1
|
Ma X, Li M, Wang X, Qi G, Wei L, Zhang D. Sialylation in the gut: From mucosal protection to disease pathogenesis. Carbohydr Polym 2024; 343:122471. [PMID: 39174097 DOI: 10.1016/j.carbpol.2024.122471] [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: 05/07/2024] [Revised: 06/19/2024] [Accepted: 07/07/2024] [Indexed: 08/24/2024]
Abstract
Sialylation, a crucial post-translational modification of glycoconjugates, entails the attachment of sialic acid (SA) to the terminal glycans of glycoproteins and glycolipids through a tightly regulated enzymatic process involving various enzymes. This review offers a comprehensive exploration of sialylation within the gut, encompassing its involvement in mucosal protection and its impact on disease progression. The sialylation of mucins and epithelial glycoproteins contributes to the integrity of the intestinal mucosal barrier. Furthermore, sialylation regulates immune responses in the gut, shaping interactions among immune cells, as well as their activation and tolerance. Additionally, the gut microbiota and gut-brain axis communication are involved in the role of sialylation in intestinal health. Altered sialylation patterns have been implicated in various intestinal diseases, including inflammatory bowel disease (IBD), colorectal cancer (CRC), and other intestinal disorders. Emerging research underscores sialylation as a promising avenue for diagnostic, prognostic, and therapeutic interventions in intestinal diseases. Potential strategies such as sialic acid supplementation, inhibition of sialidases, immunotherapy targeting sialylated antigens, and modulation of sialyltransferases have been utilized in the treatment of intestinal diseases. Future research directions will focus on elucidating the molecular mechanisms underlying sialylation alterations, identifying sialylation-based biomarkers, and developing targeted interventions for precision medicine approaches.
Collapse
Affiliation(s)
- Xueni Ma
- Key Laboratory of Digestive Diseases, Lanzhou University Second Hospital, Lanzhou, China; The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Muyang Li
- Key Laboratory of Digestive Diseases, Lanzhou University Second Hospital, Lanzhou, China; The Second Clinical Medical College, Lanzhou University, Lanzhou, China
| | - Xiaochun Wang
- Department of Gastroenterology, Gansu Provincial Hospital, Lanzhou, China
| | - Guoqing Qi
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, China
| | - Lina Wei
- Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, China
| | - Dekui Zhang
- Key Laboratory of Digestive Diseases, Lanzhou University Second Hospital, Lanzhou, China; Department of Gastroenterology, Lanzhou University Second Hospital, Lanzhou, China.
| |
Collapse
|
2
|
Green N, Chan C, Ooi CY. The gastrointestinal microbiome, small bowel bacterial overgrowth, and microbiome modulators in cystic fibrosis. Pediatr Pulmonol 2024; 59 Suppl 1:S70-S80. [PMID: 39105345 DOI: 10.1002/ppul.26913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 01/12/2024] [Accepted: 01/31/2024] [Indexed: 08/07/2024]
Abstract
People with cystic fibrosis (pwCF) have an altered gastrointestinal microbiome. These individuals also demonstrate propensity toward developing small intestinal bacterial overgrowth (SIBO). The dysbiosis present has intestinal and extraintestinal implications, including potential links with the higher rates of gastrointestinal malignancies described in CF. Given these implications, there is growing interest in therapeutic options for microbiome modulation. Alternative therapies, including probiotics and prebiotics, and current CF transmembrane conductance regulator gene modulators are promising interventions for ameliorating gut microbiome dysfunction in pwCF. This article will characterize and discuss the current state of knowledge and expert opinions on gut dysbiosis and SIBO in the context of CF, before reviewing the current evidence supporting gut microbial modulating therapies in CF.
Collapse
Affiliation(s)
- Nicole Green
- Department of Pediatrics, Division of Gastroenterology and Hepatology, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA
| | - Christopher Chan
- Discipline of Paediatrics & Child Health, Randwick Clinical Campus, School of Clinical Medicine, UNSW Medicine & Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Chee Y Ooi
- Discipline of Paediatrics & Child Health, Randwick Clinical Campus, School of Clinical Medicine, UNSW Medicine & Health, University of New South Wales, Sydney, New South Wales, Australia
- Department of Gastroenterology, Sydney Children's Hospital, Randwick, New South Wales, Australia
| |
Collapse
|
3
|
Fitzjerrells RL, Ollberding NJ, Mangalam AK. Looking at the full picture, using topic modeling to observe microbiome communities associated with disease. GUT MICROBES REPORTS 2024; 1:1-11. [PMID: 39183943 PMCID: PMC11340690 DOI: 10.1080/29933935.2024.2378067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/24/2024] [Accepted: 07/01/2024] [Indexed: 08/27/2024]
Abstract
The microbiome, a complex micro-ecosystem, helps the host with various vital physiological processes. Alterations of the microbiome (dysbiosis) have been linked with several diseases, and generally, differential abundance testing between the healthy and patient groups is performed to identify important bacteria. However, providing a singular species of bacteria to an individual as treatment has not been as successful as fecal microbiota transplant therapy, where the entire microbiome of a healthy individual is transferred. These observations suggest that a combination of bacteria might be crucial for the beneficial effects. Here we provide the framework to utilize topic modeling, an unsupervised machine learning approach, to identify a community of bacteria related to health or disease. Specifically, we used our previously published gut microbiome data of patients with multiple sclerosis (MS), a neurodegenerative disease linked to a dysbiotic gut microbiome. We identified communities of bacteria associated with MS, including genera previously discovered, but also others that would have been overlooked by differential abundance testing. This method can be a useful tool for analyzing the microbiome, and it should be considered along with the commonly utilized differential abundance tests to better understand the role of the gut microbiome in health and disease.
Collapse
Affiliation(s)
- Rachel L. Fitzjerrells
- Interdisciplinary Graduate Program in Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Nicholas J. Ollberding
- Division of Biostatistics and Epidemiology; Cincinnati Children’s Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA
| | - Ashutosh K. Mangalam
- Interdisciplinary Graduate Program in Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Iowa City VA Health Care System, 601 US-6 W, Iowa City, IA 52246, USA
| |
Collapse
|
4
|
Mohr AE, Jasbi P, van Woerden I, Chi J, Gu H, Bruening M, Whisner CM. Microbial Ecology and Metabolism of Emerging Adulthood: Gut Microbiome Insights from a College Freshman Cohort. GUT MICROBES REPORTS 2024; 1:1-23. [PMID: 39221110 PMCID: PMC11361303 DOI: 10.1080/29933935.2024.2387936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The human gut microbiome (GM) undergoes dynamic changes throughout life, transitioning from infancy to adulthood. Despite improved understanding over the past years about how genetics, lifestyle, and the external environment impact the GM, limited research has explored the GM's evolution during late-stage adolescence, especially among college students. This study addresses this gap by investigating the longitudinal dynamics of fecal microbial, functional, and metabolomic signatures in a diverse group of first-year, dormitory-housed college students. A total of 485 stool samples from 246 participants were analyzed, identifying four primary GM community types, predominantly led by Bacteroides (66.8% of samples), as well as Blautia and Prevotella. The Prevotella/Bacteroides (P/B) ratio emerged as a robust GM composition indicator, predictively associated with 15 metabolites. Notably, higher P/B ratios correlated negatively with p-cresol sulfate and cholesterol sulfate, implying potential health implications, while positively correlating with kynurenic acid. Distinct GM transition and stability patterns were found from a detailed longitudinal subset of 93 participants over an academic year. Parasutterella and the Ruminococcus gnavus group exhibited positive associations with compositional variability, whereas Faecalibacterium and Eubacterium ventriosum group displayed negative associations, the latter suggesting stabilizing roles in the GM. Most notably, nearly half of the longitudinal cohort experienced GM community shifts, emphasizing long-term GM adaptability. Comparing individuals with stable community types to those undergoing transitions, we observed significant differences in microbial composition and diversity, signifying substantial shifts in the microbiota during transitions. Although diet-related variables contributed to some observed variance, diet did not independently predict the probability of switching between community types within the study's timeframe via multi-state Markov modeling. Furthermore, exploration of stability within dynamic microbiomes among the longitudinal cohort experiencing shifts in community types revealed that microbiome taxa at the genus level exhibited significantly higher total variance than estimated functional and fecal metabolomic features. This suggests tight control of function and metabolism, despite community shifting. Overall, this study highlights the dynamic nature of the late-stage adolescent GM, the role of core taxa, metabolic pathways, the fecal metabolome, and lifestyle and dietary factors, contributing to our understanding of GM assembly and potential health implications during this life phase.
Collapse
Affiliation(s)
- Alex E. Mohr
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paniz Jasbi
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Center for Personalized Diagnostics, School of Molecular Sciences, Arizona State University, Tempe, AZ USA
| | - Irene van Woerden
- Community and Public Health, Idaho State University, Pocatello, ID, USA
| | - Jinhua Chi
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Meg Bruening
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Department of Nutritional Sciences, College of Health and Human Development, Pennsylvania State University, University Park, PA, USA
| | - Corrie M. Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Health Through Microbiomes, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| |
Collapse
|
5
|
Wang L, Deng Z, Huang J, Li T, Jiang J, Wang W, Sun Y, Deng Y. Zearalenone-induced hepatointestinal toxicity in laying hens: unveiling the role of gut microbiota and fecal metabolites. Poult Sci 2024; 103:104221. [PMID: 39241615 DOI: 10.1016/j.psj.2024.104221] [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: 04/24/2024] [Revised: 08/07/2024] [Accepted: 08/11/2024] [Indexed: 09/09/2024] Open
Abstract
Zearalenone (ZEN), a mycotoxin produced by Fusarium species, is known for its reproductive toxicity as an estrogen analogue. However, there are limited knowledge about its hepatointestinal toxicity, as well as the role that gut microbiota and metabolites play in this process. In this study, a total of 24 thirty-week-old hens were fed to investigate the hepatointestinal toxicity subjected to long-term ZEN consumption at 2.0 mg/kg for 90 d. And we employed uncultured 16S rRNA sequencing for gut microbiota and untargeted metabolomics for fecal metabolites assessment. Notably, ZEN induced significant hepatic damage, as evidenced by hepatocyte necrosis, inflammatory cell infiltrate, increased liver lipopolysaccharide (LPS) and blood aspartate aminotransferase (AST) levels (P < 0.05). The decreased villus height, disruption of simple columnar epithelial cells, and exposure of the mucosal intrinsic layer were observed in the intestine. The gut microbial community composition and metabolites differed between ZEN group and control group. ZEN group exhibited higher gut microbial diversity (P < 0.05), lower Firmicutes/Bacteroidetes ratio and Lactobacillus abundance, and higher abundance in the genus such as Bacteroidetes, Parabacteroidetes and Desulfovibrio. Metabolomic analysis showed that ZEN treatment altered biosynthesis of siderophore group nonribosomal peptides and phenylpropanoids, metabolism of amino acid, digestion and absorption of vitamin and ABC transporters. Differential metabolites suggested that ZEN increase the risk of estrogen disorder, nucleic acid degradation, intestinal oxidative stress and inflammation. Neural network analysis showed that Ruminococcus was positively correlated with glyceric acid, and Prevotella was positively correlated with phenylacetylglycine. Both metabolites were positively correlated with blood AST level (P < 0.05), suggesting that intestinal microbe Ruminococcus and Prevotella might exacerbate liver damage by producing these harmful metabolites. Overall, we conclude that ZEN has damaged hepatointestinal system and the altered gut microbiota with resultant metabolite changes contribute to the adverse hepatointestinal effects of ZEN on laying hens. This study underscores the need for monitoring and mitigating ZEN exposure in poultry diets, highlighting its broader implications for animal health and food safety.
Collapse
Affiliation(s)
- Lingling Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, Guangzhou, Guangdong 510642, PR China
| | - Zifeng Deng
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, Guangzhou, Guangdong 510642, PR China
| | - Jieying Huang
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, Guangzhou, Guangdong 510642, PR China
| | - Tingyuan Li
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, Guangzhou, Guangdong 510642, PR China
| | - Jun Jiang
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, Guangzhou, Guangdong 510642, PR China
| | - Wence Wang
- Guangdong Provincial Key Laboratory of Animal Nutrition and Regulation, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong 510642, PR China
| | - Yu Sun
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong provincial key laboratory for the development biology and environmental adaptation of agricultural organisms, Guangzhou, Guangdong 510642, PR China
| | - Yiqun Deng
- State Key Laboratory of Swine and Poultry Breeding Industry, South China Agricultural University, Guangzhou, Guangdong 510642, PR China; Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, PR China.
| |
Collapse
|
6
|
Flores JA, Antonio JM, Suntornsaratoon P, Meadows V, Bandyopadhyay S, Han J, Singh R, Balasubramanian I, Upadhyay R, Liu Y, Bonder EM, Kiela P, Su X, Ferraris R, Gao N. The arginine and nitric oxide metabolic pathway regulate the gut colonization and expansion of Ruminococcous gnavus. J Biol Chem 2024; 300:107614. [PMID: 39089585 DOI: 10.1016/j.jbc.2024.107614] [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: 01/18/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 08/04/2024] Open
Abstract
Ruminococcus gnavus is a mucolytic commensal bacterium whose increased gut colonization has been associated with chronic inflammatory and metabolic diseases in humans. Whether R. gnavus metabolites can modulate host intestinal physiology remains largely understudied. We performed untargeted metabolomic and bulk RNA-seq analyses using R. gnavus monocolonization in germ-free mice. Based on transcriptome-metabolome correlations, we tested the impact of specific arginine metabolites on intestinal epithelial production of nitric oxide (NO) and examined the effect of NO on the growth of various strains of R. gnavus in vitro and in nitric oxide synthase 2 (Nos2)-deficient mice. R. gnavus produces specific arginine, tryptophan, and tyrosine metabolites, some of which are regulated by the environmental richness of sialic acid and mucin. R. gnavus colonization promotes expression of amino acid transporters and enzymes involved in metabolic flux of arginine and associated metabolites into NO. R. gnavus induced elevated levels of NOS2, while Nos2 ablation resulted in R. gnavus expansion in vivo. The growth of various R. gnavus strains can be inhibited by NO. Specific R. gnavus metabolites modulate intestinal epithelial cell NOS2 abundance and reduce epithelial barrier function at higher concentrations. Intestinal colonization and interaction with R. gnavus are partially regulated by an arginine-NO metabolic pathway, whereby a balanced control by the gut epithelium may restrain R. gnavus growth in healthy individuals. Disruption in this arginine metabolic regulation will contribute to the expansion and blooming of R. gnavus.
