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Guo X, Zhao W, Yin D, Mei Z, Wang F, Tiedje J, Ling S, Hu S, Xu T. Aspirin altered antibiotic resistance genes response to sulfonamide in the gut microbiome of zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124566. [PMID: 39025292 DOI: 10.1016/j.envpol.2024.124566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/11/2024] [Accepted: 07/15/2024] [Indexed: 07/20/2024]
Abstract
Pharmaceuticals are widespread in aquatic environments and might contribute to the prevalence of antibiotic resistance. However, the co-effect of antibiotics and non-antibiotic pharmaceuticals on the gut microbiome of fish is poorly understood. In this study, we characterized the variation of the zebrafish gut microbiome and resistome after exposure to sulfamethoxazole (SMX) and aspirin under different treatments. SMX contributed to the significant increase in the antibiotic resistance genes (ARGs) richness and abundance with 46 unique ARGs and five mobile genetic elements (MGEs) detected. Combined exposure to SMX and aspirin enriched total ARGs abundance and rearranged microbiota under short-term exposure. Exposure time was more responsible for resistome and the gut microbiome than exposure concentrations. Perturbation of the gut microbiome contributed to the functional variation related to RNA processing and modification, cell motility, signal transduction mechanisms, and defense mechanisms. A strong significant positive correlation (R = 0.8955, p < 0.001) was observed between total ARGs and MGEs regardless of different treatments revealing the key role of MGEs in ARGs transmission. Network analysis indicated most of the potential ARGs host bacteria belonged to Proteobacteria. Our study suggested that co-occurrence of non-antibiotics and antibiotics could accelerate the spread of ARGs in gut microbial communities and MGEs played a key role.
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Affiliation(s)
- Xueping Guo
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Wanting Zhao
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Daqiang Yin
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Zhi Mei
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - James Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI, 48824, USA
| | - Siyuan Ling
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Shuangqing Hu
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China
| | - Ting Xu
- Key Laboratory of Yangtze River Water Environment, Ministry of Education, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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Deli CK, Fatouros IG, Poulios A, Liakou CA, Draganidis D, Papanikolaou K, Rosvoglou A, Gatsas A, Georgakouli K, Tsimeas P, Jamurtas AZ. Gut Microbiota in the Progression of Type 2 Diabetes and the Potential Role of Exercise: A Critical Review. Life (Basel) 2024; 14:1016. [PMID: 39202758 PMCID: PMC11355287 DOI: 10.3390/life14081016] [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: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Type 2 diabetes (T2D) is the predominant metabolic epidemic posing a major threat to global health. Growing evidence indicates that gut microbiota (GM) may critically influence the progression from normal glucose tolerance, to pre-diabetes, to T2D. On the other hand, regular exercise contributes to the prevention and/or treatment of the disease, and evidence suggests that a possible way regular exercise favorably affects T2D is by altering GM composition toward health-promoting bacteria. However, research regarding this potential effect of exercise-induced changes of GM on T2D and the associated mechanisms through which these effects are accomplished is limited. This review presents current data regarding the association of GM composition and T2D and the possible critical GM differentiation in the progression from normal glucose, to pre-diabetes, to T2D. Additionally, potential mechanisms through which GM may affect T2D are presented. The effect of exercise on GM composition and function on T2D progression is also discussed.
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Affiliation(s)
- Chariklia K. Deli
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Ioannis G. Fatouros
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Athanasios Poulios
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Christina A. Liakou
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Dimitrios Draganidis
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Konstantinos Papanikolaou
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Anastasia Rosvoglou
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Athanasios Gatsas
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Kalliopi Georgakouli
- Department of Dietetics and Nutrition, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece;
| | - Panagiotis Tsimeas
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
| | - Athanasios Z. Jamurtas
- Department of Physical Education and Sport Science, School of Physical Education, Sport Science, and Dietetics, University of Thessaly, 42100 Trikala, Greece; (I.G.F.); (A.P.); (C.A.L.); (D.D.); (K.P.); (A.R.); (A.G.); (P.T.); (A.Z.J.)
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Yin LL, Qi PQ, Hu YF, Fu XJ, He RS, Wang MM, Deng YJ, Xiong SY, Yu QW, Hu JP, Zhou L, Zhou ZB, Xiong Y, Deng H. Dysbiosis promotes recurrence of adenomatous polyps in the distal colorectum. World J Gastrointest Oncol 2024; 16:3600-3623. [PMID: 39171160 PMCID: PMC11334022 DOI: 10.4251/wjgo.v16.i8.3600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/19/2024] [Accepted: 06/14/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Colorectal polyps, which are characterized by a high recurrence rate, represent preneoplastic conditions of the intestine. Due to unclear mechanisms of pathogenesis, first-line therapies for non-hereditary recurrent colorectal polyps are limited to endoscopic resection. Although recent studies suggest a mechanistic link between intestinal dysbiosis and polyps, the exact compositions and roles of bacteria in the mucosa around the lesions, rather than feces, remain unsettled. AIM To clarify the composition and diversity of bacteria in the mucosa surrounding or 10 cm distal to recurrent intestinal polyps. METHODS Mucosal samples were collected from four patients consistently with adenomatous polyps (Ade), seven consistently with non-Ade (Pol), ten with current Pol but previous Ade, and six healthy individuals, and bacterial patterns were evaluated by 16S rDNA sequencing. Linear discriminant analysis and Student's t-tests were used to identify the genus-level bacteria differences between groups with different colorectal polyp phenotypes. Pearson's correlation coefficients were used to evaluate the correlation between intestinal bacteria at the genus level and clinical indicators. RESULTS The results confirmed a decreased level of probiotics and an enrichment of pathogenic bacteria in patients with all types of polyps compared to healthy individuals. These changes were not restricted to the mucosa within 0.5 cm adjacent to the polyps, but also existed in histologically normal tissue 10 cm distal from the lesions. Significant differences in bacterial diversity were observed in the mucosa from individuals with normal conditions, Pol, and Ade. Increased abundance of Gram-negative bacteria, including Klebsiella, Plesiomonas, and Cronobacter, was observed in Pol group and Ade group, suggesting that resistance to antibiotics may be one risk factor for bacterium-related harmful environment. Meanwhile, age and gender were linked to bacteria changes, indicating the potential involvement of sex hormones. CONCLUSION These preliminary results support intestinal dysbiosis as an important risk factor for recurrent polyps, especially adenoma. Targeting specific pathogenic bacteria may attenuate the recurrence of polyps.
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Affiliation(s)
- Li-Li Yin
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ping-Qian Qi
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yun-Fei Hu
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Xiao-Jun Fu
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Rui-Shan He
- The Second College of Clinical Medicine, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Meng-Meng Wang
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Yan-Juan Deng
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Su-Yi Xiong
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Qi-Wen Yu
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Jin-Ping Hu
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Lv Zhou
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Zhi-Bin Zhou
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang University, Nanchang 330006, Jiangxi Province, China
| | - Ying Xiong
- Department of General Medicine, The Second College of Clinical Medicine, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi Province, China
| | - Huan Deng
- The Affiliated Rehabilitation Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Fourth Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, Jiangxi Province, China
- Tumor Immunology Institute, Nanchang University, Nanchang 330006, Jiangxi Province, China
- The Ministry of Education Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, Jiangxi Medical College, Nanchang University, Nanchang 330031, Jiangxi Province, China
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Dinat S, Orchard A, Van Vuuren S. Antimicrobial activity of Southern African medicinal plants on Helicobacter pylori and Lactobacillus species. JOURNAL OF ETHNOPHARMACOLOGY 2024; 330:118238. [PMID: 38663780 DOI: 10.1016/j.jep.2024.118238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/07/2024] [Accepted: 04/20/2024] [Indexed: 05/02/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Numerous medicinal plants have been used traditionally in South Africa for gastric ulcer treatment. Helicobacter pylori is known for causing inflammation and the onset of gastric ulcers. While several studies explored medicinal plants against H. pylori, investigation of medicinal plants used for gastric ulcers has been neglected, as well as the effects these plants would have on bacteria occurring naturally in the gut microbiome. AIM OF THE STUDY This study aimed to investigate Southern African medicinal plants used traditionally for treating gastric ulcers against H. pylori , as well as the effects that these plants have when combined with Lactobacillus species and tested against H. pylori. METHODOLOGY Based on evidence from the ethnobotanical literature, 21 plants were collected. Their antimicrobial activity was assessed against five clinical H. pylori strains, and in combination with each of three Lactobacillus species, using the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) broth microdilution assays. Toxicity was assessed using the brine shrimp lethality assay. RESULTS Noteworthy activity was observed against at least one H. pylori strain for 12 plant species. The lowest mean MICs were from organic extracts of Carissa edulis Vahl (0.18 mg/mL) and Chironia baccifera L. (0.20 mg/mL), and aqueous extracts of Sansevieria hyacinthoides (L.) Druce (0.26 mg/mL) and Dodonaea viscosa Jacq. (0.30 mg/mL). Aqueous extracts of the investigated plants were combined with Lactobacillus species, and the majority of combinations showed increased antimicrobial activity compared with the extracts alone. Combinations of Lactobacillus rhamnosus with 18 of the 21 aqueous plant extracts showed at least a two-fold decrease in the mean MBC against all H. pylori strains tested. Lactobacillus acidophilus combined with either Protea repens L., Carpobrotus edulis (L.) L. Bolus or Warburgia salutaris (Bertol.f.) Chiov. aqueous extracts had the best anti-H. pylori activity (mean MBCs of 0.10 mg/mL for each combination). Only four organic and one aqueous extract(s) were considered toxic. CONCLUSION These results highlight the potential of medicinal plants to inhibit H. pylori growth and their role in traditional treatments for the management of ulcers. The results also indicate that aqueous extracts of these plants do not hinder the growth of bacteria that occur naturally in the gut microbiome and play a role in maintaining gut health, as well as show the potential benefit of including Lactobacillus species as potentiators of H. pylori activity.
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Affiliation(s)
- S Dinat
- Department of Pharmacy and Pharmacology, University of the Witwatersrand, Johannesburg, South Africa
| | - A Orchard
- Department of Pharmacy and Pharmacology, University of the Witwatersrand, Johannesburg, South Africa
| | - S Van Vuuren
- Department of Pharmacy and Pharmacology, University of the Witwatersrand, Johannesburg, South Africa.
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Humphrey S, Marouli A, Thümmler K, Mullin M, Pritchard L, Wall DM. Genomic characterization of prophage elements in Clostridium clostridioforme: an understudied component of the intestinal microbiome. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001486. [PMID: 39132742 PMCID: PMC11318856 DOI: 10.1099/mic.0.001486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/22/2024] [Indexed: 08/13/2024]
Abstract
Genome sequencing of Clostridium clostridioforme strain LM41 revealed the presence of an atypically high proportion of mobile genetic elements for this species, with a particularly high abundance of prophages. Bioinformatic analysis of prophage sequences sought to characterize these elements and identify prophage-linked genes contributing to enhanced fitness of the host bacteria in the dysbiotic gut. Using PHASTER, PhageScope and manual curation, this work has identified 15 prophages: 4 predicted to be intact, 2 predicted to be defective and 9 which are unclassified. Quantitative PCR (qPCR) analysis revealed spontaneous release of four of the LM41 prophages (φ1, φ2, φ4 and φ10) into the culture supernatant, with virion-like particles visualized using transmission electron microscopy. The majority (12/14) of these particles had morphology akin to podoviruses, which is consistent with morphology predictions for φ1 and φ4. We observed diversity in the lysogeny mechanisms utilized by the prophages, with examples of the classical λ-like CI/Cro system, the ICEBs1 ImmR/ImmA-like system and the Mu-like C/Ner system. Classical morons, such as toxins or immune evasion factors, were not observed. We did, however, identify a variety of genes with roles in mediating restriction modification and genetic diversity, as well as some candidate genes with potential roles in host adaptation. Despite being the most abundant entities in the intestine, there is a dearth of information about phages associated with members of the microbiome. This work begins to shed light on the contribution of these elements to the lifestyle of C. clostridioforme LM41.
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Affiliation(s)
- Suzanne Humphrey
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RW, UK
| | - Angeliki Marouli
- School of Infection and Immunity, College of Medical and Veterinary Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Katja Thümmler
- School of Infection and Immunity, College of Medical and Veterinary Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Margaret Mullin
- CAF Electron Microscopy Unit (MVLS College Research Facilities), University of Glasgow, Glasgow, G12 8QQ, UK
| | - Leighton Pritchard
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, G4 0RW, UK
| | - Daniel M. Wall
- School of Infection and Immunity, College of Medical and Veterinary Sciences, University of Glasgow, Glasgow, G12 8TA, UK
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Veseli I, Chen YT, Schechter MS, Vanni C, Fogarty EC, Watson AR, Jabri BA, Blekhman R, Willis AD, Yu MK, Fernandez-Guerra A, Fussel J, Eren AM. Microbes with higher metabolic independence are enriched in human gut microbiomes under stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.10.540289. [PMID: 37293035 PMCID: PMC10245760 DOI: 10.1101/2023.05.10.540289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health versus IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.
