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Yeruva L, Mulakala BK, Rajasundaram D, Gonzalez S, Cabrera-Rubio R, Martínez-Costa C, Collado MC. Human milk miRNAs associate to maternal dietary nutrients, milk microbiota, infant gut microbiota and growth. Clin Nutr 2023; 42:2528-2539. [PMID: 37931372 DOI: 10.1016/j.clnu.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Maternal diet influences the milk composition, yet little information is available on the impact of maternal diet on milk miRNAs expression. Further, the association of human milk miRNAs to maternal diet and milk microbiota is not explored. In addition, the role of milk miRNAs on the infant gut microbiota, infant growth and development has not been investigated. METHODS Milk samples were collected from 60 healthy lactating women at ≤15d post-partum, HTG transcriptome assay was performed to examine milk miRNA profile. Maternal clinical and dietary clusters information were available and infant anthropometric measures were followed up to one year of age. Milk and infant microbiota were analyzed by 16S rRNA gene sequencing and integrative multi-omics data analysis was performed to identify potential association between microRNA, maternal dietary nutrients and microbiota. RESULTS Discriminant analysis revealed that the milk miRNAs were clustered into groups according to the maternal protein source. Interestingly, 31 miRNAs were differentially expressed (P adj < 0.05) between maternal dietary clusters (Cluster 1: enriched in plant protein and fibers and Cluster 2: enriched in animal protein), with 30 miRNAs downregulated in the plant protein group relative to animal protein group. Pathway analysis revealed that the top enriched pathways (P adj < 0.01) were involved in cell growth and proliferation processes. Furthermore, significant features contributing to the clustering were associated with maternal dietary nutrients and milk microbiota (r > 0.70). Further, miR-378 and 320 family miRNAs involved in adipogenesis were positively correlated to the infant BMI-z-scores, weight, and weight for length-z-scores at 6 months of age. CONCLUSIONS Maternal dietary source impacts the milk miRNA expression profile. Further, miRNAs were associated with maternal dietary nutrients, milk microbiota and to the infant gut microbiota and infant growth and development. CLINICAL TRIAL The study is registered in ClinicalTrials.gov. The identification number is NCT03552939.
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Affiliation(s)
- Laxmi Yeruva
- Microbiome and Metabolism Research Unit, USDA-ARS, SEA, Little Rock, AR, USA; Arkansas Children's Nutrition Center, Little Rock, AR, USA.
| | - Bharat Kumar Mulakala
- Microbiome and Metabolism Research Unit, USDA-ARS, SEA, Little Rock, AR, USA; Arkansas Children's Nutrition Center, Little Rock, AR, USA; Texas A&M AgriLife Institute for Advancing Health Through Agriculture, TX, USA
| | | | - Sonia Gonzalez
- Department of Functional Biology, Faculty of Medicine, University of Oviedo, Oviedo, Spain; Diet, Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (DIMISA, ISPA), Oviedo, Spain
| | - Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | | | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain.
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Güley Z, Fallico V, Cabrera-Rubio R, O’Sullivan D, Marotta M, Pennone V, Smith S, Beresford T. Diversity of the Microbiota of Traditional Izmir Tulum and Izmir Brined Tulum Cheeses and Selection of Potential Probiotics. Foods 2023; 12:3482. [PMID: 37761191 PMCID: PMC10528788 DOI: 10.3390/foods12183482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/09/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
High-throughput DNA sequencing (HTS) was used to study the microbial diversity of commercial traditional Izmir Tulum (IT) and Izmir Brined Tulum (IBT) cheeses from Izmir, Türkiye. Simultaneously, cultivation-dependent methods were used to isolate, identify and characterize bacterial strains displaying probiotic potential. At the phylum level, Firmicutes dominated the microbiota of both cheese types comprising >98% of the population. Thirty genera were observed, with Streptococcus being the most abundant genus and with Streptococcus thermophilus and S. infantarius subsp. infantarius being the most abundant species. Genera, including Bifidobacterium and Chryseobacterium, not previously associated with IT and IBT, were detected. IT cheeses displayed higher operational taxonomic units (OTUs; Richness) and diversity index (Simpson) than IBT cheeses; however, the difference between the diversity of the microbiota of IT and IBT cheese samples was not significant. Three Lacticaseibacillus paracasei strains isolated from IBT cheeses exhibited probiotic characteristics, which included capacity to survive under in vitro simulated gastrointestinal conditions, resistance to bile salts and potential to adhere to HT-29 human intestinal cells. These findings demonstrate that Tulum cheeses harbor bacterial genera not previously reported in this cheese and that some strains display probiotic characteristics.
