31 infants with biliary atresia and 20 healthy subjects were recruited. RESULTS The composition of gut microbiota in BA group was significantly different with the normal control group (P < 0.05) and the abundance ratio of Klebsiella/Bifidobacterium showed great potential for identification of BA (P < 0.01). In addition, the differential bacterial taxa were involved in lipid and vitamins metabolism. CONCLUSION Our results could provide potential non-invasive biomarker for identification of biliary atresia and contribute to the treatment in terms of ameliorating microbiota dysbiosis.
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Affiliation(s)
- Fei Liu
- Department of Pediatric Surgery, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, Guangdong, 510623, China
| | - Ru Wei
- Department of Children Health Care, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, Guangdong, 510623, China
| | - Xiaogang Xu
- Department of Pediatric Surgery, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, Guangdong, 510623, China
| | - Menglong Lan
- Department of Pediatric Surgery, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, Guangdong, 510623, China
| | - Boyuan Tao
- Department of Pediatric Surgery, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, Guangdong, 510623, China
| | - Zijian Liang
- Department of Pediatric Surgery, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, Guangdong, 510623, China
| | - Jixiao Zeng
- Department of Pediatric Surgery, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 9 Jinsui Road, Guangzhou, Guangdong, 510623, China.
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Makrakis LR, Oliveira VC, Santos ES, Nascimento C, Watanabe E, Ribeiro AB, Silva-Lovato CH. Analysis of microbial communities of ocular prostheses and anophthalmic sockets using 16S rRNA gene sequencing. Biofouling 2023; 39:555-564. [PMID: 37470406 DOI: 10.1080/08927014.2023.2236562] [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: 03/28/2023] [Revised: 06/06/2023] [Accepted: 07/07/2023] [Indexed: 07/21/2023]
Abstract
Ocular prostheses are liable to host microbial adhesion, which can favor conjunctival inflammation. Knowing the microbiota of the ocular prosthesis and anophthalmic socket is important for predicting infection-related pathogens. This study evaluated the microbiota of the prostheses and anophthalmic sockets of six individuals by 16S rRNA sequencing. The microbial abundance and diversity were analyzed using the Operational Taxonomic Units at the genus level. Forty-seven phyla, capturing 1,258 named genera, were recorded in the sample set. In both sites, the most frequent genera were Fusobacterium, Staphylococcus, Prevotella, and Streptococcus. The microbial abundance was higher for the anophthalmic socket than for the prosthesis. Alpha diversity showed no significant differences in bacterial richness or diversity between sites. Although the microbial abundance in the anophthalmic socket was higher, both sites had similar microbiota with high diversity and low dominance among the genera.
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Affiliation(s)
- L R Makrakis
- Department of Dental Materials and Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - V C Oliveira
- Department of Dental Materials and Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Human Exposome and Infectious Diseases Network-HEID, School of Nursing of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - E S Santos
- Department of Clinical Toxicological and Bromatologic Analysis, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - C Nascimento
- Department of Dental Materials and Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - E Watanabe
- Human Exposome and Infectious Diseases Network-HEID, School of Nursing of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Department of Restorative Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - A B Ribeiro
- Department of Dental Materials and Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - C H Silva-Lovato
- Department of Dental Materials and Prosthodontics, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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Wang Y, Yan Y, Thompson KN, Bae S, Accorsi EK, Zhang Y, Shen J, Vlamakis H, Hartmann EM, Huttenhower C. Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome 2021; 9:17. [PMID: 33478576 PMCID: PMC7819323 DOI: 10.1186/s40168-020-00961-3] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/06/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND High-throughput sequencing provides a powerful window into the structural and functional profiling of microbial communities, but it is unable to characterize only the viable portion of microbial communities at scale. There is as yet not one best solution to this problem. Previous studies have established viability assessments using propidium monoazide (PMA) treatment coupled with downstream molecular profiling (e.g., qPCR or sequencing). While these studies have met with moderate success, most of them focused on the resulting "viable" communities without systematic evaluations of the technique. Here, we present our work to rigorously benchmark "PMA-seq" (PMA treatment followed by 16S rRNA gene amplicon sequencing) for viability assessment in synthetic and realistic microbial communities. RESULTS PMA-seq was able to successfully reconstruct simple synthetic communities comprising viable/heat-killed Escherichia coli and Streptococcus sanguinis. However, in realistically complex communities (computer screens, computer mice, soil, and human saliva) with E. coli spike-in controls, PMA-seq did not accurately quantify viability (even relative to variability in amplicon sequencing), with its performance largely affected by community properties such as initial biomass, sample types, and compositional diversity. We then applied this technique to environmental swabs from the Boston subway system. Several taxa differed significantly after PMA treatment, while not all microorganisms responded consistently. To elucidate the "PMA-responsive" microbes, we compared our results with previous PMA-based studies and found that PMA responsiveness varied widely when microbes were sourced from different ecosystems but were reproducible within similar environments across studies. CONCLUSIONS This study provides a comprehensive evaluation of PMA-seq exploring its quantitative potential in synthetic and complex microbial communities, where the technique was effective for semi-quantitative purposes in simple synthetic communities but provided only qualitative assessments in realistically complex community samples. Video abstract.
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Affiliation(s)
- Ya Wang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Kelsey N. Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Sena Bae
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Emma K. Accorsi
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
| | - Yancong Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Jiaxian Shen
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
- Department of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Harvard University, 655 Huntington Avenue, Boston, MA 02115 USA
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