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Cui K, Wang S, Pei Y, Zhou B. Occurrence and distribution of antibiotic pollution and antibiotic resistance genes in seagrass meadow sediments based on metagenomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173438. [PMID: 38782270 DOI: 10.1016/j.scitotenv.2024.173438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 05/25/2024]
Abstract
Seagrass meadows are one of the most important coastal ecosystems that provide essential ecological and economic services. The contamination levels of antibiotic and antibiotic resistance genes (ARGs) in coastal ecosystems are severely elevated owing to anthropogenic disturbances, such as terrestrial input, aquaculture effluent, and sewage discharge. However, few studies have focused on the occurrence and distribution of antibiotics and their corresponding ARGs in this habitat. Thus, we investigated the antibiotic and ARGs profiles, microbial communities, and ARG-carrying host bacteria in typical seagrass meadow sediments collected from Swan Lake, Caofeidian shoal harbor, Qingdao Bay, and Sishili Bay in the Bohai Sea and northern Yellow Sea. The total concentrations of 30 detected antibiotics ranged from 99.35 to 478.02 μg/kg, tetracyclines were more prevalent than other antibiotics. Metagenomic analyses showed that 342 ARG subtypes associated with 22 ARG types were identified in the seagrass meadow sediments. Multidrug resistance genes and RanA were the most dominant ARG types and subtypes, respectively. Co-occurrence network analysis revealed that Halioglobus, Zeaxanthinibacter, and Aureitalea may be potential hosts at the genus level, and the relative abundances of these bacteria were higher in Sishili Bay than those in other areas. This study provided important insights into the pollution status of antibiotics and ARGs in typical seagrass meadow sediments. Effective management should be performed to control the potential ecological health risks in seagrass meadow ecosystems.
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Affiliation(s)
- Kaixuan Cui
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Shumin Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Yanzhao Pei
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Bin Zhou
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Ecology and Environmental Science, Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
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Taguer M, Xiao J, Crawford R, Shi H, Cheng MP, Citron M, Hannigan GD, Kasper SH. Spatial recovery of the murine gut microbiota after antibiotics perturbation. mBio 2024; 15:e0070724. [PMID: 38832780 PMCID: PMC11253616 DOI: 10.1128/mbio.00707-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 03/31/2024] [Indexed: 06/05/2024] Open
Abstract
Bacterial communities are highly complex, with interaction networks dictating ecosystem function. Bacterial interactions are constrained by the spatial organization of these microbial communities, yet studying the spatial organization of microbial communities at the single-cell level has been technically challenging. Here, we use the recently developed high-phylogenetic-resolution microbiota mapping by fluorescence in situ hybridization technology to image the gut microbiota at the species and single-cell level. We simultaneously image 63 different bacterial species to spatially characterize the perturbation and recovery of the gut microbiota to ampicillin and vancomycin in the cecum and distal colon of mice. To decipher the biology in this complex imaging data, we developed an analytical framework to characterize the spatial changes of the gut microbiota to a perturbation. The three-tiered analytical approach includes image-level diversity, pairwise colocalization analysis, and hypothesis-driven neighborhood analysis. Through this workflow, we identify biogeographic and antibiotic-based differences in the spatial organization of the gut microbiota. We demonstrate that the cecal microbiota has increased micrometer-scale diversity than the colon at baseline and recovers better from perturbation. Also, we identify potential foundation and keystone species that have high baseline neighborhood richness and that are associated with recovery from antibiotics. Through this workflow, we add a spatial layer to the characterization of bacterial communities and progress toward a better understanding of bacterial interactions leading to improved microbiome modulation strategies. IMPORTANCE Antibiotics have broad off-target effects on the gut microbiome. When the microbial community is unable to recover from antibiotics, it can lead to increased susceptibility to gastrointestinal infections and increased risk of immunological and metabolic diseases. In this study, we work to better understand how the gut microbiota recovers from antibiotics by employing a recent technology to image the entire bacterial community at once. Through this approach, we characterize the spatial changes in the gut microbiota after treatment with model antibiotics in both the cecum and colon of mice. We find antibiotic- and biogeographic-dependent spatial changes between bacterial species and that many of these spatial colocalizations do not recover to baseline levels even 35 days after antibiotic administration.
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Affiliation(s)
- M. Taguer
- Discovery Immunology, MRL, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - J. Xiao
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - R. Crawford
- Informatics Technology, MRL, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - H. Shi
- Kanvas Biosciences, Inc., Monmouth Junction, New Jersey, USA
| | - M. P. Cheng
- Kanvas Biosciences, Inc., Monmouth Junction, New Jersey, USA
| | - M. Citron
- Infectious Diseases and Vaccine Research, MRL, Merck & Co., Inc., West Point, Pennsylvania, USA
| | - G. D. Hannigan
- Informatics Technology, MRL, Merck & Co., Inc., Cambridge, Massachusetts, USA
| | - S. H. Kasper
- Discovery Immunology, MRL, Merck & Co., Inc., Cambridge, Massachusetts, USA
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9
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Vliex LMM, Penders J, Nauta A, Zoetendal EG, Blaak EE. The individual response to antibiotics and diet - insights into gut microbial resilience and host metabolism. Nat Rev Endocrinol 2024; 20:387-398. [PMID: 38486011 DOI: 10.1038/s41574-024-00966-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 06/16/2024]
Abstract
Antibiotic use disrupts microbial composition and activity in humans, but whether this disruption in turn affects host metabolic health is unclear. Cohort studies show associations between antibiotic use and an increased risk of developing obesity and type 2 diabetes mellitus. Here, we review available clinical trials and show the disruptive effect of antibiotic use on the gut microbiome in humans, as well as its impact on bile acid metabolism and microbial metabolites such as short-chain fatty acids. Placebo-controlled human studies do not show a consistent effect of antibiotic use on body weight and insulin sensitivity at a population level, but rather an individual-specific or subgroup-specific response. This response to antibiotic use is affected by the resistance and resilience of the gut microbiome, factors that determine the extent of disruption and the speed of recovery afterwards. Nutritional strategies to improve the composition and functionality of the gut microbiome, as well as its recovery after antibiotic use (for instance, with prebiotics), require a personalized approach to increase their efficacy. Improved insights into key factors that influence the individual-specific response to antibiotics and dietary intervention may lead to better efficacy in reversing or preventing antibiotic-induced microbial dysbiosis as well as strategies for preventing cardiometabolic diseases.
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Affiliation(s)
- Lars M M Vliex
- Department of Human Biology, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - John Penders
- Department of Medical Microbiology, Infectious Diseases and Infection Prevention, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Arjen Nauta
- FrieslandCampina, Amersfoort, The Netherlands
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Ellen E Blaak
- Department of Human Biology, NUTRIM, School for Nutrition and Translational Research in Metabolism, Maastricht University Medical Center+, Maastricht, The Netherlands.
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10
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Moussa AY. Streptomyces Endophytes in Edible Plants: New Insights into their Chemistry and Health Benefits. Chem Biodivers 2024:e202400888. [PMID: 38884446 DOI: 10.1002/cbdv.202400888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/16/2024] [Accepted: 06/17/2024] [Indexed: 06/18/2024]
Abstract
Streptomyces is the largest source of microbial antibiotics with about 50 % of marketed antimicrobial drugs originating from this genus. Endophytic streptomyces are the link between medicinal plants and the microbial world. Endophytic Streptomyces in edible plants were not targeted before despite their uniqueness and importance. In this review, we analyzed the chemical diversity of more than 150 compounds belonging to endophytic Streptomyces chemical classes such as alkaloids, polyketides, peptides, macrolides and terpenes and their biological activities. This analysis showed a dominant antimicrobial effect for most of the isolated compounds and highlighted an underestimated diversity to be studied or repurposed for other biological activities. Return to edible plants use and conducting toxicity studies to rationalize their nutraceutical potential based on their beneficial endophytes is urged. Although there are many studies for non-vertebrates, the nutraceutical potential of these plants is expected to improve the gut microbiota since they are enriched with bioactive compounds from streptomyces species. This is the first review to discuss edible plants associated streptomyces, and we prospect that many studies will follow to unravel the mysterious health benefits of streptomyces in the human microbiome and encourage the revival of a correct lifestyle for the sake of a healthier microbiome.
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Affiliation(s)
- Ashaimaa Y Moussa
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, Cairo, 11566, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University Postal address, 11566, African Union Organization Street, Abbassia, Cairo, Egypt
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11
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Verma J, Devi S, Narang A, Kaur S, Manhas RK. Probiotic potential of Streptomyces levis strain HFM-2 isolated from human gut and its antibiofilm properties against pathogenic bacteria. BMC Microbiol 2024; 24:208. [PMID: 38862894 PMCID: PMC11165917 DOI: 10.1186/s12866-024-03353-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a serious worldwide public health concern that needs immediate action. Probiotics could be a promising alternative for fighting antibiotic resistance, displaying beneficial effects to the host by combating diseases, improving growth, and stimulating the host immune responses against infection. This study was conducted to evaluate the probiotic, antibacterial, and antibiofilm potential of Streptomyces levis strain HFM-2 isolated from the healthy human gut. RESULTS In vitro antibacterial activity in the cell-free supernatant of S. levis strain HFM-2 was evaluated against different pathogens viz. K. pneumoniae sub sp. pneumoniae, S. aureus, B. subtilis, VRE, S. typhi, S. epidermidis, MRSA, V. cholerae, M. smegmatis, E. coli, P. aeruginosa and E. aerogenes. Further, the ethyl acetate extract from S. levis strain HFM-2 showed strong biofilm inhibition against S. typhi, K. pneumoniae sub sp. pneumoniae, P. aeruginosa and E. coli. Fluorescence microscopy was used to detect biofilm inhibition properties. MIC and MBC values of EtOAc extract were determined at 500 and 1000 µg/mL, respectively. Further, strain HFM-2 showed high tolerance in gastric juice, pancreatin, bile, and at low pH. It exhibited efficient adhesion properties, displaying auto-aggregation (97.0%), hydrophobicity (95.71%, 88.96%, and 81.15% for ethyl acetate, chloroform and xylene, respectively), and showed 89.75%, 86.53%, 83.06% and 76.13% co-aggregation with S. typhi, MRSA, S. pyogenes and E. coli, respectively after 60 min of incubation. The S. levis strain HFM-2 was susceptible to different antibiotics such as tetracycline, streptomycin, kanamycin, ciprofloxacin, erythromycin, linezolid, meropenem, amikacin, gentamycin, clindamycin, moxifloxacin and vancomycin, but resistant to ampicillin and penicillin G. CONCLUSION The study shows that S. levis strain HFM-2 has significant probiotic properties such as good viability in bile, gastric juice, pancreatin environment, and at low pH; proficient adhesion properties, and antibiotic susceptibility. Further, the EtOAc extract of Streptomyces levis strain HFM-2 has a potent antibiofilm and antibacterial activity against antibacterial-resistant clinical pathogens.
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Affiliation(s)
- Jaya Verma
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Sapna Devi
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Anmol Narang
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Sukhraj Kaur
- Department of Microbiology, Guru Nanak Dev University, Amritsar, Punjab, India
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12
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Flinn H, Marshall A, Holcomb M, Cruz L, Soriano S, Treangen TJ, Villapol S. Antibiotic treatment induces microbiome dysbiosis and reduction of neuroinflammation following traumatic brain injury in mice. RESEARCH SQUARE 2024:rs.3.rs-4475195. [PMID: 38946944 PMCID: PMC11213166 DOI: 10.21203/rs.3.rs-4475195/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background The gut microbiome is linked to brain pathology in cases of traumatic brain injury (TBI), yet the specific bacteria that are implicated are not well characterized. To address this gap, in this study, we induced traumatic brain injury (TBI) in male C57BL/6J mice using the controlled cortical impact (CCI) injury model. After 35 days, we administered a broad-spectrum antibiotics (ABX) cocktail (ampicillin, gentamicin, metronidazole, vancomycin) through oral gavage for 2 days to diminish existing microbiota. Subsequently, we inflicted a second TBI on the mice and analyzed the neuropathological outcomes five days later. Results Longitudinal analysis of the microbiome showed significant shifts in the diversity and abundance of bacterial genera during both acute and chronic inflammation. These changes were particularly dramatic following treatment with ABX and after the second TBI. ABX treatment did not affect the production of short-chain fatty acids (SCFA) but did alter intestinal morphology, characterized by reduced villus width and a lower count of goblet cells, suggesting potential negative impacts on intestinal integrity. Nevertheless, diminishing the intestinal microbiome reduced cortical damage, apoptotic cell density, and microglial/macrophage activation in the cortical and thalamic regions of the brain. Conclusions Our findings suggest that eliminating colonized gut bacteria via broad-spectrum ABX reduces neuroinflammation and enhances neurological outcomes in TBI despite implications to gut health.
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13
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Olteanu G, Ciucă-Pană MA, Busnatu ȘS, Lupuliasa D, Neacșu SM, Mititelu M, Musuc AM, Ioniță-Mîndrican CB, Boroghină SC. Unraveling the Microbiome-Human Body Axis: A Comprehensive Examination of Therapeutic Strategies, Interactions and Implications. Int J Mol Sci 2024; 25:5561. [PMID: 38791599 PMCID: PMC11122276 DOI: 10.3390/ijms25105561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
This review scrutinizes the intricate interplay between the microbiome and the human body, exploring its multifaceted dimensions and far-reaching implications. The human microbiome, comprising diverse microbial communities inhabiting various anatomical niches, is increasingly recognized as a critical determinant of human health and disease. Through an extensive examination of current research, this review elucidates the dynamic interactions between the microbiome and host physiology across multiple organ systems. Key topics include the establishment and maintenance of microbiota diversity, the influence of host factors on microbial composition, and the bidirectional communication pathways between microbiota and host cells. Furthermore, we delve into the functional implications of microbiome dysbiosis in disease states, emphasizing its role in shaping immune responses, metabolic processes, and neurological functions. Additionally, this review discusses emerging therapeutic strategies aimed at modulating the microbiome to restore host-microbe homeostasis and promote health. Microbiota fecal transplantation represents a groundbreaking therapeutic approach in the management of dysbiosis-related diseases, offering a promising avenue for restoring microbial balance within the gut ecosystem. This innovative therapy involves the transfer of fecal microbiota from a healthy donor to an individual suffering from dysbiosis, aiming to replenish beneficial microbial populations and mitigate pathological imbalances. By synthesizing findings from diverse fields, this review offers valuable insights into the complex relationship between the microbiome and the human body, highlighting avenues for future research and clinical interventions.