Collapse
Affiliation(s)
- Juan A Flores
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Jayson M Antonio
- Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Panan Suntornsaratoon
- Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Vik Meadows
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA; Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | | | - Jiangmeng Han
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA; Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Rajbir Singh
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | | | - Ravij Upadhyay
- Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Yue Liu
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Edward M Bonder
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA
| | - Pawel Kiela
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children's Research Center, Department of Pediatrics, University of Arizona, Tucson, Arizona, USA
| | - Xiaoyang Su
- Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Ronaldo Ferraris
- Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, New Jersey, USA; Department of Pharmacology, Physiology and Neurosciences, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.
| |
Collapse
|
7
|
Sreya PK, Hari Naga Papa Rao A, Suresh G, Sasikala C, Venkata Ramana C. Genomic and functional insights of a mucin foraging Rhodopirellula halodulae sp. nov. Syst Appl Microbiol 2024; 47:126523. [PMID: 38897058 DOI: 10.1016/j.syapm.2024.126523] [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: 02/10/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
Nine novel strains were obtained from various algal and seagrass samples. The analysis of the 16S rRNA gene-based phylogenetic tree revealed monophyletic placement of all novel strains within the Rhodopirellula genus. The type strain was identified as JC737T, which shared 99.1 % 16S rRNA gene sequence identity with Rhodopirellula baltica SH1T, while strain JC740 was designated as an additional strain. The genome sizes of strains JC737T and JC740 were 6.6 and 6.7 Mb, respectively, and the G + C content was 56.2 %. The strains cladded distinctly in the phylogenomic tree, and the ANI and dDDH values of the strain JC737T were 75.8-76.1 % and 20.8-21.3 %, respectively, in comparison to other Rhodopirellula members. The strain demonstrated a versatile degradation capability, exhibiting a diverse array of complex polysaccharides, including mucin which had not been previously identified within the members of the phylum Planctomycetota. The phylogenomic, pan-genomic, morphological, physiological, and genomic characterization of the strain lead to the proposal to describe the strain as Rhodopirellula halodulae sp. nov.
Collapse
Affiliation(s)
- P K Sreya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Atham Hari Naga Papa Rao
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | - Gandham Suresh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India
| | | | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India.
| |
Collapse
|
8
|
Shen J, Li J, Zhang Y, Mei X, Xue C, Chang Y. Characterization of an α-L-fucosidase in marine bacterium Wenyingzhuangia fucanilytica: new evidence on the catalytic sites of GH95 family glycosidases. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38932571 DOI: 10.1002/jsfa.13659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 05/08/2024] [Accepted: 06/01/2024] [Indexed: 06/28/2024]
Abstract
BACKGROUND α-l-Fucose confers unique functions for fucose-containing biomolecules such as human milk oligosaccharides. α-l-Fucosidases can serve as desirable tools in the application of fucosylated saccharides. Discovering novel α-l-fucosidases and elucidating their enzyme properties are always worthy tasks. RESULTS A GH95 family α-l-fucosidase named Afc95A_Wf was cloned from the genome of the marine bacterium Wenyingzhuangia fucanilytica and expressed in Escherichia coli. It exhibited maximum activity at 40 °C and pH 7.5. Afc95A_Wf defined a different substrate specificity among reported α-l-fucosidases, which was capable of hydrolyzing α-fucoside in CNP-fucose, Fucα1-2Galβ1-4Glc and Galβ1-4(Fucα1-3)Glc, and showed a preference for α1,2-fucosidic linkage. It adopted Asp residue in the amino acid sequence at position 391, which was distinct from the previously acknowledged residue of Asn. The predicted tertiary structure and site-directed mutagenesis revealed that Asp391 participates in the catalysis of Afc95A_Wf. The differences in the substrate specificity and catalytic site shed light on that Afc95A_Wf adopted a novel mechanism in catalysis. CONCLUSION A GH95 family α-l-fucosidase (Afc95A_Wf) was cloned and expressed. It showed a cleavage preference for α1,2-fucosidic linkage to α1,3-fucosidic linkage. Afc95A_Wf demonstrated a different substrate specificity and a residue at an important catalytic site compared with known GH95 family proteins, which revealed the occurrence of diversity on catalytic mechanisms in the GH95 family. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- Jingjing Shen
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Jiajing Li
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| |
Collapse
|
9
|
Raba G, Luis AS, Schneider H, Morell I, Jin C, Adamberg S, Hansson GC, Adamberg K, Arike L. Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota. iScience 2024; 27:110093. [PMID: 38947523 PMCID: PMC11214529 DOI: 10.1016/j.isci.2024.110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/29/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
A diet lacking dietary fibers promotes the expansion of gut microbiota members that can degrade host glycans, such as those on mucins. The microbial foraging on mucin has been associated with disruptions of the gut-protective mucus layer and colonic inflammation. Yet, it remains unclear how the co-utilization of mucin and dietary fibers affects the microbiota composition and metabolic activity. Here, we used 14 dietary fibers and porcine colonic and gastric mucins to study the dynamics of mucin and dietary fiber utilization by the human fecal microbiota in vitro. Combining metaproteome and metabolites analyses revealed the central role of the Bacteroides genus in the utilization of complex fibers together with mucin while Akkermansia muciniphila was the main utilizer of sole porcine colonic mucin but not gastric mucin. This study gives a broad overview of the colonic environment in response to dietary and host glycan availability.
Collapse
Affiliation(s)
- Grete Raba
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Ana S. Luis
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Hannah Schneider
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Indrek Morell
- Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Gunnar C. Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
- Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia
| | - Liisa Arike
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| |
Collapse
|
10
|
Yang X, Huang J, Peng J, Wang P, Wong FS, Wang R, Wang D, Wen L. Gut microbiota from B-cell-specific TLR9-deficient NOD mice promote IL-10 + Breg cells and protect against T1D. Front Immunol 2024; 15:1413177. [PMID: 38903498 PMCID: PMC11187306 DOI: 10.3389/fimmu.2024.1413177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of insulin-producing β cells. Toll-like receptor 9 (TLR9) plays a role in autoimmune diseases, and B cell-specific TLR9 deficiency delays T1D development. Gut microbiota are implicated in T1D, although the relationship is complex. However, the impact of B cell-specific deficiency of TLR9 on intestinal microbiota and the impact of altered intestinal microbiota on the development of T1D are unclear. Objectives This study investigated how gut microbiota and the intestinal barrier contribute to T1D development in B cell-specific TLR9-deficient NOD mice. Additionally, this study explored the role of microbiota in immune regulation and T1D onset. Methods The study assessed gut permeability, gene expression related to gut barrier integrity, and gut microbiota composition. Antibiotics depleted gut microbiota, and fecal samples were transferred to germ-free mice. The study also examined IL-10 production, Breg cell differentiation, and their impact on T1D development. Results B cell-specific TLR9-deficient NOD mice exhibited increased gut permeability and downregulated gut barrier-related gene expression. Antibiotics restored gut permeability, suggesting microbiota influence. Altered microbiota were enriched in Lachnospiraceae, known for mucin degradation. Transferring this microbiota to germ-free mice increased gut permeability and promoted IL-10-expressing Breg cells. Rag-/- mice transplanted with fecal samples from Tlr9 fl/fl Cd19-Cre+ mice showed delayed diabetes onset, indicating microbiota's impact. Conclusion B cell-specific TLR9 deficiency alters gut microbiota, increasing gut permeability and promoting IL-10-expressing Breg cells, which delay T1D. This study uncovers a link between TLR9, gut microbiota, and immune regulation in T1D, with implications for microbiota-targeted T1D therapies.
Collapse
Affiliation(s)
- Xin Yang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Juan Huang
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Jian Peng
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Pai Wang
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
- Department of Gastrocolorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - F. Susan Wong
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Ruirui Wang
- Shanghai Innovation Center of Traditional Chinese Medicine (TCM) Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Wen
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| |
Collapse
|
11
|
Hilliard MA, Sela DA. Transmission and Persistence of Infant Gut-Associated Bifidobacteria. Microorganisms 2024; 12:879. [PMID: 38792709 PMCID: PMC11124121 DOI: 10.3390/microorganisms12050879] [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: 03/22/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024] Open
Abstract
Bifidobacterium infantis are the primary colonizers of the infant gut, yet scientific research addressing the transmission of the genus Bifidobacterium to infants remains incomplete. This review examines microbial reservoirs of infant-type Bifidobacterium that potentially contribute to infant gut colonization. Accordingly, strain inheritance from mother to infant via the fecal-oral route is likely contingent on the bifidobacterial strain and phenotype, whereas transmission via the vaginal microbiota may be restricted to Bifidobacterium breve. Additional reservoirs include breastmilk, horizontal transfer from the environment, and potentially in utero transfer. Given that diet is a strong predictor of Bifidobacterium colonization in early life and the absence of Bifidobacterium is observed regardless of breastfeeding, it is likely that additional factors are responsible for bifidobacterial colonization early in life.
Collapse
Affiliation(s)
- Margaret A. Hilliard
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA;
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - David A. Sela
- Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA;
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
- Department of Nutrition, University of Massachusetts, Amherst, MA 01003, USA
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Department of Microbiology & Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA 01605, USA
| |
Collapse
|
12
|
Lai Y, Tang W, Luo X, Zheng H, Zhang Y, Wang M, Yu G, Yang M. Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis. Front Immunol 2024; 15:1369116. [PMID: 38711505 PMCID: PMC11070502 DOI: 10.3389/fimmu.2024.1369116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 04/01/2024] [Indexed: 05/08/2024] Open
Abstract
Objective Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in AS in order to discover the microbiome-metabolome interface in AS. Based on prospective cohort studies, we further explored the impact of the tumor necrosis factor inhibitor (TNFi) on the gut microbiota and metabolites in AS. Methods To further understand the gut microbiota and metabolites in AS, along with the influence of TNFi, we initiated a prospective cohort study. Fecal samples were collected from 29 patients with AS before and after TNFi therapy and 31 healthy controls. Metagenomic and metabolomic experiments were performed on the fecal samples; moreover, validation experiments were conducted based on the association between the microbiota and metabolites. Results A total of 7,703 species were annotated using the metagenomic sequencing system and by profiling the microbial community taxonomic composition, while 50,046 metabolites were identified using metabolite profiling. Differential microbials and metabolites were discovered between patients with AS and healthy controls. Moreover, TNFi was confirmed to partially restore the gut microbiota and the metabolites. Multi-omics analysis of the microbiota and metabolites was performed to determine the associations between the differential microbes and metabolites, identifying compounds such as oxypurinol and biotin, which were correlated with the inhibition of the pathogenic bacteria Ruminococcus gnavus and the promotion of the probiotic bacteria Bacteroides uniformis. Through experimental studies, the relationship between microbes and metabolites was further confirmed, and the impact of these two types of microbes on the enterocytes and the inflammatory cytokine interleukin-18 (IL-18) was explored. Conclusion In summary, multi-omics exploration elucidated the impact of TNFi on the gut microbiota and metabolites and proposed a novel therapeutic perspective: supplementation of compounds to inhibit potential pathogenic bacteria and to promote potential probiotics, therefore controlling inflammation in AS.
Collapse
Affiliation(s)
- Yupeng Lai
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Wenli Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiao Luo
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Huihui Zheng
- Department of Pharmacy, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yanpeng Zhang
- Department of Laboratory, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Meiying Wang
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Guangchuang Yu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Min Yang
- Department of Rheumatology and Immunology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| |
Collapse
|
13
|
Sonnert ND, Rosen CE, Ghazi AR, Franzosa EA, Duncan-Lowey B, González-Hernández JA, Huck JD, Yang Y, Dai Y, Rice TA, Nguyen MT, Song D, Cao Y, Martin AL, Bielecka AA, Fischer S, Guan C, Oh J, Huttenhower C, Ring AM, Palm NW. A host-microbiota interactome reveals extensive transkingdom connectivity. Nature 2024; 628:171-179. [PMID: 38509360 DOI: 10.1038/s41586-024-07162-0] [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: 05/07/2022] [Accepted: 02/05/2024] [Indexed: 03/22/2024]
Abstract
The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown1-3. Classical pathogens often invade host tissues and modulate immune responses through interactions with human extracellular and secreted proteins (the 'exoproteome'). Commensal microorganisms may also facilitate niche colonization and shape host biology by engaging host exoproteins; however, direct exoproteome-microbiota interactions remain largely unexplored. Here we developed and validated a novel technology, BASEHIT, that enables proteome-scale assessment of human exoproteome-microbiome interactions. Using BASEHIT, we interrogated more than 1.7 million potential interactions between 519 human-associated bacterial strains from diverse phylogenies and tissues of origin and 3,324 human exoproteins. The resulting interactome revealed an extensive network of transkingdom connectivity consisting of thousands of previously undescribed host-microorganism interactions involving 383 strains and 651 host proteins. Specific binding patterns within this network implied underlying biological logic; for example, conspecific strains exhibited shared exoprotein-binding patterns, and individual tissue isolates uniquely bound tissue-specific exoproteins. Furthermore, we observed dozens of unique and often strain-specific interactions with potential roles in niche colonization, tissue remodelling and immunomodulation, and found that strains with differing host interaction profiles had divergent interactions with host cells in vitro and effects on the host immune system in vivo. Overall, these studies expose a previously unexplored landscape of molecular-level host-microbiota interactions that may underlie causal effects of indigenous microorganisms on human health and disease.
