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Tanca A, Palomba A, Fiorito G, Abbondio M, Pagnozzi D, Uzzau S. Metaproteomic portrait of the healthy human gut microbiota. NPJ Biofilms Microbiomes 2024; 10:54. [PMID: 38944645 PMCID: PMC11214629 DOI: 10.1038/s41522-024-00526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/11/2024] [Indexed: 07/01/2024] Open
Abstract
Gut metaproteomics can provide direct evidence of microbial functions actively expressed in the colonic environments, contributing to clarify the role of the gut microbiota in human physiology. In this study, we re-analyzed 10 fecal metaproteomics datasets of healthy individuals from different continents and countries, with the aim of identifying stable and variable gut microbial functions and defining the contribution of specific bacterial taxa to the main metabolic pathways. The "core" metaproteome included 182 microbial functions and 83 pathways that were identified in all individuals analyzed. Several enzymes involved in glucose and pyruvate metabolism, along with glutamate dehydrogenase, acetate kinase, elongation factors G and Tu and DnaK, were the proteins with the lowest abundance variability in the cohorts under study. On the contrary, proteins involved in chemotaxis, response to stress and cell adhesion were among the most variable functions. Random-effect meta-analysis of correlation trends between taxa, functions and pathways revealed key ecological and molecular associations within the gut microbiota. The contribution of specific bacterial taxa to the main biological processes was also investigated, finding that Faecalibacterium is the most stable genus and the top contributor to anti-inflammatory butyrate production in the healthy gut microbiota. Active production of other mucosal immunomodulators facilitating host tolerance was observed, including Roseburia flagellin and lipopolysaccharide biosynthetic enzymes expressed by members of Bacteroidota. Our study provides a detailed picture of the healthy human gut microbiota, contributing to unveil its functional mechanisms and its relationship with nutrition, immunity, and environmental stressors.
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Affiliation(s)
- Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Giovanni Fiorito
- Clinical Bioinformatic Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Unit of Microbiology and Virology, University Hospital of Sassari, Sassari, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.
- Unit of Microbiology and Virology, University Hospital of Sassari, Sassari, Italy.
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2
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El Morr Y, Fürstenheim M, Mestdagh M, Franciszkiewicz K, Salou M, Morvan C, Dupré T, Vorobev A, Jneid B, Premel V, Darbois A, Perrin L, Mondot S, Colombeau L, Bugaut H, du Halgouet A, Richon S, Procopio E, Maurin M, Philippe C, Rodriguez R, Lantz O, Legoux F. MAIT cells monitor intestinal dysbiosis and contribute to host protection during colitis. Sci Immunol 2024; 9:eadi8954. [PMID: 38905325 PMCID: PMC7616241 DOI: 10.1126/sciimmunol.adi8954] [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: 05/25/2023] [Accepted: 05/29/2024] [Indexed: 06/23/2024]
Abstract
Intestinal inflammation shifts microbiota composition and metabolism. How the host monitors and responds to such changes remains unclear. Here, we describe a protective mechanism by which mucosal-associated invariant T (MAIT) cells detect microbiota metabolites produced upon intestinal inflammation and promote tissue repair. At steady state, MAIT ligands derived from the riboflavin biosynthesis pathway were produced by aerotolerant bacteria residing in the colonic mucosa. Experimental colitis triggered luminal expansion of riboflavin-producing bacteria, leading to increased production of MAIT ligands. Modulation of intestinal oxygen levels suggested a role for oxygen in inducing MAIT ligand production. MAIT ligands produced in the colon rapidly crossed the intestinal barrier and activated MAIT cells, which expressed tissue-repair genes and produced barrier-promoting mediators during colitis. Mice lacking MAIT cells were more susceptible to colitis and colitis-driven colorectal cancer. Thus, MAIT cells are sensitive to a bacterial metabolic pathway indicative of intestinal inflammation.
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Affiliation(s)
- Yara El Morr
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Mariela Fürstenheim
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
- Université Paris Cité, Paris, France
| | - Martin Mestdagh
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | | | - Marion Salou
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Claire Morvan
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015Paris, France
| | - Thierry Dupré
- Laboratoire de Biochimie, Hôpital Bichat AP-HP, Université de Paris, Paris, France
| | - Alexey Vorobev
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Bakhos Jneid
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Virginie Premel
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Aurélie Darbois
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Laetitia Perrin
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Stanislas Mondot
- Institut Micalis, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ludovic Colombeau
- CNRS UMR 3666, INSERM U1143, Chemical Biology of Cancer Laboratory, PSL University, Institut Curie, 75005Paris, France
| | - Hélène Bugaut
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | | | - Sophie Richon
- Institut Curie, PSL Research University, CNRS UMR144, Paris, France
| | - Emanuele Procopio
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Mathieu Maurin
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
| | - Catherine Philippe
- Institut Micalis, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Raphael Rodriguez
- CNRS UMR 3666, INSERM U1143, Chemical Biology of Cancer Laboratory, PSL University, Institut Curie, 75005Paris, France
| | - Olivier Lantz
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
- Laboratoire d’immunologie clinique, Institut Curie, 75005Paris, France
- Centre d’investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris, France
| | - François Legoux
- Institut Curie, PSL University, Inserm U932, Immunity and Cancer, Paris, France
- INSERM ERL1305, CNRS UMR6290, Université de Rennes, Institut de Génétique & Développement de Rennes, Rennes, France
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3
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Partipilo G, Bowman EK, Palmer EJ, Gao Y, Ridley RS, Alper HS, Keitz BK. Single-Cell Phenotyping of Extracellular Electron Transfer via Microdroplet Encapsulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598847. [PMID: 38915652 PMCID: PMC11195189 DOI: 10.1101/2024.06.13.598847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Electroactive organisms contribute to metal cycling, pollutant removal, and other redox-driven environmental processes. Studying this phenomenon in high-throughput is challenging since extracellular reduction cannot easily be traced back to its cell of origin within a mixed population. Here, we describe the development of a microdroplet emulsion system to enrich EET-capable organisms. We validated our system using the model electroactive organism S. oneidensis and describe the tooling of a benchtop microfluidic system for oxygen-limited processes. We demonstrated enrichment of EET-capable phenotypes from a mixed wild-type and EET-knockout population. As a proof-of-concept application, bacteria were collected from iron sedimentation from Town Lake (Austin, TX) and subjected to microdroplet enrichment. We observed an increase in EET-capable organisms in the sorted population that was distinct when compared to a population enriched in a bulk culture more closely akin to traditional techniques for discovering EET-capable bacteria. Finally, two bacterial species, C. sakazakii and V. fessus not previously shown to be electroactive, were further cultured and characterized for their ability to reduce channel conductance in an organic electrochemical transistor (OECT) and to reduce soluble Fe(III). We characterized two bacterial species not previously shown to exhibit electrogenic behavior. Our results demonstrate the utility of a microdroplet emulsions for identifying putative EET-capable bacteria and how this technology can be leveraged in tandem with existing methods.
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Affiliation(s)
- Gina Partipilo
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Emily K. Bowman
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, 78712
| | - Emma J. Palmer
- Civil, Architectural, and Environmental Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Yang Gao
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Rodney S. Ridley
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
| | - Benjamin K. Keitz
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712
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4
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Muramatsu MK, Winter SE. Nutrient acquisition strategies by gut microbes. Cell Host Microbe 2024; 32:863-874. [PMID: 38870902 PMCID: PMC11178278 DOI: 10.1016/j.chom.2024.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
The composition and function of the gut microbiota are intimately tied to nutrient acquisition strategies and metabolism, with significant implications for host health. Both dietary and host-intrinsic factors influence community structure and the basic modes of bacterial energy metabolism. The intestinal tract is rich in carbon and nitrogen sources; however, limited access to oxygen restricts energy-generating reactions to fermentation. By contrast, increased availability of electron acceptors during episodes of intestinal inflammation results in phylum-level changes in gut microbiota composition, suggesting that bacterial energy metabolism is a key driver of gut microbiota function. In this review article, we will illustrate diverse examples of microbial nutrient acquisition strategies in the context of habitat filters and anatomical location and the central role of energy metabolism in shaping metabolic strategies to support bacterial growth in the mammalian gut.
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Affiliation(s)
- Matthew K Muramatsu
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis, Davis, CA 95616, USA
| | - Sebastian E Winter
- Department of Internal Medicine, Division of Infectious Diseases, UC Davis, Davis, CA 95616, USA.
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5
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Flint HJ, Louis P, Duncan SH. Why does increased microbial fermentation in the human colon shift toward butyrate? AIMS Microbiol 2024; 10:311-319. [PMID: 38919716 PMCID: PMC11194621 DOI: 10.3934/microbiol.2024016] [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: 03/05/2024] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 06/27/2024] Open
Abstract
The microbial community of the human large intestine mainly ferments dietary fiber to short chain fatty acids (SCFAs), which are efficiently absorbed by the host. The three major SCFAs (acetate, propionate, and butyrate) have different fates within the body and different effects on health. A recent analysis of 10 human volunteer studies established that the proportions of these SCFA in fecal samples significantly shifted towards butyrate as the overall concentration of SCFA increased. Butyrate plays a key role in gut health and is preferentially utilized as an energy source by the colonic epithelium. Here we discuss possible mechanisms that underlie this 'butyrate shift'; these include the selection for butyrate-producing bacteria within the microbiota by certain types of fiber, and the possibility of additional butyrate formation from lactate and acetate by metabolite cross-feeding. However, a crucial factor appears to be the pH in the proximal colon, which decreases as the SCFA concentrations increase. A mildly acidic pH has been shown to have an important impact on microbial competition and on the stoichiometry of butyrate production. Understanding these complex interactions has been greatly aided by the refinement of theoretical models of the colonic microbiota that assume a small number (10) of microbial functional groups (MFGs).
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Affiliation(s)
| | | | - Sylvia H. Duncan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, UK AB25 2ZD
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Li H, Huang Y, Liang L, Li H, Li S, Feng Y, Feng S, Wu K, Wu F. The relationship between the gut microbiota and oxidative stress in the cognitive function of schizophrenia: A pilot study in China. Schizophr Res 2024; 267:444-450. [PMID: 38643725 DOI: 10.1016/j.schres.2024.03.053] [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: 11/27/2023] [Revised: 03/22/2024] [Accepted: 03/31/2024] [Indexed: 04/23/2024]
Abstract
Cognitive impairment is a core symptom of schizophrenia. The gut microbiota (GM) and oxidative stress may play important roles in the pathophysiological mechanisms of cognitive impairment. This study aimed to explore the relationship between GM and oxidative stress in the cognitive function of schizophrenia. GM obtained by 16S RNA sequencing and serum superoxide dismutase (SOD) levels from schizophrenia patients (N = 68) and healthy controls (HCs, N = 72) were analyzed. All psychiatric symptoms were assessed using the Positive and Negative Syndrome Scale (PANSS). Cognitive function was assessed using the MATRICS Consensus Cognitive Battery (MCCB). Correlation analysis was used to explore the relationship between GM, SOD, and cognitive function. Machine learning models were used to identify potential biomarkers. Compared to HCs, the relative abundances of Collinsella, undefined Ruminococcus, Lactobacillus, Eubacterium, Mogibacterium, Desulfovibrio, Bulleidia, Succinivibrio, Corynebacterium, and Atopobium were higher in patients with schizophrenia, but Faecalibacterium, Anaerostipes, Turicibacter, and Ruminococcus were lower. In patients with schizophrenia, the positive factor, general factor, and total score of MCCB positively correlated with Lactobacillus, Collinsella, and Lactobacillus, respectively; SOD negatively correlated with Eubacterium, Collinsella, Lactobacillus, Corynebacterium, Bulleidia, Mogibacterium, and Succinivibrio, but positively correlated with Faecalibacterium, Ruminococcus, and MCCB verbal learning index scores; Faecalibacterium and Turicibacter were positively correlated with MCCB visual learning index scores and speed of processing index scores, respectively. Our findings revealed a correlation between SOD and GM and confirmed that cognitive dysfunction in patients with schizophrenia involves abnormal SOD levels and GM changes.
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Affiliation(s)
- Hehua Li
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yuanyuan Huang
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liqin Liang
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China
| | - Hanqiu Li
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shijia Li
- Swammerdam Institute for Life Sciences (SILS)-University of Amsterdam, Amsterdam, the Netherlands
| | - Yangdong Feng
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Shixuan Feng
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China
| | - Kai Wu
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, Guangzhou, China; Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China.
| | - Fengchun Wu
- The Affiliated Brain Hospital of Guangzhou Medical University, Guangzhou, China; Guangdong Engineering Technology Research Center for Translational Medicine of Mental Disorders, Guangzhou, China; Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou Medical University, Guangzhou, China.
