1
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Zhang H, Lu Y, Zhang Y, Dong J, Jiang S, Tang Y. DHA-enriched phosphatidylserine ameliorates cyclophosphamide-induced liver injury via regulating the gut-liver axis. Int Immunopharmacol 2024; 140:112895. [PMID: 39133957 DOI: 10.1016/j.intimp.2024.112895] [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: 06/11/2024] [Revised: 07/24/2024] [Accepted: 08/05/2024] [Indexed: 09/01/2024]
Abstract
OBJECTIVE This study explores the therapeutic effects and mechanisms of DHA-enriched phosphatidylserine (DHA-PS) on liver injury induced by cyclophosphamide (CTX) in mice, focusing on the gut-liver axis. METHODS A mouse model was established by administering CTX (80 mg/kg) intraperitoneally for 5 days. DHA-PS (50 or 100 mg/kg) was administered for the next 7 days to assess its reparative impact on liver damage. RESULTS The findings revealed significant improvements in liver biochemical indices, inflammatory markers, and oxidative stress levels in the mice treated with DHA-PS. Through non-targeted metabolomics analysis, DHA-PS mitigated CTX-induced metabolic disruptions by modulating lipid, amino acid, and pyrimidine metabolism. Immunofluorescence analysis further confirmed that DHA-PS reduced the expression of liver-associated inflammatory proteins by inhibiting the TLR4/NF-κB pathway. Additionally, DHA-PS restored the intestinal barrier, evidenced by adjustments in the levels of intestinal lipopolysaccharide (LPS), secretory immunoglobulin A (sIgA), and tight junction proteins (Claudin-1, Occludin, and ZO-1). It also improved gut microbiota balance by enhancing microbial diversity, increasing beneficial bacteria, and altering community structures. CONCLUSION These results suggest that DHA-PS could be a potential therapeutic agent or functional food for CTX-induced liver injury through its regulation of the gut-liver axis.
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Affiliation(s)
- Honglei Zhang
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Yun Lu
- Medical Department, The Second Affiliated Hospital of Jiaxing University, Jiaxing, 314000, China.
| | - Yuanlei Zhang
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jiayu Dong
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Su Jiang
- ECA Healthcare Inc, Shanghai, 201101, China
| | - Yunping Tang
- School of Food and Pharmacy, Zhejiang Ocean University, Zhoushan, 316022, China.
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2
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Long J, Saw M, Zhang P, Wang L, Li L, Ren H, Liu C, Ma Z, Zhang J, Wang B. Role of tenofovir dipivoxil in gut microbiota recovery from HBV-infection induced dysbiosis. BMC Microbiol 2024; 24:359. [PMID: 39304810 DOI: 10.1186/s12866-024-03457-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 08/06/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Studies have found dysbiosis of the gut microbiota in individuals infected with the hepatitis B virus (HBV). Tenofovir dipivoxil (TDF) is one of the preferred oral antiviral drugs used for the treatment of chronic hepatitis B (CHB), but the extent to which TDF is able to affect the gut microbiota and inflammatory factors of a patient remains largely unexplored. In this study, we collected stool samples from HBV patients prior to medication and from CHB patients treated with TDF. RESULTS The gut microbiota and inflammatory factors were assessed in 42 healthy subjects (HC group), 109 HBV-infected subjects, including 48 CHB patients who were not medicated with nucleoside analogue drugs (No-NAs group), and 61 CHB patients who were medicated with TDF (TDF group). 16 S rRNA sequencing revealed that TDF treatment caused significant changes in the gut microbiota of HBV-infected individuals; however, the gut microbiota of HBV-infected individuals did not fully recover to a pre-dysbiosis state. The relative abundance of Bacteroidota gradually decreased from the HC group to the No-NAs and TDF groups. The relative abundance of Fusobacteriota was significantly higher in the No-NAs group than in the HC group. At the genus level, Dialister, Eubacterium_hallii_group, Halomonas, Collinsella, Sphingomonas, Xanthomonadaceae_unclassified, and Rhizobiaceae_unclassified were overrepresented; while the abundance of Bacteroides and Fusobacterium decreased significantly in the No-NAs and TDF groups. CONCLUSIONS This study showed that TDF treatment significantly improved the regulation of the gut microbiota and aided in dysbiosis recovery. We did not observe significant improvement in serum inflammatory factor concentrations, which may be related to the relatively short duration of TDF administration in this study.
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Affiliation(s)
- Jianfei Long
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Maximilian Saw
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China.
| | - Pan Zhang
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Li Wang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Ling Li
- Department of Pharmacy, Jing'an District Central Hospital, Fudan University, Shanghai, China
| | - Hongyan Ren
- Shanghai Mobio Biomedical Technology Co., Shanghai, China
| | - Chao Liu
- Shanghai Mobio Biomedical Technology Co., Shanghai, China
| | - Zhenxuan Ma
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiming Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China.
- Department of Infectious Diseases, Jing'An Branch of Huashan Hospital, Fudan University, Shanghai, China.
| | - Bin Wang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China.
- Department of Pharmacy, Jing'an District Central Hospital, Fudan University, Shanghai, China.
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3
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Demirturk M, Cinar MS, Avci FY. The immune interactions of gut glycans and microbiota in health and disease. Mol Microbiol 2024; 122:313-330. [PMID: 38703041 DOI: 10.1111/mmi.15267] [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: 10/13/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/06/2024]
Abstract
The human digestive system harbors a vast diversity of commensal bacteria and maintains a symbiotic relationship with them. However, imbalances in the gut microbiota accompany various diseases, such as inflammatory bowel diseases (IBDs) and colorectal cancers (CRCs), which significantly impact the well-being of populations globally. Glycosylation of the mucus layer is a crucial factor that plays a critical role in maintaining the homeostatic environment in the gut. This review delves into how the gut microbiota, immune cells, and gut mucus layer work together to establish a balanced gut environment. Specifically, the role of glycosylation in regulating immune cell responses and mucus metabolism in this process is examined.
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Affiliation(s)
- Mahmut Demirturk
- Department of Biochemistry, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Mukaddes Sena Cinar
- Department of Biochemistry, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Fikri Y Avci
- Department of Biochemistry, Emory Vaccine Center, Emory University School of Medicine, Atlanta, Georgia, USA
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4
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Wu XQ, Chen XM, Pan YY, Sun C, Tian JX, Qian AD, Niu XT, Kong YD, Li M, Wang GQ. Changes of intestinal barrier in the process of intestinal inflammation induced by Aeromonas hydrophila in snakehead (Channa argus). FISH & SHELLFISH IMMUNOLOGY 2024; 152:109775. [PMID: 39019126 DOI: 10.1016/j.fsi.2024.109775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/19/2024]
Abstract
Bacterial intestinal inflammation frequently occurs in cultured fish. Nevertheless, research on intestinal barrier dysfunction in the process of intestinal inflammation is deficient. In this study, we explored the changes of intestinal inflammation induced by Aeromonas hydrophila (A. hydrophila) in snakehead and the relationship between intestinal barrier and inflammation. Snakehead [(13.05 ± 2.39) g] were infected via anus with A. hydrophila. Specimens were collected for analysis at 0, 1, 3, 7 and 21 d post-injection. The results showed that with the increase of exposure time, the hindgut underwent stages of normal function, damage, damage deterioration, repair and recovery. Relative to 0 d, the levels of IL-1β and TNF-α in serum, and the expression of nod1, tlr1, tlr5, nf-κb, tnf-α and il-1β in intestine were significantly increased, and showed an upward then downward pattern over time. However, the expression of tlr2 and il-10 were markedly decreased, and showed the opposite trend. In addition, with the development of intestinal inflammation, the diversity and richness of species, and the levels of phylum and genus in intestine were obviously altered. The levels of trypsin, LPS, AMS, T-SOD, CAT, GPx, AKP, LZM and C3 in intestine were markedly reduced, and displayed a trend of first decreasing and then rebounding. The ultrastructure observation showed that the microvilli and tight junction structure of intestinal epithelial cells experienced normal function initially, then damage, and finally recovery over time. The expression of claudin-3 and zo-1 in intestine were significantly decreased, and showed a trend of first decreasing and then rebounding. Conversely, the expression of mhc-i, igm, igt and pigr in intestine were markedly increased, and displayed a trend of increasing first and then decreasing. The above results revealed the changes in intestinal barrier during the occurrence and development of intestinal inflammation, which provided a theoretical basis for explaining the relationship between the two.
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Affiliation(s)
- Xue-Qin Wu
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Xiu-Mei Chen
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
| | - Yi-Yu Pan
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Chuang Sun
- Fisheries Technology Extension Station of Baicheng, Jilin Province, Baicheng, 137000, China
| | - Jia-Xin Tian
- College of Life Sciences, Tonghua Normal University, Tonghua, 134002, China
| | - Ai-Dong Qian
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Xiao-Tian Niu
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Yi-di Kong
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Min Li
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China
| | - Gui-Qin Wang
- College of Animal Science and Technology, Jilin Provincial Key Laboratory of Animal Nutrition and Feed Science, Key Laboratory for Animal Production, Product Quality and Safety of Ministry of Education, Jilin Agricultural University, Changchun, 130118, China.
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5
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Huang YY, Price MN, Hung A, Gal-Oz O, Tripathi S, Smith CW, Ho D, Carion H, Deutschbauer AM, Arkin AP. Barcoded overexpression screens in gut Bacteroidales identify genes with roles in carbon utilization and stress resistance. Nat Commun 2024; 15:6618. [PMID: 39103350 DOI: 10.1038/s41467-024-50124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/28/2024] [Indexed: 08/07/2024] Open
Abstract
A mechanistic understanding of host-microbe interactions in the gut microbiome is hindered by poorly annotated bacterial genomes. While functional genomics can generate large gene-to-phenotype datasets to accelerate functional discovery, their applications to study gut anaerobes have been limited. For instance, most gain-of-function screens of gut-derived genes have been performed in Escherichia coli and assayed in a small number of conditions. To address these challenges, we develop Barcoded Overexpression BActerial shotgun library sequencing (Boba-seq). We demonstrate the power of this approach by assaying genes from diverse gut Bacteroidales overexpressed in Bacteroides thetaiotaomicron. From hundreds of experiments, we identify new functions and phenotypes for 29 genes important for carbohydrate metabolism or tolerance to antibiotics or bile salts. Highlights include the discovery of a D-glucosamine kinase, a raffinose transporter, and several routes that increase tolerance to ceftriaxone and bile salts through lipid biosynthesis. This approach can be readily applied to develop screens in other strains and additional phenotypic assays.
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Affiliation(s)
- Yolanda Y Huang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, USA.
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Allison Hung
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Omree Gal-Oz
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Surya Tripathi
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Christopher W Smith
- Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Davian Ho
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Héloïse Carion
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Bioengineering, University of California-Berkeley, Berkeley, CA, USA.