Collapse
Affiliation(s)
- Nicole D Sonnert
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Connor E Rosen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew R Ghazi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - John D Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yi Yang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tyler A Rice
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mytien T Nguyen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Deguang Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yiyun Cao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anjelica L Martin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Agata A Bielecka
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Suzanne Fischer
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron M Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
14
|
Li S, Chen M, Wang Z, Abudourexiti W, Zhang L, Ding C, Ding L, Gong J. Ant may well destroy a whole dam: glycans of colonic mucus barrier disintegrated by gut bacteria. Microbiol Res 2024; 281:127599. [PMID: 38219635 DOI: 10.1016/j.micres.2023.127599] [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: 09/25/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
The colonic mucus layer plays a critical role in maintaining the integrity of the colonic mucosal barrier, serving as the primary defense against colonic microorganisms. Predominantly composed of mucin 2 (MUC2), a glycosylation-rich protein, the mucus layer forms a gel-like coating that covers the colonic epithelium surface. This layer provides a habitat for intestinal microorganisms, which can utilize mucin glycans present in the mucus layer as a sustainable source of nutrients. Additionally, metabolites produced by the microbiota during the metabolism of mucus glycans have a profound impact on host health. Under normal conditions, the production and consumption of mucus maintain a dynamic balance. However, several studies have demonstrated that certain factors, such as dietary fiber deficiency, can enhance the metabolism of mucus glycans by gut bacteria, thereby disturbing this balance and weakening the mucus barrier function of the mucus layer. To better understand the occurrence and development of colon-related diseases, it is crucial to investigate the complex metabolic patterns of mucus glycosylation by intestinal microorganisms. Our objective was to comprehensively review these patterns in order to clarify the effects of mucus layer glycan metabolism by intestinal microorganisms on the host.
Collapse
Affiliation(s)
- Song Li
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Mingfei Chen
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Zhongyuan Wang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Waresi Abudourexiti
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Liang Zhang
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, Jiangsu, China
| | - Chao Ding
- Department of General Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Jianfeng Gong
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China.
| |
Collapse
|
15
|
Lordan C, Roche AK, Delsing D, Nauta A, Groeneveld A, MacSharry J, Cotter PD, van Sinderen D. Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond. Microbiol Mol Biol Rev 2024; 88:e0009423. [PMID: 38206006 PMCID: PMC10966949 DOI: 10.1128/mmbr.00094-23] [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] [Indexed: 01/12/2024] Open
Abstract
SUMMARYHuman milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing neonate. Certain bifidobacterial species, being among the earliest gut colonizers of breast-fed infants, have an adapted functional capacity to metabolize various HMO structures. This ability is typically observed in infant-associated bifidobacteria, as opposed to bifidobacteria associated with a mature microbiota. In recent years, information has been gleaned regarding how these infant-associated bifidobacteria as well as certain other taxa are able to assimilate HMOs, including the mechanistic strategies enabling their acquisition and consumption. Additionally, complex metabolic interactions occur between microbes facilitated by HMOs, including the utilization of breakdown products released from HMO degradation. Interest in HMO-mediated changes in microbial composition and function has been the focal point of numerous studies, in recent times fueled by the availability of individual biosynthetic HMOs, some of which are now commonly included in infant formula. In this review, we outline the main HMO assimilatory and catabolic strategies employed by infant-associated bifidobacteria, discuss other taxa that exhibit breast milk glycan degradation capacity, and cover HMO-supported cross-feeding interactions and related metabolites that have been described thus far.
Collapse
Affiliation(s)
- Cathy Lordan
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
| | - Aoife K. Roche
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Arjen Nauta
- FrieslandCampina, Amersfoort, the Netherlands
| | | | - John MacSharry
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
16
|
Xue K, Zhang G, Li Z, Zeng X, Li Z, Wang F, Zhang X, Lin C, Mao C. Dissecting the association between gut microbiota and hypertrophic scarring: a bidirectional Mendelian randomization study. Front Microbiol 2024; 15:1345717. [PMID: 38577682 PMCID: PMC10991740 DOI: 10.3389/fmicb.2024.1345717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
Hypertrophic scars affect a significant number of individuals annually, giving rise to both cosmetic concerns and functional impairments. Prior research has established that an imbalance in the composition of gut microbes, termed microbial dysbiosis, can initiate the progression of various diseases through the intricate interplay between gut microbiota and the host. However, the precise nature of the causal link between gut microbiota and hypertrophic scarring remains uncertain. In this study, after compiling summary data from genome-wide association studies (GWAS) involving 418 instances of gut microbiota and hypertrophic scarring, we conducted a bidirectional Mendelian randomization (MR) to investigate the potential existence of a causal relationship between gut microbiota and the development of hypertrophic scar and to discern the directionality of causation. By utilizing MR analysis, we identified seven causal associations between gut microbiome and hypertrophic scarring, involving one positive and six negative causal directions. Among them, Intestinimonas, Ruminococcus2, Barnesiella, Dorea, Desulfovibrio piger, and Ruminococcus torques act as protective factors against hypertrophic scarring, while Eubacterium rectale suggests a potential role as a risk factor for hypertrophic scars. Additionally, sensitivity analyses of these results revealed no indications of heterogeneity or pleiotropy. The findings of our MR study suggest a potential causative link between gut microbiota and hypertrophic scarring, opening up new ways for future mechanistic research and the exploration of nanobiotechnology therapies for skin disorders.
Collapse
Affiliation(s)
- Kaikai Xue
- Key Laboratory of Orthopedics of Zhejiang Province, Department of Orthopedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Burn, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guojian Zhang
- Key Laboratory of Orthopedics of Zhejiang Province, Department of Orthopedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Burn, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zihao Li
- Key Laboratory of Orthopedics of Zhejiang Province, Department of Orthopedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Burn, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangtao Zeng
- Key Laboratory of Orthopedics of Zhejiang Province, Department of Orthopedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
- Department of Burn, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zi Li
- Key Laboratory of Orthopedics of Zhejiang Province, Department of Orthopedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fulin Wang
- Key Laboratory of Orthopedics of Zhejiang Province, Department of Orthopedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xingxing Zhang
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cai Lin
- Department of Burn, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cong Mao
- Key Laboratory of Orthopedics of Zhejiang Province, Department of Orthopedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
17
|
Balouei F, Stefanon B, Martello E, Atuahene D, Sandri M, Meineri G. Supplementation with Silybum marianum Extract, Synbiotics, Omega-3 Fatty Acids, Vitamins, and Minerals: Impact on Biochemical Markers and Fecal Microbiome in Overweight Dogs. Animals (Basel) 2024; 14:579. [PMID: 38396547 PMCID: PMC10886211 DOI: 10.3390/ani14040579] [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: 11/28/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Overweight and obese dogs can develop metabolic dysfunction, characterized by an inflammatory response and involvement of liver functions. If a modulation of the gut microbiome and its interaction with the gut-liver axis is implicated in the development of metabolic dysfunction, exploration becomes necessary. Over the past decade, diverse therapeutic approaches have emerged to target pathogenic factors involved in metabolic dysfunction. This study investigated the impact of a supplement with hepatoprotective activity, containing extracts of Silybum marianum, prebiotics, probiotics, n-3 polyunsaturated fatty acids, vitamins, and minerals on hematological markers of liver functions and inflammation, as well as on the intestinal microbiota of 10 overweight adult dogs over a 35-day time span. Animals underwent clinical and laboratory evaluations every 7 days, both before the administration of the supplement (T0) and after 7, 14, 21, 28, and 35 days (T1, T2, T3, T4, and T5). In comparison to T0, a significant (p < 0.05) decrease in ALP, glucose, direct bilirubin, and CRP was observed from T3 to T5. The alpha diversity of the fecal microbiota significantly decreased (p < 0.05) only at T1, with high variability observed between dogs. Total short-chain fatty acid and lactic acid were also lower at T1 (p < 0.05) compared to the other times of sampling. The beta diversity of the fecal microbiota failed to show a clear pattern in relation to the sampling times. These results of blood parameters in overweight dogs show a reduction of the inflammation and an improvement of metabolic status during the study period, but the effective contribution of the supplement in this clinical outcome deserves further investigation. Furthermore, the considerable individual variability observed in the microbiome hinders the confident detection of supplement effects.
Collapse
Affiliation(s)
- Fatemeh Balouei
- Department of Agrifood, Environmental and Animal Science, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (F.B.); (M.S.)
| | - Bruno Stefanon
- Department of Agrifood, Environmental and Animal Science, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (F.B.); (M.S.)
| | - Elisa Martello
- Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, Nottingham City Hospital Campus, Nottingham NG5 1PB, UK;
| | - David Atuahene
- Department of Veterinary Sciences, School of Agriculture and Veterinary Medicine, University of Turin, Grugliasco, 10095 Turin, Italy; (D.A.); (G.M.)
| | - Misa Sandri
- Department of Agrifood, Environmental and Animal Science, University of Udine, Via delle Scienze 206, 33100 Udine, Italy; (F.B.); (M.S.)
| | - Giorgia Meineri
- Department of Veterinary Sciences, School of Agriculture and Veterinary Medicine, University of Turin, Grugliasco, 10095 Turin, Italy; (D.A.); (G.M.)
| |
Collapse
|
18
|
Álvarez-Herms J, González-Benito A, Corbi F, Odriozola A. What if gastrointestinal complications in endurance athletes were gut injuries in response to a high consumption of ultra-processed foods? Please take care of your bugs if you want to improve endurance performance: a narrative review. Eur J Appl Physiol 2024; 124:383-402. [PMID: 37839038 DOI: 10.1007/s00421-023-05331-z] [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: 03/15/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
To improve performance and recovery faster, athletes are advised to eat more often than usual and consume higher doses of simple carbohydrates, during and after exercise. Sports energetic supplements contain food additives, such as artificial sweeteners, emulsifiers, acidity regulators, preservatives, and salts, which could be harmful to the gut microbiota and impair the intestinal barrier function. The intestinal barrier plays a critical function in bidirectionally regulation of the selective transfer of nutrients, water, and electrolytes, while preventing at the same time, the entrance of harmful substances (selective permeability). The gut microbiota helps to the host to regulate intestinal homeostasis through metabolic, protective, and immune functions. Globally, the gut health is essential to maintain systemic homeostasis in athletes, and to ensure proper digestion, metabolization, and substrate absorption. Gastrointestinal complaints are an important cause of underperformance and dropout during endurance events. These complications are directly related to the loss of gut equilibrium, mainly linked to microbiota dysbiosis and leaky gut. In summary, athletes must be cautious with the elevated intake of ultra-processed foods and specifically those contained on sports nutrition supplements. This review points out the specific nutritional interventions that should be implemented and/or discontinued depending on individual gut functionality.
Collapse
Affiliation(s)
- Jesús Álvarez-Herms
- Phymolab (Physiology and Molecular Laboratory), Collado Hermoso, Segovia, Spain.
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Bilbao, Spain.
| | - A González-Benito
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - F Corbi
- Institut Nacional d'Educació Física de Catalunya (INEFC), University of Lleida (UdL), Lleida, Spain
| | - A Odriozola
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| |
Collapse
|
19
|
Gargari G, Mantegazza G, Cremon C, Taverniti V, Valenza A, Barbaro MR, Marasco G, Duncan R, Fiore W, Ferrari R, De Vitis V, Barbara G, Guglielmetti S. Collinsella aerofaciens as a predictive marker of response to probiotic treatment in non-constipated irritable bowel syndrome. Gut Microbes 2024; 16:2298246. [PMID: 38178601 PMCID: PMC10773624 DOI: 10.1080/19490976.2023.2298246] [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: 07/11/2023] [Accepted: 12/19/2023] [Indexed: 01/06/2024] Open
Abstract
Probiotics are exploited for adjuvant treatment in IBS, but reliable guidance for selecting the appropriate probiotic to adopt for different forms of IBS is lacking. We aimed to identify markers for recognizing non-constipated (NC) IBS patients that may show significant clinical improvements upon treatment with the probiotic strain Lacticaseibacillus paracasei DG (LDG). To this purpose, we performed a post-hoc analysis of samples collected during a multicenter, double-blind, parallel-group, placebo-controlled trial in which NC-IBS patients were randomized to receive at least 24 billion CFU LDG or placebo capsules b.i.d. for 12 weeks. The primary clinical endpoint was the composite response based on improved abdominal pain and fecal type. The fecal microbiome and serum markers of intestinal (PV1 and zonulin), liver, and kidney functions were investigated. We found that responders (R) in the probiotic arm (25%) differed from non-responders (NR) based on the abundance of 18 bacterial taxa, including the families Coriobacteriaceae, Dorea spp. and Collinsella aerofaciens, which were overrepresented in R patients. These taxa also distinguished R (but not NR) patients from healthy controls. Probiotic intervention significantly reduced the abundance of these bacteria in R, but not in NR. Analogous results emerged for C. aerofaciens from the analysis of data from a previous trial on IBS with the same probiotic. Finally, C. aerofaciens was positively correlated with the plasmalemmal vesicle associated protein-1 (PV-1) and the markers of liver function. In conclusion, LDG is effective on NC-IBS patients with NC-IBS with a greater abundance of potential pathobionts. Among these, C. aerofaciens has emerged as a potential predictor of probiotic efficacy.