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7
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Nguélé AT, Carrara C, Mozzicafreddo M, Chen H, Piersanti A, Salum SS, Ali SM, Miceli C. Association between Food or Nutrients and Gut Microbiota in Healthy and Helminth-Infected Women of Reproductive Age from Zanzibar, Tanzania. Nutrients 2024; 16:1266. [PMID: 38732513 PMCID: PMC11085056 DOI: 10.3390/nu16091266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Modulating the gut microbiota is recognised as one strategy for preventing and fighting diseases. While the significant impact of diet on the gut microbiota's composition and function has been extensively researched, there is a notable lack of studies on the interactions between diet, microbiota, and helminth infections. Here, we used a combination of self-reported food intake and a 16S rDNA sequencing approach to analyse the composition of the gut microbiota in women of reproductive age from the two main islands of the Zanzibar archipelago, where helminth infections are endemic. We also applied a Spearman correlation analysis to food/nutrients and gut microbiota. Our results reveal that, despite close ethnic and cultural ties, the participants' gut microbiota differs depending on their location. A nutrient intake analysis revealed deficiencies in minerals and vitamins, indicating an imbalanced diet. A correlation analysis identified bacterial taxa consistently correlated with specific food or nutrients in healthy women from both locations, and in two types of helminth infections. Escherichia/Shigella abundances, usually associated with Trichuris trichiura infection, consistently correlated with insufficient levels of vitamins B2 and B12. In conclusion, our findings suggest that the increased consumption of specific food like cassava and fish, as well as essential nutrients such as calcium, B vitamins, and vitamin A, may modulate the gut microbiota of populations residing in regions where helminth infections are endemic.
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Affiliation(s)
- Aristide Toussaint Nguélé
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
| | - Chiara Carrara
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
| | - Matteo Mozzicafreddo
- Department of Clinical and Molecular Sciences, Marche Polytechnic University, 60126 Ancona, Italy;
| | - Hongliang Chen
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
- College of Veterinary Medicine, Jilin Provincial Engineering Research Center of Animal Probiotics, Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun 130118, China
| | - Angela Piersanti
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
| | - Salum Seif Salum
- School of Health and Medical Sciences, State University of Zanzibar, Zanzibar 146, Tanzania;
| | - Said M. Ali
- Public Health Laboratory Ivo de Carneri, Chake Chake 122, Tanzania;
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, 62032 Camerino, Italy; (A.T.N.); (C.C.); (H.C.); (A.P.)
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Zhang WW, Thakur K, Zhang JG, Wei ZJ. Riboflavin ameliorates intestinal inflammation via immune modulation and alterations of gut microbiota homeostasis in DSS-colitis C57BL/6 mice. Food Funct 2024; 15:4109-4121. [PMID: 38597225 DOI: 10.1039/d4fo00835a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
While there have been advancements in understanding the direct and indirect impact of riboflavin (B2) on intestinal inflammation, the precise mechanisms are still unknown. This study focuses on evaluating the effects of riboflavin (B2) supplementation on a colitis mouse model induced with 3% dextran sodium sulphate (DSS). We administered three different doses of oral B2 (VB2L, VB2M, and VB2H) and assessed its impact on various physiological and biochemical parameters associated with colitis. Mice given any of the three doses exhibited relative improvement in the symptoms and intestinal damage. This was evidenced by the inhibition of the pro-inflammatory cytokines TNF-α, IL-1β, and CALP, along with an increase in the anti-inflammatory cytokine IL-10. B2 supplementation also led to a restoration of oxidative homeostasis, as indicated by a decrease in myeloperoxidase (MPO) and malondialdehyde (MDA) levels and an increase in reduced glutathione (GSH) and catalase (CAT) activities. B2 intervention showed positive effects on intestinal barrier function, confirmed by increased expression of tight junction proteins (occludin and ZO-1). B2 was linked to an elevated relative abundance of Actinobacteriota, Desulfobacterota, and Verrucomicrobiota. Notably, Verrucomicrobiota showed a significant increase in the VB2H group, reaching 15.03% relative abundance. Akkermansia exhibited a negative correlation with colitis and might be linked to anti-inflammatory function. Additionally, a remarkable increase in n-butyric acid, i-butyric acid, and i-valeric acid was reported in the VB2H group. The ameliorating role of B2 in gut inflammation can be attributed to immune system modulation as well as alterations in the gut microbiota composition, along with elevated levels of fecal SCFAs.
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Affiliation(s)
- Wang-Wei Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China.
| | - Kiran Thakur
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China.
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China
| | - Jian-Guo Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China.
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China
| | - Zhao-Jun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China.
- School of Biological Science and Engineering, North Minzu University, Yinchuan 750021, People's Republic of China
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Bernard M, Lecoeur A, Coville JL, Bruneau N, Jardet D, Lagarrigue S, Meynadier A, Calenge F, Pascal G, Zerjal T. Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions. Sci Rep 2024; 14:8210. [PMID: 38589474 PMCID: PMC11001975 DOI: 10.1038/s41598-024-58374-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 03/28/2024] [Indexed: 04/10/2024] Open
Abstract
The gut microbiota is known to play an important role in energy harvest and is likely to affect feed efficiency. In this study, we used 16S metabarcoding sequencing to analyse the caecal microbiota of laying hens from feed-efficient and non-efficient lines obtained by divergent selection for residual feed intake. The two lines were fed either a commercial wheat-soybean based diet (CTR) or a low-energy, high-fibre corn-sunflower diet (LE). The analysis revealed a significant line x diet interaction, highlighting distinct differences in microbial community composition between the two lines when hens were fed the CTR diet, and more muted differences when hens were fed the LE diet. Our results are consistent with the hypothesis that a richer and more diverse microbiota may play a role in enhancing feed efficiency, albeit in a diet-dependent manner. The taxonomic differences observed in the microbial composition seem to correlate with alterations in starch and fibre digestion as well as in the production of short-chain fatty acids. As a result, we hypothesise that efficient hens are able to optimise nutrient absorption through the activity of fibrolytic bacteria such as Alistipes or Anaerosporobacter, which, via their production of propionate, influence various aspects of host metabolism.
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Affiliation(s)
- Maria Bernard
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
- INRAE, SIGENAE, 78350, Jouy-en-Josas, France.
| | - Alexandre Lecoeur
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jean-Luc Coville
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Nicolas Bruneau
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Deborah Jardet
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Annabelle Meynadier
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Fanny Calenge
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Géraldine Pascal
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Tatiana Zerjal
- INRAE, AgroParisTech, GABI, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
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10
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Liao C, Wang L, Quon G. Microbiome-based classification models for fresh produce safety and quality evaluation. Microbiol Spectr 2024; 12:e0344823. [PMID: 38445872 PMCID: PMC10986475 DOI: 10.1128/spectrum.03448-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/17/2024] [Indexed: 03/07/2024] Open
Abstract
Small sample sizes and loss of sequencing reads during the microbiome data preprocessing can limit the statistical power of differentiating fresh produce phenotypes and prevent the detection of important bacterial species associated with produce contamination or quality reduction. Here, we explored a machine learning-based k-mer hash analysis strategy to identify DNA signatures predictive of produce safety (PS) and produce quality (PQ) and compared it against the amplicon sequence variant (ASV) strategy that uses a typical denoising step and ASV-based taxonomy strategy. Random forest-based classifiers for PS and PQ using 7-mer hash data sets had significantly higher classification accuracy than those using the ASV data sets. We also demonstrated that the proposed combination of integrating multiple data sets and leveraging a 7-mer hash strategy leads to better classification performance for PS and PQ compared to the ASV method but presents lower PS classification accuracy compared to the feature-selected ASV-based taxonomy strategy. Due to the current limitation of generating taxonomy using the 7-mer hash strategy, the ASV-based taxonomy strategy with remarkably less computing time and memory usage is more efficient for PS and PQ classification and applicable for important taxa identification. Results generated from this study lay the foundation for future studies that wish and need to incorporate and/or compare different microbiome sequencing data sets for the application of machine learning in the area of microbial safety and quality of food. IMPORTANCE Identification of generalizable indicators for produce safety (PS) and produce quality (PQ) improves the detection of produce contamination and quality decline. However, effective sequencing read loss during microbiome data preprocessing and the limited sample size of individual studies restrain statistical power to identify important features contributing to differentiating PS and PQ phenotypes. We applied machine learning-based models using individual and integrated k-mer hash and amplicon sequence variant (ASV) data sets for PS and PQ classification and evaluated their classification performance and found that random forest (RF)-based models using integrated 7-mer hash data sets achieved significantly higher PS and PQ classification accuracy. Due to the limitation of taxonomic analysis for the 7-mer hash, we also developed RF-based models using feature-selected ASV-based taxonomic data sets, which performed better PS classification than those using the integrated 7-mer hash data set. The RF feature selection method identified 480 PS indicators and 263 PQ indicators with a positive contribution to the PS and PQ classification.
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Affiliation(s)
- Chao Liao
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Luxin Wang
- Department of Food Science and Technology, University of California Davis, Davis, California, USA
| | - Gerald Quon
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California, USA
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11
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Nejati M, Soheili M, Salami M, Khedri M. The effect of redox bacteria on the programmed cell death-1 cancer immunotherapy. Res Pharm Sci 2024; 19:228-237. [PMID: 39035583 PMCID: PMC11257211 DOI: 10.4103/rps.rps_28_23] [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: 02/16/2023] [Revised: 07/12/2023] [Accepted: 12/18/2023] [Indexed: 07/23/2024] Open
Abstract
Background and purpose Extracellular electron transferring (EET) or redox bacteria employ a shuttle of flavins to transfer electrons to the oxygen in the intestinal mucosa. Although clinical studies suggest that the gut microbiome modulates the efficiency of immune checkpoint therapy in patients with cancer, the modulation mechanisms have not been well-characterized yet. Experimental approach In the present study, the oral gavage administration of Shewanella oneidensis MR-1 as a prototypic EET bacteria was assayed in a mouse model of lung cancer to determine the effect of EET bacterium on the efficacy of the programmed cell death protein 1 (PD1)-immune checkpoint therapy. Findings/Results It was indicated that in vitro EET from S. oneidensis was mediated by riboflavins that were supplied through extrinsic sources. Co-administration of S. oneidensis and anti-PD 1 antibodies represent better tumor remission compared to the single-administration of each one; however, no statistically significant change was observed in the tumor volume. Conclusion and implications More detailed studies are needed to definitively confirm the therapeutic effects of electrogenic bacteria in patients with cancer. Given the findings of the present study, increasing flavin compounds or EET bacteria in the intestine may provide novel strategies for modulating cancer immunotherapy.
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Affiliation(s)
- Majid Nejati
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Masoud Soheili
- Physiology Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Mahmoud Salami
- Physiology Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Mostafa Khedri
- Department of Clinical Laboratory Sciences, School of Allied Medical Sciences, Kashan University of Medical Sciences, Kashan, Iran
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12
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Naradasu D, Miran W, Okamoto A. Electrochemical Characterization of Two Gut Microbial Strains Cooperatively Promoting Multiple Sclerosis Pathogenesis. Microorganisms 2024; 12:257. [PMID: 38399661 PMCID: PMC10892914 DOI: 10.3390/microorganisms12020257] [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: 12/21/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/25/2024] Open
Abstract
In this study, we explored the extracellular electron transfer (EET) capabilities of two bacterial strains, OTU0001 and OTU0002, which are demonstrated in biofilm formation in mouse gut and the induction of autoimmune diseases like multiple sclerosis. OTU0002 displayed significant electrogenic behaviour, producing microbial current on an indium tin-doped oxide electrode surface, particularly in the presence of glucose, with a current density of 60 nA/cm2. The presence of cell-surface redox substrate potentially mediating EET was revealed by the redox-based staining method and electrochemical voltammetry assay. However, medium swapping analyses and the addition of flavins, a model redox mediator, suggest that the current production is dominated by soluble endogenous redox substrates in OTU0002. Given redox substrates were detected at the cell surface, the secreted redox molecule may interact with the cellular surface of OTU0002. In contrast to OTU0002, OTU0001 did not exhibit notable electrochemical activity, lacking cell-surface redox molecules. Further, the mixture of the two strains did not increase the current production from OTU0001, suggesting that OTU0001 does not support the EET mechanism of OTU0002. The present work revealed the coexistence of EET and non-EET capable pathogens in multi-species biofilm.
