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Peng Y, Zhao Q, Chen S, Li Z, An D, Zhang X. Potential contributions of keystone species to intestinal ecosystem in patients with Crohn's disease. J Appl Microbiol 2024; 135:lxae086. [PMID: 38549423 DOI: 10.1093/jambio/lxae086] [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: 11/10/2023] [Revised: 02/26/2024] [Accepted: 03/27/2024] [Indexed: 04/12/2024]
Abstract
AIMS Ravelling the central but poorly understood issue that potential contributions of keystone species to intestinal ecosystem functioning of patients with certain life-altering diseases including Crohn's disease (CD). METHODS AND RESULTS In this study, a combination of 16S rRNA gene amplicon sequencing and amplicon-oriented metagenomic profiling was applied to gain insights into the shifts in bacterial community composition at different stages of CD course, and explore the functional roles of identified keystone species in intestinal microecosystem. Our results showed significant alterations in structure and composition of gut microbiota between CD patients and healthy control (HC) (P < 0.05), but was no difference at active and remission stages. Whole-community-based comprehensive analyses were employed to identify the differential species such as Escherichia coli, Anaerostipes hadrus, and Eubacterium hallii in CD patients, with healthy populations as the control. Metagenome-wide functional analyses further revealed that the relative abundance of specialized metabolism-related genes such as cynS, frdB, serA, and gltB from these bacterial species in CD group was significantly different (P < 0.05) from that in HC, and highlighted the potential roles of the keystone species in regulating the accumulation of important metabolites such as succinate, formate, ammonia, L-glutamate, and L-serine, which might have an effect on homeostasis of intestinal ecosystem. CONCLUSIONS The findings identify several potential keystone species that may influence the intestinal microecosystem functioning of CD patients and provide some reference for future CD treatment.
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Affiliation(s)
- Yuzhu Peng
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410006, China
| | - Qi Zhao
- Department of Respiratory and Critical Care Medicine, Tangdu Hospital of Air Force Military Medical University, Xi'an 710038, China
| | - Shuijiao Chen
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhenyu Li
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410006, China
| | - Di An
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410006, China
| | - Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha 410006, China
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2
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Hoang J, Gilbertson-White S, Cady N, Yadav M, Shahi S, Aguilar L, Mangalam AK, Cherwin C. Preliminary Analysis of Gut Microbiome and Gastrointestinal Symptom Burden in Breast Cancer Patients Receiving Chemotherapy Compared to Healthy Controls. Biol Res Nurs 2024; 26:219-230. [PMID: 37830211 PMCID: PMC11145515 DOI: 10.1177/10998004231205277] [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] [Indexed: 10/14/2023]
Abstract
BACKGROUND Alterations in the naturally occurring bacteria of the gut, known as the gastrointestinal (GI) microbiome, may influence GI symptoms in women with breast cancer. OBJECTIVE This work aims to describe GI symptom occurrence, duration, severity, and distress and measures of the GI microbiome among women with breast cancer receiving chemotherapy compared to age- and sex-matched healthy controls. INTERVENTIONS/METHODS 22 women with breast cancer receiving chemotherapy and 17 healthy control women provided stool specimens and GI symptom data using the modified Memorial Symptom Assessment Scale (MSAS). The fecal microbiome was profiled by metagenomic sequencing of 16S Ribosomal RNA (rRNA). GI microbiome was compared between groups using alpha-diversity (Observed OTU number and Shannon index), beta-diversity (UniFrac distances), and relative abundance of select genera. RESULTS GI symptoms with high symptom reports among breast cancer patients included nausea, diarrhea, flatulence, dry mouth, taste change, and poor appetite. Indices of differential abundance (beta diversity) significantly distinguished between breast cancer patients and healthy controls. Unique bacterial features differentiating the 2 groups were Prevotella_9, Akkermansia, Lachnospira, Lachnospiraceae_NK4A136, Lachnoclostridium, and Oscillibacter. CONCLUSIONS Gut bacteria are associated with GI inflammation and mucus degradation, suggesting the potential role of the GI microbiome in GI symptom burden. Understanding the influence of GI bacteria on gut health and symptoms will help harness the enormous potential of the GI microbiome as a future diagnostic and therapeutic agent to reduce the symptom burden associated with chemotherapy.
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Affiliation(s)
- Jemmie Hoang
- College of Nursing, University of Iowa, Iowa City, IA, USA
| | | | - Nicole Cady
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Meeta Yadav
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Shailesh Shahi
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Leeann Aguilar
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Ashutosh K. Mangalam
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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Wang H, Yan G, Wu Y, Zhuoma D, Liu Z, Gao X, Wang X. Fecal microbiota related to postoperative endoscopic recurrence in patients with Crohn's disease. Gastroenterol Rep (Oxf) 2024; 12:goae017. [PMID: 38524186 PMCID: PMC10960934 DOI: 10.1093/gastro/goae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/05/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Background Postoperative recurrence (POR) remains a major challenge for patients with Crohn's disease (CD). Gut microbial dysbiosis has been reported to be involved in the pathogenesis of POR. This study aims to investigate the relationship between fecal microbiome and endoscopic recurrence in patients with CD after ileocolonic resection. Methods This is a cross-sectional study. Fecal samples were collected from 52 patients with CD after surgical intervention from 6 to 12 months before endoscopic examination. Endoscopic recurrence was defined as Rutgeerts score ≥ i2. The microbiome was analyzed by sequencing the V3-V4 hypervariable regions of the 16S rRNA gene. Results A total of 52 patients were included and classified into POR (n = 27) and non-POR (n = 25) groups. Compared with the non-POR group, the POR group had a significantly lower community richness (Chao1 index: 106.5 vs 124, P = 0.013) and separated microbial community (P = 0.007 for Adonis, P = 0.032 for Anosim), combined with different distribution of 16 gut microbiotas and decrease of 11 predicted metabolic pathways (P < 0.05). Lactobacillus and Streptococcus were identified to closely correlate to non-POR (P < 0.05) after controlling for confounding factors. Kaplan-Meier analysis indicated that the patients with higher abundance of Streptococcus experienced longer remission periods (P < 0.01), but this was not for Lactobacillus. The predicted ethylmalonyl-coA pathway related to increased amount of succinate was positively correlated with Streptococcus (r > 0.5, P < 0.05). Conclusions The characteristic alterations of fecal microbiota are associated with postoperative endoscopic recurrence in patients with CD; particularly, high abundance of Streptococcus may be closely related to endoscopic remission.