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Affiliation(s)
- Gabriel Olteanu
- Department of Clinical Laboratory and Food Safety, Faculty of Pharmacy, University of Medicine and Pharmacy Carol Davila, 020956 Bucharest, Romania;
| | - Maria-Alexandra Ciucă-Pană
- Department of Cardiology, Carol Davila University of Medicine and Pharmacy, Bagdasar-Arseni Emergency Hospital, 050474 Bucharest, Romania;
| | - Ștefan Sebastian Busnatu
- Department of Cardio-Thoracic Pathology, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
| | - Dumitru Lupuliasa
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (D.L.); (S.M.N.)
| | - Sorinel Marius Neacșu
- Department of Pharmaceutical Technology and Bio-Pharmacy, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania; (D.L.); (S.M.N.)
| | - Magdalena Mititelu
- Department of Clinical Laboratory and Food Safety, Faculty of Pharmacy, University of Medicine and Pharmacy Carol Davila, 020956 Bucharest, Romania;
| | - Adina Magdalena Musuc
- Institute of Physical Chemistry—Ilie Murgulescu, Romanian Academy, 060021 Bucharest, Romania
| | - Corina-Bianca Ioniță-Mîndrican
- Department of Toxicology, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 020945 Bucharest, Romania;
| | - Steluța Constanța Boroghină
- Department of Complementary Sciences, History of Medicine and Medical Culture, Carol Davila University of Medicine and Pharmacy, 050474 Bucharest, Romania;
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14
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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15
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Koo H, Morrow CD. Bacteroidales-Specific Antimicrobial Genes Can Influence the Selection of the Dominant Fecal Strain of Bacteroides vulgatus and Bacteroides uniformis from the Gastrointestinal Tract Microbial Community. Life (Basel) 2024; 14:555. [PMID: 38792577 PMCID: PMC11121782 DOI: 10.3390/life14050555] [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: 03/13/2024] [Revised: 04/21/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024] Open
Abstract
Bacteroides vulgatus and Bacteroides uniformis are known to be abundant in the human fecal microbial community. Although these strains typically remain stable over time in humans, disruption of this microbial community following antibiotics resulted in the transient change to new strains suggesting that a complex, dynamic strain community exists in humans. To further study the selection of dominant fecal microbial strains from the gastrointestinal tract (GIT) community, we analyzed three longitudinal metagenomic sequencing data sets using BLAST+ to identify genes encoding Bacteroidales-specific antimicrobial proteins (BSAP) that have known functions to restrict species-specific replication of B. uniformis (BSAP-2) or B. vulgatus (BSAP-3) and have been postulated to provide a competitive advantage in microbial communities. In the HMP (Human Microbiome Project) data set, we found fecal samples from individuals had B. vulgatus or B. uniformis with either complete or deleted BSAP genes that did not change over time. We also examined fecal samples from two separate longitudinal data sets of individuals who had been given either single or multiple antibiotics. The BSAP gene pattern from most individuals given either single or multiple antibiotics recovered to be the same as the pre-antibiotic strain. However, in a few individuals, we found incomplete BSAP-3 genes at early times during the recovery that were replaced by B. vulgatus with the complete BSAP-3 gene, consistent with the function of the BSAP to specifically restrict Bacteroides spp. The results of these studies provide insights into the fluxes that occur in the Bacteroides spp. GIT community following perturbation and the dynamics of the selection of a dominant fecal strain of Bacteroides spp.
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Affiliation(s)
- Hyunmin Koo
- Department of Genetics, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, Hugh Kaul Precision Medicine Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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16
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Kolzhetsov N, Markelova N, Frolova M, Alikina O, Glazunova O, Safonova L, Kalashnikova I, Yudin V, Makarov V, Keskinov A, Yudin S, Troshina D, Rechkina V, Shcherbakova V, Shavkunov K, Ozoline O. Enterotype-Dependent Probiotic-Mediated Changes in the Male Rat Intestinal Microbiome In Vivo and In Vitro. Int J Mol Sci 2024; 25:4558. [PMID: 38674145 PMCID: PMC11049970 DOI: 10.3390/ijms25084558] [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: 03/04/2024] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Beneficial properties of lactic acid bacteria have been known long ago, but particular interest in probiotics has arisen in the last two decades due to the understanding of the important role of intestinal microflora in human life. Thus, the ability of probiotics to support healthy homeostasis of gut microbiomes has received particular attention. Here, we evaluated the effect of a probiotic consisting of Bifidobacterium longum and Lacticaseibacillus paracasei on the gut microbiome of male rats, assessed their persistence in the fecal biota, and compared probiotic-mediated changes in vitro and in vivo. As expected, microbiomes of two enterotypes were identified in the feces of 21 animals, and it turned out that even a single dose of the probiotic altered the microbial composition. Upon repeated administration, the E1 biota temporarily acquired properties of the E2 type. Being highly sensitive to the intervention of probiotic bacteria at the phylum and genus levels, the fecal microbiomes retained the identity of their enterotypes when transferred to a medium optimized for gut bacteria. For the E2 biota, even similarities between probiotic-mediated reactions in vitro and in vivo were detected. Therefore, fecal-derived microbial communities are proposed as model consortia to optimize the response of resident bacteria to various agents.
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Affiliation(s)
- Nikolay Kolzhetsov
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Natalia Markelova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Maria Frolova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Alikina
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Glazunova
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Lubov Safonova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Irina Kalashnikova
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Vladimir Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Valentin Makarov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Anton Keskinov
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Sergey Yudin
- Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical and Biological Agency, 119121 Moscow, Russia; (L.S.); (I.K.); (V.Y.); (V.M.); (A.K.); (S.Y.)
| | - Daria Troshina
- Faculty of Biotechnology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Viktoria Rechkina
- Laboratory of Anaerobic Microorganisms, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (V.R.); (V.S.)
| | - Viktoria Shcherbakova
- Laboratory of Anaerobic Microorganisms, Institute of Biochemistry and Physiology of Microorganisms of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (V.R.); (V.S.)
| | - Konstantin Shavkunov
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
| | - Olga Ozoline
- Laboratory of Functional Genomics of Prokaryotes, Institute of Cell Biophysics of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Russia; (N.K.); (N.M.); (M.F.); (O.A.); (O.G.); (K.S.)
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17
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Garrigues Q, Mugnier A, Chastant S, Sicard F, Martin JC, Svilar L, Castex M, Ramis-Vidal MG, Rovere N, Michaud L, David P, Mansalier E, Rodiles A, Mila H, Apper E. The supplementation of female dogs with live yeast Saccharomyces cerevisiae var. boulardii CNCM I-1079 acts as gut stabilizer at whelping and modulates immunometabolic phenotype of the puppies. Front Nutr 2024; 11:1366256. [PMID: 38680531 PMCID: PMC11048480 DOI: 10.3389/fnut.2024.1366256] [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: 01/08/2024] [Accepted: 03/29/2024] [Indexed: 05/01/2024] Open
Abstract
Time around parturition is a stressful period for both bitches and their puppies. The use of probiotics has been proposed, e.g., in pigs, to improve health status of sows, their reproductive performances and in turn, the health and performance of their progeny. The objective of the present study was to evaluate the impact, on both dams and puppies, of a supplementation of bitches with the live yeast Saccharomyces cerevisiae var. boulardii CNCM I-1079 (SB-1079) during the second part of the gestation and the lactation period. A total of 36 bitches of medium and large-sized breeds were enrolled. They were divided into two groups, one of which received 1.3 × 109 colony forming units of live yeast per day. At dam's level, SB-1079 yeast shaped a different microbiota structure between the two groups just after whelping, impacted alpha diversity and some plasma metabolites related to energy metabolism. Regarding reproductive performances, SB-1079 improved gross energy of the colostrum (1.4 vs. 1.2 kcal of ME/g) as well as the concentration of protein in milk at Day 7 after parturition (10.4 vs. 7.6%). SB-1079 also reduced the odds of having low birth weight in the litter. At puppy's level, a modulation of immunometabolic phenotype is suggested by the observation of increased growth rates during the early pediatric period (i.e., between 21 and 56 days of life, 225 vs. 190%) and a decrease of the IL-8:IL-10 ratio after vaccination against rabies (4.2 vs. 16.9). Our findings suggest that SB-1079 supplementation during gestation and lactation has the potential to enhance health of bitches and in turn health of puppies through maternal programming.
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Affiliation(s)
| | | | | | - Flavie Sicard
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
- CriBioM, Aix Marseille Université, Marseille, France
| | | | - Ljubica Svilar
- Aix-Marseille Université, C2VN, INRAE, INSERM, Marseille, France
- CriBioM, Aix Marseille Université, Marseille, France
| | | | - Manuel Guillermo Ramis-Vidal
- Department of Animal Production, Faculty of Veterinary Medicine, University of Murcia, Murcia, Spain
- Instituo Murciano de Investigación en Biomedicina (IMIB), Murcia, Spain
| | - Nicoletta Rovere
- Department of HASFS, VESPA, University of Veterinary, Milan, Italy
| | | | - Pauline David
- NeoCare, ENVT, Université de Toulouse, Toulouse, France
| | | | | | - Hanna Mila
- NeoCare, ENVT, Université de Toulouse, Toulouse, France
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18
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Brar NK, Dhariwal A, Åmdal HA, Junges R, Salvadori G, Baker JL, Edlund A, Petersen FC. Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome. NPJ Biofilms Microbiomes 2024; 10:37. [PMID: 38565843 PMCID: PMC10987642 DOI: 10.1038/s41522-024-00507-7] [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: 08/28/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.
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Affiliation(s)
- N K Brar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - A Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - H A Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - R Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - G Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - J L Baker
- Department of Oral Rehabilitation & Biosciences, Oregon Health & Science University, Portland, OR, USA
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - A Edlund
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego School of Medicine, La Jolla, CA, USA
| | - F C Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway.
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19
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Bhardwaj G, Riadi Y, Afzal M, Bansal P, Kaur H, Deorari M, Tonk RK, Almalki WH, Kazmi I, Alzarea SI, Kukreti N, Thangavelu L, Saleem S. The hidden threat: Environmental toxins and their effects on gut microbiota. Pathol Res Pract 2024; 255:155173. [PMID: 38364649 DOI: 10.1016/j.prp.2024.155173] [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: 12/11/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/18/2024]
Abstract
The human gut microbiota (GM), which consists of a complex and diverse ecosystem of bacteria, plays a vital role in overall wellness. However, the delicate balance of this intricate system is being compromised by the widespread presence of environmental toxins. The intricate connection between contaminants in the environment and human well-being has garnered significant attention in recent times. Although many environmental pollutants and their toxicity have been identified and studied in laboratory settings and animal models, there is insufficient data concerning their relevance to human physiology. Consequently, research on the toxicity of environmental toxins in GM has gained prominence in recent years. Various factors, such as air pollution, chemicals, heavy metals, and pesticides, have a detrimental impact on the composition and functioning of the GM. This comprehensive review aims to comprehend the toxic effects of numerous environmental pollutants, including antibiotics, endocrine-disrupting chemicals, heavy metals, and pesticides, on GM by examining recent research findings. The current analysis concludes that different types of environmental toxins can lead to GM dysbiosis and have various potential adverse effects on the well-being of animals. We investigate the alterations to the GM composition induced by contaminants and their impact on overall well-being, providing a fresh perspective on research related to pollutant exposure.
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Affiliation(s)
- Gautam Bhardwaj
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar sector-3, M-B Road, New Delhi 110017, India
| | - Yassine Riadi
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka 560069, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh 247341, India; Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand 831001, India
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Rajiv Kumar Tonk
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar sector-3, M-B Road, New Delhi 110017, India.
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589 Jeddah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341 Sakaka, Aljouf, Saudi Arabia
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Lakshmi Thangavelu
- Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, India
| | - Shakir Saleem
- Department of Public Health. College of Health Sciences, Saudi Electronic University, Riyadh, Saudi Arabia.
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20
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DI Pierro F, Bertuccioli A, Cazzaniga M, Matera M, Cavecchia I, Gerardi V, Piccirelli S, Salvi D, Pugliano CL, Cesaro P, Spada C, Guasti L, Zerbinati N. Can microbiota analysis help intercept cases of colon cancer in case of occult blood negativity, also suggesting possible pharmacological intervention strategies? Minerva Gastroenterol (Torino) 2024; 70:109-112. [PMID: 37889113 DOI: 10.23736/s2724-5985.23.03578-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Affiliation(s)
- Francesco DI Pierro
- Scientific Department, Velleja Research, Milan, Italy -
- Department of Medicine and Surgery, University of Insubria, Varese, Italy -
| | - Alexander Bertuccioli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Pesaro-Urbino, Italy
| | | | | | | | - Viviana Gerardi
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Stefania Piccirelli
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Daniele Salvi
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Cecilia L Pugliano
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Paola Cesaro
- Section of Digestive Endoscopy and Gastroenterology, Fondazione Poliambulanza, Brescia, Italy
| | - Cristiano Spada
- Unit of Digestive Endoscopy, IRCCS A. Gemelli University Polyclinic Foundation, Rome, Italy
| | - Luigina Guasti
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Nicola Zerbinati
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
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21
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Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore RM, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Ruscheweyh HJ, Sunagawa S, Mclellan SL, Willis AD, Comstock LE, Eren AM. A cryptic plasmid is among the most numerous genetic elements in the human gut. Cell 2024; 187:1206-1222.e16. [PMID: 38428395 DOI: 10.1016/j.cell.2024.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/03/2023] [Accepted: 01/25/2024] [Indexed: 03/03/2024]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.