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Affiliation(s)
- Divya Naradasu
- Oral Microbiology, Bristol Dental School, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol BS1 3NY, UK;
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
| | - Waheed Miran
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- School of Chemical and Materials Engineering, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Ibaraki, Japan;
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba 305-0044, Ibaraki, Japan
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo 060-8628, Hokkaido, Japan
- Graduate School of Science and Engineering, College of Science and Engineering, University of Tsukuba, 1-1-1 Tennodai, Tsukuba 305-8573, Ibaraki, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Kanagawa, Japan
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13
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Bircher L, Sourabié AM, Paurevic M, Hochuli J, Geirnaert A, Navas C, Drogue B, Lacroix C. Faecalibacterium duncaniae A2-165 growth is strongly promoted by yeast extract and vitamin B5 in cGMP medium. Microb Biotechnol 2024; 17:e14374. [PMID: 38019136 PMCID: PMC10832529 DOI: 10.1111/1751-7915.14374] [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: 07/19/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/30/2023] Open
Abstract
Several gut microbial species within the Faecalibacterium genus have emerged as promising next-generation probiotics (NGP) due to their multifunctional protective effects against gastrointestinal and systemic disorders. To enable clinical studies and further applications, improved methods for cultivating Faecalibacterium must be developed in compliance with current Good Manufacturing Practice regulations, which is complicated by its oxygen sensitivity and complex nutritional requirements. Different yeast-based nutrients (YBNs), including yeast extracts (YEs) and yeast peptones (YPs), are ubiquitously used when cultivating microbes to supply a broad range of macro- and micronutrients. In this study, we evaluated six experimental YBNs, namely three YEs, two YPs and a yeast cell wall product (YCW), and eight B-vitamins in the cultivation of Faecalibacterium duncaniae A2-165, former Faecalibacterium prausnitzii, using growth assays in microtitre plates, dose-effect studies in Hungate tube fermentations and fully controlled bioreactor experiments. We demonstrated that YEs promote F. duncaniae A2-165 growth in a nutritionally limited medium, while YPs and YCW lacked essential growth factors for enabling cell propagation. High cell density was obtained in controlled bioreactors using a medium containing 2-4% of a selected YE and 1% casein peptone (3.4 ± 1.7 × 109 -5.1 ± 1.3 × 109 cells mL-1 ). Among all tested B-vitamins, we identified B5 as a strong growth promoter. Replacing casein peptone with YP and supplementing with vitamin B5 further increased biomass by approximately 50% (6.8 ± 1.7 × 109 cells mL-1 ). Hence, empirical selection of YE, YP and B5 allowed formulation of a high-yielding animal allergen-free nutritive medium to produce F. duncaniae A2-165. Selecting nutritionally suitable YBNs and combining these with other key nutrients are important steps for optimizing production of NGP with high yields and lower cost.
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Affiliation(s)
- Lea Bircher
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Alain M. Sourabié
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Marijana Paurevic
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Janina Hochuli
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Annelies Geirnaert
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
| | - Chloé Navas
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Benoît Drogue
- Science Technology and Innovation DepartmentProcelys by LeSaffreMaisons‐AlfortFrance
| | - Christophe Lacroix
- Department Health Science and Technology, Laboratory of Food Biotechnology, Institute of Food, Nutrition and HealthETH ZurichZürichSwitzerland
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14
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Wang Y, Sharma A, Weber KM, Topper E, Appleton AA, Gustafson D, Clish CB, Kaplan RC, Burk RD, Qi Q, Peters BA. The menopause-related gut microbiome: associations with metabolomics, inflammatory protein markers, and cardiometabolic health in women with HIV. Menopause 2024; 31:52-64. [PMID: 38086007 PMCID: PMC10841550 DOI: 10.1097/gme.0000000000002287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
OBJECTIVE This study aimed to identify menopause-related gut microbial features, as well as their related metabolites and inflammatory protein markers, and link with cardiometabolic risk factors in women with and without HIV. METHODS In the Women's Interagency HIV Study, we performed shotgun metagenomic sequencing on 696 stool samples from 446 participants (67% women with HIV), and quantified plasma metabolomics and serum proteomics in a subset (~86%). We examined the associations of menopause (postmenopausal vs premenopausal) with gut microbial features in a cross-sectional repeated-measures design and further evaluated those features in relation to metabolites, proteins, and cardiometabolic risk factors. RESULTS Different overall gut microbial composition was observed by menopausal status in women with HIV only. We identified a range of gut microbial features that differed between postmenopausal and premenopausal women with HIV (but none in women without HIV), including abundance of 32 species and functional potentials involving 24 enzymatic reactions and lower β-glucuronidase bacterial gene ortholog. Specifically, highly abundant species Faecalibacterium prausnitzii , Bacteroides species CAG:98 , and Bifidobacterium adolescentis were depleted in postmenopausal versus premenopausal women with HIV. Menopause-depleted species (mainly Clostridia ) in women with HIV were positively associated with several glycerophospholipids, while negatively associated with imidazolepropionic acid and fibroblast growth factor 21. Mediation analysis suggested that menopause may decrease plasma phosphatidylcholine plasmalogen C36:1 and C36:2 levels via reducing abundance of species F. prausnitzii and Acetanaerobacterium elongatum in women with HIV. Furthermore, waist-to-hip ratio was associated with menopause-related microbes, metabolites, and fibroblast growth factor 21 in women with HIV. CONCLUSIONS Menopause was associated with a differential gut microbiome in women with HIV, related to metabolite and protein profiles that potentially contribute to elevated cardiometabolic risk.
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Affiliation(s)
- Yi Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anjali Sharma
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Elizabeth Topper
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Allison A. Appleton
- Department of Epidemiology and Biostatistics, University at Albany School of Public Health, Rensselaer, NY, USA
| | - Deborah Gustafson
- Department of Neurology, State University of New York Downstate Health Sciences University, Brooklyn, NY, USA
| | | | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics & Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Brandilyn A. Peters
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
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15
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Van Den Ham KM, Little MR, Bednarski OJ, Fusco EM, Mandal RK, Mitra R, Li S, Doumbo S, Doumtabe D, Kayentao K, Ongoiba A, Traore B, Crompton PD, Schmidt NW. Creation of a non-Western humanized gnotobiotic mouse model through the transplantation of rural African fecal microbiota. Microbiol Spectr 2023; 11:e0155423. [PMID: 37819130 PMCID: PMC10714993 DOI: 10.1128/spectrum.01554-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/05/2023] [Indexed: 10/13/2023] Open
Abstract
IMPORTANCE There is increasing evidence that microbes residing within the intestines (gut microbiota) play important roles in the well-being of humans. Yet, there are considerable challenges in determining the specific role of gut microbiota in human diseases owing to the complexity of diverse internal and environmental factors that can contribute to diseases. Mice devoid of all microorganisms (germ-free mice) can be colonized with human stool samples to examine the specific contribution of the gut microbiota to a disease. These approaches have been primarily focused on stool samples obtained from individuals in Western countries. Thus, there is limited understanding as to whether the same methods used to colonize germ-free mice with stool from Western individuals would apply to the colonization of germ-free mice with stool from non-Western individuals. Here, we report the results from colonizing germ-free mice with stool samples of Malian children.
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Affiliation(s)
- Kristin M. Van Den Ham
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Morgan R. Little
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Olivia J. Bednarski
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Elizabeth M. Fusco
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rabindra K. Mandal
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Riten Mitra
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, USA
| | - Shanping Li
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Safiatou Doumbo
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Didier Doumtabe
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Kassoum Kayentao
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Aissata Ongoiba
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Boubacar Traore
- Mali International Center of Excellence in Research, Malaria Research and Training Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Peter D. Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
| | - Nathan W. Schmidt
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
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16
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Loveikyte R, Bourgonje AR, van Goor H, Dijkstra G, van der Meulen-de Jong AE. The effect of iron therapy on oxidative stress and intestinal microbiota in inflammatory bowel diseases: A review on the conundrum. Redox Biol 2023; 68:102950. [PMID: 37918126 PMCID: PMC10643537 DOI: 10.1016/j.redox.2023.102950] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 10/28/2023] [Indexed: 11/04/2023] Open
Abstract
One in five patients with Inflammatory Bowel Disease (IBD) suffers from anemia, most frequently caused by iron deficiency. Anemia and iron deficiency are associated with worse disease outcomes, reduced quality of life, decreased economic participation, and increased healthcare costs. International guidelines and consensus-based recommendations have emphasized the importance of treating anemia and iron deficiency. In this review, we draw attention to the rarely discussed effects of iron deficiency and iron therapy on the redox status, the intestinal microbiota, and the potential interplay between them, focusing on the clinical implications for patients with IBD. Current data are scarce, inconsistent, and do not provide definitive answers. Nevertheless, it is imperative to rule out infections and discern iron deficiency anemia from other types of anemia to prevent untargeted oral or intravenous iron supplementation and potential side effects, including oxidative stress. Further research is necessary to establish the clinical significance of changes in the redox status and the intestinal microbiota following iron supplementation.
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Affiliation(s)
- R Loveikyte
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands; Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - A R Bourgonje
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; The Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - H van Goor
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - G Dijkstra
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - A E van der Meulen-de Jong
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
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17
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Bosch B, Hartikainen A, Ronkainen A, Scheperjans F, Arkkila P, Satokari R. Development of a Protocol for Anaerobic Preparation and Banking of Fecal Microbiota Transplantation Material: Evaluation of Bacterial Richness in the Cultivated Fraction. Microorganisms 2023; 11:2901. [PMID: 38138045 PMCID: PMC10745795 DOI: 10.3390/microorganisms11122901] [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: 10/11/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Fecal microbiota transplantation (FMT) has shown highly variable results in indications beyond recurrent Clostridioides difficile infection. Microbiota dysbiosis in many diseases is characterized by the depletion of strictly anaerobic bacteria, which may be crucial for FMT efficacy. We developed a protocol to ensure anaerobic conditions during the entire transplant preparation and banking process, from material collection to administration. The protocol necessitates an anaerobic cabinet, i.e., a non-standard laboratory equipment. We analyzed the population of viable anaerobes by combining cultivation and 16S rRNA gene profiling during the transplant preparation, and after 4, 8, and 12 months of anaerobic or aerobic storage at -80 °C, 78% of fecal species were captured via cultivation. Our findings suggest that strictly anaerobic transplant preparation and storage may preserve species richness better than oxic conditions, but the overall difference was not significant. However, specific anaerobes such as Neglecta and Anaerotruncus were affected by the oxygen exposure. A storage time of up to 12 months did not affect the presence of cultivated taxa. Noteworthy, our analysis focused on the richness of cultivated anaerobes rather than their abundance, which may have been affected. The benefits of the developed anaerobic protocol in FMT for specific indications remain to be demonstrated in clinical trials.
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Affiliation(s)
- Berta Bosch
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (A.H.); (A.R.)
| | - Anna Hartikainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (A.H.); (A.R.)
| | - Aki Ronkainen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (A.H.); (A.R.)
| | - Filip Scheperjans
- Department of Neurology, Helsinki University Hospital, 00290 Helsinki, Finland;
- Clinicum, University of Helsinki, 00290 Helsinki, Finland;
| | - Perttu Arkkila
- Clinicum, University of Helsinki, 00290 Helsinki, Finland;
- Department of Gastroenterology, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Reetta Satokari
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; (A.H.); (A.R.)
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18
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Nandy A, Farkas D, Pepió-Tárrega B, Martinez-Crespiera S, Borràs E, Avignone-Rossa C, Di Lorenzo M. Influence of carbon-based cathodes on biofilm composition and electrochemical performance in soil microbial fuel cells. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2023; 16:100276. [PMID: 37206316 PMCID: PMC10189395 DOI: 10.1016/j.ese.2023.100276] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 05/21/2023]
Abstract
Increasing energy demands and environmental pollution concerns press for sustainable and environmentally friendly technologies. Soil microbial fuel cell (SMFC) technology has great potential for carbon-neutral bioenergy generation and self-powered electrochemical bioremediation. In this study, an in-depth assessment on the effect of several carbon-based cathode materials on the electrochemical performance of SMFCs is provided for the first time. An innovative carbon nanofibers electrode doped with Fe (CNFFe) is used as cathode material in membrane-less SMFCs, and the performance of the resulting device is compared with SMFCs implementing either Pt-doped carbon cloth (PtC), carbon cloth, or graphite felt (GF) as the cathode. Electrochemical analyses are integrated with microbial analyses to assess the impact on both electrogenesis and microbial composition of the anodic and cathodic biofilm. The results show that CNFFe and PtC generate very stable performances, with a peak power density (with respect to the cathode geometric area) of 25.5 and 30.4 mW m-2, respectively. The best electrochemical performance was obtained with GF, with a peak power density of 87.3 mW m-2. Taxonomic profiling of the microbial communities revealed differences between anodic and cathodic communities. The anodes were predominantly enriched with Geobacter and Pseudomonas species, while cathodic communities were dominated by hydrogen-producing and hydrogenotrophic bacteria, indicating H2 cycling as a possible electron transfer mechanism. The presence of nitrate-reducing bacteria, combined with the results of cyclic voltammograms, suggests microbial nitrate reduction occurred on GF cathodes. The results of this study can contribute to the development of effective SMFC design strategies for field implementation.
