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Tang-Wing C, Mohanty I, Bryant M, Makowski K, Melendez D, Dorrestein PC, Knight R, Caraballo-Rodríguez AM, Allaband C, Jenné K. Impact of diet change on the gut microbiome of common marmosets ( Callithrix jacchus). mSystems 2024; 9:e0010824. [PMID: 38975760 PMCID: PMC11334461 DOI: 10.1128/msystems.00108-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/01/2024] [Indexed: 07/09/2024] Open
Abstract
Gastrointestinal diseases are the most frequently reported clinical problems in captive common marmosets (Callithrix jacchus), often affecting the health and welfare of the animal and ultimately their use as a research subject. The microbiome has been shown to be intimately connected to diet and gastrointestinal health. Here, we use shotgun metagenomics and untargeted metabolomics in fecal samples of common marmosets collected before, during, and after a dietary transition from a biscuit to a gel diet. The overall health of marmosets, measured as weight recovery and reproductive outcome, improved after the diet transition. Moreover, each marmoset pair had significant shifts in the microbiome and metabolome after the diet transition. In general, we saw a decrease in Escherichia coli and Prevotella species and an increase in Bifidobacterium species. Untargeted metabolic profiles indicated that polyamine levels, specifically cadaverine and putrescine, were high after diet transition, suggesting either an increase in excretion or a decrease in intestinal reabsorption at the intestinal level. In conclusion, our data suggest that Bifidobacterium species could potentially be useful as probiotic supplements to the laboratory marmoset diet. Future studies with a larger sample size will be beneficial to show that this is consistent with the diet change. IMPORTANCE Appropriate diet and health of the common marmoset in captivity are essential both for the welfare of the animal and to improve experimental outcomes. Our study shows that a gel diet compared to a biscuit diet improves the health of a marmoset colony, is linked to increases in Bifidobacterium species, and increases the removal of molecules associated with disease. The diet transition had an influence on the molecular changes at both the pair and time point group levels, but only at the pair level for the microbial changes. It appears to be more important which genes and functions present changed rather than specific microbes. Further studies are needed to identify specific components that should be considered when choosing an appropriate diet and additional supplementary foods, as well as to validate the benefits of providing probiotics. Probiotics containing Bifidobacterium species appear to be useful as probiotic supplements to the laboratory marmoset diet, but additional work is needed to validate these findings.
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Affiliation(s)
- Cassandra Tang-Wing
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Ipsita Mohanty
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Katherine Makowski
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
| | - Daira Melendez
- Bioinformatics Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA
| | | | - Celeste Allaband
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Keith Jenné
- Animal Care Program, University of California, San Diego, La Jolla, California, USA
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2
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Li J, Gao X, Sun X, Li H, Wei J, Lv L, Zhu L. Investigating the causal role of the gut microbiota in esophageal cancer and its subtypes: a two-sample Mendelian randomization study. BMC Cancer 2024; 24:416. [PMID: 38575885 PMCID: PMC10996172 DOI: 10.1186/s12885-024-12205-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/29/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Through research on the gut microbiota (GM), increasing evidence has indicated that the GM is associated with esophageal cancer (ESCA). However, the specific cause-and-effect relationship remains unclear. In this study, Mendelian randomization (MR) analysis was applied to investigate the causal relationship between the GM and ESCA, including its subtypes. METHODS We collected information on 211 GMs and acquired data on ESCA and its subtypes through genome-wide association studies (GWASs). The causal relationship was primarily assessed using the inverse variance weighted (IVW) method. Additionally, we applied the weighted median estimator (WME) method, MR-Egger method, weighted mode, and simple mode to provide further assistance. Subsequent to these analyses, sensitivity analysis was conducted using the MR-Egger intercept test, MR-PRESSO global test, and leave-one-out method. RESULT Following our assessment using five methods and sensitivity analysis, we identified seven GMs with potential causal relationships with ESCA and its subtypes. At the genus level, Veillonella and Coprobacter were positively correlated with ESCA, whereas Prevotella9, Eubacterium oxidoreducens group, and Turicibacter were negatively correlated with ESCA. In the case of esophageal adenocarcinoma (EAC), Flavonifractor exhibited a positive correlation, while Actinomyces exhibited a negative correlation. CONCLUSION Our study revealed the potential causal relationship between GM and ESCA and its subtypes, offering novel insights for the advancement of ESCA diagnosis and treatment.