Collapse
Affiliation(s)
- Giorgio Gargari
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Giacomo Mantegazza
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Cesare Cremon
- Dipartimento di Scienze Mediche e Chirurgiche, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Valentina Taverniti
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Alice Valenza
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Maria Raffaella Barbaro
- Dipartimento di Scienze Mediche e Chirurgiche, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Giovanni Marasco
- Dipartimento di Scienze Mediche e Chirurgiche, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Robin Duncan
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | | | | | | | - Giovanni Barbara
- Dipartimento di Scienze Mediche e Chirurgiche, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Simone Guglielmetti
- Division of Food Microbiology and Bioprocesses, Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| |
Collapse
|
20
|
Gao H, He C, Xin S, Hua R, Du Y, Wang B, Gong F, Yu X, Pan L, Liang C, Gao L, Shang H, Xu JD. Rhubarb extract rebuilding the mucus homeostasis and regulating mucin-associated flora to relieve constipation. Exp Biol Med (Maywood) 2023; 248:2449-2463. [PMID: 38073524 PMCID: PMC10903230 DOI: 10.1177/15353702231211859] [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: 04/23/2023] [Accepted: 08/21/2023] [Indexed: 01/23/2024] Open
Abstract
In clinical trials, rhubarb extract (Rb) was demonstrated to efficiently alleviate constipation. We would like to find out the underlying mechanism of rhubarb relieving constipation. However, there are few studies on the effects of rhubarb on colonic mucus secretion and constipation. The aim of this study was to investigate the effects of rhubarb on colonic mucus secretion and its underlying mechanism. The mice were randomly divided into four groups. Group I was the control group and Group II was the rhubarb control group, with Rb (24 g/kg body weight [b.w.]) administered through intragastric administration for three days. Group III mice were given diphenoxylate (20 mg/kg b.w.) for five days via gavage to induce constipation. Group IV received diphenoxylate lasting five days before undergoing Rb administration for three days. The condition of the colon was evaluated using an endoscope. Particularly, the diameter of blood vessels in the colonic mucosa expanded considerably in constipation mice along with diminishing mucus output, which was in line with the observation via scanning electron microscope (SEM) and transmission electron microscope (TEM). We also performed metagenomic analysis to reveal the microbiome related to mucin gene expression level referring to mucin secretion. In conclusion, Rb relieves constipation by rebuilding mucus homeostasis and regulating the microbiome.
Collapse
Affiliation(s)
- Han Gao
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
- Department of Clinical Laboratory, Aerospace Center Hospital, Beijing 100039, China
| | - Chengwei He
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Shuzi Xin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Rongxuan Hua
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Yixuan Du
- Department of Oral Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Boya Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengrong Gong
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xinyi Yu
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Luming Pan
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Chen Liang
- Department of Clinical Medicine, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Lei Gao
- Department of Biomedical Informatics, School of Biomedical Engineering, Capital Medical University, Beijing 100069, China
| | - Hongwei Shang
- Experimental Center for Morphological Research Platform, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jing-dong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| |
Collapse
|
21
|
Low KE, Tingley JP, Klassen L, King ML, Xing X, Watt C, Hoover SER, Gorzelak M, Abbott DW. Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates. Biotechnol Adv 2023; 69:108245. [PMID: 37652144 DOI: 10.1016/j.biotechadv.2023.108245] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.
Collapse
Affiliation(s)
- Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Marissa L King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Caitlin Watt
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Monika Gorzelak
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
| |
Collapse
|
22
|
Lou YC, Rubin BE, Schoelmerich MC, DiMarco KS, Borges AL, Rovinsky R, Song L, Doudna JA, Banfield JF. Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species. Nat Commun 2023; 14:7417. [PMID: 37973815 PMCID: PMC10654741 DOI: 10.1038/s41467-023-43279-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2'-fucosyllactose (2'FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2'FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2'FL breakdown, thus critical for B. breve's growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2'FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual's microbiome.
Collapse
Affiliation(s)
- Yue Clare Lou
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Benjamin E Rubin
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Marie C Schoelmerich
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Environmental Systems Sciences, ETH Zurich, Zurich, Switzerland
| | - Kaden S DiMarco
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Adair L Borges
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Rachel Rovinsky
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Leo Song
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA, USA.
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
| |
Collapse
|
23
|
Labarthe S, Plancade S, Raguideau S, Plaza Oñate F, Le Chatelier E, Leclerc M, Laroche B. Four functional profiles for fibre and mucin metabolism in the human gut microbiome. MICROBIOME 2023; 11:231. [PMID: 37858269 PMCID: PMC10588041 DOI: 10.1186/s40168-023-01667-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 09/07/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND With the emergence of metagenomic data, multiple links between the gut microbiome and the host health have been shown. Deciphering these complex interactions require evolved analysis methods focusing on the microbial ecosystem functions. Despite the fact that host or diet-derived fibres are the most abundant nutrients available in the gut, the presence of distinct functional traits regarding fibre and mucin hydrolysis, fermentation and hydrogenotrophic processes has never been investigated. RESULTS After manually selecting 91 KEGG orthologies and 33 glycoside hydrolases further aggregated in 101 functional descriptors representative of fibre and mucin degradation pathways in the gut microbiome, we used nonnegative matrix factorization to mine metagenomic datasets. Four distinct metabolic profiles were further identified on a training set of 1153 samples, thoroughly validated on a large database of 2571 unseen samples from 5 external metagenomic cohorts and confirmed with metatranscriptomic data. Profiles 1 and 2 are the main contributors to the fibre-degradation-related metagenome: they present contrasted involvement in fibre degradation and sugar metabolism and are differentially linked to dysbiosis, metabolic disease and inflammation. Profile 1 takes over Profile 2 in healthy samples, and unbalance of these profiles characterize dysbiotic samples. Furthermore, high fibre diet favours a healthy balance between profiles 1 and profile 2. Profile 3 takes over profile 2 during Crohn's disease, inducing functional reorientations towards unusual metabolism such as fucose and H2S degradation or propionate, acetone and butanediol production. Profile 4 gathers under-represented functions, like methanogenesis. Two taxonomic makes up of the profiles were investigated, using either the covariation of 203 prevalent genomes or metagenomic species, both providing consistent results in line with their functional characteristics. This taxonomic characterization showed that profiles 1 and 2 were respectively mainly composed of bacteria from the phyla Bacteroidetes and Firmicutes while profile 3 is representative of Proteobacteria and profile 4 of methanogens. CONCLUSIONS Integrating anaerobic microbiology knowledge with statistical learning can narrow down the metagenomic analysis to investigate functional profiles. Applying this approach to fibre degradation in the gut ended with 4 distinct functional profiles that can be easily monitored as markers of diet, dysbiosis, inflammation and disease. Video Abstract.
Collapse
Affiliation(s)
- Simon Labarthe
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France.
- Univ. Bordeaux, INRAE, BIOGECO, 33610, Cestas, France.
- Inria, INRAE, Pléiade, 33400, Talence, France.
| | - Sandra Plancade
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
- UR875 MIAT, Université fédérale de Toulouse, INRAE, Castanet-Tolosan, France
| | - Sebastien Raguideau
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
- Earlham Institute, Organisms and Ecosystems, NR4 7UZ, Norwich, UK
| | | | | | - Marion Leclerc
- Université Paris-Saclay, INRAE, Micalis, 78350, Jouy-en-Josas, France
- Pendulum Therapeutics, San Francisco, USA
| | - Beatrice Laroche
- Université Paris-Saclay, INRAE, MaIAGE, 78350, Jouy-en-Josas, France
- Inria, INRAE, Musca, 91120, Palaiseau, France
| |
Collapse
|
24
|
Azzouz DF, Chen Z, Izmirly PM, Chen LA, Li Z, Zhang C, Mieles D, Trujillo K, Heguy A, Pironti A, Putzel GG, Schwudke D, Fenyo D, Buyon JP, Alekseyenko AV, Gisch N, Silverman GJ. Longitudinal gut microbiome analyses and blooms of pathogenic strains during lupus disease flares. Ann Rheum Dis 2023; 82:1315-1327. [PMID: 37365013 PMCID: PMC10511964 DOI: 10.1136/ard-2023-223929] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023]
Abstract
OBJECTIVE Whereas genetic susceptibility for systemic lupus erythematosus (SLE) has been well explored, the triggers for clinical disease flares remain elusive. To investigate relationships between microbiota community resilience and disease activity, we performed the first longitudinal analyses of lupus gut-microbiota communities. METHODS In an observational study, taxononomic analyses, including multivariate analysis of ß-diversity, assessed time-dependent alterations in faecal communities from patients and healthy controls. From gut blooms, strains were isolated, with genomes and associated glycans analysed. RESULTS Multivariate analyses documented that, unlike healthy controls, significant temporal community-wide ecological microbiota instability was common in SLE patients, and transient intestinal growth spikes of several pathogenic species were documented. Expansions of only the anaerobic commensal, Ruminococcus (blautia) gnavus (RG) occurred at times of high-disease activity, and were detected in almost half of patients during lupus nephritis (LN) disease flares. Whole genome sequence analysis of RG strains isolated during these flares documented 34 genes postulated to aid adaptation and expansion within a host with an inflammatory condition. Yet, the most specific feature of strains found during lupus flares was the common expression of a novel type of cell membrane-associated lipoglycan. These lipoglycans share conserved structural features documented by mass spectroscopy, and highly immunogenic repetitive antigenic-determinants, recognised by high-level serum IgG2 antibodies, that spontaneously arose, concurrent with RG blooms and lupus flares. CONCLUSIONS Our findings rationalise how blooms of the RG pathobiont may be common drivers of clinical flares of often remitting-relapsing lupus disease, and highlight the potential pathogenic properties of specific strains isolated from active LN patients.
Collapse
Affiliation(s)
- Doua F Azzouz
- Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Ze Chen
- Vilcek Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York, New York, USA
| | - Peter M Izmirly
- Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Lea Ann Chen
- Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Zhi Li
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, New York, USA
| | - Chongda Zhang
- Vilcek Institute of Graduate Biomedical Sciences, NYU Grossman School of Medicine, New York, New York, USA
| | - David Mieles
- Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Kate Trujillo
- Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Adriana Heguy
- Pathology, NYU Grossman School of Medicine, New York, New York, USA
| | - Alejandro Pironti
- Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Greg G Putzel
- Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Dominik Schwudke
- Division of Bioanalytical Chemsitry, Forschungszentrum Borstel Leibniz Lungenzentrum, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site: Hamburg-Lübeck, Borstel, Germany
- Airway Research Center North, Member of the German Center for Lung Research (DZL), Partner Site: Research Center Borstel, Borstel, Germany
| | - David Fenyo
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, New York, USA
| | - Jill P Buyon
- Medicine, NYU Grossman School of Medicine, New York, New York, USA
| | - Alexander V Alekseyenko
- Department of Public Health Sciences, Biomedical Informatics Center, Program for Microbiome Research, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Nicolas Gisch
- Division of Bioanalytical Chemistry, Priority Area Infections, Forschungszentrum Borstel Leibniz Lungenzentrum, Borstel, Germany
| | | |
Collapse
|
25
|
Zhou Y, Xu B, Wang L, Zhang C, Li S. Fine Particulate Matter Perturbs the Pulmonary Microbiota in Broiler Chickens. Animals (Basel) 2023; 13:2862. [PMID: 37760262 PMCID: PMC10525718 DOI: 10.3390/ani13182862] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
(1) Fine particulate matter (PM2.5) seriously affects the respiratory tract health of both animals and humans. Growing evidence indicates that the pulmonary microbiota is involved in the development of respiratory tract health; however, there is still much that is unknown about the specific changes of pulmonary microbiota caused by PM2.5 in broilers. (2) In this experiment, a total of 48 broilers were randomly divided into a control group and PM-exposure group. The experiment lasted for 21 days. Microbiota, inflammation biomarkers, and histological markers in the lungs were determined. (3) On the last day of the experiment, PM significantly disrupted the structure of lung tissue and induced chronic pulmonary inflammation by increasing IL-6, TNFα, and IFNγ expression and decreasing IL-10 expression. PM exposure significantly altered the α and β diversity of pulmonary microbiota. At the phylum level, PM exposure significantly decreased the Firmicutes abundance and increased the abundance of Actinobacteria and Proteobacteria. At the genus level, PM exposure significantly increased the abundance of Rhodococcus, Achromobacter, Pseudomonas, and Ochrobactrum. We also observed positive associations of the above altered genera with lung TNFα and IFNγ expression. (4) The results suggest that PM perturbs the pulmonary microbiota and induces chronic inflammation, and the pulmonary microbiota possibly contributes to the development of lung inflammation.
