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Kijner S, Ennis D, Shmorak S, Florentin A, Yassour M. CRISPR-Cas-based identification of a sialylated human milk oligosaccharides utilization cluster in the infant gut commensal Bacteroides dorei. Nat Commun 2024; 15:105. [PMID: 38167825 PMCID: PMC10761964 DOI: 10.1038/s41467-023-44437-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
The infant gut microbiome is impacted by early-life feeding, as human milk oligosaccharides (HMOs) found in breastmilk cannot be digested by infants and serve as nutrients for their gut bacteria. While the vast majority of HMO-utilization research has focused on Bifidobacterium species, recent studies have suggested additional HMO-utilizers, mostly Bacteroides, yet their utilization mechanism is poorly characterized. Here, we investigate Bacteroides dorei isolates from breastfed-infants and identify that polysaccharide utilization locus (PUL) 33 enables B. dorei to utilize sialylated HMOs. We perform transcriptional profiling and identity upregulated genes when growing on sialylated HMOs. Using CRISPR-Cas12 to knock-out four PUL33 genes, combined with complementation assays, we identify GH33 as the critical gene in PUL33 for sialylated HMO-utilization. This demonstration of an HMO-utilization system by Bacteroides species isolated from infants opens the way to further characterization of additional such systems, to better understand HMO-utilization in the infant gut.
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Affiliation(s)
- Sivan Kijner
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dena Ennis
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shimrit Shmorak
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Florentin
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Kuvin Center for the Study of Infectious and Tropical Diseases, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Pathak A, Angst DC, León-Sampedro R, Hall AR. Antibiotic-degrading resistance changes bacterial community structure via species-specific responses. THE ISME JOURNAL 2023; 17:1495-1503. [PMID: 37380830 PMCID: PMC10432403 DOI: 10.1038/s41396-023-01465-2] [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: 12/16/2022] [Revised: 06/15/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
Some bacterial resistance mechanisms degrade antibiotics, potentially protecting neighbouring susceptible cells from antibiotic exposure. We do not yet understand how such effects influence bacterial communities of more than two species, which are typical in nature. Here, we used experimental multispecies communities to test the effects of clinically important pOXA-48-plasmid-encoded resistance on community-level responses to antibiotics. We found that resistance in one community member reduced antibiotic inhibition of other species, but some benefitted more than others. Further experiments with supernatants and pure-culture growth assays showed the susceptible species profiting most from detoxification were those that grew best at degraded antibiotic concentrations (greater than zero, but lower than the starting concentration). This pattern was also observed on agar surfaces, and the same species also showed relatively high survival compared to most other species during the initial high-antibiotic phase. By contrast, we found no evidence of a role for higher-order interactions or horizontal plasmid transfer in community-level responses to detoxification in our experimental communities. Our findings suggest carriage of an antibiotic-degrading resistance mechanism by one species can drastically alter community-level responses to antibiotics, and the identities of the species that profit most from antibiotic detoxification are predicted by their intrinsic ability to survive and grow at changing antibiotic concentrations.
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Affiliation(s)
- Ayush Pathak
- Institute of Integrative Biology, Department of Environmental Systems Science (D-USYS), ETH Zurich, Zurich, Switzerland.
| | - Daniel C Angst
- Institute of Integrative Biology, Department of Environmental Systems Science (D-USYS), ETH Zurich, Zurich, Switzerland
| | - Ricardo León-Sampedro
- Institute of Integrative Biology, Department of Environmental Systems Science (D-USYS), ETH Zurich, Zurich, Switzerland
| | - Alex R Hall
- Institute of Integrative Biology, Department of Environmental Systems Science (D-USYS), ETH Zurich, Zurich, Switzerland
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3
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Wang C, Bai J, Chen X, Song J, Zhang Y, Wang H, Suo H. Gut microbiome-based strategies for host health and disease. Crit Rev Food Sci Nutr 2023; 64:6834-6849. [PMID: 36803092 DOI: 10.1080/10408398.2023.2176464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Host health and disease are influenced by changes in the abundance and structure of intestinal flora. Current strategies are focused on regulating the structure of intestinal flora to ensure host health by alleviating disease. However, these strategies are limited by multiple factors, such as host genotype, physiology (microbiome, immunity, and gender), intervention, and diet. Accordingly, we reviewed the prospects and limitations of all strategies regulating the structure and abundance of microflora, including probiotics, prebiotics, diet, fecal microbiota transplantation, antibiotics, and phages. Some new technologies that can improve these strategies are also introduced. Compared with other strategies, diets and prebiotics are associated with reduced risk and high security. Besides, phages have the potential for application in the targeted regulation of intestinal microbiota due to their high specificity. Notably, the variability in individual microflora and their metabolic response to different interventions should be considered. Future studies should use artificial intelligence combined with multi-omics to investigate the host genome and physiology based on factors, such as blood type, dietary habits, and exercise, in order to develop individualized intervention strategies to improve host health.