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Affiliation(s)
- Arpita Nandy
- Department of Chemical Engineering and Centre for Biosensors, Bioelectronics & Biodevices (C3Bio), University of Bath, Claverton Down, BA2 7AY, UK
| | - Daniel Farkas
- Department of Microbial Sciences, University of Surrey, Guildford, GU2 7XH, UK
| | - Belén Pepió-Tárrega
- LEITAT Technological Center, C/ de la Innovació, 2, 08225, Terrassa, Barcelona, Spain
| | | | - Eduard Borràs
- LEITAT Technological Center, C/ de la Innovació, 2, 08225, Terrassa, Barcelona, Spain
| | | | - Mirella Di Lorenzo
- Department of Chemical Engineering and Centre for Biosensors, Bioelectronics & Biodevices (C3Bio), University of Bath, Claverton Down, BA2 7AY, UK
- Corresponding author.
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19
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Nawab S, Bao Q, Ji LH, Luo Q, Fu X, Fan S, Deng Z, Ma W. The Pathogenicity of Fusobacterium nucleatum Modulated by Dietary Fibers-A Possible Missing Link between the Dietary Composition and the Risk of Colorectal Cancer. Microorganisms 2023; 11:2004. [PMID: 37630564 PMCID: PMC10458976 DOI: 10.3390/microorganisms11082004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/20/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
The dietary composition has been approved to be strongly associated with the risk of colorectal cancer (CRC), one of the most serious malignancies worldwide, through regulating the gut microbiota structure, thereby influencing the homeostasis of colonic epithelial cells by producing carcinogens, i.e., ammonia or antitumor metabolites, like butyrate. Though butyrate-producing Fusobacterium nucleatum has been considered a potential tumor driver associated with chemotherapy resistance and poor prognosis in CRC, it was more frequently identified in the gut microbiota of healthy individuals rather than CRC tumor tissues. First, within the concentration range tested, the fermentation broth of F. nucleatum exhibited no significant effects on Caco-2 and NCM460 cells viability except for a notable up-regulation of the expression of TLR4 (30.70%, p < 0.0001) and Myc (47.67%, p = 0.021) and genes encoding proinflammatory cytokines including IL1B (197.57%, p < 0.0001), IL6 (1704.51%, p < 0.0001), and IL8 (897.05%, p < 0.0001) in Caco-2 cells exclusively. Although no marked effects of polydextrose or fibersol-2 on the growth of F. nucleatum, Caco-2 and NCM460 cells were observed, once culture media supplemented with polydextrose or fibersol-2, the corresponding fermentation broths of F. nucleatum significantly inhibited the growth of Caco-2 cells up to 48.90% (p = 0.0003, 72 h, 10%) and 52.96% (p = 0.0002, 72 h, 10%), respectively in a dose-dependent manner. These two kinds of fibers considerably promoted butyrate production of F. nucleatum up to 205.67% (p < 0.0001, 6% polydextrose at 24 h) and 153.46% (p = 0.0002, 6% fibersol-2 at 12 h), which explained why and how the fermentation broths of F. nucleatum cultured with fibers suppressing the growth of Caco-2 cells. Above findings indicated that dietary fiber determined F. nucleatum to be a carcinogenic or antitumor bacterium, and F. nucleatum played an important role in the association between the dietary composition, primarily the content of dietary fibers, and the risk of CRC.
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Affiliation(s)
- Sadia Nawab
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Qelger Bao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lin-Hua Ji
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Middle Shandong Road, Shanghai 200001, China
| | - Qian Luo
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiang Fu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Shuxuan Fan
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Wei Ma
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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20
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Khan MT, Dwibedi C, Sundh D, Pradhan M, Kraft JD, Caesar R, Tremaroli V, Lorentzon M, Bäckhed F. Synergy and oxygen adaptation for development of next-generation probiotics. Nature 2023; 620:381-385. [PMID: 37532933 PMCID: PMC10412450 DOI: 10.1038/s41586-023-06378-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/27/2023] [Indexed: 08/04/2023]
Abstract
The human gut microbiota has gained interest as an environmental factor that may contribute to health or disease1. The development of next-generation probiotics is a promising strategy to modulate the gut microbiota and improve human health; however, several key candidate next-generation probiotics are strictly anaerobic2 and may require synergy with other bacteria for optimal growth. Faecalibacterium prausnitzii is a highly prevalent and abundant human gut bacterium associated with human health, but it has not yet been developed into probiotic formulations2. Here we describe the co-isolation of F. prausnitzii and Desulfovibrio piger, a sulfate-reducing bacterium, and their cross-feeding for growth and butyrate production. To produce a next-generation probiotic formulation, we adapted F. prausnitzii to tolerate oxygen exposure, and, in proof-of-concept studies, we demonstrate that the symbiotic product is tolerated by mice and humans (ClinicalTrials.gov identifier: NCT03728868 ) and is detected in the human gut in a subset of study participants. Our study describes a technology for the production of next-generation probiotics based on the adaptation of strictly anaerobic bacteria to tolerate oxygen exposures without a reduction in potential beneficial properties. Our technology may be used for the development of other strictly anaerobic strains as next-generation probiotics.
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Affiliation(s)
- Muhammad Tanweer Khan
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Metabogen, Mölndal, Sweden
| | - Chinmay Dwibedi
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Daniel Sundh
- Sahlgrenska Osteoporosis Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Meenakshi Pradhan
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jamie D Kraft
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Robert Caesar
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Mattias Lorentzon
- Sahlgrenska Osteoporosis Centre, Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Region Västra Götaland, Geriatric Medicine Clinic, Sahlgrenska University Hospital Mölndal, Mölndal, Sweden
- Mary MacKillop Institute for Health Research, Australian Catholic University, Melbourne, Victoria, Australia
| | - Fredrik Bäckhed
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
- Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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21
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Xu J, Yang Y, Li X, Ding S, Zheng L, Xiong C, Yang Y. Pleiotropic activities of succinate: The interplay between gut microbiota and cardiovascular diseases. IMETA 2023; 2:e124. [PMID: 38867936 PMCID: PMC10989957 DOI: 10.1002/imt2.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/14/2024]
Abstract
Cardiovascular diseases (CVDs) continue to be a significant contributor to global mortality, imposing a substantial burden and emphasizing the urgent need for disease control to save lives and prevent disability. With advancements in technology and scientific research, novel mechanisms underlying CVDs have been uncovered, leading to the exploration of promising treatment targets aimed at reducing the global burden of the disease. One of the most intriguing findings is the relationship between CVDs and gut microbiota, challenging the traditional understanding of CVDs mechanisms and introducing the concept of the gut-heart axis. The gut microbiota, through changes in microbial compositions and functions, plays a crucial role in influencing local and systemic effects on host physiology and disease development, with its metabolites acting as key regulators. In previous studies, we have emphasized the importance of specific metabolites such as betaine, putrescine, trimethylamine oxide, and N,N,N-trimethyl-5-aminovaleric acid in the potential treatment of CVDs. Particularly noteworthy is the gut microbiota-associated metabolite succinate, which has garnered significant attention due to its involvement in various pathophysiological pathways closely related to CVDs pathogenesis, including immunoinflammatory responses, oxidative stress, and energy metabolism. Furthermore, we have identified succinate as a potential biomarker, highlighting its therapeutic feasibility in managing aortic dissection and aneurysm. This review aims to comprehensively outline the characteristics of succinate, including its biosynthetic process, summarize the current evidence linking it to CVDs causation, and emphasize the host-microbial crosstalk involved in modulating CVDs. The insights presented here offer a novel paradigm for future management and control of CVDs.
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Affiliation(s)
- Jing Xu
- Department of Cardiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yicheng Yang
- Respiratory and Pulmonary Vascular Center, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Xin Li
- Respiratory and Pulmonary Vascular Center, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Shusi Ding
- China National Clinical Research Center for Neurological Diseases, Tiantan Hospital, Advanced Innovation Center for Human Brain ProtectionThe Capital Medical UniversityBeijingChina
| | - Lemin Zheng
- China National Clinical Research Center for Neurological Diseases, Tiantan Hospital, Advanced Innovation Center for Human Brain ProtectionThe Capital Medical UniversityBeijingChina
- The Institute of Cardiovascular Sciences and Institute of Systems Biomedicine, School of Basic Medical Sciences, Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, NHC Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Health Science CenterPeking UniversityBeijingChina
| | - Changming Xiong
- Respiratory and Pulmonary Vascular Center, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Yuejin Yang
- Department of Cardiology, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular DiseasesChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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22
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Botin T, Ramirez-Chamorro L, Vidic J, Langella P, Martin-Verstraete I, Chatel JM, Auger S. The Tolerance of Gut Commensal Faecalibacterium to Oxidative Stress Is Strain Dependent and Relies on Detoxifying Enzymes. Appl Environ Microbiol 2023; 89:e0060623. [PMID: 37382539 PMCID: PMC10370306 DOI: 10.1128/aem.00606-23] [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] [Received: 04/12/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
Obligate anaerobic bacteria in genus Faecalibacterium are among the most dominant taxa in the colon of healthy individuals and contribute to intestinal homeostasis. A decline in the abundance of this genus is associated with the occurrence of various gastrointestinal disorders, including inflammatory bowel diseases. In the colon, these diseases are accompanied by an imbalance between the generation and elimination of reactive oxygen species (ROS), and oxidative stress is closely linked to disruptions in anaerobiosis. In this work, we explored the impact of oxidative stress on several strains of faecalibacteria. An in silico analysis of complete genomes of faecalibacteria revealed the presence of genes encoding O2- and/or ROS-detoxifying enzymes, including flavodiiron proteins, rubrerythrins, reverse rubrerythrins, superoxide reductases, and alkyl peroxidase. However, the presence and the number of these detoxification systems varied greatly among faecalibacteria. These results were confirmed by O2 stress survival tests, in which we found that strains differed widely in their sensitivity. We showed the protective role of cysteine, which limited the production of extracellular O2•- and improved the survival of Faecalibacterium longum L2-6 under high O2 tension. In the strain F. longum L2-6, we observed that the expression of genes encoding detoxifying enzymes was upregulated in the response to O2 or H2O2 stress but with different patterns of regulation. Based on these results, we propose a first model of the gene regulatory network involved in the response to oxidative stress in F. longum L2-6. IMPORTANCE Commensal bacteria in the genus Faecalibacterium have been proposed for use as next-generation probiotics, but efforts to cultivate and exploit the potential of these strains have been limited by their sensitivity to O2. More broadly, little is known about how commensal and health-associated bacterial species in the human microbiome respond to the oxidative stress that occurs as a result of inflammation in the colon. In this work, we provide insights regarding the genes that encode potential mechanisms of protection against O2 or ROS stress in faecalibacteria, which may facilitate future advances in work with these important bacteria.
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Affiliation(s)
- Tatiana Botin
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Luis Ramirez-Chamorro
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Jasmina Vidic
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Philippe Langella
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Laboratoire Pathogénèse des Bactéries Anaérobies, Paris, France
- Institut Universitaire de France, Paris, France
| | - Jean-Marc Chatel
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
| | - Sandrine Auger
- Université Paris Saclay, INRAE, AgroParisTech, UMR1319, MICALIS, Jouy-en-Josas, France
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23
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Yang S, Liu G, Savelkoul HFJ, Jansen CA, Li B. Mini-review: microbiota have potential to prevent PEDV infection by improved intestinal barrier. Front Immunol 2023; 14:1230937. [PMID: 37503350 PMCID: PMC10369048 DOI: 10.3389/fimmu.2023.1230937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) infection poses a significant threat to the global pig industry. Current prevention and control strategies are inadequate in protecting pigs from new PEDV variants. This review aims to examine the relationship between PEDV and intestinal microbes, and investigate whether modulating intestinal microbes could affect PEDV infection. The mechanisms by which various intestinal microbes affect viral infection were initially introduced. Intestinal microbes can influence enteric viral infection through direct contact, such as binding, or by affecting interferons (IFNs) production and the intestinal barrier. Influencing the intestinal barrier by microbes can impact PEDV infection in young piglets. To narrow down the range of microbes that may influence PEDV infection, this review summarized microbes that change after infection. Short chain fatty acids (SCFAs), bacterial cell components, and toxins from microbes were identified as important mediators affecting PEDV infection. SCFAs primarily strengthen the intestinal barrier and inhibit intestinal inflammation, while bacterial cell components and toxins are more likely to damage the intestinal barrier. Therefore, this review hypothesizes that fecal transplantation, which allows the host to colonize more SCFAs-producing microbes, may prevent PEDV infection. However, these hypotheses require further proof, and the transplantation of intestinal microbes in pigs requires more exploration.