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6
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Liu X, Li S, Wang L, Ma K. Microecological regulation in HCC therapy: Gut microbiome enhances ICI treatment. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167230. [PMID: 38734322 DOI: 10.1016/j.bbadis.2024.167230] [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: 10/24/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 05/13/2024]
Abstract
The exploration of the complex mechanisms of cancer immunotherapy is rapidly evolving worldwide, and our focus is on the interaction of hepatocellular carcinoma (HCC) with immune checkpoint inhibitors (ICIs), particularly as it relates to the regulatory role of the gut microbiome. An important basis for the induction of immune responses in HCC is the presence of specific anti-tumor cells that can be activated and reinforced by ICIs, which is why the application of ICIs results in sustained tumor response rates in the majority of HCC patients. However, mechanisms of acquired resistance to immunotherapy in unresectable HCC result in no long-term benefit for some patients. The significant heterogeneity of inter-individual differences in the gut microbiome in response to treatment with ICIs makes it possible to target modulation of specific gut microbes to assist in augmenting checkpoint blockade therapies in HCC. This review focuses on the complex relationship between the gut microbiome, host immunity, and HCC, and emphasizes that manipulating the gut microbiome to improve response rates to cancer ICI therapy is a clinical strategy with unlimited potential.
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Affiliation(s)
- Xuliang Liu
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Shiyao Li
- Department of Respiratory Medicine, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Liming Wang
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China; Engineering Research Center for New Materials and Precision Treatment Technology of Malignant Tumors Therapy, The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China; Engineering Technology Research Center for Translational Medicine, The Second Affiliated Hospital, Dalian Medical University, Dalian, Liaoning, China.
| | - Kexin Ma
- Division of Hepatobiliary and Pancreatic Surgery, Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China.
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7
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Muramatsu MK, Winter SE. Nutrient acquisition strategies by gut microbes. Cell Host Microbe 2024; 32:863-874. [PMID: 38870902 PMCID: PMC11178278 DOI: 10.1016/j.chom.2024.05.011] [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: 03/25/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
The composition and function of the gut microbiota are intimately tied to nutrient acquisition strategies and metabolism, with significant implications for host health. Both dietary and host-intrinsic factors influence community structure and the basic modes of bacterial energy metabolism. The intestinal tract is rich in carbon and nitrogen sources; however, limited access to oxygen restricts energy-generating reactions to fermentation. By contrast, increased availability of electron acceptors during episodes of intestinal inflammation results in phylum-level changes in gut microbiota composition, suggesting that bacterial energy metabolism is a key driver of gut microbiota function. In this review article, we will illustrate diverse examples of microbial nutrient acquisition strategies in the context of habitat filters and anatomical location and the central role of energy metabolism in shaping metabolic strategies to support bacterial growth in the mammalian gut.
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Affiliation(s)
- Matthew K Muramatsu
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis, Davis, CA 95616, USA
| | - Sebastian E Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis, Davis, CA 95616, USA.
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8
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Yang X, Zhang J, Zhu J, Yang R, Tong Y. Molecular insights into FucR transcription factor to control the metabolism of L-fucose in Bifidobacterium longum subsp. infantis. Microbiol Res 2024; 283:127709. [PMID: 38593579 DOI: 10.1016/j.micres.2024.127709] [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: 12/13/2023] [Revised: 03/27/2024] [Accepted: 03/30/2024] [Indexed: 04/11/2024]
Abstract
Bifidobacterium longum subsp. infantis commonly colonizes the human gut and is capable of metabolizing L-fucose, which is abundant in the gut. Multiple studies have focused on the mechanisms of L-fucose utilization by B. longum subsp. infantis, but the regulatory pathways governing the expression of these catabolic processes are still unclear. In this study, we have conducted a structural and functional analysis of L-fucose metabolism transcription factor FucR derived from B. longum subsp. infantis Bi-26. Our results indicated that FucR is a L-fucose-sensitive repressor with more α-helices, fewer β-sheets, and β-turns. Transcriptional analysis revealed that FucR displays weak negative self-regulation, which is counteracted in the presence of L-fucose. Isothermal titration calorimetry indicated that FucR has a 2:1 stoichiometry with L-fucose. The key amino acid residues for FucR binding L-fucose are Asp280 and Arg331, with mutation of Asp280 to Ala resulting in a decrease in the affinity between FucR and L-fucose with the Kd value from 2.58 to 11.68 μM, and mutation of Arg331 to Ala abolishes the binding ability of FucR towards L-fucose. FucR specifically recognized and bound to a 20-bp incomplete palindrome sequence (5'-ACCCCAATTACGAAAATTTTT-3'), and the affinity of the L-fucose-loaded FucR for the DNA fragment was lower than apo-FucR. The results provided new insights into the regulating L-fucose metabolism by B. longum subsp. infantis.
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Affiliation(s)
- Xiaojun Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Zhang
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jing Zhu
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ruijin Yang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yanjun Tong
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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9
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Crouch LI, Rodrigues CS, Bakshani CR, Tavares-Gomes L, Gaifem J, Pinho SS. The role of glycans in health and disease: Regulators of the interaction between gut microbiota and host immune system. Semin Immunol 2024; 73:101891. [PMID: 39388764 DOI: 10.1016/j.smim.2024.101891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/03/2024] [Accepted: 10/03/2024] [Indexed: 10/12/2024]
Abstract
The human gut microbiota is home to a diverse collection of microorganisms that has co-evolved with the host immune system in which host-microbiota interactions are essential to preserve health and homeostasis. Evidence suggests that the perturbation of this symbiotic host-microbiome relationship contributes to the onset of major diseases such as chronic inflammatory diseases including Inflammatory Bowel Disease. The host glycocalyx (repertoire of glycans/sugar-chains at the surface of gut mucosa) constitutes a major biological and physical interface between the intestinal mucosa and microorganisms, as well as with the host immune system. Glycans are an essential niche for microbiota colonization and thus an important modulator of host-microorganism interactions both in homeostasis and in disease. In this review, we discuss the role of gut mucosa glycome as an instrumental pathway that regulates host-microbiome interactions in homeostasis but also in health to inflammation transition. We also discuss the power of mucosa glycosylation remodelling as an attractive preventive and therapeutic strategy to preserve gut homeostasis.
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Affiliation(s)
- Lucy I Crouch
- Department of Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham B15 2TT, UK.
| | - Cláudia S Rodrigues
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal; ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Cassie R Bakshani
- Department of Microbes, Infection and Microbiomes, College of Medicine and Health, University of Birmingham, Birmingham B15 2TT, UK
| | - Leticia Tavares-Gomes
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Joana Gaifem
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Salomé S Pinho
- i3S - Institute for Research and Innovation in Health, University of Porto, Porto, Portugal; ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal.
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10
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Jernfors T, Lavrinienko A, Vareniuk I, Landberg R, Fristedt R, Tkachenko O, Taskinen S, Tukalenko E, Mappes T, Watts PC. Association between gut health and gut microbiota in a polluted environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169804. [PMID: 38184263 DOI: 10.1016/j.scitotenv.2023.169804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/28/2023] [Accepted: 12/29/2023] [Indexed: 01/08/2024]
Abstract
Animals host complex bacterial communities in their gastrointestinal tracts, with which they share a mutualistic interaction. The numerous effects these interactions grant to the host include regulation of the immune system, defense against pathogen invasion, digestion of otherwise undigestible foodstuffs, and impacts on host behaviour. Exposure to stressors, such as environmental pollution, parasites, and/or predators, can alter the composition of the gut microbiome, potentially affecting host-microbiome interactions that can be manifest in the host as, for example, metabolic dysfunction or inflammation. However, whether a change in gut microbiota in wild animals associates with a change in host condition is seldom examined. Thus, we quantified whether wild bank voles inhabiting a polluted environment, areas where there are environmental radionuclides, exhibited a change in gut microbiota (using 16S amplicon sequencing) and concomitant change in host health using a combined approach of transcriptomics, histological staining analyses of colon tissue, and quantification of short-chain fatty acids in faeces and blood. Concomitant with a change in gut microbiota in animals inhabiting contaminated areas, we found evidence of poor gut health in the host, such as hypotrophy of goblet cells and likely weakened mucus layer and related changes in Clca1 and Agr2 gene expression, but no visible inflammation in colon tissue. Through this case study we show that inhabiting a polluted environment can have wide reaching effects on the gut health of affected animals, and that gut health and other host health parameters should be examined together with gut microbiota in ecotoxicological studies.
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Affiliation(s)
- Toni Jernfors
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland.
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland; Laboratory of Food Systems Biotechnology, Institute of Food, Nutrition and Health, ETH Zürich, Zürich, Switzerland
| | - Igor Vareniuk
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Rikard Fristedt
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Olena Tkachenko
- Department of Cytology, Histology and Reproductive Medicine, Taras Shevchenko National University of Kyiv, 01033, Ukraine
| | - Sara Taskinen
- Department of Mathematics and Statistics, University of Jyväskylä, FI-40014, Finland
| | - Eugene Tukalenko
- Department of Radiobiology and Radioecology, Institute for Nuclear Research of NAS of Ukraine, 020000, Ukraine
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
| | - Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, FI-40014, Finland
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11
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Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe 2024; 32:181-190.e9. [PMID: 38228143 PMCID: PMC10922750 DOI: 10.1016/j.chom.2023.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/14/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The early microbial colonization of the gastrointestinal tract can have long-term impacts on development and health. Keystone species, including Bacteroides spp., are prominent in early life and play crucial roles in maintaining the structure of the intestinal ecosystem. However, the process by which a resilient community is curated during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa in early life and regulates a commensal colonization program. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. NanH is required for vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and microbiota mediated through host-derived glycans to promote stable colonization.
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Affiliation(s)
- Ekaterina Buzun
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristija Sejane
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Renee E Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Luke R Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiaqi Zhao
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominic M McGrosso
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA 92093, USA; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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12
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Abstract
Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.
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Affiliation(s)
- Giselle McCallum
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
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13
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Aminov R, Aminova L. The role of the glycome in symbiotic host-microbe interactions. Glycobiology 2023; 33:1106-1116. [PMID: 37741057 PMCID: PMC10876039 DOI: 10.1093/glycob/cwad073] [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: 01/16/2023] [Revised: 09/13/2023] [Accepted: 09/21/2023] [Indexed: 09/25/2023] Open
Abstract
Glycosylation plays a crucial role in many aspects of cell biology, including cellular and organismal integrity, structure-and-function of many glycosylated molecules in the cell, signal transduction, development, cancer, and in a number of diseases. Besides, at the inter-organismal level of interaction, a variety of glycosylated molecules are involved in the host-microbiota recognition and initiation of downstream signalling cascades depending on the outcomes of the glycome-mediated ascertainment. The role of glycosylation in host-microbe interactions is better elaborated within the context of virulence and pathogenicity in bacterial infection processes but the symbiotic host-microbe relationships also involve substantive glycome-mediated interactions. The works in the latter field have been reviewed to a much lesser extent, and the main aim of this mini-review is to compensate for this deficiency and summarise the role of glycomics in host-microbe symbiotic interactions.