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Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan M Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY 10032, USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Biochemistry, University of Chicago, Chicago, IL 60637, USA
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA; Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zurich, Zurich 8093, Switzerland
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Laurie E Comstock
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
| | - A Murat Eren
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Marine Biological Laboratory, Woods Hole, MA 02543, USA; Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany; Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany; Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany; Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany.
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22
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Singh V, West G, Fiocchi C, Good CE, Katz J, Jacobs MR, Dichosa AEK, Flask C, Wesolowski M, McColl C, Grubb B, Ahmed S, Bank NC, Thamma K, Bederman I, Erokwu B, Yang X, Sundrud MS, Menghini P, Basson AR, Ezeji J, Viswanath SE, Veloo A, Sykes DB, Cominelli F, Rodriguez-Palacios A. Clonal Parabacteroides from Gut Microfistulous Tracts as Transmissible Cytotoxic Succinate-Commensal Model of Crohn's Disease Complications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574896. [PMID: 38260564 PMCID: PMC10802508 DOI: 10.1101/2024.01.09.574896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Crohn's disease (CD) has been traditionally viewed as a chronic inflammatory disease that cause gut wall thickening and complications, including fistulas, by mechanisms not understood. By focusing on Parabacteroides distasonis (presumed modern succinate-producing commensal probiotic), recovered from intestinal microfistulous tracts (cavernous fistulous micropathologies CavFT proposed as intermediate between 'mucosal fissures' and 'fistulas') in two patients that required surgery to remove CD-damaged ilea, we demonstrate that such isolates exert pathogenic/pathobiont roles in mouse models of CD. Our isolates are clonally-related; potentially emerging as transmissible in the community and mice; proinflammatory and adapted to the ileum of germ-free mice prone to CD-like ileitis (SAMP1/YitFc) but not healthy mice (C57BL/6J), and cytotoxic/ATP-depleting to HoxB8-immortalized bone marrow derived myeloid cells from SAMP1/YitFc mice when concurrently exposed to succinate and extracts from CavFT-derived E. coli , but not to cells from healthy mice. With unique genomic features supporting recent genetic exchange with Bacteroides fragilis -BGF539, evidence of international presence in primarily human metagenome databases, these CavFT Pdis isolates could represent to a new opportunistic Parabacteroides species, or subspecies (' cavitamuralis' ) adapted to microfistulous niches in CD.
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23
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Fayed B, Jagal J, Cagliani R, Kedia RA, Elsherbeny A, Bayraktutan H, Khoder G, Haider M. Co-administration of amoxicillin-loaded chitosan nanoparticles and inulin: A novel strategy for mitigating antibiotic resistance and preserving microbiota balance in Helicobacter pylori treatment. Int J Biol Macromol 2023; 253:126706. [PMID: 37673144 DOI: 10.1016/j.ijbiomac.2023.126706] [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: 07/06/2023] [Revised: 08/25/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
Helicobacter pylori (H. pylori) is a causative agent of various gastrointestinal diseases and eradication mainly relies on antibiotic treatment, with (AMX) being a key component. However, rising antibiotic resistance in H. pylori necessitates the use of antibiotics combination therapy, often disrupting gut microbiota equilibrium leading to further health complications. This study investigates a novel strategy utilizing AMX-loaded chitosan nanoparticles (AMX-CS NPs), co-administered with prebiotic inulin to counteract H. pylori infection while preserving microbiota health. Following microbroth dilution method, AMX displayed efficacy against H. pylori, with a MIC50 of 48.34 ± 3.3 ng/mL, albeit with a detrimental impact on Lactobacillus casei (L. casei). The co-administration of inulin (500 μg/mL) with AMX restored L. casei viability while retaining the lethal effect on H. pylori. Encapsulation of AMX in CS-NPs via ionic gelation method, resulted in particles of 157.8 ± 3.85 nm in size and an entrapment efficiency (EE) of 86.44 ± 2.19 %. Moreover, AMX-CS NPs showed a sustained drug release pattern over 72 h with no detectable toxicity on human dermal fibroblasts cell lines. Encapsulation of AMX into CS NPs also reduced its MIC50 against H. pylori, while its co-administration with inulin maintained L. casei viability. Interestingly, treatment with AMX-CS NPs also reduced the expression of the efflux pump gene hefA in H. pylori. This dual treatment strategy offers a promising approach for more selective antimicrobial treatment, minimizing disruption to healthy microbial communities while effectively addressing pathogenic threats.
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Affiliation(s)
- Bahgat Fayed
- Research Institute of Medical & Health Sciences, University of Sharjah, 27272 Sharjah, United Arab Emirates; Chemistry of Natural and Microbial Product Department, National Research Centre, Cairo 12622, Egypt
| | - Jayalakshmi Jagal
- Research Institute of Medical & Health Sciences, University of Sharjah, 27272 Sharjah, United Arab Emirates
| | - Roberta Cagliani
- Research Institute of Medical & Health Sciences, University of Sharjah, 27272 Sharjah, United Arab Emirates
| | - Reena A Kedia
- Research Institute of Medical & Health Sciences, University of Sharjah, 27272 Sharjah, United Arab Emirates
| | - Amr Elsherbeny
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom; Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Hulya Bayraktutan
- Division of Molecular Therapeutics and Formulation, School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom; Biodiscovery Institute, School of Medicine, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Ghalia Khoder
- Research Institute of Medical & Health Sciences, University of Sharjah, 27272 Sharjah, United Arab Emirates; Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, University of Sharjah, 27272 Sharjah, United Arab Emirates.
| | - Mohamed Haider
- Research Institute of Medical & Health Sciences, University of Sharjah, 27272 Sharjah, United Arab Emirates; Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, University of Sharjah, 27272 Sharjah, United Arab Emirates.
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24
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Li X, Brejnrod A, Thorsen J, Zachariasen T, Trivedi U, Russel J, Vestergaard GA, Stokholm J, Rasmussen MA, Sørensen SJ. Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults. Nat Commun 2023; 14:8526. [PMID: 38135681 PMCID: PMC10746713 DOI: 10.1038/s41467-023-44289-6] [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: 03/20/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Despite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in the latter case. Here, we use fecal metagenomic data from 662 Danish infants and 217 young adults to fill this gap. The gut resistomes are characterized by a bimodal distribution driven by E. coli composition. The typical profile of the gut resistome differs significantly between adults and infants, with the latter distinguished by higher gene and plasmid abundances. However, the predominant antibiotic resistance genes (ARGs) are the same. Antibiotic treatment reduces bacterial diversity and increased ARG and plasmid abundances in both cohorts, especially core ARGs. The effects of antibiotic treatments on the gut microbiome last longer in adults than in infants, and different antibiotics are associated with distinct impacts. Overall, this study broadens our current understanding of gut resistome dynamics and the impact of antibiotic treatment across age groups.
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Affiliation(s)
- Xuanji Li
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Asker Brejnrod
- Department of Health Technology, Technical University of Denmark, Section of Bioinformatics, 2800 Kgs, Lyngby, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Trine Zachariasen
- Department of Health Technology, Technical University of Denmark, Section of Bioinformatics, 2800 Kgs, Lyngby, Denmark
| | - Urvish Trivedi
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jakob Russel
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Gisle Alberg Vestergaard
- Department of Health Technology, Technical University of Denmark, Section of Bioinformatics, 2800 Kgs, Lyngby, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Department of Food Science, Section of Microbiology and Fermentation, University of Copenhagen, 1958, Frederiksberg C, Denmark
| | - Morten Arendt Rasmussen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
- Department of Food Science, Section of Microbiology and Fermentation, University of Copenhagen, 1958, Frederiksberg C, Denmark.
| | - Søren Johannes Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, 2100, Copenhagen, Denmark.
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25
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Ferreira ICDS, Menezes RDP, Jesus TAD, Machado ICDB, Lopes MSM, Costa AD, Araújo LBD, Röder DVDDB. Impact of intestinal colonization by Gram-negative bacteria on the incidence of bloodstream infections and lethality in critically ill neonates. J Infect Public Health 2023; 16 Suppl 1:9-18. [PMID: 37951729 DOI: 10.1016/j.jiph.2023.10.040] [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: 07/26/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Early detection of antimicrobial-resistant microorganisms is crucial to prevent subsequent invasive infections and contain their spread in the Neonatal Intensive Care Unit (NICU). This study aims to investigate the association between intestinal colonization (IC) by Gram-negative bacteria and the risk of bloodstream infection (BSI) in critically ill neonates. METHODS Data from the electronic medical records of 678 newborns admitted to a NICU Brazilian between 2018 and 2022 were retrospectively analyzed. Participants were monitored by the National Health Security Network. RESULTS Among neonates, 6.9 % had IC (56.9 % attributed to Acinetobacter baumannii); of these, 19.1 % developed BSI (66.7 % by Staphylococcus spp.). Within the A. baumannii colonization, 34.5 % occurred during an outbreak in September 2021. Colonized individuals had a longer mean length of stay (49.3 ± 26.4 days) and higher mortality rate (12.8 %) compared to non-colonized individuals (22.2 ± 16.9 days; 6.7 %, respectively). Previous use of antimicrobials and invasive devices significantly increased the risk of colonization. Colonization by drug-resistant microorganisms, along with the occurrence of BSI, was associated with increased mortality and reduced survival time. CONCLUSIONS IC contributed to the incidence of BSI, leading to more extended hospital stays and higher mortality rates. Its early detection proved to be essential to identify an outbreak and control the spread of resistant microorganisms within the NICU.
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Affiliation(s)
| | - Ralciane de Paula Menezes
- Technical Course in Clinical Analysis, Technical School of Health, Federal University of Uberlândia, Minas Gerais, Brazil.
| | - Thiago Alves de Jesus
- Undergraduate Course in Biomedicine, Institute of Biomedical Sciences, Federal University of Uberlândia, Minas Gerais, Brazil
| | - Izabella Clara de Brito Machado
- Undergraduate Course in Biomedicine, Institute of Biomedical Sciences, Federal University of Uberlândia, Minas Gerais, Brazil
| | - Mallu Santos Mendonça Lopes
- Undergraduate Course in Biomedicine, Institute of Biomedical Sciences, Federal University of Uberlândia, Minas Gerais, Brazil
| | - Aline Diulia Costa
- Undergraduate Course in Biomedicine, Institute of Biomedical Sciences, Federal University of Uberlândia, Minas Gerais, Brazil
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26
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Abbondio M, Tanca A, De Diego L, Sau R, Bibbò S, Pes GM, Dore MP, Uzzau S. Metaproteomic assessment of gut microbial and host functional perturbations in Helicobacter pylori-infected patients subjected to an antimicrobial protocol. Gut Microbes 2023; 15:2291170. [PMID: 38063474 PMCID: PMC10730194 DOI: 10.1080/19490976.2023.2291170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
The impact of therapeutic interventions on the human gut microbiota (GM) is a clinical issue of paramount interest given the strong interconnection between microbial dynamics and human health. Orally administered antibiotics are known to reduce GM biomass and modify GM taxonomic profile. However, the impact of antimicrobial therapies on GM functions and biochemical pathways has scarcely been studied. Here, we characterized the fecal metaproteome of 10 Helicobacter pylori-infected patients before (T0) and after 10 days (T1) of a successful quadruple therapy (bismuth, tetracycline, metronidazole, and rabeprazole) and 30 days after therapy cessation (T2), to investigate how GM and host functions change during the eradication and healing processes. At T1, the abundance ratio between microbial and host proteins was reversed compared with that at T0 and T2. Several pathobionts (including Klebsiella, Proteus, Enterococcus, Muribaculum, and Enterocloster) were increased at T1. Therapy reshaped the relative contributions of the functions required to produce acetate, propionate, and butyrate. Proteins related to the uptake and processing of complex glycans were increased. Microbial cross-feeding with sialic acid, fucose, and rhamnose was enhanced, whereas hydrogen sulfide production was reduced. Finally, microbial proteins involved in antibiotic resistance and inflammation were more abundant after therapy. Moreover, a reduction in host proteins with known roles in inflammation and H. pylori-mediated carcinogenesis was observed. In conclusion, our results support the use of metaproteomics to monitor drug-induced remodeling of GM and host functions, opening the way for investigating new antimicrobial therapies aimed at preserving gut environmental homeostasis.