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Affiliation(s)
- Shanshan Yang
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture, Nanjing, China
- Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture, Nanjing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Guangliang Liu
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Huub F. J. Savelkoul
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Christine A. Jansen
- Cell Biology and Immunology Group, Wageningen University and Research, Wageningen, Netherlands
| | - Bin Li
- Key Laboratory of Veterinary Biological Engineering and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture, Nanjing, China
- Jiangsu Key Laboratory for Food Quality and Safety-State, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture, Nanjing, China
- Key Laboratory Cultivation Base of Ministry of Science and Technology, Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Ministry of Agriculture, Nanjing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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24
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Martín R, Rios-Covian D, Huillet E, Auger S, Khazaal S, Bermúdez-Humarán LG, Sokol H, Chatel JM, Langella P. Faecalibacterium: a bacterial genus with promising human health applications. FEMS Microbiol Rev 2023; 47:fuad039. [PMID: 37451743 PMCID: PMC10410495 DOI: 10.1093/femsre/fuad039] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 06/08/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023] Open
Abstract
In humans, many diseases are associated with alterations in gut microbiota, namely increases or decreases in the abundance of specific bacterial groups. One example is the genus Faecalibacterium. Numerous studies have underscored that low levels of Faecalibacterium are correlated with inflammatory conditions, with inflammatory bowel disease (IBD) in the forefront. Its representation is also diminished in the case of several diseases, including colorectal cancer (CRC), dermatitis, and depression. Additionally, the relative presence of this genus is considered to reflect, at least in part, intestinal health status because Faecalibacterium is frequently present at reduced levels in individuals with gastrointestinal diseases or disorders. In this review, we first thoroughly describe updates to the taxonomy of Faecalibacterium, which has transformed a single-species taxon to a multispecies taxon over the last decade. We then explore the links discovered between Faecalibacterium abundance and various diseases since the first IBD-focused studies were published. Next, we examine current available strategies for modulating Faecalibacterium levels in the gut. Finally, we summarize the mechanisms underlying the beneficial effects that have been attributed to this genus. Together, epidemiological and experimental data strongly support the use of Faecalibacterium as a next-generation probiotic (NGP) or live biotherapeutic product (LBP).
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Affiliation(s)
- Rebeca Martín
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - David Rios-Covian
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Eugénie Huillet
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sandrine Auger
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Sarah Khazaal
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Luis G Bermúdez-Humarán
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Harry Sokol
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
- Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology Department, F-75012 Paris, France
- Paris Centre for Microbiome Medicine (PaCeMM) FHU, F-75012, Paris, France
| | - Jean-Marc Chatel
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Philippe Langella
- Paris-Saclay University, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
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25
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Pang J, Looft T, Zhang Q, Sahin O. Deciphering the Association between Campylobacter Colonization and Microbiota Composition in the Intestine of Commercial Broilers. Microorganisms 2023; 11:1724. [PMID: 37512896 PMCID: PMC10386351 DOI: 10.3390/microorganisms11071724] [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: 05/31/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Campylobacter is a major food safety concern and is transmitted mainly via poultry meat. We previously found that some commercial broiler farms consistently produced Campylobacter-negative flocks while others were consistently Campylobacter-positive for consecutive production cycles although the farms operated under similar management practices. We hypothesized that this difference in Campylobacter colonization might be associated with the gut microbiota composition. To address this, six commercial broiler farms were selected based on their Campylobacter status (three negative and three positive) to evaluate the microbiota differences between each farm category. For each farm on each production cycle (2-3 cycles), 40 ceca collected from five-week-old broilers were processed for microbiota analysis via 16S rRNA gene sequencing. Cecal microbiota species richness, phylogenetic diversity, community structure, and composition of Campylobacter-positive farms were noticeably different from those of Campylobacter-negative farms. Rikenella, Methanocorpusculum, Barnesiella, Parasutterella, and Helicobacter were significantly more abundant among Campylobacter-positive farms. In contrast, Ruminococcaceae, Streptococcus, Escherichia, Eggerthellaceae, Lactobacillus, Monoglobus, and Blausia were more abundant in Campylobacter-negative farms. Eggerthellaceae, Clostridia, Lachnospiraceae, Lactobacillus, Monoglobus, and Parabacteroides were significantly negatively correlated with Campylobacter abundance. These findings suggest that specific members of cecal microbiota may influence Campylobacter colonization in commercial broilers and may be further explored to control Campylobacter in poultry.
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Affiliation(s)
- Jinji Pang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Torey Looft
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
- National Animal Disease Center, United States Department of Agriculture, Ames, IA 50010, USA
| | - Qijing Zhang
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Orhan Sahin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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26
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Nuzum ND, Szymlek-Gay EA, Loke S, Dawson SL, Teo WP, Hendy AM, Loughman A, Macpherson H. Differences in the gut microbiome across typical ageing and in Parkinson's disease. Neuropharmacology 2023; 235:109566. [PMID: 37150399 DOI: 10.1016/j.neuropharm.2023.109566] [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: 12/22/2022] [Revised: 04/21/2023] [Accepted: 04/30/2023] [Indexed: 05/09/2023]
Abstract
The microbiota-gut-brain axis' role in Parkinson's disease (PD) pathophysiology, and how this differs from typical ageing, is poorly understood. Presently, gut-bacterial diversity, taxonomic abundance and metabolic bacterial pathways were compared across healthy young (n = 22, 18-35 years), healthy older (n = 33, 50-80 years), and PD groups (n = 18, 50-80 years) using shotgun sequencing and compositional data analysis. Associations between the gut-microbiome and PD symptoms, and between lifestyle factors (fibre intake, physical activity, and sleep) and the gut-microbiome were conducted. Alpha-diversity did not differ between PD participants and older adults, whilst beta-diversity differed between these groups. Lower abundance of Butyricimonas synergistica, a butyrate-producer, was associated with worse PD non-motor symptoms in the PD group. Regarding typical ageing, Bifidobacterium bifidum, was greater in the younger compared to older group, with no difference between the older and PD group. Abundance of metabolic pathways related to butyrate production did not differ among the groups, while 100 other metabolic pathways differed among the three groups. Sleep efficiency was positively associated with Roseburia inulinivorans in the older group. These results highlight the relevance of gut-microbiota to PD and that reduced butyrate-production may be involved with PD pathophysiology. Future studies should account for lifestyle factors when investigating gut-microbiomes across ageing and in PD.
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Affiliation(s)
- Nathan D Nuzum
- Deakin University, Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Geelong, Australia.
| | - Ewa A Szymlek-Gay
- Deakin University, Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Geelong, Australia
| | - Stella Loke
- Deakin University, School of Life and Environmental Sciences, Australia
| | - Samantha L Dawson
- Deakin University, Food & Mood Centre, IMPACT Strategic Research Centre, School of Medicine, Geelong, Australia
| | - Wei-Peng Teo
- Physical Education and Sports Science Academic Group, National Institute of Education, Nanyang Technological University, Singapore
| | - Ashlee M Hendy
- Deakin University, Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Geelong, Australia
| | - Amy Loughman
- Deakin University, Food & Mood Centre, IMPACT Strategic Research Centre, School of Medicine, Geelong, Australia
| | - Helen Macpherson
- Deakin University, Institute for Physical Activity and Nutrition (IPAN), School of Exercise and Nutrition Sciences, Geelong, Australia
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27
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You Z, Li J, Wang Y, Wu D, Li F, Song H. Advances in mechanisms and engineering of electroactive biofilms. Biotechnol Adv 2023; 66:108170. [PMID: 37148984 DOI: 10.1016/j.biotechadv.2023.108170] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/22/2023] [Accepted: 05/02/2023] [Indexed: 05/08/2023]
Abstract
Electroactive biofilms (EABs) are electroactive microorganisms (EAMs) encased in conductive polymers that are secreted by EAMs and formed by the accumulation and cross-linking of extracellular polysaccharides, proteins, nucleic acids, lipids, and other components. EABs are present in the form of multicellular aggregates and play a crucial role in bioelectrochemical systems (BESs) for diverse applications, including biosensors, microbial fuel cells for renewable bioelectricity production and remediation of wastewaters, and microbial electrosynthesis of valuable chemicals. However, naturally occurred EABs are severely limited owing to their low electrical conductivity that seriously restrict the electron transfer efficiency and practical applications. In the recent decade, synthetic biology strategies have been adopted to elucidate the regulatory mechanisms of EABs, and to enhance the formation and electrical conductivity of EABs. Based on the formation of EABs and extracellular electron transfer (EET) mechanisms, the synthetic biology-based engineering strategies of EABs are summarized and reviewed as follows: (i) Engineering the structural components of EABs, including strengthening the synthesis and secretion of structural elements such as polysaccharides, eDNA, and structural proteins, to improve the formation of biofilms; (ii) Enhancing the electron transfer efficiency of EAMs, including optimizing the distribution of c-type cytochromes and conducting nanowire assembly to promote contact-based EET, and enhancing electron shuttles' biosynthesis and secretion to promote shuttle-mediated EET; (iii) Incorporating intracellular signaling molecules in EAMs, including quorum sensing systems, secondary messenger systems, and global regulatory systems, to increase the electron transfer flux in EABs. This review lays a foundation for the design and construction of EABs for diverse BES applications.
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Affiliation(s)
- Zixuan You
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jianxun Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Yuxuan Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Deguang Wu
- Department of Brewing Engineering, Moutai Institute, Luban Ave, Renhuai 564507, Guizhou, PR China
| | - Feng Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
| | - Hao Song
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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28
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Duncan SH, Conti E, Ricci L, Walker AW. Links between Diet, Intestinal Anaerobes, Microbial Metabolites and Health. Biomedicines 2023; 11:biomedicines11051338. [PMID: 37239009 DOI: 10.3390/biomedicines11051338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/23/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
A dense microbial community resides in the human colon, with considerable inter-individual variability in composition, although some species are relatively dominant and widespread in healthy individuals. In disease conditions, there is often a reduction in microbial diversity and perturbations in the composition of the microbiota. Dietary complex carbohydrates that reach the large intestine are important modulators of the composition of the microbiota and their primary metabolic outputs. Specialist gut bacteria may also transform plant phenolics to form a spectrum of products possessing antioxidant and anti-inflammatory activities. Consumption of diets high in animal protein and fat may lead to the formation of potentially deleterious microbial products, including nitroso compounds, hydrogen sulphide, and trimethylamine. Gut anaerobes also form a range of secondary metabolites, including polyketides that may possess antimicrobial activity and thus contribute to microbe-microbe interactions within the colon. The overall metabolic outputs of colonic microbes are derived from an intricate network of microbial metabolic pathways and interactions; however, much still needs to be learnt about the subtleties of these complex networks. In this review we consider the multi-faceted relationships between inter-individual microbiota variation, diet, and health.
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Affiliation(s)
- Sylvia H Duncan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Elena Conti
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Liviana Ricci
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, UK
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Szabó C, Kachungwa Lugata J, Ortega ADSV. Gut Health and Influencing Factors in Pigs. Animals (Basel) 2023; 13:ani13081350. [PMID: 37106913 PMCID: PMC10135089 DOI: 10.3390/ani13081350] [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: 03/03/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The gastrointestinal tract (GIT) is a complex, dynamic, and critical part of the body, which plays an important role in the digestion and absorption of ingested nutrients and excreting waste products of digestion. In addition, GIT also plays a vital role in preventing the entry of harmful substances and potential pathogens into the bloodstream. The gastrointestinal tract hosts a significant number of microbes, which throughout their metabolites, directly interact with the hosts. In modern intensive animal farming, many factors can disrupt GIT functions. As dietary nutrients and biologically active substances play important roles in maintaining homeostasis and eubiosis in the GIT, this review aims to summarize the current status of our knowledge on the most important areas.