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Affiliation(s)
- Rustam Aminov
- The School of Medicine, Medical Sciences and Nutrition, Foresterhill Campus, Aberdeen AB25 2ZD, Scotland, United Kingdom
| | - Leila Aminova
- Midwest Bioprocessing Center, 801 W Main St, Peoria, IL, 61606-1877, United States
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14
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Inaba R, Vujakovic S, Bergstrom K. The gut mucus network: A dynamic liaison between microbes and the immune system. Semin Immunol 2023; 69:101807. [PMID: 37478802 DOI: 10.1016/j.smim.2023.101807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 06/24/2023] [Accepted: 07/08/2023] [Indexed: 07/23/2023]
Abstract
A complex mucus network made up of large polymers of the mucin-family glycoprotein MUC2 exists between the large intestinal microbial mass and epithelial and immune cells. This has long been understood as an innate immune defense barrier against the microbiota and other luminal threats that reinforces the barrier function of the epithelium and limits microbiota contact with the tissues. However, past and recent studies have provided new evidence of how critical the mucus network is to act as a 'liaison' between host and microbe to mediate anti-inflammatory, mutualistic interactions with the microbiota and protection from pathogens. This review summarizes historical and recent insights into the formation of the gut mucus network, how the microbes and immune system influence mucus, and in turn, how the mucus influences immune responses to the microbiota.
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Affiliation(s)
- Rain Inaba
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada
| | - Sara Vujakovic
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada
| | - Kirk Bergstrom
- Department of Biology, University of British Columbia, Okanagan Campus, 3187 University Way, Kelowna V1V 1V7, British Columbia, Canada.
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15
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Salm F, Znalesniak EB, Laskou A, Harder S, Schlüter H, Hoffmann W. Expression Profiling along the Murine Intestine: Different Mucosal Protection Systems and Alterations in Tff1-Deficient Animals. Int J Mol Sci 2023; 24:12684. [PMID: 37628863 PMCID: PMC10454331 DOI: 10.3390/ijms241612684] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Tff1 is a typical gastric peptide secreted together with the mucin, Muc5ac. Tff1-deficient (Tff1KO) mice are well known for their prominent gastric phenotype and represent a recognized model for antral tumorigenesis. Notably, intestinal abnormalities have also been reported in the past in these animals. Here, we have compared the expression of selected genes in Tff1KO mice and their corresponding wild-type littermates (RT-PCR analyses), focusing on different mucosal protection systems along the murine intestine. As hallmarks, genes were identified with maximum expression in the proximal colon and/or the duodenum: Agr2, Muc6/A4gnt/Tff2, Tff1, Fut2, Gkn2, Gkn3, Duox2/Lpo, Nox1. This is indicative of different protection systems such as Tff2/Muc6, Tff1-Fcgbp, gastrokines, fucosylation, and reactive oxygen species (ROS) in the proximal colon and/or duodenum. Few significant transcriptional changes were observed in the intestine of Tff1KO mice when compared with wild-type littermates, Clca1 (Gob5), Gkn1, Gkn2, Nox1, Tff2. We also analyzed the expression of Tff1, Tff2, and Tff3 in the pancreas, liver, and lung of Tff1KO and wild-type animals, indicating a cross-regulation of Tff gene expression. Furthermore, on the protein level, heteromeric Tff1-Fcgbp and various monomeric Tff1 forms were identified in the duodenum and a high-molecular-mass Tff2/Muc6 complex was identified in the proximal colon (FPLC, proteomics).
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Affiliation(s)
- Franz Salm
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Eva B. Znalesniak
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Aikaterini Laskou
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Sönke Harder
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Werner Hoffmann
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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16
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Buzun E, Hsu CY, Sejane K, Oles RE, Ayala AV, Loomis LR, Zhao J, Rossitto LA, McGrosso D, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early life colonization by a pioneering gut commensal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552477. [PMID: 37609270 PMCID: PMC10441351 DOI: 10.1101/2023.08.08.552477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The early microbial colonization of the gastrointestinal tract can lead to long-term impacts in development and overall human health. Keystone species, including Bacteroides spp ., play a crucial role in maintaining the structure, diversity, and function of the intestinal ecosystem. However, the process by which a defined and resilient community is curated and maintained during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa and regulates the commensal colonization program during the first weeks of life. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. After examining the dynamics between pioneer gut Bacteroides species in the murine gut, we discovered that NanH enables vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, we demonstrate that NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and the microbiota mediated through host-derived glycans to promote stable intestinal colonization.
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17
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Nilsen M, Rehbinder EM, Lødrup Carlsen KC, Haugen G, Hedlin G, Jonassen CM, Killingstad ME, Nordlund B, Ormaasen I, Skjerven HO, Snipen L, Staff AC, Söderhäll C, Sørensen R, Vettukattil R, Wilborn LM, Rudi K. A Globally Distributed Bacteroides caccae Strain Is the Most Prevalent Mother-Child Shared Bacteroidaceae Strain in a Large Scandinavian Cohort. Appl Environ Microbiol 2023; 89:e0078923. [PMID: 37338379 PMCID: PMC10370313 DOI: 10.1128/aem.00789-23] [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: 05/15/2023] [Accepted: 05/28/2023] [Indexed: 06/21/2023] Open
Abstract
Bacteroides and Phocaeicola, members of the family Bacteroidaceae, are among the first microbes to colonize the human infant gut. While it is known that these microbes can be transmitted from mother to child, our understanding of the specific strains that are shared and potentially transmitted is limited. In this study, we aimed to investigate the shared strains of Bacteroides and Phocaeicola in mothers and their infants. We analyzed fecal samples from pregnant woman recruited at 18 weeks of gestation from the PreventADALL study, as well as offspring samples from early infancy, including skin swab samples taken within 10 min after birth, the first available fecal sample (meconium), and fecal samples at 3 months of age. We screened 464 meconium samples for Bacteroidaceae, with subsequent selection of 144 mother-child pairs for longitudinal analysis, based on the presence of Bacteroidaceae, longitudinal sample availability, and delivery mode. Our results showed that Bacteroidaceae members were mainly detected in samples from vaginally delivered infants. We identified high prevalences of Phocaeicola vulgatus, Phocaeicola dorei, Bacteroides caccae, and Bacteroides thetaiotaomicron in mothers and vaginally born infants. However, at the strain level, we observed high prevalences of only two strains: a B. caccae strain and a P. vulgatus strain. Notably, the B. caccae strain was identified as a novel component of mother-child shared strains, and its high prevalence was also observed in publicly available metagenomes worldwide. Our findings suggest that mode of delivery may play a role in shaping the early colonization of the infant gut microbiota, in particular the colonization of Bacteroidaceae members. IMPORTANCE Our study provides evidence that Bacteroidaceae strains present on infants' skin within 10 min after birth, in meconium samples, and in fecal samples at 3 months of age in vaginally delivered infants are shared with their mothers. Using strain resolution analyses, we identified two strains, belonging to Bacteroides caccae and Phocaeicola vulgatus, as shared between mothers and their infants. Interestingly, the B. caccae strain showed a high prevalence worldwide, while the P. vulgatus strain was less common. Our findings also showed that vaginal delivery was associated with early colonization of Bacteroidaceae members, whereas cesarean section delivery was associated with delayed colonization. Given the potential for these microbes to influence the colonic environment, our results suggest that understanding the bacterial-host relationship at the strain level may have implications for infant health and development later in life.
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Affiliation(s)
- Morten Nilsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Eva Maria Rehbinder
- Department of Dermatology and Vaenerology, Oslo University Hospital, Oslo, Norway
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
| | - Karin C. Lødrup Carlsen
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Guttorm Haugen
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Gunilla Hedlin
- Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Björn Nordlund
- Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Ida Ormaasen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Håvard O. Skjerven
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Lars Snipen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Anne Cathrine Staff
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Obstetrics and Gynaecology, Oslo University Hospital, Oslo, Norway
| | - Cilla Söderhäll
- Astrid Lindgren Children’s Hospital, Karolinska University Hospital, Stockholm, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
| | - Regina Sørensen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Riyas Vettukattil
- University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, Oslo, Norway
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Lene Marie Wilborn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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18
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Djoko KY. Control of nutrient metal availability during host-microbe interactions: beyond nutritional immunity. J Biol Inorg Chem 2023:10.1007/s00775-023-02007-z. [PMID: 37464157 PMCID: PMC10368554 DOI: 10.1007/s00775-023-02007-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023]
Abstract
The control of nutrient availability is an essential ecological function of the host organism in host-microbe systems. Although often overshadowed by macronutrients such as carbohydrates, micronutrient metals are known as key drivers of host-microbe interactions. The ways in which host organisms control nutrient metal availability are dictated by principles in bioinorganic chemistry. Here I ponder about the actions of metal-binding molecules from the host organism in controlling nutrient metal availability to the host microbiota. I hope that these musings will encourage new explorations into the fundamental roles of metals in the ecology of diverse host-microbe systems.
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Affiliation(s)
- Karrera Y Djoko
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK.
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19
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Nuñez S, Barra M, Garrido D. Developing a Fluorescent Inducible System for Free Fucose Quantification in Escherichia coli. BIOSENSORS 2023; 13:bios13030388. [PMID: 36979599 PMCID: PMC10046853 DOI: 10.3390/bios13030388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 05/28/2023]
Abstract
L-Fucose is a monosaccharide abundant in mammalian glycoconjugates. In humans, fucose can be found in human milk oligosaccharides (HMOs), mucins, and glycoproteins in the intestinal epithelium. The bacterial consumption of fucose and fucosylated HMOs is critical in the gut microbiome assembly of infants, dominated by Bifidobacterium. Fucose metabolism is important for the production of short-chain fatty acids and is involved in cross-feeding microbial interactions. Methods for assessing fucose concentrations in complex media are lacking. Here we designed and developed a molecular quantification method of free fucose using fluorescent Escherichia coli. For this, low- and high-copy plasmids were evaluated with and without the transcription factor fucR and its respective fucose-inducible promoter controlling the reporter gene sfGFP. E. coli BL21 transformed with a high copy plasmid containing pFuc and fucR displayed a high resolution across increasing fucose concentrations and high fluorescence/OD values after 18 h. The molecular circuit was specific against other monosaccharides and showed a linear response in the 0-45 mM range. Adjusting data to the Hill equation suggested non-cooperative, simple regulation of FucR to its promoter. Finally, the biosensor was tested on different concentrations of free fucose and the supernatant of Bifidobacterium bifidum JCM 1254 supplemented with 2-fucosyl lactose, indicating the applicability of the method in detecting free fucose. In conclusion, a bacterial biosensor of fucose was validated with good sensitivity and precision. A biological method for quantifying fucose could be useful for nutraceutical and microbiological applications, as well as molecular diagnostics.
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20
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Development of the Anaerobic Microbiome in the Infant Gut. Pediatr Infect Dis J 2023:00006454-990000000-00384. [PMID: 36917032 DOI: 10.1097/inf.0000000000003905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Ninety-five percent of gut microbiota are anaerobes and vary according to age and diet. Complex carbohydrates in human milk enhance the growth of Bifidobacterium and Bacteroides in the first year. Complex carbohydrates in solid foods enhance the growth of Bacteroides and Clostridium in the second year. Short-chain fatty acids produced by Akkermansia and Faecalibacterium may reduce obesity, diabetes and IBD.