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Affiliation(s)
- Ziba Güley
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
- Department of Food Engineering, Alanya Alaaddin Keykubat University, 07425 Antalya, Türkiye
| | - Vincenzo Fallico
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
- APC Microbiome Ireland, University College Cork, T12Y120 Cork, Ireland
| | - Daniel O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
- School of Food and Nutritional Sciences, University College Cork, T12K8AF Cork, Ireland
| | - Mariarosaria Marotta
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| | - Vincenzo Pennone
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| | - Sandra Smith
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
| | - Tom Beresford
- Teagasc Food Research Centre, Moorepark, Fermoy, P61C996 Co. Cork, Ireland; (V.F.); (R.C.-R.); (D.O.); (M.M.); (V.P.); (S.S.); (T.B.)
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3
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Manara S, Selma-Royo M, Huang KD, Asnicar F, Armanini F, Blanco-Miguez A, Cumbo F, Golzato D, Manghi P, Pinto F, Valles-Colomer M, Amoroso L, Corrias MV, Ponzoni M, Raffaetà R, Cabrera-Rubio R, Olcina M, Pasolli E, Collado MC, Segata N. Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. Curr Biol 2023; 33:1939-1950.e4. [PMID: 37116481 DOI: 10.1016/j.cub.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 02/28/2023] [Accepted: 04/05/2023] [Indexed: 04/30/2023]
Abstract
The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.
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Affiliation(s)
- Serena Manara
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Marta Selma-Royo
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy; Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | - Kun D Huang
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Francesco Asnicar
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Federica Armanini
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Aitor Blanco-Miguez
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Fabio Cumbo
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Davide Golzato
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Paolo Manghi
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Federica Pinto
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Mireia Valles-Colomer
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy
| | - Loredana Amoroso
- Oncology Unit, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Maria Valeria Corrias
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Mirco Ponzoni
- Laboratory of Experimental Therapies in Oncology, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy
| | - Roberta Raffaetà
- Ca' Foscari University Venice, Department of Philosophy and Cultural Heritage and NICHE, Malcanton Marcorà, Dorsoduro 3484/D, 30123 Venice, Italy
| | - Raul Cabrera-Rubio
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain
| | - Mari Olcina
- Department of Preventive Medicine and Public Health, Faculty of Pharmacy, Universitat de València, Av. Vicent Andrés Estellés s/n, Burjassot, Valencia 46100, Spain
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Naples, Italy.
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), C/ Catedrático Agustín Escardino Benlloch, 7, 46980 Paterna, Valencia, Spain.
| | - Nicola Segata
- Department of Cellular Computational and Integrative Biology, Via Sommarive 9, Povo, Trento 38123, Italy.
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Vázquez L, Cabrera-Rubio R, Tamames J, Mayo B, Flórez AB. Assessment of short-read shotgun sequencing and microbiome analysis of faecal samples to discriminate between equol producers and non-producers. Benef Microbes 2023:1-14. [PMID: 37078124 DOI: 10.3920/bm2022.0027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Among the isoflavones and isoflavone-derived metabolites, equol, which in the human gut is synthesised from daidzein by minority bacterial populations, shows the strongest estrogenic and antioxidant activity. The beneficial effects on human health of isoflavone consumption might be partially or indeed totally attributable to this equol. Although some of the bacterial strains involved in its formation have been identified, the interplay between the composition and functionality of the gut microbiota and equol producer phenotype has hardly been studied. In this study, after shotgun metagenomic sequencing, different pipelines for the taxonomic and functional annotation of sequencing data were used in the search for similarities and differences in the faecal metagenome of equol-producing (n=3) and non-producing (n=2) women, with special focus on equol-producing taxa and their equol-associated genes. The taxonomic profiles of the samples differed significantly depending on the analytical method followed, although the microbial diversity detected by each tool was very similar at the phylum, genus and species levels. Equol-producing taxa were detected in both equol producers and non-producers, but no correlation between the abundance of equol-producing taxa and the equol producing/non-producing phenotype was found. Indeed, functional metagenomic analysis was unable to identify the genes involved in equol production, even in samples from equol producers. By aligning equol operons with the collected metagenomics data, a small number of reads mapping to equol-associated sequences were recognised in samples from both equol producers and equol non-producers, but only two reads mapping onto equol reductase-encoding genes in a sample from an equol producer. In conclusion, the taxonomic analysis of metagenomic data might not be suitable for detecting and quantifying equol-producing microbes in human faeces. Functional analysis of the data might provide an alternative. However, to detect the genetic makeup of the minority gut populations, more extensive sequencing than that achieved in the present study might be required.