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Affiliation(s)
- Csaba Szabó
- Department of Animal Nutrition and Physiology, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, Böszörményi Street 138, 4032 Debrecen, Hungary
| | - James Kachungwa Lugata
- Department of Animal Nutrition and Physiology, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, Böszörményi Street 138, 4032 Debrecen, Hungary
- Doctoral School of Animal Science, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, Böszörményi Street 138, 4032 Debrecen, Hungary
| | - Arth David Sol Valmoria Ortega
- Department of Animal Nutrition and Physiology, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, Böszörményi Street 138, 4032 Debrecen, Hungary
- Doctoral School of Animal Science, Faculty of Agriculture and Food Sciences and Environmental Management, University of Debrecen, Böszörményi Street 138, 4032 Debrecen, Hungary
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30
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Abstract
Microbial communities are shaped by positive and negative interactions ranging from competition to mutualism. In the context of the mammalian gut and its microbial inhabitants, the integrated output of the community has important impacts on host health. Cross-feeding, the sharing of metabolites between different microbes, has emergent roles in establishing communities of gut commensals that are stable, resistant to invasion, and resilient to external perturbation. In this review, we first explore the ecological and evolutionary implications of cross-feeding as a cooperative interaction. We then survey mechanisms of cross-feeding across trophic levels, from primary fermenters to H2 consumers that scavenge the final metabolic outputs of the trophic network. We extend this analysis to also include amino acid, vitamin, and cofactor cross-feeding. Throughout, we highlight evidence for the impact of these interactions on each species' fitness as well as host health. Understanding cross-feeding illuminates an important aspect of microbe-microbe and host-microbe interactions that establishes and shapes our gut communities.
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Affiliation(s)
- Elizabeth J Culp
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University School of Medicine, New Haven, CT, USA.
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31
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Firkins JL, Mitchell KE. Invited review: Rumen modifiers in today's dairy rations. J Dairy Sci 2023; 106:3053-3071. [PMID: 36935236 DOI: 10.3168/jds.2022-22644] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/23/2022] [Indexed: 03/19/2023]
Abstract
Our aim was to review feed additives that have a potential ruminal mechanism of action when fed to dairy cattle. We discuss how additives can influence ruminal fermentation stoichiometry through electron transfer mechanisms, particularly the production and usage of dihydrogen. Lactate accumulation should be avoided, especially when acidogenic conditions suppress ruminal neutral detergent fiber digestibility or lead to subclinical acidosis. Yeast products and other probiotics are purported to influence lactate uptake, but growing evidence also supports that yeast products influence expression of gut epithelial genes promoting barrier function and resulting inflammatory responses by the host to various stresses. We also have summarized methane-suppressing additives for potential usage in dairy rations. We focused on those with potential to decrease methane production without decreasing fiber digestibility or milk production. We identified some mitigating factors that need to be addressed more fully in future research. Growth factors such as branched-chain volatile fatty acids also are part of crucial cross-feeding among groups of microbes, particularly to optimize fiber digestibility in the rumen. Our developments of mechanisms of action for various rumen-active modifiers should help nutrition advisors anticipate when a benefit in field conditions is more likely.
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Affiliation(s)
- J L Firkins
- Department of Animal Sciences, The Ohio State University, Columbus 43210.
| | - K E Mitchell
- Department of Animal Sciences, The Ohio State University, Columbus 43210
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32
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Kahraman-Ilıkkan Ö. Bacterial Profile and Fatty Acid Composition of Anatolian Bee Bread Samples by Metataxonomic and Metabolomic Approach. Curr Microbiol 2023; 80:90. [PMID: 36723722 DOI: 10.1007/s00284-023-03195-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/14/2023] [Indexed: 02/02/2023]
Abstract
This study investigated the bacterial and postbiotic potential of three Anatolian bee bread samples obtained from different regions of Turkey (Marmara, Aegean, and Mediterranean) and offered for human consumption. The families most commonly found in Anatolian bee bread were Lactobacillaceae, Oscillospiraceae, Bacteroidaceae, Prevotellaceae, and Lachnospiraceae. Lactobacillus delbruckeii was highly abundant, but also other beneficial bacteria, known to be next-generation probiotics, were revealed in bee bread, such as Prevotalla copri, Faecalibacterium prausnitzii, and Akkermansia muciniphila. Apart from these beneficial bacteria, bee bread samples also harbored undesired bacteria such as Phocaeicola vulgatus, Phocaeicola dorei, and Clostridium perfringens. Fatty acid composition showed that bee bread samples had butyric acid, a short-chain fatty acid, as a postbiotic. Additionally, polyunsaturated fatty acids were also found such as alfa-linolenic acid and eicosadienoic acid. The fatty acids with the highest amounts were palmitic acid (~ 30%), stearic acid (~ 17%), and alpha-linolenic acid (~ 12%). One of the samples exhibited antimicrobial activity against Staphylococcus aureus.
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The Differing Roles of Flavins and Quinones in Extracellular Electron Transfer in Lactiplantibacillus plantarum. Appl Environ Microbiol 2023; 89:e0131322. [PMID: 36533923 PMCID: PMC9888254 DOI: 10.1128/aem.01313-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lactiplantibacillus plantarum is a lactic acid bacterium that is commonly found in the human gut and fermented food products. Despite its overwhelmingly fermentative metabolism, this microbe can perform extracellular electron transfer (EET) when provided with an exogenous quinone, 1,4-dihydroxy-2-naphthoic acid (DHNA), and riboflavin. However, the separate roles of DHNA and riboflavin in EET in L. plantarum have remained unclear. Here, we seek to understand the role of quinones and flavins in EET by monitoring iron and anode reduction in the presence and absence of these small molecules. We found that addition of either DHNA or riboflavin can support robust iron reduction, indicating electron transfer to extracellular iron occurs through both flavin-dependent and DHNA-dependent routes. Using genetic mutants of L. plantarum, we found that flavin-dependent iron reduction requires Ndh2 and EetA, while DHNA-dependent iron reduction largely relies on Ndh2 and PplA. In contrast to iron reduction, DHNA-containing medium supported more robust anode reduction than riboflavin-containing medium, suggesting electron transfer to an anode proceeds most efficiently through the DHNA-dependent pathway. Furthermore, we found that flavin-dependent anode reduction requires EetA, Ndh2, and PplA, while DHNA-dependent anode reduction requires Ndh2 and PplA. Taken together, we identify multiple EET routes utilized by L. plantarum and show that the EET route depends on access to environmental biomolecules and on the electron acceptor. This work expands our molecular-level understanding of EET in Gram-positive microbes and provides additional opportunities to manipulate EET for biotechnology. IMPORTANCE Lactic acid bacteria are named because of their nearly exclusive fermentative metabolism. Thus, the recent observation of EET activity-typically associated with anaerobic respiration-in this class of organisms has forced researchers to rethink the rules governing microbial metabolic strategies. Our identification of multiple routes for EET in L. plantarum that depend on two different redox active small molecules expands our understanding of how microbes metabolically adapt to different environments to gain an energetic edge and how these processes can be manipulated for biotechnological uses. Understanding the role of EET in lactic acid bacteria is of great importance due to the significance of lactic acid bacteria in agriculture, bioremediation, food production, and gut health. Furthermore, the maintenance of multiple EET routes speaks to the importance of this process to function under a variety of environmental conditions.
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Yu Z, Henderson IR, Guo J. Non-caloric artificial sweeteners modulate conjugative transfer of multi-drug resistance plasmid in the gut microbiota. Gut Microbes 2023; 15:2157698. [PMID: 36524841 PMCID: PMC9762752 DOI: 10.1080/19490976.2022.2157698] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Non-caloric artificial sweeteners have been widely permitted as table sugar substitutes with high intensities of sweetness. They can pass through the intestinal tract without significant metabolization and frequently encounter the gut microbiome, which is composed of diverse bacterial species and is a pool of antibiotic resistance genes (ARGs). However, little is known about whether these sweeteners could accelerate the spread of ARGs in the gut microbiome. Here, we established an in vitro conjugation model by using Escherichia coli that carries chromosome-inserted Tn7 lacIq-pLpp-mCherry and plasmid-encoded gfpmut3b gene as the donor and murine fecal bacteria as the recipient. We found that four commonly used artificial sweeteners (saccharin, sucralose, aspartame, and acesulfame potassium) can increase reactive oxygen species (ROS) production and promote plasmid-mediated conjugative transfer to the gut microbiome. Cell sorting and 16S rRNA gene amplicon sequencing analysis of fecal samples reveal that the tested sweeteners can promote the broad-host-range plasmid permissiveness to both Gram-negative and Gram-positive gut bacteria. The increased plasmid permissiveness was also validated with a human pathogen Klebsiella pneumoniae. Collectively, our study demonstrates that non-caloric artificial sweeteners can induce oxidative stress and boost the plasmid-mediated conjugative transfer of ARGs among the gut microbiota and a human pathogen. Considering the soaring consumption of these sweeteners and the abundance of mobile ARGs in the human gut, our results highlight the necessity of performing a thorough risk assessment of antibiotic resistance associated with the usage of artificial sweeteners as food additives.
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Affiliation(s)
- Zhigang Yu
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Australia
| | - Ian R Henderson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (Formerly AWMC), The University of Queensland, Brisbane, Australia
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35
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Peng K, Dong W, Luo T, Tang H, Zhu W, Huang Y, Yang X. Butyrate and obesity: Current research status and future prospect. Front Endocrinol (Lausanne) 2023; 14:1098881. [PMID: 36909336 PMCID: PMC9999029 DOI: 10.3389/fendo.2023.1098881] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 02/07/2023] [Indexed: 03/14/2023] Open
Abstract
Over the past few decades, increasing prevalence of obesity caused an enormous medical, social, and economic burden. As the sixth most important risk factor contributing to the overall burden of disease worldwide, obesity not only directly harms the human body, but also leads to many chronic diseases such as diabetes, cardiovascular diseases (CVD), nonalcoholic fatty liver disease (NAFLD), and mental illness. Weight loss is still one of the most effective strategies against obesity and related disorders. Recently, the link between intestinal microflora and metabolic health has been constantly established. Butyrate, a four-carbon short-chain fatty acid, is a major metabolite of the gut microbiota that has many beneficial effects on metabolic health. The anti-obesity activity of butyrate has been demonstrated, but its mechanisms of action have not been fully described. This review summarizes current knowledge of butyrate, including its production, absorption, distribution, metabolism, and the effect and mechanisms involved in weight loss and obesity-related diseases. The aim was to contribute to and advance our understanding of butyrate and its role in obesity. Further exploration of butyrate and its pathway may help to identify new anti-obesity.
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Affiliation(s)
- Ke Peng
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Wenjie Dong
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Taimin Luo
- Department of Pharmacy, Chengdu Seventh People’s Hospital, Chengdu, Sichuan, China
| | - Hui Tang
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Wanlong Zhu
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Yilan Huang
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
- *Correspondence: Yilan Huang, ; Xuping Yang,
| | - Xuping Yang
- Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- School of Pharmacy, Southwest Medical University, Luzhou, China
- *Correspondence: Yilan Huang, ; Xuping Yang,
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36
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Wang S, Liu B, Huang J, He H, Zhou L, He Y, Yan J, Tao A. Succinate and mitochondrial DNA trigger atopic march from atopic dermatitis to intestinal inflammation. J Allergy Clin Immunol 2022; 151:1050-1066.e7. [PMID: 36587852 DOI: 10.1016/j.jaci.2022.11.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Atopic march has long been recognized as the progression from atopic dermatitis (AD) to food allergy and asthma during infancy and childhood. However, effective blocking is hampered by the lack of specific biomarkers. OBJECTIVES We aimed to investigate the pathologic progression of atopic march trajectories from skin to gut. METHODS We built an atopic march mouse model by mechanical skin injury and percutaneous sensitization to peanut allergen. Anaphylaxis from the skin to the small intestine was then investigated by ELISA, RNA sequencing, quantitative real-time PCR, histopathologic analysis, and flow cytometry. The findings from the mice results were also verified by the serum samples of allergic pediatric patients. RESULTS After modeling, inflammation in the skin and small intestine manifested as a mixed type of TH2 and TH17. Further analysis identified elevated succinate in the circulation and expanded tuft cells with upregulated IL-25 in the small intestine, resulting in increased intestinal type 2 innate lymphoid cells and an enhanced type 2 inflammatory response. In addition, free mitochondrial DNA (mtDNA) released after tissue damage was also involved in inflammation march from injured skin to small intestine through the STING pathway. Analysis of clinical samples verified that serum concentrations of succinate and mtDNA were higher in AD allergic children than non-AD allergic children. CONCLUSIONS Succinate and mtDNA play key roles in skin-to-gut cross talk during the atopic march from AD to food allergy, and can be considered as biomarkers for risk assessment or targets for atopic march prevention strategies.