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Affiliation(s)
- Chen Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Junying Bai
- Citrus Research Institute, National Citrus Engineering Research Center, Southwest University, Chongqing, China
| | - Xiaoyong Chen
- College of Food Science, Southwest University, Chongqing, China
| | - Jiajia Song
- College of Food Science, Southwest University, Chongqing, China
| | - Yu Zhang
- College of Food Science, Southwest University, Chongqing, China
| | - Hongwei Wang
- College of Food Science, Southwest University, Chongqing, China
| | - Huayi Suo
- College of Food Science, Southwest University, Chongqing, China
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Wells K, Flynn R. Managing host-parasite interactions in humans and wildlife in times of global change. Parasitol Res 2022; 121:3063-3071. [PMID: 36066742 PMCID: PMC9446624 DOI: 10.1007/s00436-022-07649-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
Abstract
Global change in the Anthropocene has modified the environment of almost any species on earth, be it through climate change, habitat modifications, pollution, human intervention in the form of mass drug administration (MDA), or vaccination. This can have far-reaching consequences on all organisational levels of life, including eco-physiological stress at the cell and organism level, individual fitness and behaviour, population viability, species interactions and biodiversity. Host-parasite interactions often require highly adapted strategies by the parasite to survive and reproduce within the host environment and ensure efficient transmission among hosts. Yet, our understanding of the system-level outcomes of the intricate interplay of within host survival and among host parasite spread is in its infancy. We shed light on how global change affects host-parasite interactions at different organisational levels and address challenges and opportunities to work towards better-informed management of parasite control. We argue that global change affects host-parasite interactions in wildlife inhabiting natural environments rather differently than in humans and invasive species that benefit from anthropogenic environments as habitat and more deliberate rather than erratic exposure to therapeutic drugs and other control efforts.
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Affiliation(s)
- Konstans Wells
- Department of Biosciences, Swansea University, Swansea, SA28PP, UK.
| | - Robin Flynn
- Graduate Studies Office, South East Technological University, Cork Road Campus, Waterford, X91 K0EK, Ireland
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Kijner S, Kolodny O, Yassour M. Human milk oligosaccharides and the infant gut microbiome from an eco-evolutionary perspective. Curr Opin Microbiol 2022; 68:102156. [DOI: 10.1016/j.mib.2022.102156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/03/2022] [Accepted: 04/14/2022] [Indexed: 12/21/2022]
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Alam KM, Yan Y, Lin M, Islam MA, Gaber A, Hossain A. Insight rifampicin-resistant (rpoB) mutation in Pseudomonas stutzeri leads to enhance the biosynthesis of secondary metabolites to survive against harsh environments. Arch Microbiol 2022; 204:437. [PMID: 35768665 DOI: 10.1007/s00203-022-03064-9] [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: 02/18/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 11/02/2022]
Abstract
In this study, a wild-type and five distinct rifampicin-resistant (Rifr) rpoB mutants of Pseudomonas stutzeri (i.e., Q518R, D521Y, D521V, H531R and I614T) ability were investigated against harsh environments (particularly nutritional complexity). Among these, the robust Rifr phenotype of P. Stutzeri was associated only with base replacements of the amino deposits. The use of carboxylic and amino acids significantly increased in various Rifr mutants than that of wild type of P. stutzeri. The assimilation of carbon and nitrogen (N) sources of Rifr mutants' confirmed that the organism maintains the adaptation in nutritionally complex environments. Acetylene reduction assay at different times also found the variability for N-fixation in all strains. Among them, the highest nitrogenase activity was determined in mutant 'D521V'. The assimilation of carbon and nitrogen sources of P. stutzeri and its Rifr mutants ensures that the organism maintains the adaptability in nutritionally complex environments through fixing more nitrogen.
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Affiliation(s)
- Khandakar Mohiul Alam
- Soils and Nutrition Division, Bangladesh Sugarcrop Research Institute, Pabna, 6620, Bangladesh
| | - Yongliang Yan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South StHaidian District, Beijing, People's Republic of China
| | - Min Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South StHaidian District, Beijing, People's Republic of China
| | - Md Ariful Islam
- On-Farm Research Division, Bangladesh Agricultural Research Institute, Pabna, 6600, Bangladesh
| | - Ahmed Gaber
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Akbar Hossain
- Department of Agronomy, Bangladesh Wheat and Maize Research Institute, Dinajpur, 5200, Bangladesh.