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Affiliation(s)
- Jia Li
- Thoracic Surgery Department, Jinan Central Hospital, Shandong University, Jinan, 250000, China
| | - Xuedi Gao
- Thoracic Surgery Department, Jinan Mingshui Eye Hospital, Jinan, 250000, China
| | - Xiaoming Sun
- Thoracic Surgery Department, Jinan Central Hospital, Jinan, 250000, China
| | - Hao Li
- Thoracic Surgery Department, Jinan Central Hospital, Shandong First Medical University, Jinan, 250000, China
| | - Jiaheng Wei
- Thoracic Surgery Department, Weifang Medical University, Weifang, 261000, China
| | - Lin Lv
- Thoracic Surgery Department, Jinan Central Hospital, Shandong University, Jinan, 250000, China
| | - Liangming Zhu
- Thoracic Surgery Department, Jinan Central Hospital, Shandong University, Jinan, 250000, China.
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Patel H, Harris RA, Qian JH, Oezguen N, Watson A, Szigeti RG, Cho S, Ruan W, Britto S, Opekun A, Preidis G, Kellermayer R. Genetic Variation Between Small Bowel and Colon-Predominant Crohn's Disease. Cell Mol Gastroenterol Hepatol 2024; 17:1069-1071. [PMID: 38369131 PMCID: PMC11127623 DOI: 10.1016/j.jcmgh.2024.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 02/09/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Affiliation(s)
- Halee Patel
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - R Alan Harris
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justin H Qian
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas; Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, Texas
| | - Ashleigh Watson
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Reka G Szigeti
- Clinical Pathology and Genomic Medicine, Methodist Hospital, Weill Cornell Medical College, Houston, Texas
| | - Stanley Cho
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Wenly Ruan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Savini Britto
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Antone Opekun
- Department of Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Geoffrey Preidis
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Richard Kellermayer
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas; United States Department of Agriculture Children's Nutrition and Research Center, Houston, Texas.
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Liao L, Sun Y, Huang L, Ye L, Chen L, Shen M. A novel approach for exploring the regional features of vaginal fluids based on microbial relative abundance and alpha diversity. J Forensic Leg Med 2023; 100:102615. [PMID: 37995431 DOI: 10.1016/j.jflm.2023.102615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/14/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023]
Abstract
Vaginal fluids are one of the most common biological samples in forensic sexual assault cases, and their characterization is vital to narrow the scope of investigation. Presently, approaches for identifying vaginal fluids in different regions are not only rare but also have certain limitations. However, the microbiome has shown the potential to identify the source of body fluids and reveal the characteristics of individuals. In this study, 16S rRNA gene high-throughput sequencing was used to characterize the vaginal microbial community from three regions, Sichuan, Hainan and Hunan. In addition, data on relative abundance and alpha diversity were used to construct a random forest model. The results revealed that the dominant genera in the three regions were Lactobacillus, followed by Gardnerella. In addition, Ureaplasma, Nitrospira, Nocardiodes, Veillonella and g-norank-f-Vicinamibacteraceae were significantly enriched genera in Sichuan, llumatobacter was enriched in Hainan, and Pseudomonas was enriched in Hunan. The random forest classifier based on combined data on relative abundance and alpha diversity had a good ability to distinguish vaginal fluids with similar dominant microbial compositions in the three regions. The study suggests that combining high-throughput sequencing data with machine learning models has good potential for application in the biogeographic inference of vaginal fluids.