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Affiliation(s)
- Haichao Wang
- Department of Nephrology and Rheumatology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, P. R. China
| | - Guorong Yan
- Department of Phototherapy, Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, P. R. China
| | - Yaling Wu
- Department of Geriatrics, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, P. R. China
| | - Deji Zhuoma
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, P. R. China
| | - Zhanju Liu
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, P. R. China
| | - Xuefeng Gao
- Integrative Microecology Center, Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong, P. R. China
| | - Xiaolei Wang
- Department of Gastroenterology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, P. R. China
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Lawal SA, Voisin A, Olof H, Bording-Jorgensen M, Armstrong H. Diversity of the microbiota communities found in the various regions of the intestinal tract in healthy individuals and inflammatory bowel diseases. Front Immunol 2023; 14:1242242. [PMID: 38022505 PMCID: PMC10654633 DOI: 10.3389/fimmu.2023.1242242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
The severe and chronic inflammatory bowel diseases (IBD), Crohn disease and ulcerative colitis, are characterized by persistent inflammation and gut damage. There is an increasing recognition that the gut microbiota plays a pivotal role in IBD development and progression. However, studies of the complete microbiota composition (bacteria, fungi, viruses) from precise locations within the gut remain limited. In particular, studies have focused primarily on the bacteriome, with available methods limiting evaluation of the mycobiome (fungi) and virome (virus). Furthermore, while the different segments of the small and large intestine display different functions (e.g., digestion, absorption, fermentation) and varying microenvironment features (e.g., pH, metabolites), little is known about the biogeography of the microbiota in different segments of the intestinal tract or how this differs in IBD. Here, we highlight evidence of the differing microbiota communities of the intestinal sub-organs in healthy and IBD, along with method summaries to improve future studies.
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Affiliation(s)
- Samuel Adefisoye Lawal
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Athalia Voisin
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Hana Olof
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | | | - Heather Armstrong
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada
- IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
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Osawa M, Handa O, Fukushima S, Matsumoto H, Umegaki E, Inoue R, Naito Y, Shiotani A. Reduced abundance of butyric acid-producing bacteria in the ileal mucosa-associated microbiota of ulcerative colitis patients. J Clin Biochem Nutr 2023; 73:77-83. [PMID: 37534095 PMCID: PMC10390811 DOI: 10.3164/jcbn.22-86] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/16/2022] [Indexed: 08/04/2023] Open
Abstract
Compositional changes in the microbiota are associated with various inflammatory diseases, including ulcerative colitis (UC). Aim: This study aimed to investigate the mucosa-associated microbiota (MAM) in patients with UC and its difference related with disease activity and classification. Brush samples were collected from the terminal ileum and sigmoid colon during endoscopic procedures. The microbiota of samples was profiled using the Illumina MiSeq platform. The V3-V4 regions of the gene encoding 16S rRNA (460 bp) were amplified using PCR. Fifty UC patients and twenty healthy controls were enrolled. UC patients displayed significantly reduced α-diversity in both the ileum and sigmoid colon compared to controls. A difference in β-diversity in the unweighted analysis was observed between the two groups. The abundance of Lactobacillus and Veillonella was significantly higher and that of Butyricicoccus, Ruminococcus and Lachnospiraceae was significantly lower in the ileum of UC patients than in controls. The abundance of Odoribacter in the ileum was significantly lower in left-sided colitis and pancolitis patients than in proctitis patients and lower in patients with highly severe disease activity than with mild disease activity. The reduction in abundance of butyric acid-producing bacteria, especially Odoribacter, in ileal MAM may play an important role in the pathophysiology of UC.
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Affiliation(s)
- Motoyasu Osawa
- Department of Internal Medicine, Division of Gastroenterology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Osamu Handa
- Department of Internal Medicine, Division of Gastroenterology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Shinya Fukushima
- Department of Internal Medicine, Division of Gastroenterology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Hiroshi Matsumoto
- Department of Internal Medicine, Division of Gastroenterology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Eiji Umegaki
- Department of Internal Medicine, Division of Gastroenterology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Ryo Inoue
- Faculty of Agriculture, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan
| | - Yuji Naito
- Department of Human Immunology and Nutrition Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachi Hirokoji Agaru, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Akiko Shiotani
- Department of Internal Medicine, Division of Gastroenterology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
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Characteristics of the intestinal bacterial microbiota profiles in Bifidobacterium pseudocatenulatum LI09 pre-treated rats with D-galactosamine-induced liver injury. World J Microbiol Biotechnol 2023; 39:43. [DOI: 10.1007/s11274-022-03495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
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Wang XS, Li PX, Wang BS, Zhang WD, Wang WH. Integrated omics analysis reveals the immunologic characteristics of cystic Peyer's patches in the cecum of Bactrian camels. PeerJ 2023; 11:e14647. [PMID: 36643630 PMCID: PMC9835693 DOI: 10.7717/peerj.14647] [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: 08/03/2022] [Accepted: 12/06/2022] [Indexed: 01/10/2023] Open
Abstract