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21
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Ağagündüz D, Cocozza E, Cemali Ö, Bayazıt AD, Nanì MF, Cerqua I, Morgillo F, Saygılı SK, Berni Canani R, Amero P, Capasso R. Understanding the role of the gut microbiome in gastrointestinal cancer: A review. Front Pharmacol 2023; 14:1130562. [PMID: 36762108 PMCID: PMC9903080 DOI: 10.3389/fphar.2023.1130562] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
Gastrointestinal cancer represents one of the most diagnosed types of cancer. Cancer is a genetic and multifactorial disease, influenced by the host and environmental factors. It has been stated that 20% of cancer is caused by microorganisms such as Helicobacter pylori, hepatitis B and C virus, and human papillomavirus. In addition to these well-known microorganisms associated with cancer, it has been shown differences in the composition of the microbiota between healthy individuals and cancer patients. Some studies have suggested the existence of the selected microorganisms and their metabolites that can promote or inhibit tumorigenesis via some mechanisms. Recent findings have shown that gut microbiome and their metabolites can act as cancer promotors or inhibitors. It has been shown that gastrointestinal cancer can be caused by a dysregulation of the expression of non-coding RNA (ncRNA) through the gut microbiome. This review will summarize the latest reports regarding the relationship among gut microbiome, ncRNAs, and gastrointestinal cancer. The potential applications of diagnosing and cancer treatments will be discussed.
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Affiliation(s)
- Duygu Ağagündüz
- Department of Nutrition and Dietetics, Gazi University, Emek, Ankara, Turkey
| | | | - Özge Cemali
- Department of Nutrition and Dietetics, Gazi University, Emek, Ankara, Turkey
| | - Ayşe Derya Bayazıt
- Department of Nutrition and Dietetics, Gazi University, Emek, Ankara, Turkey
| | | | - Ida Cerqua
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Floriana Morgillo
- Medical Oncology, Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, Naples, Italy
| | - Suna Karadeniz Saygılı
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States,Department of Histology and Embryology, Kütahya Health Sciences University, Kütahya, Turkey
| | - Roberto Berni Canani
- Department of Translational Medical Science and ImmunoNutritionLab at CEINGE Biotechnologies Research Center and Task Force for Microbiome Studies, University of Naples Federico II, Naples, Italy
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States,*Correspondence: Raffaele Capasso, ; Paola Amero,
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy,*Correspondence: Raffaele Capasso, ; Paola Amero,
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22
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Kim J, Cheong YE, Yu S, Jin YS, Kim KH. Strain engineering and metabolic flux analysis of a probiotic yeast Saccharomyces boulardii for metabolizing L-fucose, a mammalian mucin component. Microb Cell Fact 2022; 21:204. [PMID: 36207743 PMCID: PMC9541068 DOI: 10.1186/s12934-022-01926-x] [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: 08/08/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022] Open
Abstract
Background Saccharomyces boulardii is a probiotic yeast that exhibits antimicrobial and anti-toxin activities. Although S. boulardii has been clinically used for decades to treat gastrointestinal disorders, several studies have reported weak or no beneficial effects of S. boulardii administration in some cases. These conflicting results of S. boulardii efficacity may be due to nutrient deficiencies in the intestine that make it difficult for S. boulardii to maintain its metabolic activity. Results To enable S. boulardii to overcome any nutritional deficiencies in the intestine, we constructed a S. boulardii strain that could metabolize l-fucose, a major component of mucin in the gut epithelium. The fucU, fucI, fucK, and fucA from Escherichia coli and HXT4 from S. cerevisiae were overexpressed in S. boulardii. The engineered S. boulardii metabolized l-fucose and produced 1,2-propanediol under aerobic and anaerobic conditions. It also produced large amounts of 1,2-propanediol under strict anaerobic conditions. An in silico genome-scale metabolic model analysis was performed to simulate the growth of S. boulardii on l-fucose, and elementary flux modes were calculated to identify critical metabolic reactions for assimilating l-fucose. As a result, we found that the engineered S. boulardii consumes l-fucose via (S)-lactaldehyde-(S)-lactate-pyruvate pathway, which is highly oxygen dependent. Conclusion To the best of our knowledge, this is the first study in which S. cerevisiae and S. boulardii strains capable of metabolizing l-fucose have been constructed. This strategy could be used to enhance the metabolic activity of S. boulardii and other probiotic microorganisms in the gut. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01926-x.
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Affiliation(s)
- Jungyeon Kim
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea
| | - Yu Eun Cheong
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea
| | - Sora Yu
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841, Republic of Korea. .,Department of Food Bioscience and Technology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
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23
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Liu Y, Zhu Y, Wang H, Wan L, Zhang W, Mu W. Strategies for Enhancing Microbial Production of 2'-Fucosyllactose, the Most Abundant Human Milk Oligosaccharide. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11481-11499. [PMID: 36094047 DOI: 10.1021/acs.jafc.2c04539] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Human milk oligosaccharides (HMOs), a group of structurally diverse unconjugated glycans in breast milk, act as important prebiotics and have plenty of unique health effects for growing infants. 2'-Fucosyllactose (2'-FL) is the most abundant HMO, accounting for approximately 30%, among approximately 200 identified HMOs with different structures. 2'-FL can be enzymatically produced by α1,2-fucosyltransferase, using GDP-l-fucose as donor and lactose as acceptor. Metabolic engineering strategies have been widely used for enhancement of GDP-l-fucose supply and microbial production of 2'-FL with high productivity. GDP-l-fucose supply can be enhanced by two main pathways, including de novo and salvage pathways. 2'-FL-producing α1,2-fucosyltransferases have widely been identified from various microorganisms. Metabolic pathways for 2'-FL synthesis can be basically constructed by enhancing GDP-l-fucose supply and introducing α1,2-fucosyltransferase. Various strategies have been attempted to enhance 2'-FL production, such as acceptor enhancement, donor enhancement, and improvement of the functional expression of α1,2-fucosyltransferase. In this review, current progress in GDP-l-fucose synthesis and bacterial α1,2-fucosyltransferases is described in detail, various metabolic engineering strategies for enhancing 2'-FL production are comprehensively reviewed, and future research focuses in biotechnological production of 2'-FL are suggested.
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Affiliation(s)
- Yuanlin Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Hao Wang
- Bloomage Biotechnology Corp., Ltd., Jinan, Shandong 250010, People's Republic of China
| | - Li Wan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, People's Republic of China
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Joffré E, Xiao X, Correia MSP, Nookaew I, Sasse S, Globisch D, Zhu B, Sjöling Å. Analysis of Growth Phases of Enterotoxigenic Escherichia coli Reveals a Distinct Transition Phase before Entry into Early Stationary Phase with Shifts in Tryptophan, Fucose, and Putrescine Metabolism and Degradation of Neurotransmitter Precursors. Microbiol Spectr 2022; 10:e0175521. [PMID: 35876501 PMCID: PMC9431495 DOI: 10.1128/spectrum.01755-21] [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: 03/03/2022] [Indexed: 11/20/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in children and adults in endemic areas. Gene regulation of ETEC during growth in vitro and in vivo needs to be further evaluated, and here we describe the full transcriptome and metabolome of ETEC during growth from mid-logarithmic growth to early stationary phase in rich medium (LB medium). We identified specific genes and pathways subjected to rapid transient alterations in gene expression and metabolite production during the transition from logarithmic to stationary growth. The transient phase was found to be different from the subsequent induction of early stationary phase-induced genes. The transient phase was characterized by the repression of genes and metabolites involved in organic substance transport. Genes involved in fucose and putrescine metabolism were upregulated, and genes involved in iron transport were repressed. Expression of toxins and colonization factors were not changed, suggesting retained virulence from mid-logarithmic to the start of the stationary phase. Metabolomic analyses showed that the transient phase was characterized by a drop of intracellular amino acids, e.g., l-tyrosine, l-tryptophan, l-phenylalanine, l-leucine, and l-glutamic acid, followed by increased levels at induction of stationary phase. A pathway enrichment analysis of the entire combined transcriptome and metabolome revealed that significant pathways during progression from logarithmic to early stationary phase are involved in the degradation of neurotransmitters aminobutyrate (GABA) and precursors of 5-hydroxytryptamine (serotonin). This work provides a comprehensive framework for further studies on transcriptional and metabolic regulation in pathogenic E. coli. IMPORTANCE We show that E. coli, exemplified by the pathogenic subspecies enterotoxigenic E. coli (ETEC), undergoes a stepwise transcriptional and metabolic transition into the stationary phase. At a specific entry point, E. coli induces activation and repression of specific pathways. This leads to a rapid decrease of intracellular levels of certain amino acids. The resulting metabolic activity leads to an intense but short peak of indole production, suggesting that this is the previously described "indole peak," rapid decrease of intermediate molecules of bacterial neurotransmitters, increased putrescine and fucose uptake, increased glutathione levels, and decreased iron uptake. This specific transient shift in gene expression and metabolome is short-lived and disappears when bacteria enter the early stationary phase. We suggest that these changes mainly prepare bacteria for ceased growth, but based on the pathways involved, we could suggest that this transient phase substantially influences survival and virulence.
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Affiliation(s)
- Enrique Joffré
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Xue Xiao
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Mário S. P. Correia
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Samantha Sasse
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Daniel Globisch
- Department of Chemistry - BMC, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
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25
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Nasr D, Moein M, Niforatos S, Nasr S, Ombada M, Khokhar F, Shahnawaz M, Poudyal B, Bou Zerdan M, Dutta D, Saidi RF, Lim SH. Piperacillin/Tazobactam and Meropenem Use Increases the Risks for Acute Graft Rejection Following First Kidney Transplantation. J Clin Med 2022; 11:jcm11102726. [PMID: 35628853 PMCID: PMC9147076 DOI: 10.3390/jcm11102726] [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: 04/27/2022] [Revised: 05/01/2022] [Accepted: 05/10/2022] [Indexed: 12/04/2022] Open
Abstract
Many broad-spectrum antibiotics (BSA) alter the intestinal microbiome that regulates adaptive immune responses. We hypothesized that BSA use before and early after kidney transplant may affect acute graft rejection (AGR). We carried out a retrospective cohort study on all patients who underwent kidney transplants in our institution. Patient demographics, clinical data, diagnosis, and treatment history were collected. Antibiotic use within 2 months prior to transplant and during the hospital admissions for transplant, as well as antibiotic types were recorded. A total of 357 consecutive first transplants were included for analysis. Median age was 52 years (range 7–76). A total of 67 patients received living donor and 290 deceased donor kidneys. A total of 19 patients received BSA within two months prior to transplant and 55 patients during the hospital admission for the transplant. With a median follow-up of 1270 days, 38 episodes of biopsy-proven AGR were recorded. There was no difference in the AGR rates during the first year between patients who received BSA and those who did not. However, the use of piperacillin/tazobactam or meropenem (PM) was associated with increased risks for the development of AGR, irrespective of the source of the donor grafts. Time to development of AGR was also shorter. Our data, therefore, suggest that the use of PM BSA prior to and immediately after kidney transplant increases the risks for AGR.