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Diep TT, Bizley S, Edwards AD. 3D-Printed Dip Slides Miniaturize Bacterial Identification and Antibiotic Susceptibility Tests Allowing Direct Mastitis Sample Analysis. MICROMACHINES 2022; 13:mi13060941. [PMID: 35744555 PMCID: PMC9231150 DOI: 10.3390/mi13060941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023]
Abstract
The early detection of antimicrobial resistance remains an essential step in the selection and optimization of antibiotic treatments. Phenotypic antibiotic susceptibility testing including the measurement of minimum inhibitory concentration (MIC) remains critical for surveillance and diagnostic testing. Limitations to current testing methods include bulky labware and laborious methods. Furthermore, the requirement of a single strain of bacteria to be isolated from samples prior to antibiotic susceptibility testing delays results. The mixture of bacteria present in a sample may also have an altered resistance profile to the individual strains, and so measuring the susceptibility of the mixtures of organisms found in some samples may be desirable. To enable simultaneous MIC and bacterial species detection in a simple and rapid miniaturized format, a 3D-printed frame was designed for a multi-sample millifluidic dip-slide device that combines panels of identification culture media with a range of antibiotics (Ampicillin, Amoxicillin, Amikacin, Ceftazidime, Cefotaxime, Ofloxacin, Oxytetracycline, Streptomycin, Gentamycin and Imipenem) diluted in Muëller-Hinton Agar. Our proof-of-concept evaluation confirmed that the direct detection of more than one bacterium parallel to measuring MIC in samples is possible, which is validated using reference strains E. coli ATCC 25922, Klebsiella pneumoniae ATCC 13883, Pseudomonas aeruginosa ATCC 10145, and Staphylococcus aureus ATCC 12600 and with mastitis milk samples collected from Reading University Farm. When mixtures were tested, a MIC value was obtained that reflected the most resistant organism present (i.e., highest MIC), suggesting it may be possible to estimate a minimum effective antibiotic concentration for mixtures directly from samples containing multiple pathogens. We conclude that this simple miniaturized approach to the rapid simultaneous identification and antibiotic susceptibility testing may be suitable for directly testing agricultural samples, which is achieved through shrinking conventional tests into a simple "dip-and-incubate" device that can be 3D printed anywhere.
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Kijner S, Cher A, Yassour M. The Infant Gut Commensal Bacteroides dorei Presents a Generalized Transcriptional Response to Various Human Milk Oligosaccharides. Front Cell Infect Microbiol 2022; 12:854122. [PMID: 35372092 PMCID: PMC8971754 DOI: 10.3389/fcimb.2022.854122] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/22/2022] [Indexed: 12/22/2022] Open
Abstract
Human milk oligosaccharides (HMOs) are a family of glycans found in breastmilk with over 200 identified structures. Despite being the third-largest solid component in breastmilk, HMOs are indigestible by infants, and they serve as food for the infant gut bacteria. Most research thus far has focused on Bifidobacterium species that harbor many glycoside hydrolases (GHs) tailored to break the carbon bonds in HMO molecules. However, there are additional microbes in the infant gut, such as Bacteroides species, with increasing evidence that they, too, are able to break-down HMOs. To study the unbiased impact of breastfeeding on the infant gut microbiome, we need to investigate the underlying mechanisms of HMO utilization by all members of the infant gut. Here, we developed an optimized system for isolating Bacteroides strains from infant stool samples. We then examined the HMO utilization capacity of multiple Bacteroides isolates by performing growth curves on six common HMOs (2’-FL, DFL, 3’-SL, 6’-SL, LNT, LNnT). Isolates often displayed similar growth characteristics on similarly-structured HMOs, like sialylated or fucosylated sugars. We identified variation in HMO utilization across multiple strains of the same species, and chose to focus here on a Bacteroides dorei isolate that was able to utilize the test HMOs. We performed RNA sequencing on B. dorei cultures, comparing the transcriptional profile in minimal media supplemented with glucose or HMOs. We showed that B. dorei employs an extensive metabolic response to HMOs. Surprisingly, there was no clear up-regulation for most GH families previously known to break-down HMOs, possibly because they were almost exclusively described in Bifidobacterium species. Instead, B. dorei exhibits a generalized response to HMOs, markedly up-regulating several shared GH families across all conditions. Within each GH family, B. dorei displays a consistent pattern of up-regulation of some genes with down-regulation of the others. This response pattern to HMOs has yet to be described in other commensals of the infant gut. Our work highlights the importance of expanding the HMO-microbiome studies beyond Bifidobacterium species, sheds light on the differences across Bacteroides strains in terms of HMO utilization, and paves the way to understanding the mechanisms enabling Bacteroides HMO utilization.