Bactrian camels have specific mucosa-associated lymphoid tissue (MALT) throughout the large intestine, with species-unique cystic Peyer's patches (PPS) as the main type of tissue. However, detailed information about the molecular characteristics of PPS remains unclear. This study applied a transcriptomic analysis, untargeted metabolomics, and 16S rDNA sequencing to compare the significant differences between PPS and the adjacent normal intestine tissues (NPPS) during the healthy stage of three young Bactrian camels. The results showed that samples from PPS could be easily differentiated from the NPPS samples based on gene expression profile, metabolites, and microbial composition, separately indicated using dimension reduction methods. A total of 7,568 up-regulated and 1,266 down-regulated differentially expressed genes (DEGs) were detected, and an enrichment analysis found 994 DEGs that participated in immune-related functions, and a co-occurance network analysis identified nine hub genes (BTK, P2RX7, Pax5, DSG1, PTPN2, DOCK11, TBX21, IL10, and HLA-DOB) during multiple immunologic processes. Further, PPS and NPPS both had a similar pattern of most compounds among all profiles of metabolites, and only 113 differentially expressed metabolites (DEMs) were identified, with 101 of these being down-regulated. Deoxycholic acid (DCA; VIP = 37.96, log2FC = -2.97, P = 0), cholic acid (CA; VIP = 13.10, log2FC = -2.10, P = 0.01), and lithocholic acid (LCA; VIP = 12.94, log2FC = -1.63, P = 0.01) were the highest contributors to the significant dissimilarities between groups. PPS had significantly lower species richness (Chao1), while Firmicutes (35.92% ± 19.39%), Bacteroidetes (31.73% ± 6.24%), and Proteobacteria (13.96% ± 16.21%) were the main phyla across all samples. The LEfSe analysis showed that Lysinibacillus, Rikenellaceae_RC9_gut_group, Candidatus_Stoquefichus, Mailhella, Alistipes, and Ruminococcaceae_UCG_005 were biomarkers of the NPPS group, while Escherichia_Shigella, Synergistes, Pyramidobacter, Odoribacter, Methanobrevibacter, Cloacibacillus, Fusobacterium, and Parabacteroides were significantly higher in the PPS group. In the Procrustes analysis, the transcriptome changes between groups showed no significant correlations with metabolites or microbial communities, whereas the alteration of metabolites significantly correlated with the alteration of the microbial community. In the co-occurrence network, seven DEMs (M403T65-neg, M329T119-neg, M309T38-neg, M277T42-2-neg, M473T27-neg, M747T38-1-pos, and M482t187-pos) and 14 genera (e.g., Akkermansia, Candidatus-Stoquefichus, Caproiciproducens, and Erysipelatoclostridium) clustered much more tightly, suggesting dense interactions. The results of this study provide new insights into the understanding of the immune microenvironment of the cystic PPS in the cecum of Bactrian camels.
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Affiliation(s)
- Xiao shan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Pei xuan Li
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Bao shan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wang dong Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wen hui Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, Gansu, China
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Cao P, Chen Q, Shi C, Wang L, Gong Z. Fusobacterium nucleatum promotes the development of acute liver failure by inhibiting the NAD + salvage metabolic pathway. Gut Pathog 2022; 14:29. [PMID: 35765030 PMCID: PMC9238040 DOI: 10.1186/s13099-022-00503-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute liver failure (ALF) patients are often accompanied by severe energy metabolism abnormalities and intestinal microecological imbalance. The intestinal mucosal barrier is severely damaged. Intestinal endotoxin can induce intestinal endotoxemia through the "Gut-Liver axis". More and more evidence shows that members of the gut microbiota, especially Fusobacterium nucleatum (F. nucleatum), are related to inflammatory bowel disease, but whether F. nucleatum is involved in the development of ALF and whether it affects the liver energy metabolism is unclear. METHODS This study first detected the abundance of F. nucleatum and its effect on ALF disease, and explored whether F. nucleatum aggravated liver inflammation in vitro and in vivo. RESULTS Our data showed that liver tissues of ALF patients contained different abundances of F. nucleatum, which were related to the degree of liver inflammation. In addition, we found that F. nucleatum infection affected the energy metabolism of the liver during the development of ALF, inhibited the synthesis pathway of nicotinamide adenine dinucleotide (NAD+)'s salvage metabolism, and promoted inflammatory damage in the liver. In terms of mechanism, F. nucleatum inhibited NAD+ and the NAD+-dependent SIRT1/AMPK signaling pathway, and promoted liver damage of ALF. CONCLUSIONS Fusobacterium nucleatum coordinates a molecular network including NAD+ and SIRT1 to control the progress of ALF. Detection and targeting of F. nucleatum and its related pathways may provide valuable insights for the treatment of ALF.
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Affiliation(s)
- Pan Cao
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, 238 Jie Fang Road, Wuhan, 430060, People's Republic of China
| | - Qian Chen
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, 238 Jie Fang Road, Wuhan, 430060, People's Republic of China
| | - Chunxia Shi
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, 238 Jie Fang Road, Wuhan, 430060, People's Republic of China
| | - Luwen Wang
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, 238 Jie Fang Road, Wuhan, 430060, People's Republic of China
| | - Zuojiong Gong
- Department of Infectious Diseases, Renmin Hospital of Wuhan University, 238 Jie Fang Road, Wuhan, 430060, People's Republic of China.
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Radhakrishnan ST, Alexander JL, Mullish BH, Gallagher KI, Powell N, Hicks LC, Hart AL, Li JV, Marchesi JR, Williams HRT. Systematic review: the association between the gut microbiota and medical therapies in inflammatory bowel disease. Aliment Pharmacol Ther 2022; 55:26-48. [PMID: 34751954 DOI: 10.1111/apt.16656] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/21/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND The gut microbiota has been implicated in the pathogenesis of inflammatory bowel disease (IBD), with Faecalibacterium prausnitizii associated with protection, and certain genera (including Shigella and Escherichia) associated with adverse features. The variability of patient response to medical therapies in IBD is incompletely understood. Given the recognised contribution of the microbiota to treatment efficacy in other conditions, there may be interplay between the gut microbiota, IBD medical therapy and IBD phenotype. AIMS To evaluate the bidirectional relationship between IBD medical therapies and the gut microbiota. METHODS We conducted a systematic search of MEDLINE and EMBASE. All original studies analysing interactions between the gut microbiota and established IBD medical therapies were included. RESULTS We screened 1296 records; 19 studies were eligible. There was heterogeneity in terms of sample analysis, treatment protocols, and outcome reporting. Increased baseline α-diversity was observed in responders versus non-responders treated with exclusive enteral nutrition (EEN), infliximab, ustekinumab or vedolizumab. Higher baseline Faecalibacterium predicted response to infliximab and ustekinumab. A post-treatment increase in Faecalibacterium prausnitzii was noted in responders to aminosalicylates, anti-TNF medications and ustekinumab; conversely, this species decreased in responders to EEN. Escherichia was a consistent marker of unfavourable drug response, and its presence in the gut mucosa correlated with inflammation in aminosalicylate-treated patients. CONCLUSIONS Both gut microbiota diversity and specific taxonomic features (including high abundance of Faecalibacterium) are associated with the efficacy of a range of IBD therapies. These findings hold promise for a potential role for the gut microbiota in explaining the heterogeneity of patient response to IBD treatments.
