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Shimomura Y, Sugi Y, Kume A, Tanaka W, Yoshihara T, Matsuura T, Komiya Y, Ogata Y, Suda W, Hattori M, Higurashi T, Nakajima A, Matsumoto M. Strain-level detection of Fusobacterium nucleatum in colorectal cancer specimens by targeting the CRISPR-Cas region. Microbiol Spectr 2023; 11:e0512322. [PMID: 37819098 PMCID: PMC10714804 DOI: 10.1128/spectrum.05123-22] [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: 12/13/2022] [Accepted: 08/25/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE Fusobacterium nucleatum is one of the predominant oral bacteria in humans. However, this bacterium is enriched in colorectal cancer (CRC) tissues and may be involved in CRC development. Our previous research suggested that F. nucleatum is present in CRC tissues originating from the oral cavity using a traditional strain-typing method [arbitrarily primed polymerase chain reaction (AP-PCR)]. First, using whole-genome sequencing, this study confirmed an exemplary similarity between the oral and tumoral strains derived from each patient with CRC. Second, we successfully developed a method to genotype this bacterium at the strain level, targeting the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated system, which is hypervariable (defined as F. nucleatum-strain genotyping PCR). This method can identify F. nucleatum strains in cryopreserved samples and is significantly superior to traditional AP-PCR, which can only be performed on isolates. The new methods have great potential for application in etiological studies of F. nucleatum in CRC.
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Affiliation(s)
- Yumi Shimomura
- Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Tokyo, Japan
| | - Yutaka Sugi
- Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Tokyo, Japan
| | - Aiko Kume
- Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Tokyo, Japan
| | - Wataru Tanaka
- Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Tokyo, Japan
| | - Tsutomu Yoshihara
- Department of Gastroenterology and Hepatology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Tetsuya Matsuura
- Department of Gastroenterology and Hepatology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Yasuhiko Komiya
- Department of Gastroenterology and Hepatology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Yusuke Ogata
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Wataru Suda
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masahira Hattori
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Takuma Higurashi
- Department of Gastroenterology and Hepatology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Atsushi Nakajima
- Department of Gastroenterology and Hepatology, Yokohama City University School of Medicine, Yokohama, Japan
| | - Mitsuharu Matsumoto
- Dairy Science and Technology Institute, Kyodo Milk Industry Co. Ltd., Tokyo, Japan
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Chu Y, Meng Q, Yu J, Zhang J, Chen J, Kang Y. Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages. Microbiol Spectr 2023; 11:e0455122. [PMID: 36951555 PMCID: PMC10101075 DOI: 10.1128/spectrum.04551-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/06/2023] [Indexed: 03/24/2023] Open
Abstract
The vast population of bacterial phages or viruses (virome) plays pivotal roles in the ecology of human microbial flora and health conditions. Obstacles, including poor viral sequence inference, strain-sensitive virus-host relationship, and the high diversity among individuals, hinder the in-depth understanding of the human virome. We conducted longitudinal studies of the virome based on constructing a high-quality personal reference metagenome (PRM). By applying long-read sequencing for representative samples, we could build a PRM of high continuity that allows accurate annotation and abundance estimation of viruses and bacterial species in all samples of the same individual by aligning short sequencing reads to the PRM. We applied this approach to a series of fecal samples collected for 6 months from a 2-year-old boy who had experienced a 2-month flare-up of atopic eczema (dermatitis) in this period. We identified 31 viral strains in the patient's gut microbiota and deciphered their strain-level relationship to their bacterial hosts. Among them, a lytic crAssphage developed into a dozen substrains and coordinated downregulation in the catabolism of aromatic amino acids (AAAs) in their host bacteria which govern the production of immune-active AAA derivates. The metabolic alterations confirmed based on metabolomic assays cooccurred with symptom remission. Our PRM-based analysis provides an easy approach for deciphering the dynamics of the strain-level human gut virome in the context of entire microbiota. Close temporal correlations among virome alteration, microbial metabolism, and disease remission suggest a potential mechanism for how bacterial phages in microbiota are intimately related to human health. IMPORTANCE The vast populations of viruses or bacteriophages in human gut flora remain mysterious. However, poor annotation and abundance estimation remain obstacles to strain-level analysis and clarification of their roles in microbiome ecology and metabolism associated with human health and diseases. We demonstrate that a personal reference metagenome (PRM)-based approach provides strain-level resolution for analyzing the gut microbiota-associated virome. When applying such an approach to longitudinal samples collected from a 2-year-old boy who has experienced a 2-month flare-up of atopic eczema, we observed thriving substrains of a lytic crAssphage, showing temporal correlation with downregulated catabolism of aromatic amino acids, lower production of immune-active metabolites, and remission of the disease. The PRM-based approach is practical and powerful for strain-centric analysis of the human gut virome, and the underlying mechanism of how strain-level virome dynamics affect disease deserves further investigation.