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Affiliation(s)
- Lili Liao
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China; Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yunxia Sun
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Litao Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Linying Ye
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Mei Shen
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
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5
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Yan XY, Yao JP, Li YQ, Xiao XJ, Yang WQ, Chen SJ, Tang TC, Yang YQ, Qu L, Hou YJ, Chen M, Li Y. Effects of acupuncture on gut microbiota and short-chain fatty acids in patients with functional constipation: a randomized placebo-controlled trial. Front Pharmacol 2023; 14:1223742. [PMID: 37719865 PMCID: PMC10502303 DOI: 10.3389/fphar.2023.1223742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/19/2023] Open
Abstract
Objective: To comprehensively evaluate the effect of acupuncture on gut microbiota, identify specific microbes closely related to the clinical efficacy of acupuncture, and explored the role of short-chain fatty acids (SCFAs). Methods: A randomized placebo-controlled trial was conducted with 80 FC patients and 28 healthy controls (HCs). FC patients randomly received 16 acupuncture (n = 40) or sham acupuncture (n = 40) sessions over 4 weeks; HCs received no treatment. The change in the proportion of patients with mean weekly complete spontaneous bowel movements (CSBMs) was considered as the primary outcome measure. Moreover, the composition and the predictive metabolic function of the gut microbiota from feceal samples were analyzed by 16S rRNA gene sequencing, while feceal SCFAs were identified via gas chromatography-mass spectrometry (GC-MS). Results: Compared to sham acupuncture, acupuncture significantly increased the proportion of CSBM responders, and improved spontaneous bowel movements (SBMs), straining, stool consistency, and quality of life. Moreover, Sequencing of 16S rRNA genes revealed that acupuncture improved β-diversity and restored the composition of gut microbiota. Specifically, the abundance of beneficial bacteria such as g_Lactobacillus increased while that of pathogenic bacteria such as g_Pseudomonas decreased after acupuncture, which were significantly correlated with alleviated symptoms. Moreover, ten microbes including g_Coprobacter, g_Lactobacillus, and g_Eubacterium_coprostanoligenes_group might be considered acupuncture-specific microbes, and formed a stable interaction network. Additionally, GC-MS analysis indicated that acupuncture increased the content of butyrate acid in the gut, which was positively correlated with an increase in defecation frequency and a decrease in acupuncture-related pathogens. Finally, acupuncture specific-microbes including g_Coprobacter, g_Lactobacillus, g_Pseudomonas, g_Eubacterium_coprostanoligenes_group, g_Erysipelotrichaceae_UCG.003, g_Prevotellaceae_UCG.001, and g_Rolstonia could accurately predict the clinical efficacy of acupuncture (AUC = 0.918). Conclusion: Acupuncture could effectively improve clinical symptoms in FC patients, and was associated with gut microbiota reshaping and increased butyrate acid levels. Moreover, key microbial genera such as g_Coprobacter and g_Lactobacillus was predictive of acupuncture efficacy in treating FC. Future studies are required to validate the causal relationship between key microbial genera and acupuncture clinical efficacy, and should explore further metabolic pathways for designing personalized treatment strategies. Clinical Trial Registration: http://www.chictr.org.cn, Identifier: ChiCTR2100048831.