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Affiliation(s)
- Shiva T Radhakrishnan
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - James L Alexander
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Benjamin H Mullish
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Kate I Gallagher
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Nick Powell
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Lucy C Hicks
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Ailsa L Hart
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Inflammatory Bowel Disease Unit, St Mark's Hospital, London, UK
| | - Jia V Li
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Horace R T Williams
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
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10
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Wang JK, Yan B, Zhao JM, Yuan LP. Effect of gut microbiota from Henoch-Schönlein Purpura patients on acid-sensitive ion channel 3 expression and intestinal motility in germ-free rats. BMC Pediatr 2021; 21:536. [PMID: 34852816 PMCID: PMC8638173 DOI: 10.1186/s12887-021-03013-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 11/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It has been proven that gut microbiota alterations are involved in the development of Henoch-Schönlein Purpura (HSP). However, the pathogenesis of HSP hasn't been eluciated. This study was to investigate the impact of gut microbiota from HSP on ASIC3 expression and interactions between microbiota and ASIC3 expression in the development of HSP. METHODS Feces collected from HSP and healthy children at the First Affiliated Hospital of Anhui Medical University were made into fecal microbial solutions. Germ-free rats were randomly assigned to either the control or HSP groups. The HSP group of rats were administered the fecal microbiota solution of HSP children, while the control group rats were administered the fecal microbiota solution of healthy children. Abdominal withdrawal reflex (AWR) and intestinal propulsion rate of the rats were used to determine visceral sensitivity. Composition of the gut microbiota of HSP children was determined using 16S rRNA gene sequencing. ASIC3 expression in the colon was ascertained through qRT-PCR as well as western blotting analysis. RESULTS The results showed a reduction in the number of species and abundance in the intestinal microbiota of children with HSP. Visceral sensitivity and intestinal propulsion rate of HSP group rats increased significantly, compared with the control group. Colon ASIC3 mRNA and protein levels in the HSP group were found to be upregulated. The microbiota dysbiosis of HSP patients could stimulate ASIC3 expression in the colon of Germ-free rats, which in turn affected intestinal motility. CONCLUSIONS These results suggested that HSP children had intestinal microbiota disorder, which might affect gut motility by down-regulating colon ASIC3 expression in rats.
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Affiliation(s)
- Jin-Kun Wang
- Department of Pediatrics, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Bo Yan
- Department of Medical Technology, Anhui Medical College, Hefei, 230026, China
| | - Jun-Mei Zhao
- Department of Pediatrics, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China
| | - Li-Ping Yuan
- Department of Pediatrics, First Affiliated Hospital of Anhui Medical University, Hefei, 230022, China.
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11
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Di Pierro F. Gut Microbiota Parameters Potentially Useful in Clinical Perspective. Microorganisms 2021; 9:microorganisms9112402. [PMID: 34835527 PMCID: PMC8623243 DOI: 10.3390/microorganisms9112402] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
Interest in gut microbiota analyses is at an all-time high. Gut microbiota is thought to relate to an increasing range of diseases of interest to physicians and nutritionists. Overweight, obesity, response to diet, metabolic syndrome, low grade inflammation, diabetes and colon neoplasms could maybe be observed in microbiota if affordable markers were available. Possible biomarkers like the Firmicutes/Bacteroidetes ratio, the Gram-positive/Gram-negative ratio, the Prevotella/Bacteroides ratio, and the Fusobacterium nucleatum/Faecalibacterium prausnitzii ratio are here reviewed in a narrative way in the attempt to highlight their possible future role in routine practice and clinically relevant diagnostics.
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Affiliation(s)
- Francesco Di Pierro
- Digestive Endoscopy & Gastroenterology, Fondazione Poliambulanza, 25124 Brescia, Italy;
- UNICAM, Camerino University, 62032 Camerino, Italy
- Scientific Department, Velleja Research, 20124 Milan, Italy
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12
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Karpinska-Leydier K, Amirthalingam J, Alshowaikh K, Iroshani Jayarathna A, Salibindla DBAMR, Paidi G, Ergin HE. Correlation Between the Gut Microbiome and Immunotherapy Response in Inflammatory Bowel Disease: A Systematic Review of the Literature. Cureus 2021; 13:e16808. [PMID: 34350086 PMCID: PMC8325948 DOI: 10.7759/cureus.16808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/01/2021] [Indexed: 11/09/2022] Open
Abstract
Inflammatory bowel disease (IBD) is an autoimmune disease associated with dysbiosis within the gastrointestinal tract. Characteristic taxonomic shifts of microbial populations are observed in disease progression and remission; however, despite similarities, there are many differences among individuals presenting with IBD including IBD subset, clinical course, and response to therapy. Much is still unknown about how these taxonomic shifts interact with immunotherapy and how genetic variants contribute. In this systematic review, we aimed to compile information on the interactions of the gut microbiome with immunotherapy in the course of disease and treatment of IBD patients. This systematic review was conducted as per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and the PubMed database was methodically screened for literature search including keywords and Medical Subject Headings (MeSH) terms for relevant articles. The quality appraisal was completed using the Cochrane Tool, Newcastle-Ottawa checklist, and the Scale for the Assessment of Narrative Review Articles (SANRA) checklist, as appropriate, and 11 relevant articles were included in this systematic review. Our review concludes that although there are characteristic taxonomic shifts between diseased and healthy patients, genetic variants are an important consideration in the predictive quality of disease and treatment decisions. The comparison between interactions of microbial populations and treatment in addition to the role of genetic variants may provide insight into treatment non-responders. Due to our limitations in current knowledge including the complexity of the microcosm, ethnic genetic variations among human populations, and our focus on relevant articles published in English over the past six years, we may have missed relevant studies. Future studies should focus on the comparison between Western and other cultural populations as well as further implementation of Genome-Wide Association Studies (GWAS) in clinical predictability.