Collapse
Affiliation(s)
| | | | | | | | - Shaoyu Li
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Y.Z.); (B.X.); (L.W.); (C.Z.)
| |
Collapse
|
26
|
Liu Y, Chen S, Wang J, Shao B, Fang J, Cao J. The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea. Microorganisms 2023; 11:2156. [PMID: 37764000 PMCID: PMC10536192 DOI: 10.3390/microorganisms11092156] [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: 08/08/2023] [Revised: 08/17/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillota are widely distributed in various environments, owing to their versatile metabolic capabilities and remarkable adaptation strategies. Recent studies reported that Bacillota species were highly enriched in cold seep sediments, but their metabolic capabilities, ecological functions, and adaption mechanisms in the cold seep habitats remained obscure. In this study, we conducted a systematic analysis of the complete genome of a novel Bacillota bacterium strain M8S5, which we isolated from cold seep sediments of the South China Sea at a depth of 1151 m. Phylogenetically, strain M8S5 was affiliated with the genus Abyssisolibacter within the phylum Bacillota. Metabolically, M8S5 is predicted to utilize various carbon and nitrogen sources, including chitin, cellulose, peptide/oligopeptide, amino acids, ethanolamine, and spermidine/putrescine. The pathways of histidine and proline biosynthesis were largely incomplete in strain M8S5, implying that its survival strictly depends on histidine- and proline-related organic matter enriched in the cold seep ecosystems. On the other hand, strain M8S5 contained the genes encoding a variety of extracellular peptidases, e.g., the S8, S11, and C25 families, suggesting its capabilities for extracellular protein degradation. Moreover, we identified a series of anaerobic respiratory genes, such as glycine reductase genes, in strain M8S5, which may allow it to survive in the anaerobic sediments of cold seep environments. Many genes associated with osmoprotectants (e.g., glycine betaine, proline, and trehalose), transporters, molecular chaperones, and reactive oxygen species-scavenging proteins as well as spore formation may contribute to its high-pressure and low-temperature adaptations. These findings regarding the versatile metabolic potentials and multiple adaptation strategies of strain M8S5 will expand our understanding of the Bacillota species in cold seep sediments and their potential roles in the biogeochemical cycling of deep marine ecosystems.
Collapse
Affiliation(s)
- Ying Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- The Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, College of Marine Sciences, Beibu Gulf University, Qinzhou 535000, China
| | - Songze Chen
- Shenzhen Ecological and Environmental Monitoring Center of Guangdong Province, Shenzhen 518049, China;
| | - Jiahua Wang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Baoying Shao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266000, China
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai 201306, China; (Y.L.); (J.W.); (B.S.)
| |
Collapse
|
27
|
Shrode RL, Ollberding NJ, Mangalam AK. Looking at the Full Picture: Utilizing Topic Modeling to Determine Disease-Associated Microbiome Communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.21.549984. [PMID: 37546903 PMCID: PMC10401927 DOI: 10.1101/2023.07.21.549984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The microbiome is a complex micro-ecosystem that provides the host with pathogen defense, food metabolism, and other vital processes. Alterations of the microbiome (dysbiosis) have been linked with a number of diseases such as cancers, multiple sclerosis (MS), Alzheimer's disease, etc. Generally, differential abundance testing between the healthy and patient groups is performed to identify important bacteria (enriched or depleted in one group). However, simply providing a singular species of bacteria to an individual lacking that species for health improvement has not been as successful as fecal matter transplant (FMT) therapy. Interestingly, FMT therapy transfers the entire gut microbiome of a healthy (or mixture of) individual to an individual with a disease. FMTs do, however, have limited success, possibly due to concerns that not all bacteria in the community may be responsible for the healthy phenotype. Therefore, it is important to identify the community of microorganisms linked to the health as well as the disease state of the host. Here we applied topic modeling, a natural language processing tool, to assess latent interactions occurring among microbes; thus, providing a representation of the community of bacteria relevant to healthy vs. disease state. Specifically, we utilized our previously published data that studied the gut microbiome of patients with relapsing-remitting MS (RRMS), a neurodegenerative autoimmune disease that has been linked to a variety of factors, including a dysbiotic gut microbiome. With topic modeling we identified communities of bacteria associated with RRMS, including genera previously discovered, but also other taxa that would have been overlooked simply with differential abundance testing. Our work shows that topic modeling can be a useful tool for analyzing the microbiome in dysbiosis and that it could be considered along with the commonly utilized differential abundance tests to better understand the role of the gut microbiome in health and disease.
Collapse
Affiliation(s)
- Rachel L. Shrode
- Department of Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Nicholas J. Ollberding
- Division of Biostatistics and Epidemiology; Cincinnati Children’s Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, USA
| | - Ashutosh K. Mangalam
- Department of Informatics, University of Iowa, Iowa City, IA, 52242, USA
- College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- University of Iowa, 25 S Grand Ave, 1080-ML, Iowa City, IA, 52246, USA
- Clinician Scientist, Iowa City VA Health Care System, 601 US-6 W, Iowa City, IA 52246, USA
| |
Collapse
|
28
|
Dedon LR, Hilliard MA, Rani A, Daza-Merchan ZT, Story G, Briere CE, Sela DA. Fucosylated Human Milk Oligosaccharides Drive Structure-Specific Syntrophy between Bifidobacterium infantis and Eubacterium hallii within a Modeled Infant Gut Microbiome. Mol Nutr Food Res 2023; 67:e2200851. [PMID: 36938958 PMCID: PMC11010582 DOI: 10.1002/mnfr.202200851] [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: 12/05/2022] [Revised: 03/23/2023] [Indexed: 03/21/2023]
Abstract
SCOPE Fucosylated human milk oligosaccharides (fHMOs) are metabolized by Bifidobacterium infantis and promote syntrophic interactions between microbiota that colonize the infant gut. The role of fHMO structure on syntrophic interactions and net microbiome function is not yet fully understood. METHODS AND RESULTS Metabolite production and microbial populations are tracked during mono- and co-culture fermentations of 2'fucosyllactose (2'FL) and difucosyllactose (DFL) by two B. infantis strains and Eubacterium hallii. This is also conducted in an in vitro modeled microbiome supplemented by B. infantis and/or E. hallii. Metabolites are quantified by high performance liquid chromatography. Total B. infantis and E. hallii populations are quantified through qRT-PCR and community composition through 16S amplicon sequencing. Differential metabolism of 2'FL and DFL by B. infantis strains gives rise to strain- and fHMO structure-specific syntrophy with E. hallii. Within the modeled microbial community, fHMO structure does not strongly alter metabolite production in aggregate, potentially due to functional redundancy within the modeled community. In contrast, community composition is dependent on fHMO structure. CONCLUSION Whereas short chain fatty acid production is not significantly altered by the specific fHMO structure introduced to the modeled community, specific fHMO structure influences the composition of the gut microbiome.
Collapse
Affiliation(s)
- Liv R. Dedon
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | - Margaret A. Hilliard
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
- Organismic and Evolutionary Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA United States
| | - Asha Rani
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | | | - Galaxie Story
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
| | - Carrie-Ellen Briere
- Elaine Marieb College of Nursing, University of Massachusetts Amherst, Amherst, MA, United States
| | - David A. Sela
- Department of Food Science, University of Massachusetts Amherst, Amherst, MA United States
- Department of Nutrition, University of Massachusetts Amherst, Amherst, MA, United States
- Department of Microbiology and Physiological Systems and Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, United States
| |
Collapse
|
29
|
Endika MF, Barnett DJM, Klostermann CE, Schols HA, Arts ICW, Penders J, Nauta A, Smidt H, Venema K. Microbiota-dependent influence of prebiotics on the resilience of infant gut microbiota to amoxicillin/clavulanate perturbation in an in vitro colon model. Front Microbiol 2023; 14:1131953. [PMID: 37275167 PMCID: PMC10232780 DOI: 10.3389/fmicb.2023.1131953] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/21/2023] [Indexed: 06/07/2023] Open
Abstract
Antibiotic exposure disturbs the developing infant gut microbiota. The capacity of the gut microbiota to recover from this disturbance (resilience) depends on the type of antibiotic. In this study, infant gut microbiota was exposed to a combination of amoxicillin and clavulanate (amoxicillin/clavulanate) in an in vitro colon model (TIM-2) with fecal-derived microbiota from 1-month-old (1-M; a mixed-taxa community type) as well as 3-month-old (3-M; Bifidobacterium dominated community type) breastfed infants. We investigated the effect of two common infant prebiotics, 2'-fucosyllactose (2'-FL) or galacto-oligosaccharides (GOS), on the resilience of infant gut microbiota to amoxicillin/clavulanate-induced changes in microbiota composition and activity. Amoxicillin/clavulanate treatment decreased alpha diversity and induced a temporary shift of microbiota to a community dominated by enterobacteria. Moreover, antibiotic treatment increased succinate and lactate in both 1- and 3-M colon models, while decreasing the production of short-chain (SCFA) and branched-chain fatty acids (BFCA). The prebiotic effect on the microbiota recovery depended on the fermenting capacity of antibiotic-exposed microbiota. In the 1-M colon model, the supplementation of 2'-FL supported the recovery of microbiota and restored the production of propionate and butyrate. In the 3-M colon model, GOS supplementation supported the recovery of microbiota and increased the production of acetate and butyrate.
Collapse
Affiliation(s)
- Martha F. Endika
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - David J. M. Barnett
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
- Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, Netherlands
| | - Cynthia E. Klostermann
- Biobased Chemistry and Technology, Wageningen University and Research, Wageningen, Netherlands
| | - Henk A. Schols
- Laboratory of Food Chemistry, Wageningen University and Research, Wageningen, Netherlands
| | - Ilja C. W. Arts
- Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Koen Venema
- Centre for Healthy Eating and Food Innovation (HEFI), Maastricht University—Campus Venlo, Venlo, Netherlands
| |
Collapse
|
30
|
Yao Y, Qi X, Jia Y, Ye J, Chu X, Wen Y, Cheng B, Cheng S, Liu L, Liang C, Wu C, Wang X, Ning Y, Wang S, Zhang F. Evaluating the interactive effects of dietary habits and human gut microbiome on the risks of depression and anxiety. Psychol Med 2023; 53:3047-3055. [PMID: 35074039 DOI: 10.1017/s0033291721005092] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Gut microbiome and dietary patterns have been suggested to be associated with depression/anxiety. However, limited effort has been made to explore the effects of possible interactions between diet and microbiome on the risks of depression and anxiety. METHODS Using the latest genome-wide association studies findings in gut microbiome and dietary habits, polygenic risk scores (PRSs) analysis of gut microbiome and dietary habits was conducted in the UK Biobank cohort. Logistic/linear regression models were applied for evaluating the associations for gut microbiome-PRS, dietary habits-PRS, and their interactions with depression/anxiety status and Patient Health Questionnaire (PHQ-9)/Generalized Anxiety Disorder-7 (GAD-7) score by R software. RESULTS We observed 51 common diet-gut microbiome interactions shared by both PHQ score and depression status, such as overall beef intake × genus Sporobacter [hurdle binary (HB)] (PPHQ = 7.88 × 10-4, Pdepression status = 5.86 × 10-4); carbohydrate × genus Lactococcus (HB) (PPHQ = 0.0295, Pdepression status = 0.0150). We detected 41 common diet-gut microbiome interactions shared by GAD score and anxiety status, such as sugar × genus Parasutterella (rank normal transformed) (PGAD = 5.15 × 10-3, Panxiety status = 0.0347); tablespoons of raw vegetables per day × family Coriobacteriaceae (HB) (PGAD = 6.02 × 10-4, Panxiety status = 0.0345). Some common significant interactions shared by depression and anxiety were identified, such as overall beef intake × genus Sporobacter (HB). CONCLUSIONS Our study results expanded our understanding of how to comprehensively consider the relationships for dietary habits-gut microbiome interactions with depression and anxiety.
Collapse
Affiliation(s)
- Yao Yao
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P. R. China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Jing Ye
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiaomeng Chu
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Cuiyan Wu
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xi Wang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Yujie Ning
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Sen Wang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| |
Collapse
|
31
|
Zheng S, Zhao X, Huang J, Tian Q, Xu S, Bo R, Liu M, Li J. Eugenol alleviates Salmonella Typhimurium-infected cecal injury by modulating cecal flora and tight junctions accompanied by suppressing inflammation. Microb Pathog 2023; 179:106113. [PMID: 37062493 DOI: 10.1016/j.micpath.2023.106113] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/13/2023] [Indexed: 04/18/2023]
Abstract
BACKGROUND Salmonella enterica serovar Typhimurium (ST) mainly exists in poultry and poultry related products, which are common sources of human salmonellosis. So, ST is an important zoonotic pathogen that threatens public health and safety. Eugenol has been noted for its antibacterial and anti-inflammatory properties, and it is expected to develop into an antibacterial therapy in vivo. METHODS Herein, the effects of eugenol against ST infection in terms of intestinal flora, cecal tight junction, and cecal inflammation in broilers was evaluated in this study. RESULTS The results showed that oral eugenol pretreatment obviously relieved the histopathological changes and ultrastructural injury of cecum caused by ST infection. Further analysis found that eugenol lessened the number of ST in the cecum, restrained Proteobacteria and Ruminococcus, and kept the ratio of Firmicutes to Bacteroidetes (F/B), improved the relative abundance of Alistipes compared to the infection control. Moreover, eugenol sustained the expression of ZO-1, claudin-1, and occluding tight junction proteins, reduced the mRNA levels of myeloid differentiation factor 88 (MyD88), toll-like receptor-4 (TLR4) and inducible nitric oxide synthesis (iNOS), suppressed the phosphorylation of p65 and IκBα in the NF-κB signaling pathway, as well as the mRNA levels of TNF-α, IL-1β, IL-2, and IL-18 in the cecum tissue. CONCLUSION Taken together, eugenol could protect broilers against ST infection via maintaining intestinal flora, tight junctions involved in mucosal barrier function, then accordingly limiting the excessive inflammation, finally contributed to improving relative weight gains and survival rates of broilers.