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Affiliation(s)
- Xiang-Yun Yan
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jun-Peng Yao
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan-Qiu Li
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xian-Jun Xiao
- School of Health Preservation and Rehabilitation, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wan-Qing Yang
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Si-Jue Chen
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tai-Chun Tang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu-Qing Yang
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liu Qu
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yu-Jun Hou
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Min Chen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ying Li
- School of Acupuncture and Tuina, Chengdu University of Traditional Chinese Medicine, Chengdu, China
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6
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Mannion A, Sheh A, Shen Z, Dzink-Fox J, Piazuelo MB, Wilson KT, Peek R, Fox JG. Shotgun Metagenomics of Gastric Biopsies Reveals Compositional and Functional Microbiome Shifts in High- and Low-Gastric-Cancer-Risk Populations from Colombia, South America. Gut Microbes 2023; 15:2186677. [PMID: 36907988 PMCID: PMC10026914 DOI: 10.1080/19490976.2023.2186677] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
Along with Helicobacter pylori infection, the gastric microbiota is hypothesized to modulate stomach cancer risk in susceptible individuals. Whole metagenomic shotgun sequencing (WMS) is a sequencing approach to characterize the microbiome with advantages over traditional culture and 16S rRNA sequencing including identification of bacterial and non-bacterial taxa, species/strain resolution, and functional characterization of the microbiota. In this study, we used WMS to survey the microbiome in extracted DNA from antral gastric biopsy samples from Colombian patients residing in the high-risk gastric cancer town Túquerres (n = 10, H. pylori-positive = 7) and low-risk town of Tumaco (n = 10, H. pylori-positive = 6). Kraken2/Bracken was used for taxonomic classification and abundance. Functional gene profiles were inferred by InterProScan and KEGG analysis of assembled contigs and gene annotation. The most abundant taxa represented bacteria, non-human eukaryota, and viral genera found in skin, oral, food, and plant/soil environments including Staphylococus, Streptococcus, Bacillus, Aspergillus, and Siphoviridae. H. pylori was the predominant taxa present in H. pylori-positive samples. Beta diversity was significantly different based on H. pylori-status, risk group, and sex. WMS detected more bacterial taxa than 16S rRNA sequencing and aerobic, anaerobic, and microaerobic culture performed on the same gastric biopsy samples. WMS identified significant differences in functional profiles found between H. pylori-status, but not risk or sex groups. H. pylori-positive samples were significantly enriched for H. pylori-specific genes including virulence factors such as vacA, cagA, and urease, while carbohydrate and amino acid metabolism genes were enriched in H. pylori-negative samples. This study shows WMS has the potential to characterize the taxonomy and function of the gastric microbiome as risk factors for H. pylori-associated gastric disease. Future studies will be needed to compare and validate WMS versus traditional culture and 16S rRNA sequencing approaches for characterization of the gastric microbiome.
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Affiliation(s)
- Anthony Mannion
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Alexander Sheh
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Zeli Shen
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - JoAnn Dzink-Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - M. Blanca Piazuelo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T Wilson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard Peek
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James G. Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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7
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Yamazaki Y, Moriya S, Kawarai S, Morita H, Kikusui T, Iriki A. Effects of enhanced insect feeding on the faecal microbiota and transcriptome of a family of captive common marmosets (Callithrix jacchus). PLoS One 2022; 17:e0279380. [PMID: 36548292 PMCID: PMC9779035 DOI: 10.1371/journal.pone.0279380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
Common marmosets have been widely used in biomedical research for years. Nutritional control is an important factor in managing their health, and insect intake would be beneficial for that purpose because common marmosets frequently feed on insects in natural habitats. Here, we examined the effect of enhanced insect feeding on the gut by analysing the faecal microbiota and transcripts of captive marmosets. A family consisting of six marmosets was divided into two groups. During the seven-day intervention period, one group (the insect feeding group, or Group IF) was fed one cricket and one giant mealworm per marmoset per day, while the other (the control group, or Group C) was not fed these insects. RNA was extracted from faecal samples to evaluate the ecology and transcripts of the microbiota, which were then compared among time points before (Pre), immediately after (Post), and two weeks after the intervention (Follow_up) using total RNA sequencing. The gut microbiota of marmosets showed Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria as dominant phyla. Linear discriminant analysis showed differential characteristics of microbiota with and without insect feeding treatment. Further analysis of differentially expressed genes revealed increases and decreases in Bacteroidetes and Firmicutes, respectively, corresponding to the availability of insects under both Post and Follow_up conditions. Significant changes specific to insect feeding were also detected within the transcriptome, some of which were synchronized with the fluctuations in the microbiota, suggesting a functional correlation or interaction between the two. The rapid changes in the microbiota and transcripts may be achieved by the microbiota community originally developed in the wild through marmosets' feeding ecology. The results were informative for identifying the physiological impact of insect feeding to produce a better food regimen and for detecting transcripts that are currently unidentifiable.