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Affiliation(s)
- Dayana Nasr
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
| | - Mahmoudreza Moein
- Department of Surgery, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (M.M.); (R.F.S.)
| | - Stephanie Niforatos
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
| | - Sandy Nasr
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
| | - Mulham Ombada
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
| | - Farzam Khokhar
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
| | - Myera Shahnawaz
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
| | - Bhavya Poudyal
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
| | - Maroun Bou Zerdan
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
| | - Dibyendu Dutta
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
- Division of Hematology and Oncology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Reza F. Saidi
- Department of Surgery, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (M.M.); (R.F.S.)
| | - Seah H. Lim
- Department of Medicine, SUNY Upstate Medical University, Syracuse, NY 13210, USA; (D.N.); (S.N.); (S.N.); (M.O.); (F.K.); (M.S.); (B.P.); (M.B.Z.); (D.D.)
- Division of Hematology and Oncology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Correspondence:
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Bergstrom K, Xia L. The barrier and beyond: Roles of intestinal mucus and mucin-type O-glycosylation in resistance and tolerance defense strategies guiding host-microbe symbiosis. Gut Microbes 2022; 14:2052699. [PMID: 35380912 PMCID: PMC8986245 DOI: 10.1080/19490976.2022.2052699] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Over the past two decades, our appreciation of the gut mucus has moved from a static lubricant to a dynamic and essential component of the gut ecosystem that not only mediates the interface between host tissues and vast microbiota, but regulates how this ecosystem functions to promote mutualistic symbioses and protect from microbe-driven diseases. By delving into the complex chemistry and biology of the mucus, combined with innovative in vivo and ex vivo approaches, recent studies have revealed novel insights into the formation and function of the mucus system, the O-glycans that make up this system, and how they mediate two major host-defense strategies - resistance and tolerance - to reduce damage caused by indigenous microbes and opportunistic pathogens. This current review summarizes these findings by highlighting the emerging roles of mucus and mucin-type O-glycans in influencing host and microbial physiology with an emphasis on host defense strategies against bacteria in the gastrointestinal tract.
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Affiliation(s)
- Kirk Bergstrom
- Department of Biology, University of British Columbia, Okanagan Campus, 3333 University Way, Kelowna, British ColumbiaV1V 1V7, Canada,Kirk Bergstrom Department of Biology, University of British Columbia, 3333 University Way, Kelowna, B.C. Canada
| | - Lijun Xia
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, OK, Oklahoma73104, USA,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, OK, Oklahoma73104, USA,CONTACT Lijun Xia Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, OK, Oklahoma73104, USA
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27
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Wardman JF, Bains RK, Rahfeld P, Withers SG. Carbohydrate-active enzymes (CAZymes) in the gut microbiome. Nat Rev Microbiol 2022; 20:542-556. [PMID: 35347288 DOI: 10.1038/s41579-022-00712-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 12/13/2022]
Abstract
The 1013-1014 microorganisms present in the human gut (collectively known as the human gut microbiota) dedicate substantial percentages of their genomes to the degradation and uptake of carbohydrates, indicating the importance of this class of molecules. Carbohydrates function not only as a carbon source for these bacteria but also as a means of attachment to the host, and a barrier to infection of the host. In this Review, we focus on the diversity of carbohydrate-active enzymes (CAZymes), how gut microorganisms use them for carbohydrate degradation, the different chemical mechanisms of these CAZymes and the roles that these microorganisms and their CAZymes have in human health and disease. We also highlight examples of how enzymes from this treasure trove have been used in manipulation of the microbiota for improved health and treatment of disease, in remodelling the glycans on biopharmaceuticals and in the potential production of universal O-type donor blood.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rajneesh K Bains
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Rahfeld
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. .,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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28
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Karimi P, Bakhtiarizadeh MR, Salehi A, Izadnia HR. Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken. Sci Rep 2022; 12:2558. [PMID: 35169237 PMCID: PMC8847365 DOI: 10.1038/s41598-022-06528-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.
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Affiliation(s)
- Parastoo Karimi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Hamid Reza Izadnia
- Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran
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29
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Gut microbiome alteration as a diagnostic tool and associated with inflammatory response marker in primary liver cancer. Hepatol Int 2022; 16:99-111. [DOI: 10.1007/s12072-021-10279-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/12/2021] [Indexed: 12/14/2022]
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30
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Jensen SK, Pærregaard SI, Brandum EP, Jørgensen AS, Hjortø GM, Jensen BAH. OUP accepted manuscript. Gastroenterol Rep (Oxf) 2022; 10:goac008. [PMID: 35291443 PMCID: PMC8915887 DOI: 10.1093/gastro/goac008] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/07/2022] [Accepted: 02/16/2022] [Indexed: 11/24/2022] Open
Abstract
Organismal survival depends on a well-balanced immune system and maintenance of host–microbe mutualism. The fine-tuned relationship between the gut microbiota and host immunity is constantly challenged by opportunistic bacteria testing the integrity of gastrointestinal (GI) barrier defenses. Barrier dysfunction reduces immunological tolerance towards otherwise innocuous microbes; it is a process that may instigate chronic inflammation. Paradoxically, sustained inflammation further diminishes barrier function, enabling bacterial translocation to extra-intestinal tissues. Once translocated, these bacteria stimulate systemic inflammation, thereby compromising organ function. While genetic risk alleles associate with barrier dysfunction, environmental stressors are key triggers of GI inflammation and associated breakdown in immune tolerance towards resident gut microbes. As dietary components dictate substrate availability, they also orchestrate microbiota composition and function, including migratory and pro-inflammatory potential, thus holding the capacity to fuel both GI and extra-intestinal inflammation. Additionally, Western diet consumption may weaken barrier defenses via curbed Paneth cell function and diminished host-defense peptide secretion. This review focuses on intervenable niches of host–microbe interactions and mucosal immunity with the ambition to provide a framework of plausible strategies to improve barrier function and regain tolerance in the inflamed mucosa via nutritional intervention.
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Affiliation(s)
- Sune K Jensen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Simone I Pærregaard
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emma P Brandum
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Astrid S Jørgensen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Gertrud M Hjortø
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Benjamin A H Jensen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Corresponding author. Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, Build. 22.5.39, Copenhagen N 2200, Denmark. Tel: +45-35330188;
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31
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Khan I, Bai Y, Zha L, Ullah N, Ullah H, Shah SRH, Sun H, Zhang C. Mechanism of the Gut Microbiota Colonization Resistance and Enteric Pathogen Infection. Front Cell Infect Microbiol 2021; 11:716299. [PMID: 35004340 PMCID: PMC8733563 DOI: 10.3389/fcimb.2021.716299] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/26/2021] [Indexed: 12/26/2022] Open
Abstract
The mammalian gut microbial community, known as the gut microbiota, comprises trillions of bacteria, which co-evolved with the host and has an important role in a variety of host functions that include nutrient acquisition, metabolism, and immunity development, and more importantly, it plays a critical role in the protection of the host from enteric infections associated with exogenous pathogens or indigenous pathobiont outgrowth that may result from healthy gut microbial community disruption. Microbiota evolves complex mechanisms to restrain pathogen growth, which included nutrient competition, competitive metabolic interactions, niche exclusion, and induction of host immune response, which are collectively termed colonization resistance. On the other hand, pathogens have also developed counterstrategies to expand their population and enhance their virulence to cope with the gut microbiota colonization resistance and cause infection. This review summarizes the available literature on the complex relationship occurring between the intestinal microbiota and enteric pathogens, describing how the gut microbiota can mediate colonization resistance against bacterial enteric infections and how bacterial enteropathogens can overcome this resistance as well as how the understanding of this complex interaction can inform future therapies against infectious diseases.
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Affiliation(s)
- Israr Khan
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China
- Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Yanrui Bai
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China
- Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Lajia Zha
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China
- Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Naeem Ullah
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
| | - Habib Ullah
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
- Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Syed Rafiq Hussain Shah
- Department of Microecology, School of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Hui Sun
- Cuiying Biomedical Research Centre, Lanzhou University Second Hospital, Lanzhou, China
| | - Chunjiang Zhang
- School of Life Sciences, Lanzhou University, Lanzhou, China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, Lanzhou University, Lanzhou, China
- Gansu Key Laboratory of Functional Genomics and Molecular Diagnosis, Lanzhou University, Lanzhou, China
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32
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Su Z, Lu L, Chen F, Chen J, Chen X. Gut Microbiota and Sunitinib-Induced Diarrhea in Metastatic Renal Cell Carcinoma: A Pilot Study. Cancer Manag Res 2021; 13:8663-8672. [PMID: 34849023 PMCID: PMC8612664 DOI: 10.2147/cmar.s328451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/29/2021] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Sunitinib-induced diarrhea seriously affects the prognosis of patients with metastatic renal cell carcinoma (mRCC) and reduces their quality of life. We aim to explore and find the relationship between sunitinib-induced diarrhea and gut microbiota. METHODS Feces were collected from 31 mRCC patients receiving sunitinib treatment. To characterize the feces gut microbiome profiles of patients, the V3-V4 region of 16S rRNA sequencing was carried out in this study. RESULTS Gut microbial diversity was decreased both in the severe diarrhea group and in the sunitinib-post group. The microbial composition with higher abundance of Bacteroides (mucus degrading bacteria) and lower abundance of Faecalibacterium, Oscillospira, Ruminococcaceae, Eubacterium and Coriobacteriaceae (butyrate-producing bacteria) were found in patients with diarrhea. Interestingly, the abundance of Actinobacteria was decreased in patients receiving sunitinib with severe diarrhea. CONCLUSION This study reported an association between gut microbiota and sunitinib-induced diarrhea. Defects of the butyrate-producing bacteria and the increase in Bacteroides may be the physiological basis of sunitinib-induced diarrhea.
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Affiliation(s)
- Zhimin Su
- Department of Oncology, 900th Hospital of PLA, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350024, People’s Republic of China
- Department of Medical Oncology, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, 361015, People’s Republic of China
| | - Linbin Lu
- Department of Oncology, 900th Hospital of PLA, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350024, People’s Republic of China
| | - Fuyu Chen
- Department of Substation Maintenance Center, State Grid Quanzhou Electric Power Supply Company, Quanzhou, 362000, People’s Republic of China
| | - Jianhui Chen
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, 350024, People’s Republic of China
| | - Xiong Chen
- Department of Oncology, 900th Hospital of PLA, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, 350024, People’s Republic of China
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Ladaycia A, Passirani C, Lepeltier E. Microbiota and nanoparticles: Description and interactions. Eur J Pharm Biopharm 2021; 169:220-240. [PMID: 34736984 DOI: 10.1016/j.ejpb.2021.10.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/12/2021] [Accepted: 10/26/2021] [Indexed: 12/15/2022]
Abstract
The healthy human body is inhabited with a large number of bacteria, forming natural flora. It is even estimated that for a human body, its amount of DNA is less important that its bacterial genetic material. This flora plays major roles in the sickness and health of the human body and any change in its composition may lead to different diseases. Nanoparticles are widely used in numerous fields: cosmetics, food, industry, and as drug delivery carrier in the medical field. Being included in these various applications, nanoparticles may interact with the human body at various levels and with different mechanisms. These interactions differ depending on the nanoparticle nature, its structure, its concentration and manifest in different ways on the microbiota, leading to its destabilization, its restoring or showing no toxic effect. Nanoparticles may also be used as a vehicle to regulate the microbiota or to treat some of its diseases.