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Affiliation(s)
- Yanan Chu
- Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Qingren Meng
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Jun Yu
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Zhang
- Department of Pediatric, Peking University Third Hospital, Beijing, China
| | - Jing Chen
- Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
| | - Yu Kang
- Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation, Beijing, China
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Liu P, Hu S, He Z, Feng C, Dong G, An S, Liu R, Xu F, Chen Y, Ying X. Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome. Front Microbiol 2022; 13:828254. [PMID: 35602026 PMCID: PMC9119422 DOI: 10.3389/fmicb.2022.828254] [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: 12/03/2021] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have been proposed to decipher strains in metagenomes. However, strain-level complexity is far from being well characterized up to date. As the indicator of strain-level complexity, metagenomic single-nucleotide polymorphisms (SNPs) have been utilized to disentangle conspecific strains. Lots of SNP-based tools have been developed to identify strains in metagenomes. However, the sufficient sequencing depth for SNP and strain-level analysis remains unclear. We conducted ultra-deep sequencing of the human gut microbiome and constructed an unbiased framework to perform reliable SNP analysis. SNP profiles of the human gut metagenome by ultra-deep sequencing were obtained. SNPs identified from conventional and ultra-deep sequencing data were thoroughly compared and the relationship between SNP identification and sequencing depth were investigated. The results show that the commonly used shallow-depth sequencing is incapable to support a systematic metagenomic SNP discovery. In contrast, ultra-deep sequencing could detect more functionally important SNPs, which leads to reliable downstream analyses and novel discoveries. We also constructed a machine learning model to provide guidance for researchers to determine the optimal sequencing depth for their projects (SNPsnp, https://github.com/labomics/SNPsnp). To conclude, the SNP profiles based on ultra-deep sequencing data extend current knowledge on metagenomics and highlights the importance of evaluating sequencing depth before starting SNP analysis. This study provides new ideas and references for future strain-level investigations.