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Affiliation(s)
- L Vázquez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011-Oviedo, Asturias, Spain
| | - R Cabrera-Rubio
- Alimentary Pharmabiotic Centre (APC), Microbiome Institute, University College Cork, Cork, Ireland
- Moorepark Teagasc Food Research Centre, Fermoy, Ireland
| | - J Tamames
- Departamento de Biología de Sistemas, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Cantoblanco, Madrid, Spain
| | - B Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011-Oviedo, Asturias, Spain
| | - A B Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares s/n, 33300-Villaviciosa, Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Avenida de Roma s/n, 33011-Oviedo, Asturias, Spain
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5
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Samarra A, Esteban-Torres M, Cabrera-Rubio R, Bernabeu M, Arboleya S, Gueimonde M, Collado MC. Maternal-infant antibiotic resistance genes transference: what do we know? Gut Microbes 2023; 15:2194797. [PMID: 37020319 PMCID: PMC10078139 DOI: 10.1080/19490976.2023.2194797] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Resistance to antibiotics is becoming a worldwide threat as infections caused by multidrug-resistant pathogenic microorganisms can overcome antibiotic treatments and spread quickly in the population. In the context of early life, newborns are at increased risk as their immune system is still under development, so infections and acquisition of resistance during childhood have short- and long-term consequences for the health. The moment of birth is the first exposure of infants to possible antibiotic-resistant microorganisms that may colonize their gut and other body sites. Different factors including mode of delivery, previous antibiotic exposure of the mother, gestational age and consumption of antibiotics in early-life have been described to modulate the neonate's microbiota, and thus, the resistome. Other factors, such as lactation, also impact the establishment and development of gut microbiota, but little is known about the role of breastmilk in transferring Antibiotic Resistant Genes (ARG). A deeper understanding of vertical transmission of antibiotic resistance from mothers to their offspring is necessary to determine the most effective strategies for reducing antibiotic resistance in the early life. In this review, we aim to present the current perspective on antibiotic resistances in mother-infant dyads, as well as a new insight on the study of the human gut and breastmilk resistome, and current strategies to overcome this public health problem, toward highlighting the gaps of knowledge that still need to be closed.
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Affiliation(s)
- Anna Samarra
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
| | - Maria Esteban-Torres
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
| | - Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
| | - Manuel Bernabeu
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
- Vicerectorat de Recerca, Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry, Dairy Research Institute- National Research Council (IPLA-CSIC), Villaviciosa, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry, Dairy Research Institute- National Research Council (IPLA-CSIC), Villaviciosa, Spain
| | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology- National Research Council (IATA-CSIC), Valencia, Spain
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6
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Güley Z, Fallico V, Cabrera-Rubio R, Cotter PD, Beresford T. Identification of Streptococcus infantarius subsp. infantarius as the species primarily responsible for acid production in Izmir Brined Tulum Cheese from the Aegean Region of Türkiye. Food Res Int 2022; 160:111707. [DOI: 10.1016/j.foodres.2022.111707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/02/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022]
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Selma-Royo M, Calvo-Lerma J, Bäuerl C, Esteban-Torres M, Cabrera-Rubio R, Collado MC. Human milk microbiota: what did we learn in the last 20 years? Microbiome Res Rep 2022; 1:19. [PMID: 38046359 PMCID: PMC10688795 DOI: 10.20517/mrr.2022.05] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/06/2022] [Accepted: 04/29/2022] [Indexed: 12/05/2023]
Abstract
Human milk (HM) is the gold standard for infant nutrition during the first months of life. Beyond its nutritional components, its complex bioactive composition includes microorganisms, their metabolites, and oligosaccharides, which also contribute to gut colonization and immune system maturation. There is growing evidence of the beneficial effects of bacteria present in HM. However, current research presents limited data on the presence and functions of other organisms. The potential biological impacts on maternal and infant health outcomes, the factors contributing to milk microbes' variations, and the potential functions in the infant's gut remain unclear. This review provides a global overview of milk microbiota, what the actual knowledge is, and what the gaps and challenges are for the next years.