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Affiliation(s)
- Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Laura De Diego
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Rosangela Sau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Stefano Bibbò
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Giovanni Mario Pes
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Maria Pina Dore
- Department of Medicine, Surgery and Pharmacy, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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27
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Fishbein SRS, Mahmud B, Dantas G. Antibiotic perturbations to the gut microbiome. Nat Rev Microbiol 2023; 21:772-788. [PMID: 37491458 DOI: 10.1038/s41579-023-00933-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
Antibiotic-mediated perturbation of the gut microbiome is associated with numerous infectious and autoimmune diseases of the gastrointestinal tract. Yet, as the gut microbiome is a complex ecological network of microorganisms, the effects of antibiotics can be highly variable. With the advent of multi-omic approaches for systems-level profiling of microbial communities, we are beginning to identify microbiome-intrinsic and microbiome-extrinsic factors that affect microbiome dynamics during antibiotic exposure and subsequent recovery. In this Review, we discuss factors that influence restructuring of the gut microbiome on antibiotic exposure. We present an overview of the currently complex picture of treatment-induced changes to the microbial community and highlight essential considerations for future investigations of antibiotic-specific outcomes. Finally, we provide a synopsis of available strategies to minimize antibiotic-induced damage or to restore the pretreatment architectures of the gut microbial community.
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Affiliation(s)
- Skye R S Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bejan Mahmud
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Division of Laboratory and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA.
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28
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Goubet AG, Rouanne M, Derosa L, Kroemer G, Zitvogel L. From mucosal infection to successful cancer immunotherapy. Nat Rev Urol 2023; 20:682-700. [PMID: 37433926 DOI: 10.1038/s41585-023-00784-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 07/13/2023]
Abstract
The clinical management of advanced malignancies of the upper and lower urinary tract has been revolutionized with the advent of immune checkpoint blockers (ICBs). ICBs reinstate or bolster pre-existing immune responses while creating new T cell specificities. Immunogenic cancers, which tend to benefit more from immunotherapy than cold tumours, harbour tumour-specific neoantigens, often associated with a high tumour mutational burden, as well as CD8+ T cell infiltrates and ectopic lymphoid structures. The identification of beneficial non-self tumour antigens and natural adjuvants is the focus of current investigation. Moreover, growing evidence suggests that urinary or intestinal commensals, BCG and uropathogenic Escherichia coli influence long-term responses in patients with kidney or bladder cancer treated with ICBs. Bacteria infecting urothelium could be a prominent target for T follicular helper cells and B cells, linking innate and cognate CD8+ memory responses. In the urinary tract, commensal flora differ between healthy and tumoural mucosae. Although antibiotics can affect the prognosis of urinary tract malignancies, bacteria can have a major influence on cancer immunosurveillance. Beyond their role as biomarkers, immune responses against uropathogenic commensals could be harnessed for the design of future immunoadjuvants that can be advantageously combined with ICBs.
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Affiliation(s)
- Anne-Gaëlle Goubet
- Gustave Roussy, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Center, Lausanne, Switzerland
| | - Mathieu Rouanne
- Gustave Roussy, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lisa Derosa
- Gustave Roussy, Villejuif, France
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicetre, France
| | - Guido Kroemer
- Gustave Roussy, Villejuif, France
- Equipe labellisée par la Ligue contre le Cancer, Université de Paris Cité, Sorbonne Université, Institut Universitaire de France, Inserm U1138, Centre de Recherche des Cordeliers, Paris, France
- Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, Villejuif, France
| | - Laurence Zitvogel
- Gustave Roussy, Villejuif, France.
- Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée - Ligue Nationale contre le Cancer, Villejuif, France.
- Faculté de Médecine, Université Paris-Saclay, Kremlin-Bicetre, France.
- Center of Clinical Investigations for In Situ Biotherapies of Cancer (BIOTHERIS) INSERM, CIC1428, Villejuif, France.
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Sartelli M, Barie PS, Coccolini F, Abbas M, Abbo LM, Abdukhalilova GK, Abraham Y, Abubakar S, Abu-Zidan FM, Adebisi YA, Adamou H, Afandiyeva G, Agastra E, Alfouzan WA, Al-Hasan MN, Ali S, Ali SM, Allaw F, Allwell-Brown G, Amir A, Amponsah OKO, Al Omari A, Ansaloni L, Ansari S, Arauz AB, Augustin G, Awazi B, Azfar M, Bah MSB, Bala M, Banagala ASK, Baral S, Bassetti M, Bavestrello L, Beilman G, Bekele K, Benboubker M, Beović B, Bergamasco MD, Bertagnolio S, Biffl WL, Blot S, Boermeester MA, Bonomo RA, Brink A, Brusaferro S, Butemba J, Caínzos MA, Camacho-Ortiz A, Canton R, Cascio A, Cassini A, Cástro-Sanchez E, Catarci M, Catena R, Chamani-Tabriz L, Chandy SJ, Charani E, Cheadle WG, Chebet D, Chikowe I, Chiara F, Cheng VCC, Chioti A, Cocuz ME, Coimbra R, Cortese F, Cui Y, Czepiel J, Dasic M, de Francisco Serpa N, de Jonge SW, Delibegovic S, Dellinger EP, Demetrashvili Z, De Palma A, De Silva D, De Simone B, De Waele J, Dhingra S, Diaz JJ, Dima C, Dirani N, Dodoo CC, Dorj G, Duane TM, Eckmann C, Egyir B, Elmangory MM, Enani MA, Ergonul O, Escalera-Antezana JP, Escandon K, Ettu AWOO, Fadare JO, Fantoni M, Farahbakhsh M, Faro MP, Ferreres A, Flocco G, Foianini E, Fry DE, Garcia AF, Gerardi C, Ghannam W, Giamarellou H, Glushkova N, Gkiokas G, Goff DA, Gomi H, Gottfredsson M, Griffiths EA, Guerra Gronerth RI, Guirao X, Gupta YK, Halle-Ekane G, Hansen S, Haque M, Hardcastle TC, Hayman DTS, Hecker A, Hell M, Ho VP, Hodonou AM, Isik A, Islam S, Itani KMF, Jaidane N, Jammer I, Jenkins DR, Kamara IF, Kanj SS, Jumbam D, Keikha M, Khanna AK, Khanna S, Kapoor G, Kapoor G, Kariuki S, Khamis F, Khokha V, Kiggundu R, Kiguba R, Kim HB, Kim PK, Kirkpatrick AW, Kluger Y, Ko WC, Kok KYY, Kotecha V, Kouma I, Kovacevic B, Krasniqi J, Krutova M, Kryvoruchko I, Kullar R, Labi KA, Labricciosa FM, Lakoh S, Lakatos B, Lansang MAD, Laxminarayan R, Lee YR, Leone M, Leppaniemi A, Hara GL, Litvin A, Lohsiriwat V, Machain GM, Mahomoodally F, Maier RV, Majumder MAA, Malama S, Manasa J, Manchanda V, Manzano-Nunez R, Martínez-Martínez L, Martin-Loeches I, Marwah S, Maseda E, Mathewos M, Maves RC, McNamara D, Memish Z, Mertz D, Mishra SK, Montravers P, Moro ML, Mossialos E, Motta F, Mudenda S, Mugabi P, Mugisha MJM, Mylonakis E, Napolitano LM, Nathwani D, Nkamba L, Nsutebu EF, O’Connor DB, Ogunsola S, Jensen PØ, Ordoñez JM, Ordoñez CA, Ottolino P, Ouedraogo AS, Paiva JA, Palmieri M, Pan A, Pant N, Panyko A, Paolillo C, Patel J, Pea F, Petrone P, Petrosillo N, Pintar T, Plaudis H, Podda M, Ponce-de-Leon A, Powell SL, Puello-Guerrero A, Pulcini C, Rasa K, Regimbeau JM, Rello J, Retamozo-Palacios MR, Reynolds-Campbell G, Ribeiro J, Rickard J, Rocha-Pereira N, Rosenthal VD, Rossolini GM, Rwegerera GM, Rwigamba M, Sabbatucci M, Saladžinskas Ž, Salama RE, Sali T, Salile SS, Sall I, Kafil HS, Sakakushev BE, Sawyer RG, Scatizzi M, Seni J, Septimus EJ, Sganga G, Shabanzadeh DM, Shelat VG, Shibabaw A, Somville F, Souf S, Stefani S, Tacconelli E, Tan BK, Tattevin P, Rodriguez-Taveras C, Telles JP, Téllez-Almenares O, Tessier J, Thang NT, Timmermann C, Timsit JF, Tochie JN, Tolonen M, Trueba G, Tsioutis C, Tumietto F, Tuon FF, Ulrych J, Uranues S, van Dongen M, van Goor H, Velmahos GC, Vereczkei A, Viaggi B, Viale P, Vila J, Voss A, Vraneš J, Watkins RR, Wanjiru-Korir N, Waworuntu O, Wechsler-Fördös A, Yadgarova K, Yahaya M, Yahya AI, Xiao Y, Zakaria AD, Zakrison TL, Zamora Mesia V, Siquini W, Darzi A, Pagani L, Catena F. Ten golden rules for optimal antibiotic use in hospital settings: the WARNING call to action. World J Emerg Surg 2023; 18:50. [PMID: 37845673 PMCID: PMC10580644 DOI: 10.1186/s13017-023-00518-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 09/23/2023] [Indexed: 10/18/2023] Open
Abstract
Antibiotics are recognized widely for their benefits when used appropriately. However, they are often used inappropriately despite the importance of responsible use within good clinical practice. Effective antibiotic treatment is an essential component of universal healthcare, and it is a global responsibility to ensure appropriate use. Currently, pharmaceutical companies have little incentive to develop new antibiotics due to scientific, regulatory, and financial barriers, further emphasizing the importance of appropriate antibiotic use. To address this issue, the Global Alliance for Infections in Surgery established an international multidisciplinary task force of 295 experts from 115 countries with different backgrounds. The task force developed a position statement called WARNING (Worldwide Antimicrobial Resistance National/International Network Group) aimed at raising awareness of antimicrobial resistance and improving antibiotic prescribing practices worldwide. The statement outlined is 10 axioms, or "golden rules," for the appropriate use of antibiotics that all healthcare workers should consistently adhere in clinical practice.
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Berglund F, Rodríguez-Molina D, Gradisteanu Pircalabioru G, Blaak H, Chifiriuc MC, Czobor Barbu I, Flach CF, Gheorghe-Barbu I, Măruțescu L, Popa M, de Roda Husman AM, Wengenroth L, Schmitt H, Larsson DGJ. The resistome and microbiome of wastewater treatment plant workers - The AWARE study. ENVIRONMENT INTERNATIONAL 2023; 180:108242. [PMID: 37816267 DOI: 10.1016/j.envint.2023.108242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Urban wastewater treatment plants harbor a large collection of antibiotic resistant enteric bacteria. It is therefore reasonable to hypothesize that workers at such plants would possess a more diverse set of resistant enteric bacteria, compared to the general population. To address this hypothesis, we have compared the fecal microbiome and resistome of 87 workers at wastewater treatment plants (WWTPs) from Romania and the Netherlands to those of 87 control individuals, using shotgun metagenomics. Controlling for potential confounders, neither the total antibiotic resistance gene (ARG) abundance, nor the overall bacterial composition were significantly different between the two groups. If anything, the ARG richness was slightly lower in WWTP workers, and in a stratified analysis the total ARG abundance was significantly lower in Dutch workers compared to Dutch control participants. We identified country of residence, together with recent antibiotic intake in the Dutch population, as the largest contributing factors to the total abundance of ARGs. A striking side-finding was that sex was associated with carriage of disinfectant resistance genes, with women in both Romania and the Netherlands having significantly higher abundance compared to men. A follow up investigation including an additional 313 publicly available samples from healthy individuals from three additional countries showed that the difference was significant for three genes conferring resistance to chemicals commonly used in cosmetics and cleaning products. We therefore hypothesize that the use of cosmetics and, possibly, cleaning products leads to higher abundance of disinfectant resistance genes in the microbiome of the users. Altogether, this study shows that working at a WWTP does not lead to a higher abundance or diversity of ARGs and no large shifts in the overall gut microbial composition in comparison to participants not working at a WWTP. Instead, other factors such as country of residence, recent antibiotic intake and sex seem to play a larger role.
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Affiliation(s)
- Fanny Berglund
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Daloha Rodríguez-Molina
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU (Ludwig-Maximilians-Universität) Munich, Munich, Germany
| | - Gratiela Gradisteanu Pircalabioru
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania; Academy of Romanian Scientists, Bucharest, Romania
| | - Hetty Blaak
- Centre of Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Mariana-Carmen Chifiriuc
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania; Academy of Romanian Scientists, Bucharest, Romania
| | - Ilda Czobor Barbu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Irina Gheorghe-Barbu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania
| | - Luminița Măruțescu
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania
| | - Marcela Popa
- Department of Microbiology and Immunology, Faculty of Biology, University of Bucharest and the Academy of Romanian Scientists, Bucharest, Romania
| | - Ana Maria de Roda Husman
- Centre of Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Laura Wengenroth
- Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU (Ludwig-Maximilians-Universität) Munich, Munich, Germany
| | - Heike Schmitt
- Centre of Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden.