Collapse
Affiliation(s)
- ShuMei Zheng
- School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, PR China
| | - Xin Zhao
- School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, PR China
| | - JunJie Huang
- School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, PR China
| | - QiMing Tian
- School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, PR China
| | - ShuYa Xu
- School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, PR China
| | - RuoNan Bo
- School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, PR China
| | - MingJiang Liu
- School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, PR China
| | - JinGui Li
- School of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu, 225009, PR China.
| |
Collapse
|
32
|
Anso I, Naegeli A, Cifuente JO, Orrantia A, Andersson E, Zenarruzabeitia O, Moraleda-Montoya A, García-Alija M, Corzana F, Del Orbe RA, Borrego F, Trastoy B, Sjögren J, Guerin ME. Turning universal O into rare Bombay type blood. Nat Commun 2023; 14:1765. [PMID: 36997505 PMCID: PMC10063614 DOI: 10.1038/s41467-023-37324-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/09/2023] [Indexed: 04/01/2023] Open
Abstract
AbstractRed blood cell antigens play critical roles in blood transfusion since donor incompatibilities can be lethal. Recipients with the rare total deficiency in H antigen, the Oh Bombay phenotype, can only be transfused with group Oh blood to avoid serious transfusion reactions. We discover FucOB from the mucin-degrading bacteria Akkermansia muciniphila as an α-1,2-fucosidase able to hydrolyze Type I, Type II, Type III and Type V H antigens to obtain the afucosylated Bombay phenotype in vitro. X-ray crystal structures of FucOB show a three-domain architecture, including a GH95 glycoside hydrolase. The structural data together with site-directed mutagenesis, enzymatic activity and computational methods provide molecular insights into substrate specificity and catalysis. Furthermore, using agglutination tests and flow cytometry-based techniques, we demonstrate the ability of FucOB to convert universal O type into rare Bombay type blood, providing exciting possibilities to facilitate transfusion in recipients/patients with Bombay phenotype.
Collapse
|
33
|
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.
Collapse
|
34
|
O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases. Essays Biochem 2023; 67:331-344. [PMID: 36912232 PMCID: PMC10154620 DOI: 10.1042/ebc20220153] [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: 12/12/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/14/2023]
Abstract
Inflammatory bowel diseases (IBD) are modern diseases, with incidence rising around the world. They are associated with perturbation of the intestinal microbiota, and with alteration and crossing of the mucus barrier by the commensal bacteria that feed on it. In the process of mucus catabolism and invasion by gut bacteria, carbohydrate-active enzymes (CAZymes) play a critical role since mucus is mainly made up by O- and N-glycans. Moreover, the occurrence of IBD seems to be associated with low-fiber diets. Conversely, supplementation with oligosaccharides, such as human milk oligosaccharides (HMOs), which are structurally similar to intestinal mucins and could thus compete with them towards bacterial mucus-degrading CAZymes, has been suggested to prevent inflammation. In this mini-review, we will establish the current state of knowledge regarding the identification and characterization of mucus-degrading enzymes from both cultured and uncultured species of gut commensals and enteropathogens, with a particular focus on the present technological opportunities available to further the discovery of mucus-degrading CAZymes within the entire gut microbiome, by coupling microfluidics with metagenomics and culturomics. Finally, we will discuss the challenges to overcome to better assess how CAZymes targeting specific functional oligosaccharides could be involved in the modulation of the mucus-driven cross-talk between gut bacteria and their host in the context of IBD.
Collapse
|
35
|
Crost EH, Coletto E, Bell A, Juge N. Ruminococcus gnavus: friend or foe for human health. FEMS Microbiol Rev 2023; 47:fuad014. [PMID: 37015876 PMCID: PMC10112845 DOI: 10.1093/femsre/fuad014] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 02/06/2023] [Accepted: 04/03/2023] [Indexed: 04/06/2023] Open
Abstract
Ruminococcus gnavus was first identified in 1974 as a strict anaerobe in the gut of healthy individuals, and for several decades, its study has been limited to specific enzymes or bacteriocins. With the advent of metagenomics, R. gnavus has been associated both positively and negatively with an increasing number of intestinal and extraintestinal diseases from inflammatory bowel diseases to neurological disorders. This prompted renewed interest in understanding the adaptation mechanisms of R. gnavus to the gut, and the molecular mediators affecting its association with health and disease. From ca. 250 publications citing R. gnavus since 1990, 94% were published in the last 10 years. In this review, we describe the biological characterization of R. gnavus, its occurrence in the infant and adult gut microbiota and the factors influencing its colonization of the gastrointestinal tract; we also discuss the current state of our knowledge on its role in host health and disease. We highlight gaps in knowledge and discuss the hypothesis that differential health outcomes associated with R. gnavus in the gut are strain and niche specific.
Collapse
Affiliation(s)
- Emmanuelle H Crost
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Erika Coletto
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Andrew Bell
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| | - Nathalie Juge
- Quadram Institute Bioscience, Rosalind Franklin Road, Colney, Norwich NR4 7UQ, United Kingdom
| |
Collapse
|
36
|
Koh JH, Lee EH, Cha KH, Pan CH, Kim D, Kim WU. Factors associated with the composition of the gut microbiome in patients with established rheumatoid arthritis and its value for predicting treatment responses. Arthritis Res Ther 2023; 25:32. [PMID: 36864473 PMCID: PMC9979421 DOI: 10.1186/s13075-023-03013-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/14/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND We aimed to investigate the gut microbiota of patients with established rheumatoid arthritis (RA) who have been managed with disease-modifying anti-rheumatic drugs (DMARDs) for a long time. We focused on factors that might affect composition of the gut microbiota. Furthermore, we investigated whether gut microbiota composition predicts future clinical responses to conventional synthetic DMARDs (csDMARDs) in patients with an insufficient response to initial therapy. METHODS We recruited 94 patients with RA and 30 healthy participants. Fecal gut microbiome was analyzed by 16S rRNA amplificon sequencing; the resulting raw reads were processed based on QIIME2. Calypso online software was used for data visualization and to compare microbial composition between groups. For RA patients with moderate-to-high disease activity, treatment was changed after stool collection, and responses were observed 6 months later. RESULTS The composition of the gut microbiota in patients with established RA was different from that of healthy participants. Young RA patients (< 45 years) had reduced richness, evenness, and distinct gut microbial compositions when compared with older RA patients and healthy individuals. Disease activity and rheumatoid factor levels were not associated with microbiome composition. Overall, biological DMARDs and csDMARDs, except sulfasalazine and TNF inhibitors, respectively, were not associated with the gut microbial composition in patients with established RA. However, the combination of Subdoligranulum and Fusicatenibacter genera was associated with a future good response to second-line csDMARDs in patients who showed an insufficient response to first-line csDMARDs. CONCLUSION Gut microbial composition in patients with established RA is different from that in healthy individuals. Thus, the gut microbiome has the potential to predict responses of some RA patients to csDMARDs.
Collapse
Affiliation(s)
- Jung Hee Koh
- Division of Rheumatology, Department of Internal Medicine, School of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.,Center for Integrative Rheumatoid Transcriptomics and Dynamics, School of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Eun Ha Lee
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, 25451, Republic of Korea
| | - Kwang Hyun Cha
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, 25451, Republic of Korea
| | - Cheol-Ho Pan
- Natural Product Informatics Research Center, KIST Gangneung Institute of Natural Products, Gangneung, 25451, Republic of Korea
| | - Donghyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Republic of Korea. .,Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul, Republic of Korea.
| | - Wan-Uk Kim
- Division of Rheumatology, Department of Internal Medicine, School of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea. .,Center for Integrative Rheumatoid Transcriptomics and Dynamics, School of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
| |
Collapse
|
37
|
Microbiome Features Differentiating Unsupervised-Stratification-Based Clusters of Patients with Abnormal Glycometabolism. mBio 2023; 14:e0348722. [PMID: 36651735 PMCID: PMC9973283 DOI: 10.1128/mbio.03487-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The alteration of gut microbiota structure plays a pivotal role in the pathogenesis of abnormal glycometabolism. However, the microbiome features identified in patient groups stratified solely based on glucose levels remain controversial among different studies. In this study, we stratified 258 participants (discovery cohort) into three clusters according to an unsupervised method based on 16 clinical parameters involving the levels of blood glucose, insulin, and lipid. We found 67 cluster-specific microbiome features (i.e., amplicon sequence variants [ASVs]) based on 16S rRNA gene V3-V4 region sequencing. Specifically, ASVs belonging to Barnesville and Alistipes were enriched in cluster 1, in which participants had the lowest blood glucose levels, high insulin sensitivity, and a high-fecal short-chain fatty acid concentration. ASVs belonging to Prevotella copri and Ruminococcus gnavus were enriched in cluster 2, which was characterized by a moderate level of blood glucose, serious insulin resistance, and high levels of cholesterol and triglyceride. Cluster 3 was characterized by a high level of blood glucose and insulin deficiency, enriched with ASVs in P. copri and Bacteroides vulgatus. In addition, machine learning classifiers using the 67 cluster-specific ASVs were used to distinguish individuals in one cluster from those in the other two clusters both in discovery and testing cohorts (n = 83). Therefore, microbiome features identified based on the unsupervised stratification of patients with more inclusive clinical parameters may better reflect microbiota alterations associated with the progression of abnormal glycometabolism. IMPORTANCE The gut microbiota is altered in patients with type 2 diabetes (T2D) and prediabetes. The association of particular bacteria with T2D, however, varied among studies, which has made it challenging to develop precision medicine approaches for the prevention and alleviation of T2D. Blood glucose level is the only parameter in clustering patients when identifying the T2D-related bacteria in previous studies. This stratification ignores the fact that patients within the same blood glucose range differ in their insulin resistance and dyslipidemia, which also may be related to disordered gut microbiota. In addition to parameters of blood glucose levels, we also used additional parameters involving insulin and lipid levels to stratify participants into three clusters and further identified cluster-specific microbiome features. We further validated the association between these microbiome features and glycometabolism with an independent cohort. This study highlights the importance of stratification of patients with blood glucose, insulin, and lipid levels when identifying the microbiome features associated with the progression of abnormal glycometabolism.
Collapse
|
38
|
Rezende RM, Cox LM, Moreira TG, Liu S, Boulenouar S, Dhang F, LeServe DS, Nakagaki BN, Lopes JR, Tatematsu BK, Lemos L, Mayrink J, Lobo ELC, Guo L, Oliveira MG, Kuhn C, Weiner HL. Gamma-delta T cells modulate the microbiota and fecal micro-RNAs to maintain mucosal tolerance. MICROBIOME 2023; 11:32. [PMID: 36814316 PMCID: PMC9948450 DOI: 10.1186/s40168-023-01478-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gamma-delta (γδ) T cells are a major cell population in the intestinal mucosa and are key mediators of mucosal tolerance and microbiota composition. Little is known about the mechanisms by which intestinal γδ T cells interact with the gut microbiota to maintain tolerance. RESULTS We found that antibiotic treatment impaired oral tolerance and depleted intestinal γδ T cells, suggesting that the gut microbiota is necessary to maintain γδ T cells. We also found that mice deficient for γδ T cells (γδ-/-) had an altered microbiota composition that led to small intestine (SI) immune dysregulation and impaired tolerance. Accordingly, colonizing WT mice with γδ-/- microbiota resulted in SI immune dysregulation and loss of tolerance whereas colonizing γδ-/- mice with WT microbiota normalized mucosal immune responses and restored mucosal tolerance. Moreover, we found that SI γδ T cells shaped the gut microbiota and regulated intestinal homeostasis by secreting the fecal micro-RNA let-7f. Importantly, oral administration of let-7f to γδ-/- mice rescued mucosal tolerance by promoting the growth of the γδ-/--microbiota-depleted microbe Ruminococcus gnavus. CONCLUSIONS Taken together, we demonstrate that γδ T cell-selected microbiota is necessary and sufficient to promote mucosal tolerance, is mediated in part by γδ T cell secretion of fecal micro-RNAs, and is mechanistically linked to restoration of mucosal immune responses. Video Abstract.