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Affiliation(s)
| | - Jashvini Amirthalingam
- Neurology, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Khadija Alshowaikh
- Obstetrics and Gynecology, California Institute of Behavioral Neurosciences & Psychology, Fairfield , USA
| | | | | | - Gokul Paidi
- Internal Medicine, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
| | - Huseyin Ekin Ergin
- General Practice, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
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13
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He C, Wang H, Yu C, Peng C, Shu X, Liao W, Zhu Z. Alterations of Gut Microbiota in Patients With Intestinal Tuberculosis That Different From Crohn's Disease. Front Bioeng Biotechnol 2021; 9:673691. [PMID: 34295880 PMCID: PMC8290844 DOI: 10.3389/fbioe.2021.673691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/11/2021] [Indexed: 01/01/2023] Open
Abstract
Intestinal tuberculosis (ITB) and Crohn's disease (CD) are chronic inflammatory bowel disorders that are associated with dysregulated mucosal immunity. The gut microbiota plays an important role in the regulation of host immunity and inflammatory response. Although mounting evidence has linked CD with the dysbiosis of gut microbiota, the characteristic profiles of mucosal bacteria in ITB remain unclear. The aim of this study was to assess the alterations of the gut microbiota in ITB and compare the microbial structure of ITB with CD. A total of 71 mucosal samples were collected from patients with ITB, CD, and healthy controls (HC), and then, 16S rRNA gene sequencing was performed. The overall composition of gut microbiota in ITB was strikingly different from HC, with the dominance of Proteobacteria and reduction of Firmicutes. Of note, the short-chain fatty acids (SCFAs)-producing bacteria such as Faecalibacterium, Roseburia, and Ruminococcus were decreased in ITB relative to HC, while Klebsiella and Pseudomonas were enriched. Multiple predictive functional modules were altered in ITB, including the over-representation of lipopolysaccharide biosynthesis, bacterial invasion of epithelial cells, and pathogenic Escherichia coli infection that can promote inflammation. Additionally, the microbial structure in CD was distinctly different from ITB, characterized by lower alpha diversity and increased abundance of Bacteroides, Faecalibacterium, Collinsella, and Klebsiella. These four bacterial markers distinguished ITB from CD with an area under the curve of 97.6%. This study established the compositional and functional perturbation of the gut microbiome in ITB and suggested the potential for using gut microbiota as biomarkers to differentiate ITB from CD.
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Affiliation(s)
- Cong He
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Huan Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chen Yu
- Department of Radiology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chao Peng
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xu Shu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wangdi Liao
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenhua Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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14
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Zha H, Liu F, Ling Z, Chang K, Yang J, Li L. Multiple bacteria associated with the more dysbiotic genitourinary microbiomes in patients with type 2 diabetes mellitus. Sci Rep 2021; 11:1824. [PMID: 33469094 PMCID: PMC7815922 DOI: 10.1038/s41598-021-81507-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 01/07/2021] [Indexed: 02/08/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) influences the human health and can cause significant illnesses. The genitourinary microbiome profiles in the T2DM patients remain poorly understood. In the current study, a series of bioinformatic and statistical analyses were carried out to determine the multiple bacteria associated with the more dysbiotic genitourinary microbiomes (i.e., those with lower dysbiosis ratio) in T2DM patients, which were sequenced by Illumina-based 16S rRNA gene amplicon sequencing. All the genitourinary microbiomes from 70 patients with T2DM were clustered into three clusters of microbiome profiles, i.e., Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, with Cluster_3_T2DM at the most dysbiotic genitourinary microbial status. The three clustered T2DM microbiomes were determined with different levels of alpha diversity indices, and driven by distinct urinalysis variables. OTU12_Clostridiales and OTU28_Oscillospira were likely to drive the T2DM microbiomes to more dysbiotic status, while OTU34_Finegoldia could play a vital role in maintaining the least dysbiotic T2DM microbiome (i.e., Cluster_1_T2DM). The functional metabolites K08300_ribonuclease E, K01223_6-phospho-beta-glucosidase and K00029_malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) were most associated with Cluster_1_T2DM, Cluster_2_T2DM and Cluster_3_T2DM, respectively. The characteristics and multiple bacteria associated with the more dysbiotic genitourinary microbiomes in T2DM patients may help with the better diagnosis and management of genitourinary dysbiosis in T2DM patients.
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Affiliation(s)
- Hua Zha
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China ,grid.9654.e0000 0004 0372 3343School of Biological Sciences, The University of Auckland, Auckland, New Zealand ,grid.9654.e0000 0004 0372 3343Institute of Marine Science, The University of Auckland, Auckland, New Zealand
| | - Fengping Liu
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China ,grid.258151.a0000 0001 0708 1323School of Medicine, Jiangnan University, Wuxi, China
| | - Zongxin Ling
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China
| | - Kevin Chang
- grid.9654.e0000 0004 0372 3343Department of Statistics, The University of Auckland, Auckland, New Zealand
| | - Jiezuan Yang
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China
| | - Lanjuan Li
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou, 310000 China
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15
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Fukushima S, Shiotani A, Matsumoto H, Handa O, Handa Y, Osawa M, Murao T, Umegaki E, Kawano M, Inoue R, Naito Y. Comparison of mucosa-associated microbiota in Crohn’s disease patients with and without anti-tumor necrosis factor-α therapy. J Clin Biochem Nutr 2021; 70:182-188. [PMID: 35400819 PMCID: PMC8921723 DOI: 10.3164/jcbn.21-41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/16/2021] [Indexed: 11/22/2022] Open
Abstract
Most studies on the gut microbiome of Crohn’s disease have been conducted using feces, instead of intestinal mucus to analyze the mucosa-associated microbiota. To investigate the characteristics of mucosa-associated microbiota in Crohn’s disease patients and the effect of anti-tumor necrosis factor (TNF)-α therapy on mucosa-associated microbiota, we analyzed microbiota in Crohn’s disease patients using brushing samples taken from terminal ileum. The recruited subjects were 18 Crohn’s disease patients and 13 controls. There were 10 patients with anti-TNF-α therapy in Crohn’s disease group. Crohn’s disease patients had significantly reduced α-diversity in Shannon index compared to the controls. The comparative analysis of the taxonomic composition at the genus level between the Crohn’s disease group and the controls indicated that butyrate-producing bacteria were less abundant in the Crohn’s disease group compared to the controls. There were no differences in the diversity between the patients taking anti-TNF-α therapy and the patients without. The comparative analysis of the taxonomic composition at the genus level between the two groups indicated that some of anti-inflammatory bacteria were less abundant in the anti-TNF-α therapy group than the other. Reduction of specific bacteria producing anti-inflammatory molecules, especially butyrate-producing bacteria may play important roles in the pathophysiology of Crohn’s disease.