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Domzaridou E, Van Staa T, Renehan AG, Cook N, Welfare W, Ashcroft DM, Palin V. The Impact of Oral Antibiotics Prior to Cancer Diagnosis on Overall Patient Survival: Findings from an English Population-Based Cohort Study. Curr Oncol 2023; 30:8434-8443. [PMID: 37754529 PMCID: PMC10528751 DOI: 10.3390/curroncol30090614] [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: 07/29/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND There is limited evidence in humans as to whether antibiotics impact the effectiveness of cancer treatments. Rodent studies have shown that disruption in gut microbiota due to antibiotics decreases cancer therapy effectiveness. We evaluated the associations between the antibiotic treatment of different time periods before cancer diagnoses and long-term mortality. METHODS Using the Clinical Practice Research Datalink GOLD, linked to the Cancer Registry's and the Office for National Statistics' mortality records, we delineated a study cohort that involved cancer patients who were prescribed antibiotics 0-3 months; 3-24 months; or more than 24 months before cancer diagnosis. Patients' exposure to antibiotics was compared according to the recency of prescriptions and time-to-event (all-cause mortality) by applying Cox models. RESULTS 111,260 cancer patients from England were included in the analysis. Compared with antibiotic prescriptions that were issued in the past, patients who had been prescribed antibiotics shortly before cancer diagnosis presented an increased hazard ratio (HR) for mortality. For leukaemia, the HR in the Cancer Registry was 1.32 (95% CI 1.16-1.51), for lymphoma it was 1.22 (1.08-1.36), for melanoma it was 1.28 (1.10-1.49), and for myeloma it was 1.19 (1.04-1.36). Increased HRs were observed for cancer of the uterus, bladder, and breast and ovarian and colorectal cancer. CONCLUSIONS Antibiotics that had been issued within the three months prior to cancer diagnosis may reduce the effectiveness of chemotherapy and immunotherapy. Judicious antibiotic prescribing is needed among cancer patients.
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Affiliation(s)
- Eleni Domzaridou
- National Institute for Health and Care Research Greater Manchester Patient Safety Research Collaboration, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
| | - Tjeerd Van Staa
- Centre for Health Informatics, Division of Informatics, Imaging and Data Science, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (T.V.S.); (V.P.)
- Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Andrew G. Renehan
- Centre for Health Informatics, Manchester Cancer Research Centre, University of Manchester, Manchester M13 9PL, UK;
| | - Natalie Cook
- Division of Cancer Science, School of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Christie NHS Foundation Trust, Wilmslow Road, Manchester M20 4BX, UK
| | - William Welfare
- Public Health England Northwest, 3 Piccadilly Place, London Road, Manchester M1 3BN, UK;
| | - Darren M. Ashcroft
- National Institute for Health and Care Research Greater Manchester Patient Safety Research Collaboration, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK;
- Centre for Pharmacoepidemiology and Drug Safety, Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Victoria Palin
- Centre for Health Informatics, Division of Informatics, Imaging and Data Science, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK; (T.V.S.); (V.P.)
- Maternal and Fetal Research Centre, Division of Developmental Biology and Medicine, University of Manchester, St Marys Hospital, Oxford Road, Manchester M13 9WL, UK
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Chen J, Zhu J, Lu W, Wang H, Pan M, Tian P, Zhao J, Zhang H, Chen W. Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance. Nutrients 2023; 15:3925. [PMID: 37764709 PMCID: PMC10536327 DOI: 10.3390/nu15183925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic treatment can lead to a loss of diversity of gut microbiota and may adversely affect gut microbiota composition and host health. Previous studies have indicated that the recovery of gut microbes from antibiotic-induced disruption may be guided by specific microbial species. We expect to predict recovery or non-recovery using these crucial species or other indices after antibiotic treatment only when the gut microbiota changes. This study focused on this prediction problem using a novel ensemble learning framework to identify a set of common and reasonably predictive recovery-associated bacterial species (p-RABs), enabling us to predict the host microbiome recovery status under broad-spectrum antibiotic treatment. Our findings also propose other predictive indicators, suggesting that higher taxonomic and functional diversity may correlate with an increased likelihood of successful recovery. Furthermore, to explore the validity of p-RABs, we performed a metabolic support analysis and identified Akkermansia muciniphila and Bacteroides uniformis as potential key supporting species for reconstruction interventions. Experimental results from a C57BL/6J male mouse model demonstrated the effectiveness of p-RABs in facilitating intestinal microbial reconstitution. Thus, we proved the reliability of the new p-RABs and validated a practical intervention scheme for gut microbiota reconstruction under antibiotic disturbance.
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Affiliation(s)
- Jing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingluo Pan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Peijun Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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Chen J, Siliceo SL, Ni Y, Nielsen HB, Xu A, Panagiotou G. Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions. MICROBIOME 2023; 11:178. [PMID: 37553697 PMCID: PMC10408196 DOI: 10.1186/s40168-023-01604-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 06/19/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND A growing body of evidence suggests that the gut microbiota is strongly linked to general human health. Microbiome-directed interventions, such as diet and exercise, are acknowledged as a viable and achievable strategy for preventing disorders and improving human health. However, due to the significant inter-individual diversity of the gut microbiota between subjects, lifestyle recommendations are expected to have distinct and highly variable impacts to the microbiome structure. RESULTS Here, through a large-scale meta-analysis including 1448 shotgun metagenomics samples obtained longitudinally from 396 individuals during lifestyle studies, we revealed Bacteroides stercoris, Prevotella copri, and Bacteroides vulgatus as biomarkers of microbiota's resistance to structural changes, and aromatic and non-aromatic amino acid biosynthesis as important regulator of microbiome dynamics. We established criteria for distinguishing between significant compositional changes from normal microbiota fluctuation and classified individuals based on their level of response. We further developed a machine learning model for predicting "responders" and "non-responders" independently of the type of intervention with an area under the curve of up to 0.86 in external validation cohorts of different ethnicities. CONCLUSIONS We propose here that microbiome-based stratification is possible for identifying individuals with highly plastic or highly resistant microbial structures. Identifying subjects that will not respond to generalized lifestyle therapeutic interventions targeting the restructuring of gut microbiota is important to ensure that primary end-points of clinical studies are reached. Video Abstract.
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Affiliation(s)
- Jiarui Chen
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute -Microbiome Dynamics, Jena, Germany
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
| | - Sara Leal Siliceo
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute -Microbiome Dynamics, Jena, Germany
| | - Yueqiong Ni
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute -Microbiome Dynamics, Jena, Germany
| | - Henrik B Nielsen
- Clinical Microbiomics, Fruebjergvej 3, 2100, Copenhagen, Denmark
| | - Aimin Xu
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Medicine, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong S.A.R., China
| | - Gianni Panagiotou
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute -Microbiome Dynamics, Jena, Germany.
- Department of Medicine, The University of Hong Kong, Hong Kong S.A.R., China.
- Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany.
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Frioux C, Ansorge R, Özkurt E, Ghassemi Nedjad C, Fritscher J, Quince C, Waszak SM, Hildebrand F. Enterosignatures define common bacterial guilds in the human gut microbiome. Cell Host Microbe 2023; 31:1111-1125.e6. [PMID: 37339626 DOI: 10.1016/j.chom.2023.05.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/03/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023]
Abstract
The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.
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Affiliation(s)
- Clémence Frioux
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK; Inria, University of Bordeaux, INRAE, 33400 Talence, France.
| | - Rebecca Ansorge
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Ezgi Özkurt
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | | | - Joachim Fritscher
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Christopher Quince
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo 0318, Norway; Department of Neurology, University of California, San Francisco, San Francisco, CA 94148, USA; Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Falk Hildebrand
- Food, Microbiome, and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ Norwich, Norfolk, UK; Digital Biology, Earlham Institute NR4 7UZ Norwich, Norfolk, UK.
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Casadei E, Mani A, Cisco M, Vågnes Ø, Salinas I, Patel S. Sex-dependent effects of mechanical delousing on the skin microbiome of broodstock Atlantic salmon (Salmo salar L.). Sci Rep 2023; 13:10824. [PMID: 37402791 DOI: 10.1038/s41598-023-37670-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/26/2023] [Indexed: 07/06/2023] Open
Abstract
Delousing strategies, including mechanical delousing, are typically used to treat Atlantic salmon (Salmo salar) sea lice infestations. In this study, we evaluate the impact of mechanical delousing (Hydrolicer) on the skin bacterial microbiome of broodstock female and male Atlantic salmon. 16S rDNA sequencing of salmon skin microbial communities was performed immediately before delousing, right after delousing and 2 and 13 days post-delousing (dpd). The skin bacterial community of female salmon was more diverse than that of males at the start of the experiment. Overall, hydrolycer caused losses in alpha diversity in females and increases in alpha diversity in males. Hydrolicer also caused rapid shifts in the skin microbial community composition immediately after delicing in a sex-specific manner. There was a decrease in abundance of Proteobacteria and Bacteriodetes in both female and male salmon, whereas Firmicutes and Tenericutes abundances increased. Interestingly, the female community recovered faster, while the male community remained dysbiotic 13 dpd due to expansions in Bacteroidetes (Pseudomonadaceae) and Firmicutes. Our data suggest that female broodstock are more resilient to Hydrolicer treatment due to their more diverse skin microbiota community, and that sex influences the skin microbial community and therefore host health outcomes during common farming manipulations.
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Affiliation(s)
- Elisa Casadei
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Amir Mani
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Mariela Cisco
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Øyvind Vågnes
- Vaxxinova Norway, Kong Christian Frederiks Plass 3, 5006, Bergen, Norway
- Blue Analytics AS, Kong Christian Frederiks Plass 3, 5006, Bergen, Norway
| | - Irene Salinas
- Department of Biology, Center for Evolutionary and Theoretical Immunology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Sonal Patel
- Vaxxinova Norway, Kong Christian Frederiks Plass 3, 5006, Bergen, Norway.
- Norwegian Veterinary Institute, Thormøhlens Gate 53C, 5006, Bergen, Norway.
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Sun P, Wang M, Zheng W, Li S, Zhu X, Chai X, Zhao S. Unbalanced diets enhance the complexity of gut microbial network but destabilize its stability and resistance. STRESS BIOLOGY 2023; 3:20. [PMID: 37676325 PMCID: PMC10441997 DOI: 10.1007/s44154-023-00098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/05/2023] [Indexed: 09/08/2023]
Abstract
Stability is a fundamental ecological property of the gut microbiota and is associated with host health. Numerous studies have shown that unbalanced dietary components disturb the gut microbial composition and thereby contribute to the onset and progression of disease. However, the impact of unbalanced diets on the stability of the gut microbiota is poorly understood. In the present study, four-week-old mice were fed a plant-based diet high in refined carbohydrates or a high-fat diet for four weeks to simulate a persistent unbalanced diet. We found that persistent unbalanced diets significantly reduced the gut bacterial richness and increased the complexity of bacterial co-occurrence networks. Furthermore, the gut bacterial response to unbalanced diets was phylogenetically conserved, which reduced network modularity and enhanced the proportion of positive associations between community taxon, thereby amplifying the co-oscillation of perturbations among community species to destabilize gut microbial communities. The disturbance test revealed that the gut microbiota of mice fed with unbalanced diets was less resistant to antibiotic perturbation and pathogenic bacteria invasion. This study may fill a gap in the mechanistic understanding of the gut microbiota stability in response to diet and provide new insights into the gut microbial ecology.
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Affiliation(s)
- Penghao Sun
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Mengli Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Wei Zheng
- College of Resources and Environment Sciences, Northwest A&F University, Yangling, China
| | - Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Xiaoyan Zhu
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| | - Xuejun Chai
- College of Basic Medicine, Xi'an Medical University, Xi'an, China.
| | - Shanting Zhao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China.
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Qi X, Zhang Y, Zhang Y, Luo F, Song K, Wang G, Ling F. Vitamin B 12 produced by Cetobacterium somerae improves host resistance against pathogen infection through strengthening the interactions within gut microbiota. MICROBIOME 2023; 11:135. [PMID: 37322528 PMCID: PMC10268390 DOI: 10.1186/s40168-023-01574-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/15/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND Pathogen infections seriously affect host health, and the use of antibiotics increases the risk of the emergence of drug-resistant bacteria and also increases environmental and health safety risks. Probiotics have received much attention for their excellent ability to prevent pathogen infections. Particularly, explaining mechanism of action of probiotics against pathogen infections is important for more efficient and rational use of probiotics and the maintenance of host health. RESULTS Here, we describe the impacts of probiotic on host resistance to pathogen infections. Our findings revealed that (I) the protective effect of oral supplementation with B. velezensis against Aeromonas hydrophila infection was dependent on gut microbiota, specially the anaerobic indigenous gut microbe Cetobacterium; (II) Cetobacterium was a sensor of health, especially for fish infected with pathogenic bacteria; (III) the genome resolved the ability of Cetobacterium somerae CS2105-BJ to synthesize vitamin B12 de novo, while in vivo and in vitro metabolism assays also showed the ability of Cetobacterium somerae CS2105-BJ to produce vitamin B12; (IV) the addition of vitamin B12 significantly altered the gut redox status and the gut microbiome structure and function, and then improved the stability of the gut microbial ecological network, and enhanced the gut barrier tight junctions to prevent the pathogen infection. CONCLUSION Collectively, this study found that the effect of probiotics in enhancing host resistance to pathogen infections depended on function of B12 produced by an anaerobic indigenous gut microbe, Cetobacterium. Furthermore, as a gut microbial regulator, B12 exhibited the ability to strengthen the interactions within gut microbiota and gut barrier tight junctions, thereby improving host resistance against pathogen infection. Video Abstract.
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Affiliation(s)
- Xiaozhou Qi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yong Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yilin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fei Luo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Kaige Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Gaoxue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
| | - Fei Ling
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China.
