1
|
Ai B, Mei Y, Liang D, Wang T, Cai H, Yu D. Uncovering the special microbiota associated with occurrence and progression of gastric cancer by using RNA-sequencing. Sci Rep 2023; 13:5722. [PMID: 37029259 PMCID: PMC10082026 DOI: 10.1038/s41598-023-32809-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/03/2023] [Indexed: 04/09/2023] Open
Abstract
Gastric cancer (GC) has been identified as the third deadly cancer in the world. Accumulating researches suggest a potential role of microorganisms in tumorigenesis. However, the composition of microbiota in GC tissues is not clear and it changes throughout the different stages of GC remain mostly elusive. Our study integrated RNA-Seq data of 727 samples derived from gastric tissues across four datasets and revealed its microbial composition. In order to remove the false positive results, core taxa were defined and characterized. Based on it, we analyzed the influence of biological factors on its composition. The pan-microbiome of gastric tissues was estimated to be over than 1400 genera. Seventeen core genera were identified. Among them, Helicobacter, Lysobacter were significantly enriched in normal tissues, while Pseudomonas was enriched in tumor tissues. Interestingly, Acinetobacter, Pasteurella, Streptomyces, Chlamydia, and Lysobacter, showed a significant increase trend during tumor development and formed strong intra/inter-correlations among them or with other genera. Furthermore, we found that tumor stage played an important role in altering the microbial composition of GC tissues. This study provides support for the in-depth study of tumor microbiome, and the specific microbiome excavated provides a possibility for the subsequent identification of potential biomarkers for GC.
Collapse
Affiliation(s)
- Bin Ai
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Yue Mei
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Dong Liang
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Tengjiao Wang
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China
| | - Hui Cai
- Department of Gastrointestinal Surgery, Changhai Hospital, Shanghai, China.
| | - Dong Yu
- Department of Precision Medicine, Translational Medicine Research Center, Naval Medical University, Shanghai, China.
- Shanghai Key Laboratory of Cell Engineering, Shanghai, China.
| |
Collapse
|
2
|
Abdelhafiz Y, Fernandes JMO, Donati C, Pindo M, Kiron V. Intergenerational Transfer of Persistent Bacterial Communities in Female Nile Tilapia. Front Microbiol 2022; 13:879990. [PMID: 35655994 PMCID: PMC9152445 DOI: 10.3389/fmicb.2022.879990] [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: 02/20/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022] Open
Abstract
Resident microbial communities that can support various host functions play a key role in their development and health. In fishes, microbial symbionts are vertically transferred from the parents to their progeny. Such transfer of microbes in mouthbrooder fish species has not been reported yet. Here, we employed Nile tilapia (Oreochromis niloticus) to investigate the vertical transmission of microbes across generations using a 16S rRNA amplicon sequencing approach, based on the presence of bacteria in different generations. Our analysis revealed that the core microbiome in the buccal cavity and posterior intestine of parents shapes the gut microbiome of the progeny across generations. We speculate that the route of this transmission is via the buccal cavity. The identified core microbiome bacteria, namely Nocardioides, Propionibacterium, and Sphingomonas have been reported to play an essential role in the health and development of offspring. These core microbiome members could have specific functions in fish, similar to mammals.
Collapse
Affiliation(s)
- Yousri Abdelhafiz
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | | | - Claudio Donati
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Massimo Pindo
- Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Viswanath Kiron
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| |
Collapse
|
3
|
Dwiyanto J, Ayub Q, Lee SM, Foo SC, Chong CW, Rahman S. Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective. Microb Genom 2021; 7:000619. [PMID: 34463609 PMCID: PMC8549367 DOI: 10.1099/mgen.0.000619] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 10/19/2020] [Accepted: 06/01/2021] [Indexed: 12/24/2022] Open
Abstract
Ethnicity is consistently reported as a strong determinant of human gut microbiota. However, the bulk of these studies are from Western countries, where microbiota variations are mainly driven by relatively recent migration events. Malaysia is a multicultural society, but differences in gut microbiota persist across ethnicities. We hypothesized that migrant ethnic groups continue to share fundamental gut traits with the population in the country of origin due to shared cultural practices despite subsequent geographical separation. To test this hypothesis, the 16S rRNA gene amplicons from 16 studies comprising three major ethnic groups in Malaysia were analysed, covering 636 Chinese, 248 Indian and 123 Malay individuals from four countries (China, India, Indonesia and Malaysia). A confounder-adjusted permutational multivariate analysis of variance (PERMANOVA) detected a significant association between ethnicity and the gut microbiota (PERMANOVA R2=0.005, pseudo-F=2.643, P=0.001). A sparse partial least squares - discriminant analysis model trained using the gut microbiota of individuals from China, India and Indonesia (representation of Chinese, Indian and Malay ethnic group, respectively) showed a better-than-random performance in classifying Malaysian of Chinese descent, although the performance for Indian and Malay were modest (true prediction rate, Chinese=0.60, Indian=0.49, Malay=0.44). Separately, differential abundance analysis singled out Ligilactobacillus as being elevated in Indians. We postulate that despite the strong influence of geographical factors on the gut microbiota, cultural similarity due to a shared ethnic origin drives the presence of a shared gut microbiota composition. The interplay of these factors will likely depend on the circumstances of particular groups of migrants.