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Affiliation(s)
- Shan Wang
- Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China
| | - Bowen Liu
- Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China
| | - Jiahao Huang
- Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China
| | - Huiru He
- Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China
| | - Linghui Zhou
- Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China
| | - Ying He
- Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China
| | - Jie Yan
- Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China
| | - Ailin Tao
- Second Affiliated Hospital, State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy and Clinical Immunology, Guangzhou Medical University, Guangzhou, China.
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Abstract
Extracellular electron transfer (EET) is a process via which certain microorganisms, such as bacteria, exchange electrons with extracellular materials by creating an electrical link across their membranes. EET has been studied for the reactions on solid materials such as minerals and electrodes with implication in geobiology and biotechnology. EET-capable bacteria exhibit broad phylogenetic diversity, and some are found in environments with various types of electron acceptors/donors not limited to electrodes or minerals. Oxygen has also been shown to serve as the terminal electron acceptor for EET of Pseudomonas aeruginosa and Faecalibacterium prausnitzii. However, the physiological significance of such oxygen-terminating EETs, as well as the mechanisms underlying them, remain unclear. In order to understand the physiological advantage of oxygen-terminating EET and its link with energy metabolism, in this review, we compared oxygen-terminating EET with aerobic respiration, fermentation, and electrode-terminating EET. We also summarized benefits and limitations of oxygen-terminating EET in a biofilm setting, which indicate that EET capability enables bacteria to create a niche in the anoxic zone of aerobic biofilms, thereby remodeling bacterial metabolic activities in biofilms.
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38
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Abstract
Chickens are in constant interaction with their environment, e.g., bedding and litter, and their microbiota. However, how litter microbiota develops over time and whether bedding and litter microbiota may affect the cecal microbiota is not clear. We addressed these questions using sequencing of V3/V4 variable region of 16S rRNA genes of cecal, bedding, and litter samples from broiler breeder chicken flocks for 4 months of production. Cecal, bedding, and litter samples were populated by microbiota of distinct composition. The microbiota in the bedding material did not expand in the litter. Similarly, major species from litter microbiota did not expand in the cecum. Only cecal microbiota was found in the litter forming approximately 20% of total litter microbiota. A time-dependent development of litter microbiota was observed. Escherichia coli, Staphylococcus saprophyticus, and Weissella jogaejeotgali were characteristic of fresh litter during the first month of production. Corynebacterium casei, Lactobacillus gasseri, and Lactobacillus salivarius dominated in a 2-month-old litter, Brevibacterium, Brachybacterium, and Sphingobacterium were characteristic for 3-month-old litter, and Salinococcus, Dietzia, Yaniella, and Staphylococcus lentus were common in a 4-month-old litter. Although the development was likely determined by physicochemical conditions in the litter, it might be interesting to test some of these species for active modification of litter to improve the chicken environment and welfare. IMPORTANCE Despite intimate contact, the composition of bedding, litter, and cecal microbiota differs considerably. Species characteristic for litter microbiota at different time points of chicken production were identified thus opening the possibility for active manipulation of litter microbiota.
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Liu S, Li Y, Song Y, Wu X, Baloch Z, Xia X. The diversity of vaginal microbiome in women infected with single HPV and multiple genotype HPV infections in China. Front Cell Infect Microbiol 2022; 12:642074. [PMID: 36601309 PMCID: PMC9806233 DOI: 10.3389/fcimb.2022.642074] [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: 12/15/2020] [Accepted: 11/07/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction The human papillomavirus (HPV) is the leading cause of cervical cancer globally. However, its microbial composition and association with the types of HPV infection remain elusive. Methods This study was designed to characterize the vaginal microbiota of 53 HPV-infected and 16 normal women (control group) by using high-throughput sequencing with the Illumina platform. Results In this study, the five leading phyla were Firmicutes (73.9%), Actinobacteriota (12.8%), Proteobacteria (6.2%), Fusobacteria (3.5%), and Bacteroidota (3.1%). We found that single HPV genotype-positive women had higher α-microbial diversity compared with HPV-negative and multiple HPV-positive women. In women with a single HPV genotype infection, the HPV-16 infection had significantly higher α-diversity than other genotype infections. In multiple HPV genotype-positive women, the highest α-diversity was found in women positive for HR-HR HPV genotype infection, compared with other infections. Furthermore, in single- and multiple-genotype infections, the abundance of s_unclassified_g_Lactobacillus decreased whereas the abundance of s_Gardnerella_vaginalis increased compared with control. Additionally, s_unclassified_f_Rhizobiaceae and s_sneathia_sanguinegens were only found in HPV-infected women. Conclusion This study showed that the type of HPV infection was associated with the composition of the vaginal microbiota. Further studies on HPV genotypes and vaginal microbiota are necessary to uncover more mysteries of their association and provide a promising therapeutic target as well as low-cost future therapeutic strategies.
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Affiliation(s)
- Shufa Liu
- Faculty of Life Science and Technology and Yunnan Provincial Center for Molecular Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yuanyue Li
- Department of Gynecology, The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China,Yunnan Provincial Key Laboratory of Clinical Virology, Kunming, Yunnan, China
| | - Yuzhu Song
- Faculty of Life Science and Technology and Yunnan Provincial Center for Molecular Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Xiaomei Wu
- Department of Gynecology, The First People’s Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology and Yunnan Provincial Center for Molecular Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China,*Correspondence: Zulqarnain Baloch, ; Xueshan Xia,
| | - Xueshan Xia
- Faculty of Life Science and Technology and Yunnan Provincial Center for Molecular Medicine, Kunming University of Science and Technology, Kunming, Yunnan, China,*Correspondence: Zulqarnain Baloch, ; Xueshan Xia,
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Hazan S, Dave S, Papoutsis AJ, Deshpande N, Howell MC, Martin LM. Vitamin C improves gut Bifidobacteria in humans. Future Microbiol 2022. [PMID: 36475828 DOI: 10.2217/fmb-2022-0209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aims: Numerous beneficial effects of vitamin C (ascorbic acid) supplementation have been reported in the literature. However, data on its effects toward the gut microbiome are limited. We assessed the effect of vitamin C supplementation on the abundance of beneficial bacterial species in the gut microbiome. Materials and methods: Stool samples were analyzed for relative abundance of gut microbiome bacteria using next-generation sequencing-based profiling and metagenomic shotgun analysis. Results: Supplementation with vitamin C increased the abundance of bacteria of the genus Bifidobacterium (p = 0.0001) and affected various species. Conclusion: The beneficial effects of vitamin C supplementation may be attributed to modulation of the gut microbiome and the consequent health benefits thereof.
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Affiliation(s)
- Sabine Hazan
- ProgenaBIome, LLC, Ventura, CA 93003, USA
- Mcrobiome Research Foundation, Ventura, CA 93003, USA
| | - Sonya Dave
- Mcrobiome Research Foundation, Ventura, CA 93003, USA
| | | | | | | | - Leisha Ma Martin
- Texas A&M University - Corpus Christi, Department of Life Sciences, Corpus Christi, TX 78412, USA
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Guberman-Pfeffer MJ. Assessing Thermal Response of Redox Conduction for Anti-Arrhenius Kinetics in a Microbial Cytochrome Nanowire. J Phys Chem B 2022; 126:10083-10097. [PMID: 36417757 PMCID: PMC9743091 DOI: 10.1021/acs.jpcb.2c06822] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A micrometers-long helical homopolymer of the outer-membrane cytochrome type S (OmcS) from Geobacter sulfurreducens is proposed to transport electrons to extracellular acceptors in an ancient respiratory strategy of biogeochemical and technological significance. OmcS surprisingly exhibits higher conductivity upon cooling (anti-Arrhenius kinetics), an effect previously attributed to H-bond restructuring and heme redox potential shifts. Herein, the temperature sensitivity of redox conductivity is more thoroughly examined with conventional and constant-redox and -pH molecular dynamics and quantum mechanics/molecular mechanics. A 30 K drop in temperature constituted a weak perturbation to electron transfer energetics, changing electronic couplings (⟨Hmn⟩), reaction free energies (ΔGmn), reorganization energies (λmn), and activation energies (Ea) by at most |0.002|, |0.050|, |0.120|, and |0.045| eV, respectively. Changes in ΔGmn reflected -0.07 ± 0.03 V shifts in redox potentials that were caused in roughly equal measure by altered electrostatic interactions with the solvent and protein. Changes in intraprotein H-bonding reproduced the earlier observations. Single-particle diffusion and multiparticle steady-state flux models, parametrized with Marcus theory rates, showed that biologically relevant incoherent hopping cannot qualitatively or quantitatively describe electrical conductivity measured by atomic force microscopy in filamentous OmcS. The discrepancy is attributed to differences between solution-phase simulations and solid-state measurements and the need to model intra- and intermolecular vibrations explicitly.
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Affiliation(s)
- Matthew J. Guberman-Pfeffer
- Department
of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, Connecticut06510, United States,Microbial
Sciences Institute, Yale University, 840 West Campus Drive, West Haven, Connecticut06516, United States,
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Exploring Freeze-Drying as Strategy to Enhance Viability of Faecalibacterium duncaniae DSM 17677 upon Aerobic Storage and Gastrointestinal Conditions. Pharmaceutics 2022; 14:pharmaceutics14122735. [PMID: 36559229 PMCID: PMC9785611 DOI: 10.3390/pharmaceutics14122735] [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: 10/27/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 12/12/2022] Open
Abstract
Faecalibacterium duncaniae is an intestinal commensal bacterium proposed as a next-generation probiotic due to its promising outcomes in the treatment and prevention of several human diseases, which demonstrate its multiple contributions to the host’s health. However, its strict anaerobic nature has created several hurdles in the development of functional foods, nutraceuticals, and biotherapeutic products. Herein, we explored freeze-dried formulations containing prebiotics, cryoprotectants, and antioxidant agents as a technological strategy to enhance the viability of F. duncaniae DSM 17677 upon aerobic storage and gastrointestinal tract conditions. Our results indicate that freeze-dried F. duncaniae in a matrix containing inulin, sucrose, cysteine, and riboflavin survived at levels higher than 106 CFU/g and around 105 CFU/g after 1 and 4 days of aerobic storage at room temperature, respectively. Thus, the freeze-dried formulation with inulin, sucrose, cysteine, and riboflavin presents as a protective strategy to improve F. duncaniae viability under aerobic environments. Nevertheless, incorporation of a suitable coating aimed at protecting F. duncaniae against the detrimental gastrointestinal passage effects is urgently required, given its high susceptibility to extreme acidic pH values and bile.
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Alpino GDCÁ, Pereira-Sol GA, Dias MDME, Aguiar ASD, Peluzio MDCG. Beneficial effects of butyrate on brain functions: A view of epigenetic. Crit Rev Food Sci Nutr 2022; 64:3961-3970. [PMID: 36287024 DOI: 10.1080/10408398.2022.2137776] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Brain functions are influenced by the presence, activity, and metabolism of the gut microbiota through the gut-microbiota-brain (GMB) axis. The consumption of a fiber-rich diet increases the content of short-chain fatty acids (SCFAs) from bacterial fermentation in the colon. Among SCFAs, butyrate stands out because of its wide array of biological functions, such as ability to influence brain functions. Pharmacologically, sodium butyrate (NaB) regulates gene expression in the brain, where it has several beneficial effects ranging from neurodegenerative diseases to behavioral disorders through inhibitors of histone deacetylases (HDACis). In this context, we review the mechanisms of action of the two types of butyrate on brain functions, with an emphasis on the epigenetic approach. Both types of butyrate are potentially interesting for the prevention and adjuvant therapy of neurological and psychological disorders due to their neuroprotective functions. However, further studies are needed to investigate the possible neuroepigenetic effects of butyrate derived from bacterial fermentation.