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38
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Fung DLX, Li X, Leung CK, Hu P. A self-knowledge distillation-driven CNN-LSTM model for predicting disease outcomes using longitudinal microbiome data. BIOINFORMATICS ADVANCES 2023; 3:vbad059. [PMID: 37228387 PMCID: PMC10203376 DOI: 10.1093/bioadv/vbad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/03/2023] [Accepted: 05/01/2023] [Indexed: 05/27/2023]
Abstract
Motivation Human microbiome is complex and highly dynamic in nature. Dynamic patterns of the microbiome can capture more information than single point inference as it contains the temporal changes information. However, dynamic information of the human microbiome can be hard to be captured due to the complexity of obtaining the longitudinal data with a large volume of missing data that in conjunction with heterogeneity may provide a challenge for the data analysis. Results We propose using an efficient hybrid deep learning architecture convolutional neural network-long short-term memory, which combines with self-knowledge distillation to create highly accurate models to analyze the longitudinal microbiome profiles to predict disease outcomes. Using our proposed models, we analyzed the datasets from Predicting Response to Standardized Pediatric Colitis Therapy (PROTECT) study and DIABIMMUNE study. We showed the significant improvement in the area under the receiver operating characteristic curve scores, achieving 0.889 and 0.798 on PROTECT study and DIABIMMUNE study, respectively, compared with state-of-the-art temporal deep learning models. Our findings provide an effective artificial intelligence-based tool to predict disease outcomes using longitudinal microbiome profiles from collected patients. Availability and implementation The data and source code can be accessed at https://github.com/darylfung96/UC-disease-TL.
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Affiliation(s)
- Daryl L X Fung
- Department of Computer Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Xu Li
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Carson K Leung
- Department of Computer Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Watson AR, Füssel J, Veseli I, DeLongchamp JZ, Silva M, Trigodet F, Lolans K, Shaiber A, Fogarty E, Runde JM, Quince C, Yu MK, Söylev A, Morrison HG, Lee STM, Kao D, Rubin DT, Jabri B, Louie T, Eren AM. Metabolic independence drives gut microbial colonization and resilience in health and disease. Genome Biol 2023; 24:78. [PMID: 37069665 PMCID: PMC10108530 DOI: 10.1186/s13059-023-02924-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 04/07/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. RESULTS Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. CONCLUSIONS These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
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Affiliation(s)
- Andrea R Watson
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jessika Füssel
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany
| | - Iva Veseli
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Marisela Silva
- Department of Medicine, The University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Florian Trigodet
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Karen Lolans
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Alon Shaiber
- Biophysical Sciences Program, The University of Chicago, Chicago, IL, 60637, USA
| | - Emily Fogarty
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Joseph M Runde
- Department of Pediatrics, Lurie Children's Hospital of Chicago, Chicago, IL, 60611, USA
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Michael K Yu
- Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA
| | - Arda Söylev
- Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
| | - Hilary G Morrison
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Falmouth, MA, 02543, USA
| | - Sonny T M Lee
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Dina Kao
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2G3, Canada
| | - David T Rubin
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Thomas Louie
- Department of Medicine, The University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - A Murat Eren
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.
- Committee On Microbiology, The University of Chicago, Chicago, IL, 60637, USA.
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129, Oldenburg, Germany.
- Marine Biological Laboratory, Josephine Bay Paul Center, Woods Hole, Falmouth, MA, 02543, USA.
- Helmholtz Institute for Functional Marine Biodiversity, 26129, Oldenburg, Germany.
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40
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Fogarty EC, Schechter MS, Lolans K, Sheahan ML, Veseli I, Moore R, Kiefl E, Moody T, Rice PA, Yu MK, Mimee M, Chang EB, Mclellan SL, Willis AD, Comstock LE, Eren AM. A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534219. [PMID: 36993556 PMCID: PMC10055365 DOI: 10.1101/2023.03.25.534219] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.
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Affiliation(s)
- Emily C Fogarty
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Matthew S Schechter
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Karen Lolans
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Madeline L. Sheahan
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Iva Veseli
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Ryan Moore
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Evan Kiefl
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Thomas Moody
- Department of Systems Biology, Columbia University, New York, NY, 10032 USA
| | - Phoebe A Rice
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry, University of Chicago, Chicago, IL, 60637, USA
| | | | - Mark Mimee
- Committee on Microbiology, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, IL 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Sandra L Mclellan
- School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53204, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Laurie E Comstock
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
- Department of Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - A Murat Eren
- Marine Biological Laboratory, Woods Hole, MA, 02543, USA
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, 27570 Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26129 Oldenburg, Germany
- Helmholtz Institute for Functional Marine Biodiversity, 26129 Oldenburg, Germany
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Lee K, Raguideau S, Sirén K, Asnicar F, Cumbo F, Hildebrand F, Segata N, Cha CJ, Quince C. Population-level impacts of antibiotic usage on the human gut microbiome. Nat Commun 2023; 14:1191. [PMID: 36864029 PMCID: PMC9981903 DOI: 10.1038/s41467-023-36633-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.
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Affiliation(s)
- Kihyun Lee
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea
- CJ Bioscience, Seoul, 04527, Republic of Korea
| | | | - Kimmo Sirén
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Fabio Cumbo
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Falk Hildebrand
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Chang-Jun Cha
- Department of Systems Biotechnology and Center for Antibiotic Resistome, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, NR4 7UZ, UK.
- Gut Microbes and Health, Quadram Institute, Norwich, NR4 7UQ, UK.
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK.
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Bourdeau-Julien I, Castonguay-Paradis S, Rochefort G, Perron J, Lamarche B, Flamand N, Di Marzo V, Veilleux A, Raymond F. The diet rapidly and differentially affects the gut microbiota and host lipid mediators in a healthy population. MICROBIOME 2023; 11:26. [PMID: 36774515 PMCID: PMC9921707 DOI: 10.1186/s40168-023-01469-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 01/16/2023] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bioactive lipids produced by human cells or by the gut microbiota might play an important role in health and disease. Dietary intakes are key determinants of the gut microbiota, its production of short-chain (SCFAs) and branched-chain fatty acids (BCFAs), and of the host endocannabinoidome signalling, which are all involved in metabolic diseases. This hypothesis-driven longitudinal fixed sequence nutritional study, realized in healthy participants, was designed to determine if a lead-in diet affects the host response to a short-term dietary intervention. Participants received a Mediterranean diet (MedDiet) for 3 days, a 13-day lead-in controlled diet reflecting the average Canadian dietary intake (CanDiet), and once again a MedDiet for 3 consecutive days. Fecal and blood samples were collected at the end of each dietary phase to evaluate alterations in gut microbiota composition and plasma levels of endocannabinoidome mediators, SCFAs, and BCFAs. RESULTS We observed an immediate and reversible modulation of plasma endocannabinoidome mediators, BCFAs, and some SCFAs in response to both diets. BCFAs were more strongly reduced by the MedDiet when the latter was preceded by the lead-in CanDiet. The gut microbiota response was also immediate, but not all changes due to the CanDiet were reversible following a short dietary MedDiet intervention. Higher initial microbiome diversity was associated with reduced microbiota modulation after short-term dietary interventions. We also observed that BCFAs and 2-monoacylglycerols had many, but distinct, correlations with gut microbiota composition. Several taxa modulated by dietary intervention were previously associated to metabolic disorders, warranting the need to control for recent diet in observational association studies. CONCLUSIONS Our results indicate that lipid mediators involved in the communication between the gut microbiota and host metabolism exhibit a rapid response to dietary changes, which is also the case for some, but not all, microbiome taxa. The lead-in diet influenced the gut microbiome and BCFA, but not the endocannabinoidome, response to the MedDiet. A higher initial microbiome diversity favored the stability of the gut microbiota in response to dietary changes. This study highlights the importance of considering the previous diet in studies relating the gut microbiome with lipid signals involved in host metabolism. Video Abstract.
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Affiliation(s)
- Isabelle Bourdeau-Julien
- Centre Nutrition, santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), École de nutrition, Université Laval, 2440, boulevard Hochelaga, Québec, G1V 0A6 Canada
- Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, Quebec, Canada
| | - Sophie Castonguay-Paradis
- Centre Nutrition, santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), École de nutrition, Université Laval, 2440, boulevard Hochelaga, Québec, G1V 0A6 Canada
- Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, Quebec, Canada
| | - Gabrielle Rochefort
- Centre Nutrition, santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), École de nutrition, Université Laval, 2440, boulevard Hochelaga, Québec, G1V 0A6 Canada
- Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, Quebec, Canada
| | - Julie Perron
- Centre Nutrition, santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), École de nutrition, Université Laval, 2440, boulevard Hochelaga, Québec, G1V 0A6 Canada
- Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, Quebec, Canada
| | - Benoît Lamarche
- Centre Nutrition, santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), École de nutrition, Université Laval, 2440, boulevard Hochelaga, Québec, G1V 0A6 Canada
| | - Nicolas Flamand
- Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, Quebec, Canada
- Centre de recherche de l’Institut de cardiologie et de pneumologie de Québec, Faculté de médecine, Département de médecine, Université Laval, Québec, Canada
| | - Vincenzo Di Marzo
- Centre Nutrition, santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), École de nutrition, Université Laval, 2440, boulevard Hochelaga, Québec, G1V 0A6 Canada
- Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, Quebec, Canada
- Centre de recherche de l’Institut de cardiologie et de pneumologie de Québec, Faculté de médecine, Département de médecine, Université Laval, Québec, Canada
- Unité Mixte Internationale en Recherche Chimique et Biomoléculaire sur le Microbiome et son Impact Sur la Santé Métabolique et la Nutrition (UMI-MicroMeNu), Université Laval and Consiglio Nazionale delle Ricerche, Istituto di Chimica Biomolecolare, Via Campi Flegrei 34, 80078 Pozzuoli, (NA) Italy
| | - Alain Veilleux
- Centre Nutrition, santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), École de nutrition, Université Laval, 2440, boulevard Hochelaga, Québec, G1V 0A6 Canada
- Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, Quebec, Canada
| | - Frédéric Raymond
- Centre Nutrition, santé et société (NUTRISS), Institut sur la nutrition et les aliments fonctionnels (INAF), École de nutrition, Université Laval, 2440, boulevard Hochelaga, Québec, G1V 0A6 Canada
- Canada Excellence Research Chair in the Microbiome-Endocannabinoidome Axis in Metabolic Health, Quebec, Canada
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Dinat S, Orchard A, Van Vuuren S. A scoping review of African natural products against gastric ulcers and Helicobacter pylori. JOURNAL OF ETHNOPHARMACOLOGY 2023; 301:115698. [PMID: 36174808 DOI: 10.1016/j.jep.2022.115698] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE African traditional medicine is one of the oldest and most diverse practices for treating ailments and numerous natural products have been recommended for gastric ulcer treatment. Helicobacter pylori is the main causative organism implicated in several diseases, most notably in causing inflammation and the onset of gastric ulcers. Current H. pylori treatment methods are losing efficacy as H. pylori rapidly gains resistance to antibiotics. Hence, a search into natural products and their historical traditional efficacy for the treatment of gastric ulcers is of interest. AIM OF THE STUDY This review aimed to summarise the African use of natural products, including medicinal plants noted in ethnobotanical reviews, used traditionally to treat gastric ulcers, and highlights the investigations into the anti-H. pylori activity of medicinal plants and bee products found in Africa. METHODOLOGY A systematic review was carried out to identify natural products, including those used traditionally in Africa to treat gastric ulcers, and to correlate this with scientific investigations into the anti-H. pylori activity of natural products used in Africa. RESULTS A total of 107 literature sources describing the traditional use of medicinal plants in gastric ulcer treatment were found, from which 360 medicinal plants were identified. Of the plants used traditionally for gastric ulcer treatment, 11% were investigated either in vitro or in vivo for anti-ulcer and anti-H. pylori activity. Of the 122 medicinal plants eliciting antimicrobial or anti-ulcer activity, Hibiscus sabdariffa L. calyx extract and Terminalia macroptera Guill. & Perr. root extract were found to have the most noteworthy antimicrobial activity, with minimum inhibitory concentrations (MICs) of 0.01 mg/mL and 0.03 mg/mL respectively. The essential oils of Piper longum L. and Pachira aquatica Aubl. displayed the most notable in vitro anti-H. pylori activity (MIC of 0.01 mg/mL and 0.02 mg/mL). Several in vivo studies found medicinal plant extracts effective in reducing the H. pylori load along the gastric mucosa. The South African honey variants, Pure Honey and Champagne Royal Train (common names given by supplier) were the most antimicrobially effective (MIC of 0.01-10.0%, 0.63-10.00% v/v) in inhibiting H. pylori when assessed in vitro. CONCLUSION These results highlight the potential of natural products to inhibit H. pylori growth and serve as a possible stepping-stone in understanding the management of ulcers. Furthermore, effective natural product treatment or prophylactic use for preventing H. pylori growth may provide a more affordable option for African populations.
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Affiliation(s)
- S Dinat
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
| | - A Orchard
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa
| | - S Van Vuuren
- Department of Pharmacy and Pharmacology, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, Johannesburg, 2193, South Africa.
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Aggarwal N, Kitano S, Puah GRY, Kittelmann S, Hwang IY, Chang MW. Microbiome and Human Health: Current Understanding, Engineering, and Enabling Technologies. Chem Rev 2023; 123:31-72. [PMID: 36317983 PMCID: PMC9837825 DOI: 10.1021/acs.chemrev.2c00431] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Indexed: 01/12/2023]
Abstract
The human microbiome is composed of a collection of dynamic microbial communities that inhabit various anatomical locations in the body. Accordingly, the coevolution of the microbiome with the host has resulted in these communities playing a profound role in promoting human health. Consequently, perturbations in the human microbiome can cause or exacerbate several diseases. In this Review, we present our current understanding of the relationship between human health and disease development, focusing on the microbiomes found across the digestive, respiratory, urinary, and reproductive systems as well as the skin. We further discuss various strategies by which the composition and function of the human microbiome can be modulated to exert a therapeutic effect on the host. Finally, we examine technologies such as multiomics approaches and cellular reprogramming of microbes that can enable significant advancements in microbiome research and engineering.