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Affiliation(s)
| | | | | | | | | | - Maria Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia 46980, Spain
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8
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Henares D, Rocafort M, Brotons P, de Sevilla MF, Mira A, Launes C, Cabrera-Rubio R, Muñoz-Almagro C. Rapid Increase of Oral Bacteria in Nasopharyngeal Microbiota After Antibiotic Treatment in Children With Invasive Pneumococcal Disease. Front Cell Infect Microbiol 2021; 11:744727. [PMID: 34712623 PMCID: PMC8546175 DOI: 10.3389/fcimb.2021.744727] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/10/2021] [Indexed: 01/04/2023] Open
Abstract
Introduction Antibiotics are commonly prescribed to young children for treating bacterial infections such as invasive pneumococcal disease (IPD) caused by Streptococcus pneumoniae. Despite the obvious benefits of antibiotics, little is known about their possible side effects on children’s nasopharyngeal microbiota. In other ecological niches, antibiotics have been described to perturb the balanced microbiota with short- and long-term effects on children’s health. The present study aims to evaluate and compare the nasopharyngeal microbiota of children with IPD and different degree of antibiotic exposure. Methods We investigated differences in nasopharyngeal microbiota of two groups of children <18 years with IPD: children not exposed to antibiotics before sample collection (n=27) compared to children previously exposed (n=54). Epidemiological/clinical data were collected from subjects, and microbiota was characterized by Illumina sequencing of V3-V4 amplicons of the 16S rRNA gene. Results Main epidemiological/clinical factors were similar across groups. Antibiotic-exposed patients were treated during a median of 4 days (IQR: 3–6) with at least one beta-lactam (100.0%). Higher bacterial richness and diversity were found in the group exposed to antibiotics. Different streptococcal amplicon sequence variants (ASVs) were differentially abundant across groups: antibiotic use was associated to lower relative abundances of Streptococcus ASV2 and Streptococcus ASV11 (phylogenetically close to S. pneumoniae), and higher relative abundances of Streptococcus ASV3 and Streptococcus ASV12 (phylogenetically close to viridans group streptococci). ASVs assigned to typical bacteria from the oral cavity, including Veillonella, Alloprevotella, Porphyromonas, Granulicatella, or Capnocytophaga, were associated to the antibiotic-exposed group. Common nosocomial genera such as Staphylococcus, Acinetobacter, and Pseudomonas were also enriched in the group exposed to antibiotics. Conclusion Our results point toward a reduction of S. pneumoniae abundance on the nasopharynx of children with IPD after antibiotic treatment and a short-term repopulation of this altered niche by oral and nosocomial bacteria. Future research studies will have to evaluate the clinical implications of these findings and if these populations would benefit from the probiotic/prebiotic administration or even from the improvement on oral hygiene practices frequently neglected among hospitalized children.
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Affiliation(s)
- Desiree Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Muntsa Rocafort
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, University of Barcelona, Barcelona, Spain
| | - Alex Mira
- CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Health and Genomics, Center for Advanced Research in Public Health, Fundacion para el Fomento de la Investigacion Sanitaria y Biomedica de la Comunitat Valenciana (FISABIO), Valencia, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, University of Barcelona, Barcelona, Spain
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre (TEAGASC), Moorepark, Fermoy, Ireland.,APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER of Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
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9
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Henares D, Brotons P, de Sevilla MF, Fernandez-Lopez A, Hernandez-Bou S, Perez-Argüello A, Mira A, Muñoz-Almagro C, Cabrera-Rubio R. Differential nasopharyngeal microbiota composition in children according to respiratory health status. Microb Genom 2021; 7. [PMID: 34699345 PMCID: PMC8627214 DOI: 10.1099/mgen.0.000661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Acute respiratory infections (ARIs) constitute one of the leading causes of antibiotic administration, hospitalization and death among children <5 years old. The upper respiratory tract microbiota has been suggested to explain differential susceptibility to ARIs and modulate ARI severity. The aim of the present study was to investigate the relation of nasopharyngeal microbiota and other microbiological parameters with respiratory health and disease, and to assess nasopharyngeal microbiota diagnostic utility for discriminating between different respiratory health statuses. We conducted a prospective case-control study at Hospital Sant Joan de Deu (Barcelona, Spain) from 2014 to 2018. This study included three groups of children <18 years with gradual decrease of ARI severity: cases with invasive pneumococcal disease (IPD) (representative of lower respiratory tract infections and systemic infections), symptomatic controls with mild viral upper respiratory tract infections (URTI), and healthy/asymptomatic controls according to an approximate case-control ratio 1:2. Nasopharyngeal samples were collected from participants for detection, quantification and serotyping of pneumococcal DNA, viral DNA/RNA detection and 16S rRNA gene sequencing. Microbiological parameters were included on case-control classification models. A total of 140 subjects were recruited (IPD=27, URTI=48, healthy/asymptomatic control=65). Children's nasopharyngeal microbiota composition varied according to respiratory health status and infection severity. The IPD group was characterized by overrepresentation of Streptococcus pneumoniae, higher frequency of invasive pneumococcal serotypes, increased rate of viral infection and underrepresentation of potential protective bacterial species such as Dolosigranulum pigrum and Moraxella lincolnii. Microbiota-based classification models differentiated cases from controls with moderately high accuracy. These results demonstrate the close relationship existing between a child's nasopharyngeal microbiota and respiratory health, and provide initial evidence of the potential of microbiota-based diagnostics for differential diagnosis of severe ARIs using non-invasive samples.