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Affiliation(s)
| | | | | | - Osamu Handa
- Division of Gastroenterology, Kawasaki Medical School
| | - Yukiko Handa
- Division of Gastroenterology, Kawasaki Medical School
| | | | | | - Eiji Umegaki
- Division of Gastroenterology, Kawasaki Medical School
| | - Mitsuoki Kawano
- Department of Human Nutrition, Faculty of Contemporary Life Science, Chugokugakuen University
| | - Ryo Inoue
- Faculty of Agriculture, Setsunan University
| | - Yuji Naito
- Department of Human Immunology and Nutrition Science, Graduate School of Medical Science, Kyoto Prefectural University of Medicine
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16
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Sankarasubramanian J, Ahmad R, Avuthu N, Singh AB, Guda C. Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease. Front Med (Lausanne) 2020; 7:606298. [PMID: 33330572 PMCID: PMC7729129 DOI: 10.3389/fmed.2020.606298] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022] Open
Abstract
Background: Inflammatory bowel disease (IBD) represents multifactorial chronic inflammatory conditions in the gastrointestinal tract and includes Crohn's disease (CD) and ulcerative colitis (UC). Despite similarities in pathobiology and disease symptoms, UC and CD represent distinct diseases and exhibit diverse therapeutic responses. While studies have now confirmed that IBD is associated with dramatic changes in the gut microbiota, specific changes in the gut microbiome and associated metabolic effects on the host due to CD and UC are less well-understood. Methods: To address this knowledge gap, we performed an extensive unbiased meta-analysis of the gut microbiome data from five different IBD patient cohorts from five different countries using QIIME2, DIAMOND, and STAMP bioinformatics platforms. In-silico profiling of the metabolic pathways and community metabolic modeling were carried out to identify disease-specific association of the metabolic fluxes and signaling pathways. Results: Our results demonstrated a highly conserved gut microbiota community between healthy individuals and IBD patients at higher phylogenetic levels. However, at or below the order level in the taxonomic rank, we found significant disease-specific alterations. Similarly, we identified differential enrichment of the metabolic pathways in CD and UC, which included enriched pathways related to amino acid and glycan biosynthesis and metabolism, in addition to other metabolic pathways. Conclusions: In conclusion, this study highlights the prospects of harnessing the gut microbiota to improve understanding of the etiology of CD and UC and to develop novel prognostic, and therapeutic approaches.
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Affiliation(s)
- Jagadesan Sankarasubramanian
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Rizwan Ahmad
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
| | - Nagavardhini Avuthu
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Amar B. Singh
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, United States
- VA Nebraska-Western Iowa Health Care System, Omaha, NE, United States
| | - Chittibabu Guda
- Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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Zha H, Lu H, Wu J, Chang K, Wang Q, Zhang H, Li J, Luo Q, Lu Y, Li L. Vital Members in the More Dysbiotic Oropharyngeal Microbiotas in H7N9-Infected Patients. Front Med (Lausanne) 2020; 7:396. [PMID: 32850904 PMCID: PMC7433009 DOI: 10.3389/fmed.2020.00396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/24/2020] [Indexed: 01/09/2023] Open
Abstract
The dysbiosis of oropharyngeal (OP) microbiota is associated with multiple diseases, including H7N9 infection. Different OP microbial colonization states may reflect different severities or stages of disease and affect the effectiveness of the treatments. Current study aims to determine the vital bacteria that could possibly drive the OP microbiota in the H7N9 patients to more severe microbial dysbiosis state. The OP microbiotas of 42 H7N9 patients and 30 healthy subjects were analyzed by a series of bioinformatics and statistical analyses. Two clusters of OP microbiotas in H7N9 patients, i.e., Cluster_1_Diseased and Cluster_2_Diseased, were determined at two microbial colonization states by Partition Around Medoids (PAM) clustering analysis, each characterized by distinct operational taxonomic units (OTUs) and functional metabolites. Cluster_1_Diseased was determined at more severe dysbiosis status compared with Cluster_2_Diseased, while OTU143_Capnocytophaga and OTU269_Treponema acted as gatekeepers for both of the two clustered microbiotas. Nine OTUs assigned to seven taxa, i.e., Alloprevotella, Atopobium, Megasphaera, Oribacterium, Prevotella, Stomatobaculum, and Veillonella, were associated with both H7N9 patients with and without secondary bacterial lung infection in Cluster_1. In addition, two groups of healthy cohorts may have potential different susceptibilities to H7N9 infection. These findings suggest that two OP microbial colonization states of H7N9 patients were at different dysbiosis states, which may help determine the health status of H7N9 patients, as well as the susceptibility of healthy subjects to H7N9 infection.