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Affiliation(s)
- Nikhil Aggarwal
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Shohei Kitano
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
| | - Ginette Ru Ying Puah
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - Sandra Kittelmann
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Wilmar
International Limited, Singapore 138568, Singapore
| | - In Young Hwang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- Singapore
Institute of Technology, Singapore 138683, Singapore
| | - Matthew Wook Chang
- NUS
Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore 117456, Singapore
- Synthetic
Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore
- Wilmar-NUS
(WIL@NUS) Corporate Laboratory, National
University of Singapore, Singapore 117599, Singapore
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
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Dhariwal A, Haugli Bråten LC, Sturød K, Salvadori G, Bargheet A, Åmdal H, Junges R, Berild D, Zwart JA, Storheim K, Petersen FC. Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome. Gut Microbes 2023; 15:2157200. [PMID: 36576106 PMCID: PMC9809947 DOI: 10.1080/19490976.2022.2157200] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The collateral impact of antibiotics on the microbiome has attained increasing attention. However, the ecological consequences of long-term antibiotic exposure on the gut microbiome, including antibiotic resistance, are still limited. Here, we investigated long-term exposure effects to amoxicillin on the human gut microbiome and resistome. Fecal samples were collected from 20 patients receiving 3-months of amoxicillin or placebo treatment as part of a Norwegian multicenter clinical trial on chronic low back pain (AIM study). Samples were collected at baseline, last day of treatment, and 9 months after antibiotic cessation. The abundance and diversity of microbial and resistome composition were characterized using whole shotgun and functional metagenomic sequencing data. While the microbiome profiles of placebo subjects were stable over time, discernible changes in diversity and overall microbiome composition were observed after amoxicillin treatment. In particular, health-associated short-chain fatty acid producing species significantly decreased in proportion. However, these changes were short-lived as the microbiome showed overall recovery 9 months post-treatment. On the other hand, exposure to long-term amoxicillin was associated with an increase in total antimicrobial resistance gene load and diversity of antimicrobial resistance genes, with persistent changes even at 9 months post-treatment. Additionally, beta-lactam resistance was the most affected antibiotic class, suggesting a targeted response to amoxicillin, although changes at the gene level varied across individuals. Overall, our results suggest that the impact of prolonged amoxicillin exposure was more explicit and long-lasting in the fecal resistome than in microbiome composition. Such information is relevant for designing rational administration guidelines for antibiotic therapies.
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Affiliation(s)
- Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Lars Christian Haugli Bråten
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway
| | - Kjersti Sturød
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Gabriela Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Ahmed Bargheet
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Heidi Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dag Berild
- Department of Infectious Diseases, Oslo University Hospital HF, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - John-Anker Zwart
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kjersti Storheim
- Department of Research and Innovation, Division of Clinical Neuroscience, Oslo University Hospital HF, Oslo, Norway,Department of Physiotherapy, Faculty of Health Science, Oslo Metropolitan University, Oslo, Norway
| | - Fernanda Cristina Petersen
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway,CONTACT Fernanda Cristina Petersen Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
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46
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Cuozzo S, de Moreno de LeBlanc A, LeBlanc J, Hoffmann N, Tortella G. Streptomyces genus as a source of probiotics and its potential for its use in health. Microbiol Res 2023; 266:127248. [DOI: 10.1016/j.micres.2022.127248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/10/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
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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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48
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Liu A, Zhang M, Wu Y, Zhang C, Zhang Q, Su X, Zhu X, Shi W, Liu J, Zhang Y, Huang C, Yan Z, Lin J. ASPS Exhibits Anti-Rheumatic Effects by Reprogramming Gut Microbiota and Increasing Serum γ-Glutamylcysteine Level. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2205645. [PMID: 36417588 PMCID: PMC9875676 DOI: 10.1002/advs.202205645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 05/06/2023]
Abstract
Rheumatoid arthritis (RA) is an essential cause of labor loss and disability for people worldwide. Acanthopanax senticosus polysaccharide (ASPS) is one of the most important active components from A. senticosus, which exhibits various pharmacological activities such as antioxidation and immunomodulation. However, no studies have reported the application of ASPS in treating RA. This study aims to investigate the therapeutic effect of ASPS on RA and reveal its underlying mechanism. The potential therapeutic effect of ASPS against RA is initially verified in this study using the collagen-induced arthritis model. Moreover, the protective benefits of ASPS are transmitted through the fecal microbiota and blocked by simultaneous antibiotic cocktail treatment, indicating that gut microbiota may be correlated with ASPS. The 16S rRNA sequencing using feces samples and untargeted UPLC-MS metabolomics using serum samples further reveal that ASPS reprograms the arthritic progression triggered dysbiosis, enhances the expression of γ-glutamylcysteine (GGC) synthetase, and enriches the serum concentration of GGC. Furthermore, metabolites GGC is found to be able to effectively interrupt NLRP3 inflammasome activation via inhibiting ASC nucleation and therefore attenuate inflammatory arthritis. Taken together, this work highlights ASPS's therapeutic potential against RA, which mainly exhibits its effects via modulating gut microbiota and regulating GGC production.
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Affiliation(s)
- Ang Liu
- Department of OrthopaedicsSuzhou Dushu Lake HospitalDushu Lake Hospital Affiliated to Soochow UniversityMedical Center of Soochow UniversitySuzhou215125China
- Department of OrthopaedicsThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
| | - Min Zhang
- Department of PharmacyThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123China
| | - Yanglin Wu
- Department of OrthopaedicsSuzhou Dushu Lake HospitalDushu Lake Hospital Affiliated to Soochow UniversityMedical Center of Soochow UniversitySuzhou215125China
- Department of OrthopaedicsShanghai Tenth People's HospitalSchool of MedicineTongji UniversityShanghai200092China
| | - Chenhui Zhang
- Department of OrthopaedicsSuzhou Dushu Lake HospitalDushu Lake Hospital Affiliated to Soochow UniversityMedical Center of Soochow UniversitySuzhou215125China
- Department of OrthopaedicsThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
| | - Qin Zhang
- Department of OrthopaedicsSuzhou Dushu Lake HospitalDushu Lake Hospital Affiliated to Soochow UniversityMedical Center of Soochow UniversitySuzhou215125China
- Department of OrthopaedicsThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
| | - Xinlin Su
- Department of OrthopaedicsThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
| | - Xu Zhu
- Department of OrthopaedicsThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
| | - Weidong Shi
- Department of OrthopaedicsThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
| | - Jiangyun Liu
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123China
| | - Yang Zhang
- School of Biology and Food EngineeringChangshu Institute of TechnologyChangshu215500China
| | - Cheng Huang
- Department of OrthopaedicsChina‐Japan Friendship HospitalBeijing100029China
| | - Zhaowei Yan
- Department of PharmacyThe First Affiliated Hospital of Soochow UniversitySuzhou215006China
- College of Pharmaceutical SciencesSoochow UniversitySuzhou215123China
| | - Jun Lin
- Department of OrthopaedicsSuzhou Dushu Lake HospitalDushu Lake Hospital Affiliated to Soochow UniversityMedical Center of Soochow UniversitySuzhou215125China
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49
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Abed JY, Godon T, Mehdaoui F, Plante PL, Boissinot M, Bergeron MG, Bélanger RE, Muckle G, Poliakova N, Ayotte P, Corbeil J, Rousseau E. Gut metagenome profile of the Nunavik Inuit youth is distinct from industrial and non-industrial counterparts. Commun Biol 2022; 5:1415. [PMID: 36566300 PMCID: PMC9790006 DOI: 10.1038/s42003-022-04372-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/13/2022] [Indexed: 12/25/2022] Open
Abstract
Comparative metagenomics studies have highlighted differences in microbiome community structure among human populations over diverse lifestyles and environments. With their unique environmental and historical backgrounds, Nunavik Inuit have a distinctive gut microbiome with undocumented health-related implications. Using shotgun metagenomics, we explored the taxonomic and functional structure of the gut microbiome from 275 Nunavik Inuit ranging from 16 to 30-year-old. Whole-metagenome analyses revealed that Nunavik Inuit youths have a more diverse microbiome than their non-industrialized and industrialized counterparts. A comparison of k-mer content illustrated the uniqueness of the Nunavik gut microbiome. Short-chain fatty acids producing species, and carbohydrates degradation pathways dominated Inuit metagenomes. We identified a taxonomic and functional signature unique to the Nunavik gut microbiome contrasting with other populations using a random forest classifier. Here, we show that the Nunavik Inuit gut microbiome exhibits high diversity and a distinct community structure.
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Affiliation(s)
- Jehane Y. Abed
- grid.23856.3a0000 0004 1936 8390Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Centre de Recherche en Données Massives de l’Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Département de microbiologie-infectiologie et d’immunologie, Faculté de médecine, Université Laval, Québec City, QC Canada
| | - Thibaud Godon
- grid.23856.3a0000 0004 1936 8390Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Centre de Recherche en Données Massives de l’Université Laval, Québec City, QC Canada
| | - Fadwa Mehdaoui
- grid.23856.3a0000 0004 1936 8390Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Département d’informatique et génie logiciel, Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Centre Nutrition, Santé et Société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec City, QC Canada
| | - Pier-Luc Plante
- grid.23856.3a0000 0004 1936 8390Centre Nutrition, Santé et Société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec City, QC Canada
| | - Maurice Boissinot
- grid.23856.3a0000 0004 1936 8390Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC Canada
| | - Michel G. Bergeron
- grid.23856.3a0000 0004 1936 8390Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Département de microbiologie-infectiologie et d’immunologie, Faculté de médecine, Université Laval, Québec City, QC Canada
| | - Richard E. Bélanger
- grid.23856.3a0000 0004 1936 8390Axe santé des populations et pratiques optimales en santé, Centre de recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Département de pédiatrie, Faculté de médecine, Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Centre mère-enfant Soleil, CHU de Québec-Université Laval, Département de pédiatrie, Québec City, QC Canada
| | - Gina Muckle
- grid.23856.3a0000 0004 1936 8390Axe santé des populations et pratiques optimales en santé, Centre de recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390École de psychologie, Faculté des sciences sociales, Université Laval, Québec City, QC Canada
| | - Natalia Poliakova
- grid.23856.3a0000 0004 1936 8390Axe santé des populations et pratiques optimales en santé, Centre de recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, Québec City, QC Canada
| | - Pierre Ayotte
- grid.23856.3a0000 0004 1936 8390Axe santé des populations et pratiques optimales en santé, Centre de recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, Québec City, QC Canada ,grid.434819.30000 0000 8929 2775Centre de Toxicologie du Québec, Institut national de santé publique du Québec (INSPQ), Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Département de médecine sociale et préventive, Faculté de médecine, Université Laval, Québec City, QC Canada
| | - Jacques Corbeil
- grid.23856.3a0000 0004 1936 8390Centre de Recherche en Infectiologie de l’Université Laval, Axe Maladies Infectieuses et Immunitaires, Centre de Recherche du CHU de Québec-Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Centre de Recherche en Données Massives de l’Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Département de Médecine Moléculaire, Faculté de médecine, Université Laval, Québec City, QC Canada
| | - Elsa Rousseau
- grid.23856.3a0000 0004 1936 8390Centre de Recherche en Données Massives de l’Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Département d’informatique et génie logiciel, Université Laval, Québec City, QC Canada ,grid.23856.3a0000 0004 1936 8390Centre Nutrition, Santé et Société (NUTRISS), Institute of Nutrition and Functional Foods (INAF), Université Laval, Québec City, QC Canada
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50
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Leardini D, Venturelli F, Baccelli F, Cerasi S, Muratore E, Brigidi P, Pession A, Prete A, Masetti R. Pharmacomicrobiomics in Pediatric Oncology: The Complex Interplay between Commonly Used Drugs and Gut Microbiome. Int J Mol Sci 2022; 23:15387. [PMID: 36499714 PMCID: PMC9740824 DOI: 10.3390/ijms232315387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/27/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome (GM) has emerged in the last few years as a main character in several diseases. In pediatric oncological patients, GM has a role in promoting the disease, modulating the effectiveness of therapies, and determining the clinical outcomes. The therapeutic course for most pediatric cancer influences the GM due to dietary modifications and several administrated drugs, including chemotherapies, antibiotics and immunosuppressants. Interestingly, increasing evidence is uncovering a role of the GM on drug pharmacokinetics and pharmacodynamics, defining a bidirectional relationship. Indeed, the pediatric setting presents some contrasts with respect to the adult, since the GM undergoes a constant multifactorial evolution during childhood following external stimuli (such as diet modification during weaning). In this review, we aim to summarize the available evidence of pharmacomicrobiomics in pediatric oncology.
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Affiliation(s)
- Davide Leardini
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Francesco Venturelli
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Francesco Baccelli
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Sara Cerasi
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Edoardo Muratore
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Andrea Pession
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
- Pediatric Unit, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Arcangelo Prete
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
| | - Riccardo Masetti
- Pediatric Oncology and Hematology “Lalla Seràgnoli”, IRCCS Azienda Ospedaliero Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
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