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Affiliation(s)
- Yumiko Yamazaki
- Laboratory for Symbolic Cognitive Development, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
- * E-mail:
| | - Shigeharu Moriya
- Photonics Control Technology Team, RIKEN Center for Advanced Photonics, Numazu, Shizuoka, Japan
| | - Shinpei Kawarai
- Laboratory for Symbolic Cognitive Development, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
- Laboratory of Small Animal Clinics, Veterinary Teaching Hospital, Azabu University, Sagamihara, Kanagawa, Japan
| | - Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Okayama, Japan
| | - Takefumi Kikusui
- Companion Animal Research, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Atsushi Iriki
- Laboratory for Symbolic Cognitive Development, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
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8
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Shigeno Y, Liu H, Sano C, Inoue R, Niimi K, Nagaoka K. Individual variations and effects of birth facilities on the fecal microbiome of laboratory-bred marmosets (Callithrix jacchus) assessed by a longitudinal study. PLoS One 2022; 17:e0273702. [PMID: 36040908 PMCID: PMC9426884 DOI: 10.1371/journal.pone.0273702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
Laboratory animals are used for scientific research in various fields. In recent years, there has been a concern that the gut microbiota may differ among laboratory animals, which may yield different results in different laboratories where in-vivo experiments are performed. Our knowledge of the gut microbiota of laboratory-reared common marmosets (Callithrix jacchus) is limited; thus, in this study, we analyzed the daily changes in fecal microbiome composition, individual variations, and effects of the birth facility in healthy female laboratory-reared marmosets, supplied by three vendors. We showed that the marmoset fecal microbiome varied among animals from the same vendor and among animals from different vendors (birth facility), with daily changes of approximately 37%. The fecal microbiome per vendor is characterized by alpha diversity and specific bacteria, with Bifidobacterium for vendor A, Phascolarctobacterium for vendor B, and Megamonas for vendor C. Furthermore, we found that plasma progesterone concentrations and estrous cycles were not correlated with daily fecal microbiome changes. In contrast, animals with an anovulatory cycle lacked Megamonas and Desulfovibrio bacteria compared to normal estrous females. This study suggests that the source of the animal, such as breeding and housing facilities, is important for in-vivo experiments on the marmoset gut microbiota.
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Affiliation(s)
- Yuko Shigeno
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Research Resources Division, RIKEN Center for Brain Science, Saitama, Japan
| | - Hong Liu
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Chie Sano
- Research Resources Division, RIKEN Center for Brain Science, Saitama, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Applied Biological Sciences, Setsunan University, Osaka, Japan
| | - Kimie Niimi
- Research Resources Division, RIKEN Center for Brain Science, Saitama, Japan
| | - Kentaro Nagaoka
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
- * E-mail:
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9
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Sheh A, Artim SC, Burns MA, Molina-Mora JA, Lee MA, Dzink-Fox J, Muthupalani S, Fox JG. Alterations in common marmoset gut microbiome associated with duodenal strictures. Sci Rep 2022; 12:5277. [PMID: 35347206 PMCID: PMC8960757 DOI: 10.1038/s41598-022-09268-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
Chronic gastrointestinal (GI) diseases are the most common diseases in captive common marmosets (Callithrix jacchus). Despite standardized housing, diet and husbandry, a recently described gastrointestinal syndrome characterized by duodenal ulcers and strictures was observed in a subset of marmosets sourced from the New England Primate Research Center. As changes in the gut microbiome have been associated with GI diseases, the gut microbiome of 52 healthy, non-stricture marmosets (153 samples) were compared to the gut microbiome of 21 captive marmosets diagnosed with a duodenal ulcer/stricture (57 samples). No significant changes were observed using alpha diversity metrics, and while the community structure was significantly different when comparing beta diversity between healthy and stricture cases, the results were inconclusive due to differences observed in the dispersion of both datasets. Differences in the abundance of individual taxa using ANCOM, as stricture-associated dysbiosis was characterized by Anaerobiospirillum loss and Clostridium perfringens increases. To identify microbial and serum biomarkers that could help classify stricture cases, we developed models using machine