Collapse
Affiliation(s)
- Rafael M Rezende
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
| | - Laura M Cox
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Thais G Moreira
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Shirong Liu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Selma Boulenouar
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Fyonn Dhang
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Danielle S LeServe
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Brenda N Nakagaki
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Juliana R Lopes
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Bruna K Tatematsu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Luisa Lemos
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Julia Mayrink
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Eduardo L C Lobo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Lydia Guo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Marilia G Oliveira
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Chantal Kuhn
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| |
Collapse
|
39
|
Structure and function of microbial α-l-fucosidases: a mini review. Essays Biochem 2023; 67:399-414. [PMID: 36805644 PMCID: PMC10154630 DOI: 10.1042/ebc20220158] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 02/23/2023]
Abstract
Fucose is a monosaccharide commonly found in mammalian, insect, microbial and plant glycans. The removal of terminal α-l-fucosyl residues from oligosaccharides and glycoconjugates is catalysed by α-l-fucosidases. To date, glycoside hydrolases (GHs) with exo-fucosidase activity on α-l-fucosylated substrates (EC 3.2.1.51, EC 3.2.1.-) have been reported in the GH29, GH95, GH139, GH141 and GH151 families of the Carbohydrate Active Enzymes (CAZy) database. Microbes generally encode several fucosidases in their genomes, often from more than one GH family, reflecting the high diversity of naturally occuring fucosylated structures they encounter. Functionally characterised microbial α-l-fucosidases have been shown to act on a range of substrates with α-1,2, α-1,3, α-1,4 or α-1,6 fucosylated linkages depending on the GH family and microorganism. Fucosidases show a modular organisation with catalytic domains of GH29 and GH151 displaying a (β/α)8-barrel fold while GH95 and GH141 show a (α/α)6 barrel and parallel β-helix fold, respectively. A number of crystal structures have been solved in complex with ligands, providing structural basis for their substrate specificity. Fucosidases can also be used in transglycosylation reactions to synthesise oligosaccharides. This mini review provides an overview of the enzymatic and structural properties of microbial α-l-fucosidases and some insights into their biological function and biotechnological applications.
Collapse
|
40
|
Bell A, Severi E, Owen CD, Latousakis D, Juge N. Biochemical and structural basis of sialic acid utilization by gut microbes. J Biol Chem 2023; 299:102989. [PMID: 36758803 PMCID: PMC10017367 DOI: 10.1016/j.jbc.2023.102989] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
The human gastrointestinal (GI) tract harbors diverse microbial communities collectively known as the gut microbiota that exert a profound impact on human health and disease. The repartition and availability of sialic acid derivatives in the gut have a significant impact on the modulation of gut microbes and host susceptibility to infection and inflammation. Although N-acetylneuraminic acid (Neu5Ac) is the main form of sialic acids in humans, the sialic acid family regroups more than 50 structurally and chemically distinct modified derivatives. In the GI tract, sialic acids are found in the terminal location of mucin glycan chains constituting the mucus layer and also come from human milk oligosaccharides in the infant gut or from meat-based foods in adults. The repartition of sialic acid in the GI tract influences the gut microbiota composition and pathogen colonization. In this review, we provide an update on the mechanisms underpinning sialic acid utilization by gut microbes, focusing on sialidases, transporters, and metabolic enzymes.
Collapse
Affiliation(s)
- Andrew Bell
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom
| | - Emmanuele Severi
- Microbes in Health and Disease, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - C David Owen
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Dimitrios Latousakis
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom
| | - Nathalie Juge
- Quadram Institute Bioscience, Gut Microbes and Health Institute Strategic Programme, Norwich, United Kingdom.
| |
Collapse
|
41
|
Levofloxacin prophylaxis and parenteral nutrition have a detrimental effect on intestinal microbial networks in pediatric patients undergoing HSCT. Commun Biol 2023; 6:36. [PMID: 36639555 PMCID: PMC9839701 DOI: 10.1038/s42003-023-04436-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
The gut microbiome (GM) has shown to influence hematopoietic stem cell transplantation (HSCT) outcome. Evidence on levofloxacin (LVX) prophylaxis usefulness before HSCT in pediatric patients is controversial and its impact on GM is poorly characterized. Post-HSCT parenteral nutrition (PN) is oftentimes the first-line nutritional support in the neutropenic phase, despite the emerging benefits of enteral nutrition (EN). In this exploratory work, we used a global-to-local networking approach to obtain a high-resolution longitudinal characterization of the GM in 30 pediatric HSCT patients receiving PN combined with LVX prophylaxis or PN alone or EN alone. By evaluating the network topology, we found that PN, especially preceded by LVX prophylaxis, resulted in a detrimental effect over the GM, with low modularity, poor cohesion, a shift in keystone species and the emergence of modules comprising several pathobionts, such as Klebsiella spp., [Ruminococcus] gnavus, Flavonifractor plautii and Enterococcus faecium. Our pilot findings on LVX prophylaxis and PN-related disruption of GM networks should be considered in patient management, to possibly facilitate prompt recovery/maintenance of a healthy and well-wired GM. However, the impact of LVX prophylaxis and nutritional support on short- to long-term post-HSCT clinical outcomes has yet to be elucidated.
Collapse
|
42
|
Roager HM, Stanton C, Hall LJ. Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life. Gut Microbes 2023; 15:2192151. [PMID: 36942883 PMCID: PMC10038037 DOI: 10.1080/19490976.2023.2192151] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/06/2023] [Indexed: 03/23/2023] Open
Abstract
The development of infant gut microbiome is a pivotal process affecting the ecology and function of the microbiome, as well as host health. While the establishment of the infant microbiome has been of interest for decades, the focus on gut microbial metabolism and the resulting small molecules (metabolites) has been rather limited. However, technological and computational advances are now enabling researchers to profile the plethora of metabolites in the infant gut, allowing for improved understanding of how gut microbial-derived metabolites drive microbiome community structuring and host-microbial interactions. Here, we review the current knowledge on development of the infant gut microbiota and metabolism within the first year of life, and discuss how these microbial metabolites are key for enhancing our basic understanding of interactions during the early life developmental window.
Collapse
Affiliation(s)
- Henrik M. Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Catherine Stanton
- APC Microbiome Ireland, Teagasc Moorepark Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Lindsay J. Hall
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich, UK
- Intestinal Microbiome, School of Life Sciences, ZIEL – Institute for Food & Health, Technical University of Munich, Freising, Germany
- Norwich Medical School, University of East Anglia, Norwich, UK
| |
Collapse
|
43
|
Yu S, Ge X, Xu H, Tan B, Tian B, Shi Y, Dai Y, Li Y, Hu S, Qian J. Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection. Front Cell Infect Microbiol 2023; 13:1129043. [PMID: 36814443 PMCID: PMC9940757 DOI: 10.3389/fcimb.2023.1129043] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Background Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI. Methods We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples. Results We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients. Conclusion IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.
Collapse
Affiliation(s)
- Si Yu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaomeng Ge
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hui Xu
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bei Tan
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bowen Tian
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yujie Shi
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yimin Dai
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yue Li
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- *Correspondence: Yue Li, ; Songnian Hu,
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yue Li, ; Songnian Hu,
| | - Jiaming Qian
- Department of Gastroenterology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
44
|
Sun Y, Wen M, Liu Y, Wang Y, Jing P, Gu Z, Jiang T, Wang W. The human microbiome: A promising target for lung cancer treatment. Front Immunol 2023; 14:1091165. [PMID: 36817461 PMCID: PMC9936316 DOI: 10.3389/fimmu.2023.1091165] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide, and insights into its underlying mechanisms as well as potential therapeutic strategies are urgently needed. The microbiome plays an important role in human health, and is also responsible for the initiation and progression of lung cancer through its induction of inflammatory responses and participation in immune regulation, as well as for its role in the generation of metabolic disorders and genotoxicity. Here, the distribution of human microflora along with its biological functions, the relationship between the microbiome and clinical characteristics, and the role of the microbiome in clinical treatment of lung cancer were comprehensively reviewed. This review provides a basis for the current understanding of lung cancer mechanisms with a focus on the microbiome, and contributes to future decisions on treatment management.
Collapse
Affiliation(s)
- Ying Sun
- Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, China
| | - Miaomiao Wen
- Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, China
| | - Yue Liu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, China
| | - Yu Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, China
| | - Pengyu Jing
- Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, China
| | - Zhongping Gu
- Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, China
| | - Tao Jiang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, China
| | - Wenchen Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital, Air Force Medical University, Xi'an, China
| |
Collapse
|
45
|
Deswal G, Selwal MK, Nirvan H, Selwal KK. Priestia flexa KS1: A new bacterial strain isolated from human faeces implicated in mucin degradation. Int Microbiol 2022:10.1007/s10123-022-00312-2. [PMID: 36502447 DOI: 10.1007/s10123-022-00312-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
The human gut acts as a habitat for diverse microbial communities, including mucin utilizers that play a significant role in host health and diseases. In this study, a gram-positive, rod-shaped mucin degrading bacterium was isolated from human faeces that belonged to the Priestia flexa species. Priestia isolate was analyzed for mucin-degrading ability and found that the KS1 strain could grow on mucin as the sole carbon source. The experimental results of the mucolytic zone around the colony and a 58% decrease in carbohydrate concentration confirmed the ability of Priestia to degrade mucin. The intracellular and extracellular glycosidase assay data supported the above results suggesting the ability of P. flexa to produce glycan hydrolysis enzymes that convert complex mucin oligosaccharide chains into simple glycans. The survival ability of the KS1 strain in simulated gastrointestinal conditions revealed that it could tolerate low pH (≥ 50% cell viability at pH 1.0) and 0.5% bile salt concentration (≥ 85% cell viability). The strain showed low hydrophobicity towards n-hexadecane (26.51 ± 0.92%) and xylene (21.71 ± 0.54%). Moreover, the KS1 culture was resistant to cefixime, clavulanic acid/ceftazidime, nafallin, methicillin, trimethoprim, kanamycin, and nalidixic antibiotic. Our results highlight the isolation of P. flexa KS1 strain that degrade mucin under in vitro conditions and show its better acclimatization within the GI environment. Further studies are required to unearth the molecular mechanisms involved in the degradation of mucin oligosaccharides in the human gut, advancing our understanding of health and disease.
Collapse
|
46
|
Schwabkey ZI, Wiesnoski DH, Chang CC, Tsai WB, Pham D, Ahmed SS, Hayase T, Turrubiates MRO, El-Himri RK, Sanchez CA, Hayase E, Oquendo ACF, Miyama T, Halsey TM, Heckel BE, Brown AN, Jin Y, Raybaud M, Prasad R, Flores I, McDaniel L, Chapa V, Lorenzi PL, Warmoes MO, Tan L, Swennes AG, Fowler S, Conner M, McHugh K, Graf T, Jensen VB, Peterson CB, Do KA, Zhang L, Shi Y, Wang Y, Galloway-Pena JR, Okhuysen PC, Daniel-MacDougall CR, Shono Y, da Silva MB, Peled JU, van den Brink MR, Ajami N, Wargo JA, Reddy P, Valdivia RH, Davey L, Rondon G, Srour SA, Mehta RS, Alousi AM, Shpall EJ, Champlin RE, Shelburne SA, Molldrem JJ, Jamal MA, Karmouch JL, Jenq RR. Diet-derived metabolites and mucus link the gut microbiome to fever after cytotoxic cancer treatment. Sci Transl Med 2022; 14:eabo3445. [PMID: 36383683 PMCID: PMC10028729 DOI: 10.1126/scitranslmed.abo3445] [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] [Indexed: 11/17/2022]
Abstract
Not all patients with cancer and severe neutropenia develop fever, and the fecal microbiome may play a role. In a single-center study of patients undergoing hematopoietic cell transplant (n = 119), the fecal microbiome was characterized at onset of severe neutropenia. A total of 63 patients (53%) developed a subsequent fever, and their fecal microbiome displayed increased relative abundances of Akkermansia muciniphila, a species of mucin-degrading bacteria (P = 0.006, corrected for multiple comparisons). Two therapies that induce neutropenia, irradiation and melphalan, similarly expanded A. muciniphila and additionally thinned the colonic mucus layer in mice. Caloric restriction of unirradiated mice also expanded A. muciniphila and thinned the colonic mucus layer. Antibiotic treatment to eradicate A. muciniphila before caloric restriction preserved colonic mucus, whereas A. muciniphila reintroduction restored mucus thinning. Caloric restriction of unirradiated mice raised colonic luminal pH and reduced acetate, propionate, and butyrate. Culturing A. muciniphila in vitro with propionate reduced utilization of mucin as well as of fucose. Treating irradiated mice with an antibiotic targeting A. muciniphila or propionate preserved the mucus layer, suppressed translocation of flagellin, reduced inflammatory cytokines in the colon, and improved thermoregulation. These results suggest that diet, metabolites, and colonic mucus link the microbiome to neutropenic fever and may guide future microbiome-based preventive strategies.