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Affiliation(s)
- Hua Zha
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Institute of Marine Science, The University of Auckland, Auckland, New Zealand
| | - Haifeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jieyun Wu
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Plant Health and Environment Laboratory, Ministry for Primary Industries, Auckland, New Zealand
| | - Kevin Chang
- Department of Statistics, The University of Auckland, Auckland, New Zealand
| | - Qiangqiang Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jinyou Li
- Department of Geriatrics, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yanmeng Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Disease, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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18
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Microbial Signature in Adipose Tissue of Crohn's Disease Patients. J Clin Med 2020; 9:jcm9082448. [PMID: 32751800 PMCID: PMC7465250 DOI: 10.3390/jcm9082448] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 02/08/2023] Open
Abstract
Crohn’s disease (CD) is characterized by compromised immune tolerance to the intestinal commensal microbiota, intestinal barrier inflammation, and hyperplasia of creeping fat (CF) and mesenteric adipose tissue (AT), which seems to be directly related to disease activity. Gut microbiota dysbiosis might be a determining factor in CD etiology, manifesting as a low microbial diversity and a high abundance of potentially pathogenic bacteria. We tested the hypothesis that CF is a reservoir of bacteria through 16S-rRNA sequencing of several AT depots of patients with active and inactive disease and controls. We found a microbiome signature within CF and mesenteric AT from patients, but not in subcutaneous fat. We failed to detect bacterial DNA in any fat depot of controls. Proteobacteria was the most abundant phylum in both CF and mesenteric AT, and positively correlated with fecal calprotectin/C-reactive protein. Notably, the clinical status of patients seemed to be related to the microbiome signature, as those with the inactive disease showed a reduction in the abundance of pathogenic bacteria. Predictive functional profiling revealed many metabolic pathways including lipopolysaccharide biosynthesis and sulfur metabolism overrepresented in active CD relative to that in inactive CD. Our findings demonstrate that microbiota dysbiosis associated with CD pathophysiology is reflected in AT and might contribute to disease severity.
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Zha H, Chen Y, Wu J, Chang K, Lu Y, Zhang H, Xie J, Wang Q, Tang R, Li L. Characteristics of three microbial colonization states in the duodenum of the cirrhotic patients. Future Microbiol 2020; 15:855-868. [PMID: 32662659 DOI: 10.2217/fmb-2019-0270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Aim: Investigation of characteristics of different duodenal microbial colonization states in patients with liver cirrhosis (LC). Materials & methods: Deep-sequencing analyses of the 16S rRNA gene V1-V3 regions were performed. Results: Both bacterial compositions and richness were different between the three-clustered LC microbiotas, in other words, Cluster_1_LC, Cluster_2_LC and Cluster_3_LC. Cluster_1_LC were more likely at severe dysbiosis status due to its lowest modified cirrhosis dysbiosis ratio. OTU12_Prevotella and OTU10_Comamonas were most associated with Cluster_1_LC and Cluster_3_LC, respectively, while OTU38_Alloprevotella was vital in Cluster_2_LC. Pyruvate-ferredoxin/flavodoxin oxidoreductase, dihydroorotate dehydrogenase and branched-chain amino acid transport system substrate-binding protein were most associated with Cluster_1_LC, Cluster_2_LC and Cluster_3_LC, respectively. Conclusion: The three duodenal microbial colonization states had distinct representative characteristics, which might reflect the health status of cirrhotic patients.
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Affiliation(s)
- Hua Zha
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Institute of Marine Science, The University of Auckland, Auckland, New Zealand
| | - Yanfei Chen
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jieyun Wu
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Plant Health & Environment Laboratory, Ministry for Primary Industries, Auckland, New Zealand
| | - Kevin Chang
- Department of Statistics, The University of Auckland, Auckland, New Zealand
| | - Yanmeng Lu
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hua Zhang
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Jiaojiao Xie
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Qiangqiang Wang
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ruiqi Tang
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis & Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis & Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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20
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Zha H, Fang DQ, van der Reis A, Chang K, Yang LY, Xie JJ, Shi D, Xu QM, Li YT, Li LJ. Vital members in the gut microbiotas altered by two probiotic Bifidobacterium strains against liver damage in rats. BMC Microbiol 2020; 20:144. [PMID: 32503418 PMCID: PMC7275491 DOI: 10.1186/s12866-020-01827-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/19/2020] [Indexed: 02/07/2023] Open
Abstract
Background Probiotics are effective to rectify the imbalanced gut microbiota in the diseased cohorts. Two Bifidobacterium strains (LI09 and LI10) were found to alleviate D-galactosamine-induced liver damage (LD) in rats in our previous work. A series of bioinformatic and statistical analyses were performed to determine the vital bacteria in the gut microbiotas altered by the LI09 or LI10 in rats. Results Two groups of representative phylotypes could distinguish the gut microbiotas of LI09 or LI10 groups from the other groups. Among them, OTU170_Porphyromonadaceae acted as a gatekeeper in LI09 group, while OTU12_Bacteroides was determined with multiple correlations in the gut network of LI10 group. Multiple reduced OTUs associated with LC and increased OTUs associated with health were determined in LI09 or LI10 groups, among which, increased OTU51_Barnesiella and reduced OTU99_Barnesiella could be associated with the protective effects of both the two probiotics. The gut microbiotas in LI09, LI10 and positive control groups were clustered into three clusters, i.e., Cluster_1_Microbiota, Cluster_2_Microbiota and Cluster_3_Microbiota, by Partition Around Medoids clustering analysis. Cluster_2_Microbiota was determined at least dysbiotic status due to its greatest LD dysbiosis ratio, lowest levels of liver function variables and plasma cytokines compared with the two other clustered microbiotas, suggesting the treated rats in Cluster_2 were at better health status. Conclusion Our findings suggest that OTU170_Porphyromonadaceae and OTU12_Bacteroides are vital in the gut microbiotas altered by LI09 and LI10. Characteristics of the LD cohorts treated by LI09 or LI10 at different gut microbial colonization states could help monitor the cohorts’ health status.
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Affiliation(s)
- Hua Zha
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310000, China.,School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Institute of Marine Science, The University of Auckland, Auckland, New Zealand
| | - Dai-Qiong Fang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310000, China
| | - Aimee van der Reis
- Institute of Marine Science, The University of Auckland, Auckland, New Zealand
| | - Kevin Chang
- Department of Statistics, The University of Auckland, Auckland, New Zealand
| | - Li-Ya Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310000, China
| | - Jiao-Jiao Xie
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310000, China
| | - Ding Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310000, China
| | - Qiao-Mai Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310000, China
| | - Ya-Ting Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310000, China
| | - Lan-Juan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, 79 Qingchun Road, Hangzhou, 310000, China.