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Affiliation(s)
- Pu Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Shuofeng Hu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhen He
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Chao Feng
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Guohua Dong
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Sijing An
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Runyan Liu
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Fang Xu
- Yongkang First People’s Hospital, Yongkang, China
| | - Yaowen Chen
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xiaomin Ying
- Center for Computational Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
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Mahammed KS, Das AK. Design and evaluation of a simple and affordable transfer assistive device for wheelchair users in the context of developing country. Disabil Rehabil Assist Technol 2020; 17:549-554. [PMID: 32744135 DOI: 10.1080/17483107.2020.1800113] [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] [Indexed: 10/23/2022]
Abstract
PURPOSE The present study aimed at designing a simple, affordable, yet safe transfer assistive device (TAD) for lower limb impaired individuals in the context of a developing country. METHODS The preliminary study carried out, comprising a pilot survey with the involvement of stakeholder's views to design and develop the proposed device that had a unique feature. To evaluate the present TAD in terms of user's comfort of use and level of physical strain, subjects including 19 healthy students serving as "patients" have participated in a laboratory-simulated setting. Data was collected based on user's physiologic effort and rate of perceived exertion using Heart rate monitoring device (Polar RS 400 heart taster) and Borg's scale, respectively. RESULTS The data were analysed statistically and revealed that the regression equation for predicting the RPE from HR showed 31.3% of the variance in RPE was predictable from the level of HR. The ANOVA significance also indicates the model is statistically significant with (p < 0.013). Similarly, the estimated strain level has computed in terms of %HRR, and the physical strain averaged over the subjects who performed the task (n = 19) was expressed in terms of (mean ± SD) %HRR were (16.21±7.64%) which was a relatively smaller strain level as compared to the previous research report. CONCLUSION The present device found a potentially affordable solution for reducing fatigue and strain level that might develop during unassisted transfer. Similarly, the unique feature of the armpit support has contributed to dynamic contact force reduction and as double safety support.Implications for rehabilitationThe use of transfer assistive device is associated with increased patient satisfaction and privacy of usersImproved patient adherence and cooperation with caregivers in rehabilitation center.Encourages the rehabilitation settings to use transfer assistive devices instead of manual handling there by increase the recovery period.
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Affiliation(s)
- Kelifa Seid Mahammed
- Department of Design, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Amarendra Kumar Das
- Department of Design, Indian Institute of Technology Guwahati, Guwahati, Assam, India
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Ramia NE, El Kheir SM, Taha S, Mangavel C, Revol-Junelles AM, Borges F. Multilocus sequence typing of Carnobacterium maltaromaticum strains associated with fish disease and dairy products. J Appl Microbiol 2018; 126:377-387. [PMID: 30307684 DOI: 10.1111/jam.14127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 06/21/2018] [Revised: 09/18/2018] [Accepted: 09/28/2018] [Indexed: 01/15/2023]
Abstract
AIMS Carnobacterium maltaromaticum is a lactic acid bacterium of technological interest in the field of dairy ripening and food bioprotection and is generally recognized as safe in the United States. As it is associated with fish infections, the European Food Safety Agency did not include this species in the qualified presumption safety list of micro-organisms. This implies that the risk assessment for the species has to be performed at the strain level. METHODS AND RESULTS Multilocus sequence typing (MLST) is a tool that (i) potentially allows to discriminate strains isolated from diseased fish from apathogenic strains and (ii) to assess the genetic relatedness between both groups of strains. In this study, we characterized by MLST 21 C. maltaromaticum strains including 16 strains isolated from diseased fish and 5 apathogenic dairy strains isolated from cheese. The resulting population structure was investigated by integrating these new data to the previously published population structure (available at http://pubmlst.org), which represents an overall of 71 strains. CONCLUSIONS This analysis revealed that none of the strains isolated from diseased fish is assigned to a clonal complex containing cheese isolates, and that 11 strains exhibit singleton genotypes suggesting that the population of diseased fish isolates is not clonal. SIGNIFICANCE AND IMPACT OF THE STUDY This study thus provides a population structure of C. maltaromaticum that could serve in the future as a reference that could contribute to the risk assessment of C. maltaromaticum strains intended to be used in the food chain.
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Affiliation(s)
- N E Ramia
- Université de Lorraine, LIBio, Nancy, France.,Laboratoire de Biotechnologies Appliquées, EDST, Université Libanaise, Tripoli, Lebanon
| | - S M El Kheir
- Université de Lorraine, LIBio, Nancy, France.,Laboratoire de Biotechnologies Appliquées, EDST, Université Libanaise, Tripoli, Lebanon
| | - S Taha
- Laboratoire de Biotechnologies Appliquées, EDST, Université Libanaise, Tripoli, Lebanon
| | - C Mangavel
- Université de Lorraine, LIBio, Nancy, France
| | | | - F Borges
- Université de Lorraine, LIBio, Nancy, France
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