Collapse
Affiliation(s)
- Jacky Dwiyanto
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- Monash University Malaysia Genomics Facility, Bandar Sunway, Malaysia
| | - Sui Mae Lee
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Su Chern Foo
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Chun Wie Chong
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
- Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Malaysia
| |
Collapse
|
4
|
Low DY, Hejndorf S, Tharmabalan RT, Poppema S, Pettersson S. Regional Diets Targeting Gut Microbial Dynamics to Support Prolonged Healthspan. Front Microbiol 2021; 12:659465. [PMID: 33995322 PMCID: PMC8116520 DOI: 10.3389/fmicb.2021.659465] [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: 01/27/2021] [Accepted: 03/29/2021] [Indexed: 01/16/2023] Open
Abstract
In the last 150 years, we have seen a significant increase in average life expectancy, associated with a shift from infectious to non-communicable diseases. The rising incidence of these diseases, for which age is often the largest risk factor, highlights the need for contemporary societies to improve healthy ageing for their growing silver generations. As ageing is an inevitable, non-reversing and highly individualised process, we need to better understand how non-genetic factors like diet choices and commensal gut microbes can modulate the biology of ageing. In this review, we discuss how geographical and ethnic variations influence habitual dietary patterns, nutrient structure, and gut microbial profiles with potential impact on the human healthspan. Several gut microbial genera have been associated with healthy elderly populations but are highly variable across populations. It seems unlikely that a universal pro-longevity gut microbiome exists. Rather, the optimal microbiome appears to be conditional on the microbial functionality acting on regional- and ethnicity-specific trends driven by cultural food context. We also highlight dietary and microbial factors that have been observed to elicit individual and clustered biological responses. Finally, we identify next generation avenues to modify otherwise fixed host functions and the individual ageing trajectory by manipulating the malleable gut microbiome with regionally adapted, personalised food intervention regimens targeted at prolonging human healthspan.
Collapse
Affiliation(s)
- Dorrain Yanwen Low
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Sophia Hejndorf
- Department of Odontology, Karolinska Institutet, Solna, Sweden
| | | | - Sibrandes Poppema
- School of Medical and Life Sciences, Sunway University, Subang Jaya, Malaysia
| | - Sven Pettersson
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Department of Odontology, Karolinska Institutet, Solna, Sweden
- School of Medical and Life Sciences, Sunway University, Subang Jaya, Malaysia
- National Neuroscience Institute, Singapore, Singapore
| |
Collapse
|
5
|
Park CH. Changes in Gastric Microbial Composition before and after Helicobacter pylori Eradication Therapy. Korean J Helicobacter Up Gastrointest Res 2020. [DOI: 10.7704/kjhugr.2020.0028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Owing to advancements in next-generation sequencing and non-culture-based microbial research techniques, we have recognized that many bacterial taxa other than <i>Helicobacter pylori (H. pylori)</i> are present in the human stomach. Gastric microbial composition depends on gastric diseases, including gastritis, atrophic gastritis, intestinal metaplasia, and gastric cancer. Although <i>H. pylori</i> is a major factor associated with gastric cancer development, other bacterial taxa may affect gastric carcinogenesis. Because the risk of gastric cancer development can be reduced through <i>H. pylori</i> eradication, many investigators have studied the changes in the microbial composition in the stomach after <i>H. pylori</i> eradication. The gastric microbiome in patients with <i>H. pylori</i> infection typically shows abundance of <i>H. pylori</i> and a low microbial diversity index. If we treat <i>H. pylori</i>-infected patients with antibiotics, microbial diversity increases, and the relative abundance also increases in many bacterial taxa. Several studies suggested that the microbial composition in patients with <i>H. pylori</i> infection could be restored by <i>H. pylori</i> eradication therapy; however, there have been inconsistent findings of the abundant bacterial taxa after <i>H. pylori</i> eradication in patients with atrophic gastritis and intestinal metaplasia. More studies are required to reach a definitive conclusion on restoration of the microbial composition after <i>H. pylori</i> eradication according to the severity of gastric inflammation.
Collapse
|
6
|
Tziatzios G, Gkolfakis P, Papanikolaou IS, Mathur R, Pimentel M, Giamarellos-Bourboulis EJ, Triantafyllou K. Gut Microbiota Dysbiosis in Functional Dyspepsia. Microorganisms 2020; 8:E691. [PMID: 32397332 DOI: 10.3390/microorganisms8050691] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [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: 04/13/2020] [Revised: 04/28/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
Functional dyspepsia (FD) is one of the most prevalent chronic functional gastrointestinal disorders. Several distinct pathophysiological mechanisms, including gastro duodenal motor disorders, visceral hypersensitivity, brain-gut interactions, duodenal subtle inflammation, and genetic susceptibility, have been implicated in the pathogenesis of the disease, so far. However, emerging evidence suggests that both quantitative and qualitative disturbances of the gastrointestinal microbiota may also be implicated. In this context, several studies have demonstrated differences of the commensal bacterial community between patients with FD and healthy controls, while others have shown that intestinal dysbiosis might associate with disease’s symptoms severity. Elucidating these complex interactions constituting the microbiota and host crosstalk, may eventually lead to the discovery of novel, targeted therapeutic approaches that may be efficacious in treating the multiple aspects of the disorder. In this review, we summarize the data of the latest research with focus on the association between gut microbiota alterations and host regarding the pathogenesis of FD.
Collapse
|