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Affiliation(s)
- Abdallah Ladaycia
- Micro et Nanomédecines Translationnelles, MINT, UNIV Angers, UMR INSERM 1066, UMR CNRS 6021, Angers, France
| | - Catherine Passirani
- Micro et Nanomédecines Translationnelles, MINT, UNIV Angers, UMR INSERM 1066, UMR CNRS 6021, Angers, France
| | - Elise Lepeltier
- Micro et Nanomédecines Translationnelles, MINT, UNIV Angers, UMR INSERM 1066, UMR CNRS 6021, Angers, France.
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Maresca M, Alatou R, Pujol A, Nicoletti C, Perrier J, Giardina T, Simon G, Méjean V, Fons M. RadA, a MSCRAMM Adhesin of the Dominant Symbiote Ruminococcus gnavus E1, Binds Human Immunoglobulins and Intestinal Mucins. Biomolecules 2021; 11:1613. [PMID: 34827611 PMCID: PMC8615915 DOI: 10.3390/biom11111613] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 01/10/2023] Open
Abstract
Adhesion to the digestive mucosa is considered a key factor for bacterial persistence within the gut. In this study, we show that Ruminococcus gnavus E1 can express the radA gene, which encodes an adhesin of the MSCRAMMs family, only when it colonizes the gut. The RadA N-terminal region contains an all-β bacterial Ig-like domain known to interact with collagens. We observed that it preferentially binds human immunoglobulins (IgA and IgG) and intestinal mucins. Using deglycosylated substrates, we also showed that the RadA N-terminal region recognizes two different types of motifs, the protein backbone of human IgG and the glycan structure of mucins. Finally, competition assays with lectins and free monosaccharides identified Galactose and N-Acetyl-Galactosamine motifs as specific targets for the binding of RadA to mucins and the surface of human epithelial cells.
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Affiliation(s)
- Marc Maresca
- Aix Marseille University, CNRS, Centrale Marseille, ISM2, IM2B, 13007 Marseille, France; (A.P.); (C.N.); (J.P.); (T.G.)
| | - Radia Alatou
- Laboratoire de Biologie Moléculaire et Cellulaire, Université des Frères Mentouri Constantine 1, RN79 Constantine, Algeria;
| | - Ange Pujol
- Aix Marseille University, CNRS, Centrale Marseille, ISM2, IM2B, 13007 Marseille, France; (A.P.); (C.N.); (J.P.); (T.G.)
| | - Cendrine Nicoletti
- Aix Marseille University, CNRS, Centrale Marseille, ISM2, IM2B, 13007 Marseille, France; (A.P.); (C.N.); (J.P.); (T.G.)
| | - Josette Perrier
- Aix Marseille University, CNRS, Centrale Marseille, ISM2, IM2B, 13007 Marseille, France; (A.P.); (C.N.); (J.P.); (T.G.)
| | - Thierry Giardina
- Aix Marseille University, CNRS, Centrale Marseille, ISM2, IM2B, 13007 Marseille, France; (A.P.); (C.N.); (J.P.); (T.G.)
| | - Gwenola Simon
- Aix Marseille University, Université de Toulon, CNRS, IRD, MIO UM 110, 13007 Marseille, France;
| | - Vincent Méjean
- Aix Marseille University, CNRS, BIP UMR7281, IMM, IM2B, 13007 Marseille, France;
| | - Michel Fons
- Aix Marseille University, CNRS, BIP UMR7281, IMM, IM2B, 13007 Marseille, France;
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Gardner JG, Schreier HJ. Unifying themes and distinct features of carbon and nitrogen assimilation by polysaccharide-degrading bacteria: a summary of four model systems. Appl Microbiol Biotechnol 2021; 105:8109-8127. [PMID: 34611726 DOI: 10.1007/s00253-021-11614-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/20/2021] [Accepted: 09/21/2021] [Indexed: 11/24/2022]
Abstract
Our current understanding of enzymatic polysaccharide degradation has come from a huge number of in vitro studies with purified enzymes. While this vast body of work has been invaluable in identifying and characterizing novel mechanisms of action and engineering desirable traits into these enzymes, a comprehensive picture of how these enzymes work as part of a native in vivo system is less clear. Recently, several model bacteria have emerged with genetic systems that allow for a more nuanced study of carbohydrate active enzymes (CAZymes) and how their activity affects bacterial carbon metabolism. With these bacterial model systems, it is now possible to not only study a single nutrient system in isolation (i.e., carbohydrate degradation and carbon metabolism), but also how multiple systems are integrated. Given that most environmental polysaccharides are carbon rich but nitrogen poor (e.g., lignocellulose), the interplay between carbon and nitrogen metabolism in polysaccharide-degrading bacteria can now be studied in a physiologically relevant manner. Therefore, in this review, we have summarized what has been experimentally determined for CAZyme regulation, production, and export in relation to nitrogen metabolism for two Gram-positive (Caldicellulosiruptor bescii and Clostridium thermocellum) and two Gram-negative (Bacteroides thetaiotaomicron and Cellvibrio japonicus) polysaccharide-degrading bacteria. By comparing and contrasting these four bacteria, we have highlighted the shared and unique features of each, with a focus on in vivo studies, in regard to carbon and nitrogen assimilation. We conclude with what we believe are two important questions that can act as guideposts for future work to better understand the integration of carbon and nitrogen metabolism in polysaccharide-degrading bacteria. KEY POINTS: • Regardless of CAZyme deployment system, the generation of a local pool of oligosaccharides is a common strategy among Gram-negative and Gram-positive polysaccharide degraders as a means to maximally recoup the energy expenditure of CAZyme production and export. • Due to the nitrogen deficiency of insoluble polysaccharide-containing substrates, Gram-negative and Gram-positive polysaccharide degraders have a diverse set of strategies for supplementation and assimilation. • Future work needs to precisely characterize the energetic expenditures of CAZyme deployment and bolster our understanding of how carbon and nitrogen metabolism are integrated in both Gram-negative and Gram-positive polysaccharide-degrading bacteria, as both of these will significantly influence a given bacterium's suitability for biotechnology applications.
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Affiliation(s)
- Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
| | - Harold J Schreier
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.,Department of Marine Biotechnology, Institute of Marine and Environmental Technology, University of Maryland, Baltimore County, Baltimore, MD, USA
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Kidess E, Kleerebezem M, Brugman S. Colonizing Microbes, IL-10 and IL-22: Keeping the Peace at the Mucosal Surface. Front Microbiol 2021; 12:729053. [PMID: 34603258 PMCID: PMC8484919 DOI: 10.3389/fmicb.2021.729053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022] Open
Abstract
Our world is filled with microbes. Each multicellular organism has developed ways to interact with this microbial environment. Microbes do not always pose a threat; they can contribute to many processes that benefit the host. Upon colonization both host and microbes adapt resulting in dynamic ecosystems in different host niches. Regulatory processes develop within the host to prevent overt inflammation to beneficial microbes, yet keeping the possibility to respond when pathogens attempt to adhere and invade tissues. This review will focus on microbial colonization and the early (innate) host immune response, with special emphasis on the microbiota-modifying roles of IL-10 and IL-22 in the intestine. IL-10 knock out mice show an altered microbial composition, and spontaneously develop enterocolitis over time. IL-22 knock out mice, although not developing enterocolitis spontaneously, also have an altered microbial composition and increase of epithelial-adherent bacteria, mainly caused by a decrease in mucin and anti-microbial peptide production. Recently interesting links have been found between the IL-10 and IL-22 pathways. While IL-22 can function as a regulatory cytokine at the mucosal surface, it also has inflammatory roles depending on the context. For example, lack of IL-22 in the IL-10–/– mice model prevents spontaneous colitis development. Additionally, the reduced microbial diversity observed in IL-10–/– mice was also reversed in IL-10/IL-22 double mutant mice (Gunasekera et al., 2020). Since in early life, host immunity develops in parallel and in interaction with colonizing microbes, there is a need for future studies that focus on the effect of the timing of colonization in relation to the developmental phase of the host. To illustrate this, examples from zebrafish research will be compared with studies performed in mammals. Since zebrafish develop from eggs and are directly exposed to the outside microbial world, timing of the development of host immunity and subsequent control of microbial composition, is different from mammals that develop in utero and only get exposed after birth. Likewise, colonization studies using adult germfree mice might yield different results from those using neonatal germfree mice. Lastly, special emphasis will be given to the need for host genotype and environmental (co-housing) control of experiments.
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Affiliation(s)
- Evelien Kidess
- Animal Sciences Group, Host-Microbe Interactomics, Wageningen University and Research, Wageningen, Netherlands
| | - Michiel Kleerebezem
- Animal Sciences Group, Host-Microbe Interactomics, Wageningen University and Research, Wageningen, Netherlands
| | - Sylvia Brugman
- Animal Sciences Group, Host-Microbe Interactomics, Wageningen University and Research, Wageningen, Netherlands
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Bharanidharan R, Lee CH, Thirugnanasambantham K, Ibidhi R, Woo YW, Lee HG, Kim JG, Kim KH. Feeding Systems and Host Breeds Influence Ruminal Fermentation, Methane Production, Microbial Diversity and Metagenomic Gene Abundance. Front Microbiol 2021; 12:701081. [PMID: 34354694 PMCID: PMC8329423 DOI: 10.3389/fmicb.2021.701081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Our previous research revealed the advantages of separate feeding (SF) systems compared to total mixed ration (TMR) in terms of ruminal methane (CH4) production. The purpose of this experiment was to confirm the advantage of SF as a nutritional strategy for CH4 mitigation, and to determine the effects of different feeding systems (TMR and SF) on the rumen microbiome and associated metagenome of two different breeds and on CH4 emissions. We randomly allocated four Holstein (305 ± 29 kg) and four Hanwoo steers (292 ± 24 kg) to two groups; the steers were fed a commercial concentrate with tall fescue (75:25) as TMR or SF, in a crossover design (two successive 22-day periods). Neither feeding systems nor cattle breeds had an effect on the total tract digestibility of nutrients. The TMR feeding system and Hanwoo steers generated significantly more CH4 (P < 0.05) and had a higher yield [g/d and g/kg dry matter intake (DMI)] compared to the SF system and Holstein steers. A larger rumen acetate:propionate ratio was observed for the TMR than the SF diet (P < 0.05), and for Hanwoo than Holstein steers (P < 0.001), clearly reflecting a shift in the ruminal H2 sink toward CH4 production. The linear discriminant analysis (LDA) effect size (LEfSe) revealed a greater abundance (α < 0.05 and LDA > 2.0) of operational taxonomic units (OTUs) related to methanogenesis for Hanwoo steers compared to Holstein steers. Kendall’s correlation analysis revealed wide variation of microbial co-occurrence patterns between feeding systems, indicating differential H2 thermodynamics in the rumen. A metagenome analysis of rumen microbes revealed the presence of 430 differentially expressed genes, among which 17 and 27 genes exhibited positive and negative associations with CH4 production, respectively (P < 0.001). A strong interaction between feeding system and breed was observed for microbial and metagenomic abundance. Overall, these results suggest that the TMR feeding system produces more CH4, and that Hanwoo cattle are higher CH4 emitters than SF diet and Holstein cattle, respectively. Interestingly, host-associated microbial interactions differed within each breed depending on the feeding system, which indicated that breed-specific feeding systems should be taken into account for farm management.