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Affiliation(s)
| | | | | | - Aline Silva de Aguiar
- Departamento de Nutrição e Dietética, Faculdade de Nutrição Emília de Jesus Ferreiro, Universidade Federal Fluminense (UFF), Niterói, Brasil
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Zhan Q, Wang R, Thakur K, Feng JY, Zhu YY, Zhang JG, Wei ZJ. Unveiling of dietary and gut-microbiota derived B vitamins: Metabolism patterns and their synergistic functions in gut-brain homeostasis. Crit Rev Food Sci Nutr 2022; 64:4046-4058. [PMID: 36271691 DOI: 10.1080/10408398.2022.2138263] [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: 11/03/2022]
Abstract
Nutrition-gut cross-talk holds a vital position in sustaining intestinal function, and micronutrient metabolism has emerged as the foremost metabolic pathway to preserve gut homeostasis. Among micronutrients, B vitamins have evolved prior to DNA/RNA and are known for their vital roles for major evolutionary transitions in extant organisms. Despite their universal requirement and critical role, not all the three domains of life are endowed with a natural ability for de novo B vitamins synthesis. The human gut microbiome constitutes prototrophs and auxotroph which are entirely dependent on dietary intake and gut microbial production of B vitamins. The syntrophic metabolism involving cross-feeding of B vitamins and community-wide exchange between commensal bacteria elicit important changes in the diversity and composition of the human gut microbiome. Hereto, we discuss the B-vitamins sharing among prototrophic and auxotrophic gut bacteria, their absorption in small intestine and transport in distal gut, functional role in relation to the gut homeostasis and symptoms linked to their deficiency. We also briefly explore their potential involvement as psychobiotics in brain energetic metabolism (kynurenines/tryptophan pathway) for neurological functions and highlight their deficiency related malfunctioning.
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Affiliation(s)
- Qi Zhan
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Rui Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Kiran Thakur
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
- Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China
| | - Jing-Yu Feng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Yun-Yang Zhu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
| | - Jian-Guo Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
- Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China
| | - Zhao-Jun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, People's Republic of China
- Ningxia Key Laboratory for the Development and Application of Microbial Resources in Extreme Environments, School of Biological Science and Engineering, North Minzu University, Yinchuan, People's Republic of China
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Bourgonje AR. Microbial Riboflavin Biosynthesis Associates With Response to Dietary Fiber Consumption: Time to Personalize Adjunct Therapy in Patients With Inflammatory Bowel Disease? Gastroenterology 2022:S0016-5085(22)01194-5. [PMID: 36279921 DOI: 10.1053/j.gastro.2022.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
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Bourgonje AR, Otten AT, Sadaghian Sadabad M, von Martels JZH, Bulthuis MLC, Faber KN, van Goor H, Dijkstra G, Harmsen HJM. The effect of riboflavin supplementation on the systemic redox status in healthy volunteers: A post-hoc analysis of the RIBOGUT trial. Free Radic Biol Med 2022; 190:169-178. [PMID: 35973668 DOI: 10.1016/j.freeradbiomed.2022.08.008] [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: 06/21/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND Riboflavin is a redox-active vitamin that plays a pivotal role in human energy metabolism. Riboflavin may have beneficial health effects by increasing extracellular antioxidant capacity, thereby alleviating oxidative stress. Reduced levels of free thiols in blood reflect systemic oxidative stress, since they are readily oxidized by reactive species. In this study, we aimed to study the potential of riboflavin supplementation to improve the systemic redox status in healthy volunteers. METHODS This study was a post-hoc analysis of the RIBOGUT study, a randomized, double-blind, placebo-controlled human intervention trial that investigated the effect of riboflavin supplements on the gut microbiota composition of healthy individuals. Serum free thiols were quantified before and after intervention and adjusted to serum albumin levels. Changes in albumin-adjusted free thiols were analyzed, as well as potential associations with routine laboratory parameters and faecal bacterial quantification by fluorescence in-situ hybridization (FISH). RESULTS Participants were randomized to either placebo (n = 34), riboflavin 50 mg daily (n = 32), or riboflavin 100 mg daily (n = 33). At baseline, no significant differences in albumin-adjusted serum free thiols were observed. After intervention with either placebo or riboflavin, albumin-adjusted serum free thiols did not significantly change (P > 0.05), however, observed changes were inversely associated with changes in C-reactive protein (CRP) levels (r = -0.22, P < 0.05). At baseline, albumin-adjusted serum free thiols were positively associated with faecal relative abundances of Faecalibacterium prausnitzii (P < 0.01). CONCLUSION Riboflavin did not change the systemic redox status in healthy individuals as reflected by serum free thiols, but observed changes in albumin-adjusted free thiol levels were negatively associated with changes in CRP levels. Strikingly, albumin-adjusted free thiols were independently associated with relative abundances of faecal F. prausnitzii, which may suggest a potential host redox-microbiota interaction.
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Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Antonius T Otten
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Mehdi Sadaghian Sadabad
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Julius Z H von Martels
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marian L C Bulthuis
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Harry van Goor
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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Pinacho-Guendulain B, Montiel-Castro AJ, Ramos-Fernández G, Pacheco-López G. Social complexity as a driving force of gut microbiota exchange among conspecific hosts in non-human primates. Front Integr Neurosci 2022; 16:876849. [PMID: 36110388 PMCID: PMC9468716 DOI: 10.3389/fnint.2022.876849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The emergent concept of the social microbiome implies a view of a highly connected biological world, in which microbial interchange across organisms may be influenced by social and ecological connections occurring at different levels of biological organization. We explore this idea reviewing evidence of whether increasing social complexity in primate societies is associated with both higher diversity and greater similarity in the composition of the gut microbiota. By proposing a series of predictions regarding such relationship, we evaluate the existence of a link between gut microbiota and primate social behavior. Overall, we find that enough empirical evidence already supports these predictions. Nonetheless, we conclude that studies with the necessary, sufficient, explicit, and available evidence are still scarce. Therefore, we reflect on the benefit of founding future analyses on the utility of social complexity as a theoretical framework.
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Affiliation(s)
- Braulio Pinacho-Guendulain
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana (UAM), Ciudad de México, Mexico
| | - Augusto Jacobo Montiel-Castro
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- *Correspondence: Augusto Jacobo Montiel-Castro,
| | - Gabriel Ramos-Fernández
- Institute for Research on Applied Mathematics and Systems (IIMAS), National Autonomous University of Mexico (UNAM), Mexico City, Mexico
- Center for Complexity Sciences, National Autonomous University of Mexico, Mexico City, Mexico
| | - Gustavo Pacheco-López
- Department of Health Sciences, Metropolitan Autonomous University (UAM), Lerma, Mexico
- Gustavo Pacheco-López,
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Huang Z, Zhan M, Cheng G, Lin R, Zhai X, Zheng H, Wang Q, Yu Y, Xu Z. IHNV Infection Induces Strong Mucosal Immunity and Changes of Microbiota in Trout Intestine. Viruses 2022; 14:v14081838. [PMID: 36016461 PMCID: PMC9415333 DOI: 10.3390/v14081838] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
The fish intestinal mucosa is among the main sites through which environmental microorganisms interact with the host. Therefore, this tissue not only constitutes the first line of defense against pathogenic microorganisms but also plays a crucial role in commensal colonization. The interaction between the mucosal immune system, commensal microbiota, and viral pathogens has been extensively described in the mammalian intestine. However, very few studies have characterized these interactions in early vertebrates such as teleosts. In this study, rainbow trout (Oncorhynchus mykiss) was infected with infectious hematopoietic necrosis virus (IHNV) via a recently developed immersion method to explore the effects of viral infection on gut immunity and microbial community structure. IHNV successfully invaded the gut mucosa of trout, resulting in severe tissue damage, inflammation, and an increase in gut mucus. Moreover, viral infection triggered a strong innate and adaptive immune response in the gut, and RNA−seq analysis indicated that both antiviral and antibacterial immune pathways were induced, suggesting that the viral infection was accompanied by secondary bacterial infection. Furthermore, 16S rRNA sequencing also revealed that IHNV infection induced severe dysbiosis, which was characterized by large increases in the abundance of Bacteroidetes and pathobiont proliferation. Moreover, the fish that survived viral infection exhibited a reversal of tissue damage and inflammation, and their microbiome was restored to its pre−infection state. Our findings thus demonstrated that the relationships between the microbiota and gut immune system are highly sensitive to the physiological changes triggered by viral infection. Therefore, opportunistic bacterial infection must also be considered when developing strategies to control viral infection.
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Affiliation(s)
- Zhenyu Huang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengting Zhan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Gaofeng Cheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruiqi Lin
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xue Zhai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Haiou Zheng
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingchao Wang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yongyao Yu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhen Xu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- Correspondence:
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Karasova D, Faldynova M, Matiasovicova J, Sebkova A, Crhanova M, Kubasova T, Seidlerova Z, Prikrylova H, Volf J, Zeman M, Babak V, Juricova H, Rajova J, Vlasatikova L, Rysavka P, Rychlik I. Host Species Adaptation of Obligate Gut Anaerobes Is Dependent on Their Environmental Survival. Microorganisms 2022; 10:microorganisms10061085. [PMID: 35744604 PMCID: PMC9229247 DOI: 10.3390/microorganisms10061085] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 01/27/2023] Open
Abstract
The gut microbiota of warm-blooded vertebrates consists of bacterial species belonging to two main phyla; Firmicutes and Bacteroidetes. However, does it mean that the same bacterial species are found in humans and chickens? Here we show that the ability to survive in an aerobic environment is central for host species adaptation. Known bacterial species commonly found in humans, pigs, chickens and Antarctic gentoo penguins are those capable of extended survival under aerobic conditions, i.e., either spore-forming, aerotolerant or facultatively anaerobic bacteria. Such bacteria are ubiquitously distributed in the environment, which acts as the source of infection with similar probability in humans, pigs, chickens, penguins and likely any other warm-blooded omnivorous hosts. On the other hand, gut anaerobes with no specific adaptation for survival in an aerobic environment exhibit host adaptation. This is associated with their vertical transmission from mothers to offspring and long-term colonisation after administration of a single dose. This knowledge influences the design of next-generation probiotics. The origin of aerotolerant or spore-forming probiotic strains may not be that important. On the other hand, if Bacteroidetes and other host-adapted species are used as future probiotics, host preference should be considered.
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Affiliation(s)
- Daniela Karasova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Marcela Faldynova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Jitka Matiasovicova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Alena Sebkova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Magdalena Crhanova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Tereza Kubasova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Zuzana Seidlerova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Hana Prikrylova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Jiri Volf
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Michal Zeman
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Vladimir Babak
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Helena Juricova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Jana Rajova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Lenka Vlasatikova
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
| | - Petr Rysavka
- Medi Pharma Vision Ltd., 612 00 Brno, Czech Republic;
| | - Ivan Rychlik
- Veterinary Research Institute, 621 00 Brno, Czech Republic; (D.K.); (M.F.); (J.M.); (A.S.); (M.C.); (T.K.); (Z.S.); (H.P.); (J.V.); (M.Z.); (V.B.); (H.J.); (J.R.); (L.V.)
- Correspondence: ; Tel.: +420-533-331-201
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Olsson LM, Boulund F, Nilsson S, Khan MT, Gummesson A, Fagerberg L, Engstrand L, Perkins R, Uhlén M, Bergström G, Tremaroli V, Bäckhed F. Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden. Cell Host Microbe 2022; 30:726-739.e3. [PMID: 35349787 DOI: 10.1016/j.chom.2022.03.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/17/2022] [Accepted: 03/03/2022] [Indexed: 02/07/2023]
Abstract
Temporal dynamics of the gut microbiota potentially limit the identification of microbial features associated with health status. Here, we used whole-genome metagenomic and 16S rRNA gene sequencing to characterize the intra- and inter-individual variations of gut microbiota composition and functional potential of a disease-free Swedish population (n = 75) over one year. We found that 23% of the total compositional variance was explained by intra-individual variation. The degree of intra-individual compositional variability was negatively associated with the abundance of Faecalibacterium prausnitzii (a butyrate producer) and two Bifidobacterium species. By contrast, the abundance of facultative anaerobes and aerotolerant bacteria such as Escherichia coli and Lactobacillus acidophilus varied extensively, independent of compositional stability. The contribution of intra-individual variance to the total variance was greater for functional pathways than for microbial species. Thus, reliable quantification of microbial features requires repeated samples to address the issue of intra-individual variations of the gut microbiota.
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Affiliation(s)
- Lisa M Olsson
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Boulund
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Staffan Nilsson
- Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden; Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Muhammad Tanweer Khan
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anders Gummesson
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Linn Fagerberg
- Department of Proteomics, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Clinical Genomics Facility, Science for Life Laboratory, Solna, Sweden
| | - Rosie Perkins
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mathias Uhlén
- Department of Proteomics, KTH-Royal Institute of Technology, Stockholm, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Göran Bergström
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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