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Affiliation(s)
- Sivan Kijner
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Avital Cher
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- *Correspondence: Moran Yassour,
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Smith DR, Temime L, Opatowski L. Microbiome-pathogen interactions drive epidemiological dynamics of antibiotic resistance: A modeling study applied to nosocomial pathogen control. eLife 2021; 10:68764. [PMID: 34517942 PMCID: PMC8560094 DOI: 10.7554/elife.68764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/31/2021] [Indexed: 12/16/2022] Open
Abstract
The human microbiome can protect against colonization with pathogenic antibiotic-resistant bacteria (ARB), but its impacts on the spread of antibiotic resistance are poorly understood. We propose a mathematical modeling framework for ARB epidemiology formalizing within-host ARB-microbiome competition, and impacts of antibiotic consumption on microbiome function. Applied to the healthcare setting, we demonstrate a trade-off whereby antibiotics simultaneously clear bacterial pathogens and increase host susceptibility to their colonization, and compare this framework with a traditional strain-based approach. At the population level, microbiome interactions drive ARB incidence, but not resistance rates, reflecting distinct epidemiological relevance of different forces of competition. Simulating a range of public health interventions (contact precautions, antibiotic stewardship, microbiome recovery therapy) and pathogens (Clostridioides difficile, methicillin-resistant Staphylococcus aureus, multidrug-resistant Enterobacteriaceae) highlights how species-specific within-host ecological interactions drive intervention efficacy. We find limited impact of contact precautions for Enterobacteriaceae prevention, and a promising role for microbiome-targeted interventions to limit ARB spread.
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Affiliation(s)
- David Rm Smith
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France.,Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiers, Paris, France
| | - Laura Temime
- Modélisation, épidémiologie et surveillance des risques sanitaires (MESuRS), Conservatoire national des arts et métiers, Paris, France.,PACRI unit, Institut Pasteur, Conservatoire national des arts et métiers, Paris, France
| | - Lulla Opatowski
- Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion (EMAE), Paris, France.,Université Paris-Saclay, UVSQ, Inserm, CESP, Anti-infective evasion and pharmacoepidemiology team, Montigny-Le-Bretonneux, France
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O'Brien S, Baumgartner M, Hall AR. Species interactions drive the spread of ampicillin resistance in human-associated gut microbiota. EVOLUTION MEDICINE AND PUBLIC HEALTH 2021; 9:256-266. [PMID: 34447576 PMCID: PMC8385247 DOI: 10.1093/emph/eoab020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/22/2021] [Indexed: 12/23/2022]
Abstract
Background and objectives Slowing the spread of antimicrobial resistance is urgent if we are to continue treating infectious diseases successfully. There is increasing evidence microbial interactions between and within species are significant drivers of resistance. On one hand, cross-protection by resistant genotypes can shelter susceptible microbes from the adverse effects of antibiotics, reducing the advantage of resistance. On the other hand, antibiotic-mediated killing of susceptible genotypes can alleviate competition and allow resistant strains to thrive (competitive release). Here, by observing interactions both within and between species in microbial communities sampled from humans, we investigate the potential role for cross-protection and competitive release in driving the spread of ampicillin resistance in the ubiquitous gut commensal and opportunistic pathogen Escherichia coli. Methodology Using anaerobic gut microcosms comprising E.coli embedded within gut microbiota sampled from humans, we tested for cross-protection and competitive release both within and between species in response to the clinically important beta-lactam antibiotic ampicillin. Results While cross-protection gave an advantage to antibiotic-susceptible E.coli in standard laboratory conditions (well-mixed LB medium), competitive release instead drove the spread of antibiotic-resistant E.coli in gut microcosms (ampicillin boosted growth of resistant bacteria in the presence of susceptible strains). Conclusions and implications Competition between resistant strains and other members of the gut microbiota can restrict the spread of ampicillin resistance. If antibiotic therapy alleviates competition with resident microbes by killing susceptible strains, as here, microbiota-based interventions that restore competition could be a key for slowing the spread of resistance. Lay Summary Slowing the spread of global antibiotic resistance is an urgent task. In this paper, we ask how interactions between microbial species drive the spread of resistance. We show that antibiotic killing of susceptible microbes can free up resources for resistant microbes and allow them to thrive. Therefore, we should consider microbes in light of their social interactions to understand the spread of resistance.
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Affiliation(s)
- Siobhán O'Brien
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK.,Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Michael Baumgartner
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - Alex R Hall
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
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