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Affiliation(s)
- Desiree Henares
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona F de Sevilla
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Pediatric Department, Hospital Sant Joan de Deu, Barcelona, Spain
| | | | | | | | - Alex Mira
- CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,Department of Health and Genomics, Center for Advanced Research in Public Health, FISABIO, Valencia, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Hospital Sant Joan de Deu, Barcelona, Spain.,CIBER Center for Epidemiology and Public Health (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain.,School of Medicine, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre (TEAGASC), Moorepark, Fermoy, Cork, Ireland.,APC Microbiome Institute, University College Cork, County Cork, Ireland
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10
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Walshe N, Cabrera-Rubio R, Collins R, Puggioni A, Gath V, Crispie F, Cotter PD, Brennan L, Mulcahy G, Duggan V. A Multiomic Approach to Investigate the Effects of a Weight Loss Program on the Intestinal Health of Overweight Horses. Front Vet Sci 2021; 8:668120. [PMID: 34222398 PMCID: PMC8249564 DOI: 10.3389/fvets.2021.668120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Obesity is endemic in human populations in the western society, and with mounting evidence that the intestinal ecological environment plays a major role in its pathogenesis, identification of therapies based on intestinal microbiota modulation are gaining attention. Obesity in companion animals is also a common clinical problem. We set out using a multidimensional approach, to determine the effectiveness and safety of a weight loss program for horses incorporating diet restriction and exercise. In addition, we aimed to investigate the effect of this program on the overall intestinal health of overweight sedentary horses. The investigation comprised of a randomized, controlled, 6-week study of 14 overweight sedentary horses and ponies who were blocked for age, gender, and breed (controls n = 7, treatment n = 7). The treatment group were fed a restricted diet (1.4% of body weight dry matter intake) and the control group a maintenance diet (2% of body weight as dry matter intake) over the study period. The treatment group were subjected to a prescribed exercise regime, while the control group were exercised to mimic foraging conditions. Several clinical measurements were taken at the start and end of the study, including morphological parameters, ultrasound measurements of subcutaneous fat, and blood pressure. Fecal microbiota analysis was performed using 16S rRNA gene sequence analysis, and fecal metabolome was analyzed using NMR spectroscopy, on samples taken at weeks 1, 3, and 6 of the study. All horses completed the study period successfully. However, two of the treatment group had to have modified exercise regimes. The treatment group showed significant weight loss (p < 0.00001) and an associated decrease in waste circumference (p < 0.0001) when compared with the control group. The alpha-diversity of the fecal microbiota in the treatment group showed a significant increase from the start to the end of the study period (p < 0.05); however, there was no significant difference between groups at any sampling point. There were significant changes (p < 0.05) in the metabolome in both groups between the start and end of the study, but not between groups at any sampling point. Finally, the resting blood pressure of all horses was significantly lower by the end of the study.