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Affiliation(s)
- Rajaraman Bharanidharan
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Chang Hyun Lee
- Cargill Agri Purina Inc., Technology Application Center, Pyeongchang, South Korea
| | - Krishnaraj Thirugnanasambantham
- Department of Ecofriendly Livestock Science, Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea.,Pondicherry Centre for Biological Science and Educational Trust, Tamil Nadu, India
| | - Ridha Ibidhi
- Department of Ecofriendly Livestock Science, Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea
| | | | - Hong-Gu Lee
- Department of Animal Science and Technology, SangHa Life Science College, Konkuk University, Seoul, South Korea
| | - Jong Geun Kim
- Department of Ecofriendly Livestock Science, Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea.,Department of International Agricultural Technology, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, South Korea
| | - Kyoung Hoon Kim
- Department of Ecofriendly Livestock Science, Institute of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea.,Department of International Agricultural Technology, Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, South Korea
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Aviles FA, Kyndt JA. Cellulosimicrobium fucosivorans sp. nov., isolated from San Elijo Lagoon, contains a fucose metabolic pathway linked to carotenoid production. Arch Microbiol 2021; 203:4525-4538. [PMID: 34148152 DOI: 10.1007/s00203-021-02443-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/10/2021] [Accepted: 06/13/2021] [Indexed: 10/21/2022]
Abstract
Cellulosimicrobium strain SE3T was isolated from the San Elijo coastal lagoon near San Diego. A whole genome-based phylogenetic comparison shows great heterogeneity within the Cellulosimicrobium genus. Based on average nucleotide identity, whole genome-based comparison, and the presence of a unique L-fucose metabolic pathway, strain SE3T was shown to belong to a novel species within the genus, together with five other strains. The name Cellulosimicrobium fucosivorans sp. nov. is proposed, with strain SE3T as the type strain. The strain encodes a unique alpha-L-fucosidase and the L-fucose metabolic pathway is homologous to the one recently described in Campylobacter jejuni. C. fucosivorans is able to grow on L-fucose, and interestingly, the biosynthesis of the yellow carotenoid is dependent on the presence of L-fucose in the media. The ability to metabolize fucose and the linked production of carotenoids are expected to provide C. fucosivorans with a competitive advantage in the sunny coastal lagoon area.
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Affiliation(s)
- Fabiola A Aviles
- College of Science and Technology, Bellevue University, 1000 Galvin Rd. S., Bellevue, NE, 68005, USA
| | - John A Kyndt
- College of Science and Technology, Bellevue University, 1000 Galvin Rd. S., Bellevue, NE, 68005, USA.
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Kononova S, Litvinova E, Vakhitov T, Skalinskaya M, Sitkin S. Acceptive Immunity: The Role of Fucosylated Glycans in Human Host-Microbiome Interactions. Int J Mol Sci 2021; 22:ijms22083854. [PMID: 33917768 PMCID: PMC8068183 DOI: 10.3390/ijms22083854] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
The growth in the number of chronic non-communicable diseases in the second half of the past century and in the first two decades of the new century is largely due to the disruption of the relationship between the human body and its symbiotic microbiota, and not pathogens. The interaction of the human immune system with symbionts is not accompanied by inflammation, but is a physiological norm. This is achieved via microbiota control by the immune system through a complex balance of pro-inflammatory and suppressive responses, and only a disturbance of this balance can trigger pathophysiological mechanisms. This review discusses the establishment of homeostatic relationships during immune system development and intestinal bacterial colonization through the interaction of milk glycans, mucins, and secretory immunoglobulins. In particular, the role of fucose and fucosylated glycans in the mechanism of interactions between host epithelial and immune cells is discussed.
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Affiliation(s)
- Svetlana Kononova
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Correspondence:
| | - Ekaterina Litvinova
- Scientific-Research Institute of Neurosciences and Medicine, 630117 Novosibirsk, Russia;
- Siberian Federal Scientific Center of Agro-BioTechnologies, Russian Academy of Sciences, Krasnoobsk, 633501 Novosibirsk, Russia
| | - Timur Vakhitov
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
| | - Maria Skalinskaya
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Department of Internal Diseases, Gastroenterology and Dietetics, North-Western State Medical University Named after I.I. Mechnikov, 191015 St. Petersburg, Russia
| | - Stanislav Sitkin
- Department of Microbiology, State Research Institute of Highly Pure Biopreparations, 197110 St. Petersburg, Russia; (T.V.); (M.S.); (S.S.)
- Department of Internal Diseases, Gastroenterology and Dietetics, North-Western State Medical University Named after I.I. Mechnikov, 191015 St. Petersburg, Russia
- Institute of Perinatology and Pediatrics, Almazov National Medical Research Centre, 197341 St. Petersburg, Russia
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40
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Galeev A, Suwandi A, Cepic A, Basu M, Baines JF, Grassl GA. The role of the blood group-related glycosyltransferases FUT2 and B4GALNT2 in susceptibility to infectious disease. Int J Med Microbiol 2021; 311:151487. [PMID: 33662872 DOI: 10.1016/j.ijmm.2021.151487] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The glycosylation profile of the gastrointestinal tract is an important factor mediating host-microbe interactions. Variation in these glycan structures is often mediated by blood group-related glycosyltransferases, and can lead to wide-ranging differences in susceptibility to both infectious- as well as chronic disease. In this review, we focus on the interplay between host glycosylation, the intestinal microbiota and susceptibility to gastrointestinal pathogens based on studies of two exemplary blood group-related glycosyltransferases that are conserved between mice and humans, namely FUT2 and B4GALNT2. We highlight that differences in susceptibility can arise due to both changes in direct interactions, such as bacterial adhesion, as well as indirect effects mediated by the intestinal microbiota. Although a large body of experimental work exists for direct interactions between host and pathogen, determining the more complex and variable mechanisms underlying three-way interactions involving the intestinal microbiota will be the subject of much-needed future research.
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Affiliation(s)
- Alibek Galeev
- Max Planck Institute for Evolutionary Biology, Plön, Germany and Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Abdulhadi Suwandi
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany
| | - Aleksa Cepic
- Max Planck Institute for Evolutionary Biology, Plön, Germany and Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Meghna Basu
- Max Planck Institute for Evolutionary Biology, Plön, Germany and Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Plön, Germany and Institute for Experimental Medicine, Kiel University, Kiel, Germany.
| | - Guntram A Grassl
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School and German Center for Infection Research (DZIF), Hannover, Germany.
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41
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van Best N, Hornef MW. Early life host regulation of the mammalian enteric microbiota composition. Int J Med Microbiol 2021; 311:151498. [PMID: 33774478 DOI: 10.1016/j.ijmm.2021.151498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/23/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
The enteric microbiota exerts a major influence on the host. It promotes food degradation, nutrient absorption, immune maturation and protects from infection with pathogenic microorganisms. However, certain compositional alterations also enhance the risk to develop metabolic, inflammatory and immune-mediated diseases. This suggests that the enteric microbiota is subject to strong evolutionary pressure. Here, we hypothesize that endogenous, genetically determined mechanisms exist that shape and optimize the enteric microbiota. We discuss that the postnatal period as the starting point of the host-microbial interaction bears the greatest chance to identify such regulatory mechanisms and report on two recently identified ways how the neonate host favours or disfavours colonization by certain bacteria and thereby manipulates the postnatally emerging bacterial ecosystem. A better understanding of these mechanisms might ultimately help to define the features of a beneficial enteric microbiota and to develop interventional strategies to overcome adverse microbiota alterations.
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Affiliation(s)
- Niels van Best
- Institute of Medical Microbiology, RWTH University Hospital Aachen, RWTH University Aachen, Aachen, Germany; Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, the Netherlands
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen, RWTH University Aachen, Aachen, Germany.
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42
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Ladaycia A, Loretz B, Passirani C, Lehr CM, Lepeltier E. Microbiota and cancer: In vitro and in vivo models to evaluate nanomedicines. Adv Drug Deliv Rev 2021; 170:44-70. [PMID: 33388279 DOI: 10.1016/j.addr.2020.12.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/23/2020] [Accepted: 12/27/2020] [Indexed: 02/08/2023]
Abstract
Nanomedicine implication in cancer treatment and diagnosis studies witness huge attention, especially with the promising results obtained in preclinical studies. Despite this, only few nanomedicines succeeded to pass clinical phase. The human microbiota plays obvious roles in cancer development. Nanoparticles have been successfully used to modulate human microbiota and notably tumor associated microbiota. Taking the microbiota involvement under consideration when testing nanomedicines for cancer treatment might be a way to improve the poor translation from preclinical to clinical trials. Co-culture models of bacteria and cancer cells, as well as animal cancer-microbiota models offer a better representation for the tumor microenvironment and so potentially better platforms to test nanomedicine efficacy in cancer treatment. These models would allow closer representation of human cancer and might smoothen the passage from preclinical to clinical cancer studies for nanomedicine efficacy.
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43
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Fakhry SS, Rashid FA, Khudiar MM, Ismail LA, Ismail SK, Kazem RJ. Characterization of Lactobacillus species proposed as probiotics. POTRAVINARSTVO 2021. [DOI: 10.5219/1479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An isolated Lactobacillus from several various sources were identified depending on morphological, microscopically and biochemical tests in vitro analysis of probiotic properties that included: an ability to tolerate in different concentration of bile salt, survival in acidic conditions, their antimicrobial activity, and S-layer characterizations were carried out. It was noticed that isolates of Lactobacillus rhamnosus and L. delbrueckii have a broad activity of antimicrobial and found the isolate L. rhamnosus represented with a survival percentage 6.9% at pH 4.5 and 5.1% at pH 2.0) also L. rhamnosus (5.7% at pH 4.5 and 4.9% at pH 2.0) tolerated acidic media, Lactobacillus spp. has antimicrobial activity against all gram-positive and negative tested isolates. 70 kDa of S-layer protein bands were detected with whole-cell SDS-PAGE analysis, and it's predominant in cells of isolates which grown in MRS broth anaerobically. It was noticed that the collected Lactobacillus isolates could be used as probiotic.
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44
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Han Z, Thuy-Boun PS, Pfeiffer W, Vartabedian VF, Torkamani A, Teijaro JR, Wolan DW. Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome. Sci Rep 2021; 11:4763. [PMID: 33637779 PMCID: PMC7910532 DOI: 10.1038/s41598-021-83875-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
N-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.