Collapse
Affiliation(s)
- Zaker I. Schwabkey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Diana H. Wiesnoski
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wen-Bin Tsai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dung Pham
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Saira S. Ahmed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Rawan K. El-Himri
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christopher A. Sanchez
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Annette C. Frenk Oquendo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Takahiko Miyama
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Taylor M. Halsey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brooke E. Heckel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexandria N. Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yimei Jin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mathilde Raybaud
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rishika Prasad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ivonne Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Valerie Chapa
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip L. Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marc O. Warmoes
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lin Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alton G. Swennes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephanie Fowler
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret Conner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kevin McHugh
- CPRIT Scholar in Cancer Research, Austin, TX 78701, USA
- Department of Bioengineering, Rice University, Houston, TX 77251, USA
| | - Tyler Graf
- Department of Bioengineering, Rice University, Houston, TX 77251, USA
| | - Vanessa B. Jensen
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kim-Anh Do
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Liangliang Zhang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yushu Shi
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yinghong Wang
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jessica R. Galloway-Pena
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, College Station, TX 77843, USA
| | - Pablo C. Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Yusuke Shono
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marina Burgos da Silva
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jonathan U. Peled
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10021, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Marcel R.M. van den Brink
- Department of Immunology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Weill Cornell Medical College, New York, NY 10021, USA
- Adult Bone Marrow Transplantation Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nadim Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A. Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pavan Reddy
- Department of Hematology and Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710 USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710 USA
| | - Gabriela Rondon
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samer A. Srour
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rohtesh S. Mehta
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amin M. Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard E. Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Samuel A. Shelburne
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey J. Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mohamed A. Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer L. Karmouch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- CPRIT Scholar in Cancer Research, Austin, TX 78701, USA
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| |
Collapse
|
47
|
Khalid AR, Yasoob TB, Zhang Z, Zhu X, Hang S. Dietary Moringa oleifera leaf powder improves jejunal permeability and digestive function by modulating the microbiota composition and mucosal immunity in heat stressed rabbits. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80952-80967. [PMID: 35725877 DOI: 10.1007/s11356-022-20737-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Heat stress (HS) has detrimental effects on intestinal health by altering digestive and immune responses in animals. Dietary Moringa oleifera leaf powder (MOLP) has been implicated in ameliorating the impact of HS, but its effects in terms of intestinal function improvement under HS remain poorly characterized. Therefore, the current study investigated the impact of HS and MOLP supplementation on tight junction barriers, intestinal microbiota (jejunal digesta), and differentially expressed genes (DEGs) in jejunal mucosa of heat-stressed rabbits by using the next-generation sequencing techniques. A total of 21 male New Zealand White rabbits (32 weeks old mean body weight of 3318 ± 171 g) were divided into three groups (n = 7/group) as control (CON, 25 °C), heat stress (HS, 35 °C for 7 h daily), and HS with MOLP supplementation (HSM, 35 °C for 7 h daily) gavage at 200 mg/kg body weight per day for 4 weeks. The results indicated that MOLP supplementation increased mRNA expression of tight junction proteins and glutathione transferase activity, while the malonaldehyde concentration was decreased in the jejunal mucosa compared to HS group (P < 0.05). Furthermore, MOLP decreased the concentrations of lipopolysaccharide, pro-inflammatory cytokines, and myeloperoxidase compared with HS group (P < 0.05). Intestinal microbiota analysis revealed that at phyla level, the relative abundance of Bacteroidetes was higher in HSM group compared to CON and HS groups. MOLP supplementation also resulted in higher abundance of putatively health-associated genera such as Christensenellaceae R-7 gut group, Ruminococcaceae NK4A214 group, Ruminococcus 2, Lachnospiraceae NK4A136 group, and Lachnospiraceae unclassified along with higher butyrate levels in HSM group as compared to HS group. The analysis of DEGs revealed that MOLP reversed inflammatory response by downregulation of genes, such as TNFRSF13C, LBP, and COX2 in enriched KEGG pathway of NF-kβ pathway. MOLP supplementation also significantly upregulated the expression of genes in protein digestion and absorption pathway, including PRSS2, LOC100349163, CPA1, CPB1, SLC9A3, SLC1A1, and SLC7A9 in HSM group. Three genes of fibrillar collagens, i.e., COL3A1, COL5A3, and COL12A1 in protein digestion were also down-regulated in HSM group. In conclusion, MOLP supplementation could improve jejunal permeability and digestive function, positively modulate microbiota composition and mucosal immunity in heat-stressed rabbits.
Collapse
Affiliation(s)
- Abdur Rauf Khalid
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
| | - Talat Bilal Yasoob
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
| | - Zhen Zhang
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
| | - Xiaofeng Zhu
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China
| | - Suqin Hang
- National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China.
- Laboratory of Gastrointestinal Microbiology, College of Animal Science and Technology, Nanjing Agricultural University, No.1 WeiGang, Xuanwu region, Nanjing, 210095, Jiangsu, China.
| |
Collapse
|
48
|
Shin SY, Park S, Moon JM, Kim K, Kim JW, Chun J, Lee TH, Choi CH. Compositional Changes in the Gut Microbiota of Responders and Non-responders to Probiotic Treatment Among Patients With Diarrhea-predominant Irritable Bowel Syndrome: A Post Hoc Analysis of a Randomized Clinical Trial. J Neurogastroenterol Motil 2022; 28:642-654. [PMID: 36250371 PMCID: PMC9577570 DOI: 10.5056/jnm21202] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 11/21/2022] Open
Abstract
Background/Aims We aim to evaluate the differences in the microbiome of responders and non-responders, as well as predict the response to probiotic therapy, based on fecal microbiome data in patients with diarrhea-predominant irritable bowel syndrome (IBS-D). Methods A multi-strain probiotics that contains Lactobacillus acidophilus (KCTC 11906BP), Lactobacillus plantarum (KCTC11867BP), Lactobacillus rhamnosus (KCTC 11868BP), Bifidobacterium breve (KCTC 11858BP), Bifidobacterium lactis (KCTC 11903BP), Bifidobacterium longum (KCTC 11860BP), and Streptococcus thermophilus (KCTC 11870BP) were used. Patients were categorized into probiotic and placebo groups, and fecal samples were collected from all patients before and at the end of 8 weeks of treatment. The probiotic group was further divided into responders and non-responders. Responders were defined as patients who experienced adequate relief of overall irritable bowel syndrome symptoms after probiotic therapy. Fecal microbiota were investigated using Illumina MiSeq and analyzed using the EzBioCloud 16S database and microbiome pipeline (https://www.EZbiocloud.net). Results There was no significant difference in the alpha and beta diversity between the responder and non-responder groups. The abundances of the phylum Proteobacteria and genus Bacteroides significantly decreased after probiotic treatment. Bifidobacterium bifidum, Pediococcus acidilactici, and Enterococcus faecium showed a significantly higher abundance in the probiotic group after treatment compared to the placebo group. Enterococcus faecalis and Lactococcus lactis were identified as biomarkers of non-response to probiotics. The abundance of Fusicatenibacter saccharivorans significantly increased in the responders after treatment. Conclusions Probiotic treatment changes some composition of fecal bacteria in patients with IBS-D. E. faecalis and L. lactis may be prediction biomarkers for non-response to probiotics. Increased abundance of F. sccharivorans is correlated to symptom improvement by probiotics in patients with IBS-D.
Collapse
Affiliation(s)
- Seung Yong Shin
- Chung-Ang University College of Medicine, Department of Internal Medicine, Seoul, Korea
| | - Sein Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Jung Min Moon
- Chung-Ang University College of Medicine, Department of Internal Medicine, Seoul, Korea
| | - Kisung Kim
- Chung-Ang University College of Medicine, Department of Internal Medicine, Seoul, Korea
| | - Jeong Wook Kim
- Chung-Ang University College of Medicine, Department of Internal Medicine, Seoul, Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea.,School of Biological Sciences, Seoul National University, Seoul, Korea
| | - Tae Hee Lee
- Institute for Digestive Research, Digestive Disease Center Soonchunhyang University College of Medicine, Seoul, Korea
| | - Chang Hwan Choi
- Chung-Ang University College of Medicine, Department of Internal Medicine, Seoul, Korea
| | | |
Collapse
|
49
|
Lee MJ, Lai HC, Kuo YL, Chen VCH. Association between Gut Microbiota and Emotional-Behavioral Symptoms in Children with Attention-Deficit/Hyperactivity Disorder. J Pers Med 2022; 12:jpm12101634. [PMID: 36294773 PMCID: PMC9605220 DOI: 10.3390/jpm12101634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
Previous studies have explored the role of the microbiome in attention-deficit/hyperactivity disorder (ADHD). However, whether the microbiome is correlated with emotional-behavioral disturbances, the most common comorbid symptom of ADHD, remains unclear. We established a cross-sectional study in which 6- to 18-year-old children with ADHD who were receiving no medication and a healthy control group of children without ADHD were recruited to analyze their microbiome composition. Microbiota of fecal samples were collected and analyzed using a 16s rRNA gene sequencing approach. In comparison with the healthy control group, the gut microbiota in children with ADHD exhibited significantly lower beta diversity. The abundance of the phylum Proteobacteria and the genera Agathobacter, Phascolarctobacterium, Prevotella_2, Acidaminococcus, Roseburia, and Ruminococcus gnavus group was increased in the ADHD group compared with the healthy group. Linear discriminant effect size (LEfSe) analysis was used to highlight specific bacteria phylotypes that were differentially altered between the ADHD and control groups. A regression analysis was performed to investigate the association between microbiota and emotional-behavioral symptoms in children with ADHD. A significant association was noted between withdrawal and depression symptoms and Agathobacter (p = 0.044), and between rule-breaking behavior and the Ruminococcus gnavus group (p = 0.046) after adjusting for sex, age, and the ADHD core symptoms score. This study advances the knowledge of how gut microbiota composition may contribute to emotional-behavioral symptoms in children with ADHD. The detailed mechanisms underlying the role of the gut microbiota in ADHD pathophysiology still require further investigation.
Collapse
Affiliation(s)
- Min-Jing Lee
- Department of Psychiatry, Chang Gung Memorial Hospital, Chiayi Branch, Chiayi 613, Taiwan
- School of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Hsin-Chih Lai
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Microbiota Research Center and Emerging Viral Infections Research Center, Chang Gung University, Taoyuan 333, Taiwan
- Central Research Laboratory, Xiamen Chang Gung Hospital, Xiamen 361, China
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- Research Center for Chinese Herbal Medicine and Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan
| | - Yu-Lun Kuo
- Biotools Co., Ltd., New Taipei City 221, Taiwan
| | - Vincent Chin-Hung Chen
- Department of Psychiatry, Chang Gung Memorial Hospital, Chiayi Branch, Chiayi 613, Taiwan
- School of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Correspondence: ; Tel.: +886-5-3621000 (ext. 2315); Fax: +886-5-3623002
| |
Collapse
|
50
|
Riazati N, Kable ME, Newman JW, Adkins Y, Freytag T, Jiang X, Stephensen CB. Associations of microbial and indoleamine-2,3-dioxygenase-derived tryptophan metabolites with immune activation in healthy adults. Front Immunol 2022; 13:917966. [PMID: 36248784 PMCID: PMC9558171 DOI: 10.3389/fimmu.2022.917966] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background Tryptophan (Trp) metabolites from intestinal bacteria (indole, indole acetic acid [IAA] and indole propionic acid [IPA]), and the Trp metabolite kynurenine (Kyn) from the indoleamine 2,3-dioxygenase (IDO) pathway, are aryl hydrocarbon receptor (AhR) agonists and thus, can regulate immune activity via the AhR pathway. We hypothesized that plasma concentrations of these metabolites would be associated with markers of immune activation in a cohort of healthy adults in a manner consistent with AhR-mediated immune-regulation. We also hypothesized that the plasma Kyn/Trp ratio, a marker of IDO activity, would be associated with immune markers reflecting IDO activation in innate immune cells. Finally, we hypothesized that some intestinal bacteria would be associated with plasma indole, IPA and IAA, and that these bacteria themselves would be associated with immune markers. Methods A novel set of 88 immune markers, and plasma Trp metabolites, were measured in 362 healthy adults. Bacterial taxa from stool were identified by 16S rRNA gene analysis. Multiple linear regression analysis was used to identify significant associations with immune markers. Results The sum of indole and IAA was positively associated with natural killer T-cells levels. Kyn and Kyn/Trp were positively associated with neopterin and IP-10, markers of type 1 immunity, and TNF-α and C-reactive protein (CRP), markers of the acute phase response, and the regulatory cytokine IL-10. Three bacteria negatively associated with Trp metabolites were associated with markers of immune activation: the family Lachnospiraceae with higher lymphocyte counts but lower level of activated CD4 T-cells, the genus Dorea with higher production of IFN-γ by T-cells in PBMC cultures, and the genus Ruminococcus with higher production IL-6 in PBMC cultures stimulated with bacterial lipopolysaccharide (LPS). Conclusions In this cohort of healthy adults bacterial Trp metabolites were not strongly associated with immune markers. Conversely, the Kyn/Trp ratio was strongly associated with markers of systemic inflammation and the acute phase response, consistent with IDO activation in innate immune cells. Finally, commensal bacteria associated with lower plasma (and perhaps intestinal) levels of bacterial Trp metabolites were associated with greater immune activation, possibly reflecting decreased regulatory immune activity related to lower intestinal levels of bacterial indole metabolites.
Collapse
Affiliation(s)
- Niknaz Riazati
- Graduate group of Molecular, Cellular, and Integrative Physiology, University of California, Davis, Davis, CA, United States
| | - Mary E. Kable
- USDA Western Human Nutrition Research Center, University of California, Davis, Davis, CA, United States,Department of Nutrition, University of California, Davis, Davis, CA, United States
| | - John W. Newman
- USDA Western Human Nutrition Research Center, University of California, Davis, Davis, CA, United States,Department of Nutrition, University of California, Davis, Davis, CA, United States,West Coast Metabolomics Center, Genome Center, University of California, Davis, Davis, CA, United States
| | - Yuriko Adkins
- USDA Western Human Nutrition Research Center, University of California, Davis, Davis, CA, United States
| | - Tammy Freytag
- USDA Western Human Nutrition Research Center, University of California, Davis, Davis, CA, United States
| | - Xiaowen Jiang
- USDA Western Human Nutrition Research Center, University of California, Davis, Davis, CA, United States
| | - Charles B. Stephensen
- USDA Western Human Nutrition Research Center, University of California, Davis, Davis, CA, United States,Department of Nutrition, University of California, Davis, Davis, CA, United States,*Correspondence: Charles B. Stephensen,
| |
Collapse
|