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21
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Changes in the Intestinal Microbiota Are Seen Following Treatment with Infliximab in Children with Crohn's Disease. J Clin Med 2020; 9:jcm9030687. [PMID: 32143438 PMCID: PMC7141282 DOI: 10.3390/jcm9030687] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 02/08/2023] Open
Abstract
The aim of the study was to determine the impact of biological treatment with tumor necrosis factor α antibodies (anti-TNF-α) on the intestinal microbiome of children with severe Crohn's disease (CD) and to evaluate the differences in the intestinal microbiome between patients treated with biological therapy and healthy children. Microbiota composition was analyzed by 16S next-generation sequencing (NGS) and microbial profiles were compared between studied groups. Fifty-four samples (from 18 patients before and after anti-TNF-α induction therapy and 18 healthy children) were used in the sequencing analysis. Shannon's diversity index (p = 0.003, adj. p = 0.010) and observed operational taxonomic units (OTUs) (p = 0.007, adj. p = 0.015) were different between controls and patients with prior therapy for CD. Statistically significant dissimilarities between beta diversity metrics, indicating distinct community composition across groups, were observed in patients with CD before and after therapy. We did not observe any differences between controls and patients with CD after therapy. Core microbiome analysis at species level showed that 32 species were present only in patients with CD but not in controls. The results show that biological treatment is associated with changes in the intestinal microbiome of patients with CD: these changes result in an intestinal microbiome pattern similar to that seen in healthy children. Long-term observation is necessary to determine whether treatment can lead to full restoration of a healthy-like microbiome.
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22
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Cao P, Chen Y, Guo X, Chen Y, Su W, Zhan N, Dong W. Fusobacterium nucleatum Activates Endoplasmic Reticulum Stress to Promote Crohn's Disease Development via the Upregulation of CARD3 Expression. Front Pharmacol 2020; 11:106. [PMID: 32153411 PMCID: PMC7047714 DOI: 10.3389/fphar.2020.00106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/28/2020] [Indexed: 12/26/2022] Open
Abstract
There is increasing evidence that members of the gut microbiota, especially Fusobacterium nucleatum (F. nucleatum), are associated with Crohn’s disease (CD), but the specific mechanism by which F. nucleatum promotes CD development is unclear. Here, we first examined the abundance of F. nucleatum and its effects on CD disease activity and explored whether F. nucleatum aggravated intestinal inflammation and promoted intestinal mucosal barrier damage in vitro and in vivo. Our data showed that F. nucleatum was enriched in 41.21% of CD tissues from patients and was correlated with the clinical course, clinical activity, and refractory behavior of CD (P < 0.05). In addition, we found that F. nucleatum infection is involved in activating the endoplasmic reticulum stress (ERS) pathway during CD development to promote intestinal mucosal barrier destruction. Mechanistically, F. nucleatum targeted caspase activation and recruitment domain 3 (CARD3) to activate the ERS pathway and promote F. nucleatum-mediated mucosal barrier damage in vivo and in vitro. Thus, F. nucleatum coordinates a molecular network involving CARD3 and ERS to control the CD process. Measuring and targeting F. nucleatum and its associated pathways will provide valuable insight into the prevention and treatment of CD.
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Affiliation(s)
- Pan Cao
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yongyu Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xufeng Guo
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yan Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
| | - Wenhao Su
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Na Zhan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China.,Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weiguo Dong
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China.,Key Laboratory of Hubei Province for Digestive System Disease, Renmin Hospital of Wuhan University, Wuhan, China
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Elolimy A, Alharthi A, Zeineldin M, Parys C, Helmbrecht A, Loor JJ. Supply of Methionine During Late-Pregnancy Alters Fecal Microbiota and Metabolome in Neonatal Dairy Calves Without Changes in Daily Feed Intake. Front Microbiol 2019; 10:2159. [PMID: 31608024 PMCID: PMC6761860 DOI: 10.3389/fmicb.2019.02159] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 09/02/2019] [Indexed: 12/12/2022] Open
Abstract
To our knowledge, most studies demonstrating the role of manipulating maternal nutrition on hindgut (i.e., large intestine) microbiota in the offspring have been performed in non-ruminants. Whether this phenomenon exists in cattle is largely unknown. Therefore, the objectives of the current study were to evaluate the impact of maternal post-ruminal supply of methionine during late-pregnancy in dairy cows on fecal microbiota and metabolome in neonatal calves, and their association with body development and growth performance during the preweaning period. To achieve this, heifer calves, i.e., neonatal female offspring, born to Holstein cows receiving either a control (CON) diet (n = 13) or CON plus rumen-protected methionine (MET; Evonik Nutrition & Care GmbH) during the last 28 days of pregnancy were used. Fecal samples from heifers were collected from birth until 6 weeks of age, i.e., the preweaning period. Fecal microbiota was analyzed with QIIME 2 whereas fecal metabolites were measured using an untargeted LC-MS approach. At birth, MET heifers had greater (P ≤ 0.05) BW, HH, and WH. During the preweaning period, no differences between groups were detected for starter intake (P = 0.77). However, MET heifers maintained greater (P ≤ 0.05) BW, HH and tended (P = 0.06) to have greater WH and average daily gain (ADG) (P = 0.10). Fecal microbiota and metabolome profiles through 42 days of age in MET heifers indicated greater capacity for hindgut production of endogenous antibiotics and enhanced hindgut functionality and health. Enhancing maternal post-ruminal supply of methionine during late-gestation in dairy cows has a positive effect on hindgut functionality and health in their offspring through alterations in the fecal microbiota and metabolome without affecting feed intake. Those alterations could limit pathogen colonization of the hindgut while providing essential nutrients to the neonate. Together, such responses contribute to the ability of young calves to achieve better rates of nutrient utilization for growth.
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Affiliation(s)
- Ahmed Elolimy
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Animal Production, National Research Centre, Giza, Egypt
| | - Abdulrahman Alharthi
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
| | - Mohamed Zeineldin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Animal Medicine, College of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Claudia Parys
- Evonik Nutrition & Care GmbH, Hanau-Wolfgang, Germany
| | | | - Juan J. Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Department of Animal Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, United States
- Division of Nutritional Sciences, Illinois Informatics Institute, University of Illinois Urbana–Champaign, Urbana, IL, United States
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