learning algorithms (random forest, classification and regression trees, support vector machines and k-nearest neighbors) to classify microbiome, serum chemistry or complete blood count (CBC) data. Random forest (RF) models were the most accurate models and correctly classified strictures using either 9 ASVs (amplicon sequence variants), 4 serum chemistry tests or 6 CBC tests. Based on the RF model and ANCOM results, C. perfringens was identified as a potential causative agent associated with the development of strictures. Clostridium perfringens was also isolated by microbiological culture in 4 of 9 duodenum samples from marmosets with histologically confirmed strictures. Due to the enrichment of C. perfringens in situ, we analyzed frozen duodenal tissues using both 16S microbiome profiling and RNAseq. Microbiome analysis of the duodenal tissues of 29 marmosets from the MIT colony confirmed an increased abundance of Clostridium in stricture cases. Comparison of the duodenal gene expression from stricture and non-stricture marmosets found enrichment of genes associated with intestinal absorption, and lipid metabolism, localization, and transport in stricture cases. Using machine learning, we identified increased abundance of C. perfringens, as a potential causative agent of GI disease and intestinal strictures in marmosets.
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Affiliation(s)
- Alexander Sheh
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Stephen C Artim
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Merck Research Laboratories, Merck, South San Francisco, CA, USA
| | - Monika A Burns
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jose Arturo Molina-Mora
- Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Mary Anne Lee
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Sciences, Wellesley College, Wellesley, MA, USA
| | - JoAnn Dzink-Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Kramer RM, Sheh A, Toolan CH, Muthupalani S, Carrasco SE, Artim SC, Burns MA, Fox JG. Factors Affecting Hematologic and Serum Biochemical Parameters in Healthy Common Marmosets ( Callithrix jacchus). JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2022; 61:113-131. [PMID: 34996528 PMCID: PMC8956218 DOI: 10.30802/aalas-jaalas-21-000061] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 07/01/2021] [Accepted: 08/24/2021] [Indexed: 12/29/2022]
Abstract
Physiologic changes during development, aging, and pregnancy may affect clinical parameters. Previously available reference values have been based on samples that may include wild and captive marmosets, with little representation of geriatric or pregnant animals. Establishing reference values under various conditions would support better recognition of pathologic conditions in marmosets. One hundred and forty-seven (70 males and 77 females) healthy marmosets from a research colony were included in this study. Exclusion criteria were abnormal physical exam findings at the time of blood sampling, chronic medications, or clinical or pathologic evidence of disease. Reference intervals were calculated for serum chemistry and hematology. Using metadata, samples were classified based on age, sex, colony source and pregnancy status. Multiple tests indicated significant differences with varying effect sizes, indicating that developing reference intervals based on metadata can be useful. Across all the comparisons, medium or large effect sizes were observed most frequently in blood urea nitrogen (BUN), calcium, total protein, alkaline phosphatase (ALP), weight and serum albumin. We report normative clinical pathologic data for captive common marmosets through all life stages and reproductive status. Significant differences were observed in most parameters when stratifying data based on age, sex, colony source, or pregnancy, suggesting that developing reference intervals considering this information is important for clinicians.
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Affiliation(s)
- Robin M Kramer
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA
- Equal contributors
| | - Alexander Sheh
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA
- Equal contributors
| | - Carolyn H Toolan
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA
- University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA
| | | | - Sebastian E Carrasco
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA
- Current affiliation: Laboratory of Comparative Pathology, Memorial Sloan-Kettering Cancer Center/Weill Cornell Medical College, New York, NY
| | - Stephen C Artim
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA
- Current affiliation: Merck Research Laboratories, South San Francisco, CA
| | - Monika A Burns
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA
- Current affiliation: Novartis Institutes for Biomedical Research, Cambridge, MA
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA
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