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Affiliation(s)
- Zhen Han
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Peter S. Thuy-Boun
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Wayne Pfeiffer
- grid.266100.30000 0001 2107 4242San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093 USA
| | - Vincent F. Vartabedian
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Ali Torkamani
- grid.214007.00000000122199231Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA 92037 USA ,grid.214007.00000000122199231Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - John R. Teijaro
- grid.214007.00000000122199231Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037 USA
| | - Dennis W. Wolan
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037 USA ,grid.214007.00000000122199231Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037 USA
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Garber JM, Hennet T, Szymanski CM. Significance of fucose in intestinal health and disease. Mol Microbiol 2021; 115:1086-1093. [PMID: 33434389 DOI: 10.1111/mmi.14681] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/30/2020] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
The deoxyhexose sugar L-fucose is important for many biological processes within the human body and the associated microbiota. This carbohydrate is abundant in host gut mucosal surfaces, numerous microbial cell surface structures, and some dietary carbohydrates. Fucosylated oligosaccharides facilitate the establishment of a healthy microbiota and provide protection from infection. However, there are instances where pathogens can also exploit these fucosylated structures to cause infection. Furthermore, deficiencies in host fucosylation are associated with specific disease outcomes. This review focuses on our current understanding of the impact of fucosylation within the mucosal environment of the gastrointestinal tract with a specific emphasis on the mediatory effects in host-microbe interactions.
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Affiliation(s)
- Jolene M Garber
- Complex Carbohydrate Research Center and Department of Microbiology, University of Georgia, Athens, GA, USA
| | - Thierry Hennet
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Christine M Szymanski
- Complex Carbohydrate Research Center and Department of Microbiology, University of Georgia, Athens, GA, USA
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Glowacki RWP, Martens EC. If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria. J Bacteriol 2020; 203:JB.00481-20. [PMID: 33168637 PMCID: PMC8092160 DOI: 10.1128/jb.00481-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to persist, successful bacterial inhabitants of the human gut need to adapt to changing nutrient conditions, which are influenced by host diet and a variety of other factors. For members of the Bacteroidetes and several other phyla, this has resulted in diversification of a variety of enzyme-based systems that equip them to sense and utilize carbohydrate-based nutrients from host, diet, and bacterial origin. In this review, we focus first on human gut Bacteroides and describe recent findings regarding polysaccharide utilization loci (PULs) and the mechanisms of the multi-protein systems they encode, including their regulation and the expanding diversity of substrates that they target. Next, we highlight previously understudied substrates such as monosaccharides, nucleosides, and Maillard reaction products that can also affect the gut microbiota by feeding symbionts that possess specific systems for their metabolism. Since some pathogens preferentially utilize these nutrients, they may represent nutrient niches competed for by commensals and pathogens. Finally, we address recent work to describe nutrient acquisition mechanisms in other important gut species such as those belonging to the Gram-positive anaerobic phyla Actinobacteria and Firmicutes, as well as the Proteobacteria Because gut bacteria contribute to many aspects of health and disease, we showcase advances in the field of synthetic biology, which seeks to engineer novel, diet-controlled nutrient utilization pathways within gut symbionts to create rationally designed live therapeutics.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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Kwon O, Han TS, Son MY. Intestinal Morphogenesis in Development, Regeneration, and Disease: The Potential Utility of Intestinal Organoids for Studying Compartmentalization of the Crypt-Villus Structure. Front Cell Dev Biol 2020; 8:593969. [PMID: 33195268 PMCID: PMC7644937 DOI: 10.3389/fcell.2020.593969] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022] Open
Abstract
The morphology and structure of the intestinal epithelium are rearranged dynamically during development, tissue regeneration, and disease progression. The most important characteristic of intestinal epithelial morphogenesis is the repetitive compartmentalized structures of crypt-villus units, which are crucial for maintaining intestinal homeostasis and functions. Abnormal structures are known to be closely associated with disease development and progression. Therefore, understanding how intestinal crypt-villus structures are formed and grown is essential for elucidating the physiological and pathophysiological roles of the intestinal epithelium. However, a critical knowledge gap in understanding the compartmentalization of the crypt-villus axis remains when using animal models, due to obvious inter-species differences and difficulty in real-time monitoring. Recently, emerging technologies such as organoid culture, lineage tracing, and single cell sequencing have enabled the assessment of the intrinsic mechanisms of intestinal epithelial morphogenesis. In this review, we discuss the latest research on the regulatory factors and signaling pathways that play a central role in the formation, maintenance, and regeneration of crypt-villus structures in the intestinal epithelium. Furthermore, we discuss how these factors and pathways play a role in development, tissue regeneration, and disease. We further explore how the current technology of three-dimensional intestinal organoids has contributed to the understanding of crypt-villus compartmentalization, highlighting new findings related to the self-organizing-process-driven initiation and propagation of crypt-villus structures. We also discuss intestinal diseases featuring abnormalities of the crypt-villus structure to provide insights for the development of novel therapeutic strategies targeting intestinal morphogenesis and crypt-villus formation.
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Affiliation(s)
- Ohman Kwon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Tae-Su Han
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Mi-Young Son
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, South Korea
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Abstract
The Embden–Meyerhof–Parnas (EMP) and Entner–Doudoroff (ED) pathways are considered the most abundant catabolic pathways found in microorganisms, and ED enzymes have been shown to also be widespread in cyanobacteria, algae and plants. In a large number of organisms, especially common strains used in molecular biology, these pathways account for the catabolism of glucose. The existence of pathways for other carbohydrates that are relevant to biomass utilization has been recognized as new strains have been characterized among thermophilic bacteria and Archaea that are able to transform simple polysaccharides from biomass to more complex and potentially valuable precursors for industrial microbiology. Many of the variants of the ED pathway have the key dehydratase enzyme involved in the oxidation of sugar derived from different families such as the enolase, IlvD/EDD and xylose-isomerase-like superfamilies. There are the variations in structure of proteins that have the same specificity and generally greater-than-expected substrate promiscuity. Typical biomass lignocellulose has an abundance of xylan, and four different pathways have been described, which include the Weimberg and Dahms pathways initially oxidizing xylose to xylono-gamma-lactone/xylonic acid, as well as the major xylose isomerase pathway. The recent realization that xylan constitutes a large proportion of biomass has generated interest in exploiting the compound for value-added precursors, but few chassis microorganisms can grow on xylose. Arabinose is part of lignocellulose biomass and can be metabolized with similar pathways to xylose, as well as an oxidative pathway. Like enzymes in many non-phosphorylative carbohydrate pathways, enzymes involved in L-arabinose pathways from bacteria and Archaea show metabolic and substrate promiscuity. A similar multiplicity of pathways was observed for other biomass-derived sugars such as L-rhamnose and L-fucose, but D-mannose appears to be distinct in that a non-phosphorylative version of the ED pathway has not been reported. Many bacteria and Archaea are able to grow on mannose but, as with other minor sugars, much of the information has been derived from whole cell studies with additional enzyme proteins being incorporated, and so far, only one synthetic pathway has been described. There appears to be a need for further discovery studies to clarify the general ability of many microorganisms to grow on the rarer sugars, as well as evaluation of the many gene copies displayed by marine bacteria.
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Chia LW, Mank M, Blijenberg B, Aalvink S, Bongers RS, Stahl B, Knol J, Belzer C. Bacteroides thetaiotaomicron Fosters the Growth of Butyrate-Producing Anaerostipes caccae in the Presence of Lactose and Total Human Milk Carbohydrates. Microorganisms 2020; 8:E1513. [PMID: 33019531 PMCID: PMC7601031 DOI: 10.3390/microorganisms8101513] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/20/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
The development of infant gut microbiota is strongly influenced by nutrition. Human milk oligosaccharides (HMOSs) in breast milk selectively promote the growth of glycan-degrading microbes, which lays the basis of the microbial network. In this study, we investigated the trophic interaction between Bacteroides thetaiotaomicron and the butyrate-producing Anaerostipes caccae in the presence of early-life carbohydrates. Anaerobic bioreactors were set up to study the monocultures of B. thetaiotaomicron and the co-cultures of B. thetaiotaomicron with A. caccae in minimal media supplemented with lactose or a total human milk carbohydrate fraction. Bacterial growth (qPCR), metabolites (HPLC), and HMOS utilization (LC-ESI-MS2) were monitored. B. thetaiotaomicron displayed potent glycan catabolic capability with differential preference in degrading specific low molecular weight HMOSs, including the neutral trioses (2'-FL and 3-FL), neutral tetraoses (DFL, LNT, LNnT), neutral pentaoses (LNFP I, II, III, V), and acidic trioses (3'-SL and 6'-SL). In contrast, A. caccae was not able to utilize lactose and HMOSs. However, the signature metabolite of A. caccae, butyrate, was detected in co-culture with B. thetaiotaomicron. As such, A. caccae cross-fed on B. thetaiotaomicron-derived monosaccharides, acetate, and d-lactate for growth and concomitant butyrate production. This study provides a proof of concept that B. thetaiotaomicron could drive the butyrogenic metabolic network in the infant gut.
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Affiliation(s)
- Loo Wee Chia
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (L.W.C.); (S.A.); (J.K.)
| | - Marko Mank
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
| | - Bernadet Blijenberg
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (L.W.C.); (S.A.); (J.K.)
| | - Roger S. Bongers
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
| | - Bernd Stahl
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CT Utrecht, The Netherlands
| | - Jan Knol
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (L.W.C.); (S.A.); (J.K.)
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands; (M.M.); (B.B.); (R.S.B.); (B.S.)
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University and Research, 6708 WE Wageningen, The Netherlands; (L.W.C.); (S.A.); (J.K.)
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Kudelka MR, Stowell SR, Cummings RD, Neish AS. Intestinal epithelial glycosylation in homeostasis and gut microbiota interactions in IBD. Nat Rev Gastroenterol Hepatol 2020; 17:597-617. [PMID: 32710014 PMCID: PMC8211394 DOI: 10.1038/s41575-020-0331-7] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/05/2020] [Indexed: 02/08/2023]
Abstract
Inflammatory bowel disease (IBD) affects 6.8 million people globally. A variety of factors have been implicated in IBD pathogenesis, including host genetics, immune dysregulation and gut microbiota alterations. Emerging evidence implicates intestinal epithelial glycosylation as an underappreciated process that interfaces with these three factors. IBD is associated with increased expression of truncated O-glycans as well as altered expression of terminal glycan structures. IBD genes, glycosyltransferase mislocalization, altered glycosyltransferase and glycosidase expression and dysbiosis drive changes in the glycome. These glycan changes disrupt the mucus layer, glycan-lectin interactions, host-microorganism interactions and mucosal immunity, and ultimately contribute to IBD pathogenesis. Epithelial glycans are especially critical in regulating the gut microbiota through providing bacterial ligands and nutrients and ultimately determining the spatial organization of the gut microbiota. In this Review, we discuss the regulation of intestinal epithelial glycosylation, altered epithelial glycosylation in IBD and mechanisms for how these alterations contribute to disease pathobiology. We hope that this Review provides a foundation for future studies on IBD glycosylation and the emergence of glycan-inspired therapies for IBD.
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Affiliation(s)
- Matthew R Kudelka
- Medical Scientist Training Program, Emory University School of Medicine, Atlanta, GA, USA
- Department of Internal Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sean R Stowell
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA.
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