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Affiliation(s)
- Nicola Walshe
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Roisin Collins
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Antonella Puggioni
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Vivian Gath
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
- VistaMilk, Cork, Ireland
| | - Lorraine Brennan
- UCD School of Agriculture and Food Science, Conway Institute, UCD Institute of Food and Health, University College Dublin, Dublin, Ireland
| | - Grace Mulcahy
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
| | - Vivienne Duggan
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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11
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Leech J, Cabrera-Rubio R, Walsh AM, Macori G, Walsh CJ, Barton W, Finnegan L, Crispie F, O'Sullivan O, Claesson MJ, Cotter PD. Fermented-Food Metagenomics Reveals Substrate-Associated Differences in Taxonomy and Health-Associated and Antibiotic Resistance Determinants. mSystems 2020; 5:e00522-20. [PMID: 33172966 PMCID: PMC7657593 DOI: 10.1128/msystems.00522-20] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Fermented foods have been the focus of ever greater interest as a consequence of purported health benefits. Indeed, it has been suggested that consumption of these foods helps to address the negative consequences of "industrialization" of the human gut microbiota in Western society. However, as the mechanisms via which the microbes in fermented foods improve health are not understood, it is necessary to develop an understanding of the composition and functionality of the fermented-food microbiota to better harness desirable traits. Here, we considerably expand the understanding of fermented-food microbiomes by employing shotgun metagenomic sequencing to provide a comprehensive insight into the microbial composition, diversity, and functional potential (including antimicrobial resistance and carbohydrate-degrading and health-associated gene content) of a diverse range of 58 fermented foods from artisanal producers from a number of countries. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity. From the combined data set, 127 high-quality metagenome-assembled genomes (MAGs), including 10 MAGs representing putatively novel species of Acetobacter, Acidisphaera, Gluconobacter, Companilactobacillus, Leuconostoc, and Rouxiella, were generated. Potential health promoting attributes were more common in fermented foods than nonfermented equivalents, with water kefirs, sauerkrauts, and kvasses containing the greatest numbers of potentially health-associated gene clusters. Ultimately, this study provides the most comprehensive insight into the microbiomes of fermented foods to date and yields novel information regarding their relative health-promoting potential.IMPORTANCE Fermented foods are regaining popularity worldwide due in part to a greater appreciation of the health benefits of these foods and the associated microorganisms. Here, we use state-of-the-art approaches to explore the microbiomes of 58 of these foods, identifying the factors that drive the microbial composition of these foods and potential functional benefits associated with these populations. Food type, i.e., dairy-, sugar-, or brine-type fermented foods, was the primary driver of microbial composition, with dairy foods found to have the lowest microbial diversity and, notably, potential health promoting attributes were more common in fermented foods than nonfermented equivalents. The information provided here will provide significant opportunities for the further optimization of fermented-food production and the harnessing of their health-promoting potential.
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Affiliation(s)
- John Leech
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | - Guerrino Macori
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Calum J Walsh
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Wiley Barton
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
| | - Laura Finnegan
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Fermoy, Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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12
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Walshe N, Mulcahy G, Crispie F, Cabrera-Rubio R, Cotter P, Jahns H, Duggan V. Outbreak of acute larval cyathostominosis - A "perfect storm" of inflammation and dysbiosis. Equine Vet J 2020; 53:727-739. [PMID: 32920897 PMCID: PMC8246859 DOI: 10.1111/evj.13350] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/29/2020] [Accepted: 08/29/2020] [Indexed: 12/13/2022]
Abstract
Background Cyathostomins are prevalent and pathogenic intestinal helminths of horses, causing acute and chronic disease, including acute larval cyathostominosis, which has a mortality rate of 50%. Factors determining individual susceptibility to acute larval cyathostominosis are unknown. Investigation of these factors could lead to novel treatment and prevention strategies. Objectives To investigate clinicopathological and faecal microbiota changes associated with disease in individual horses in an acute larval cyathostominosis outbreak. Study design Case series. Methods The study population was a herd of 23 mixed breed horses in Ireland. The outbreak occurred in November 2018. Fourteen horses were clinically affected. Clinical status was monitored and recorded. Blood and faecal sampling allowed clinicopathological, faecal 16s rRNA gene sequencing and faecal egg count analyses. Results Two horses were euthanised, whilst 12 recovered. Common clinical signs included loose faecal consistency, weight loss and pyrexia. Consistent clinicopathological findings were borderline anaemia, leucocytosis, thrombocytosis, hyperfibrinogenaemia, hyperglobulinaemia and a reverse A: G ratio. Decreased alpha‐diversity of the faecal microbiota and greater relative abundance of the genus Streptococcus, class Bacilli, order Lactobacillales and family Streptococcaceae, and family Prevotelleceae was found in clinically affected horses compared to their clinically normal cohorts. An increase in obligate fibrolytic bacteria was seen in the clinically normal group compared to the clinical group. Histopathological findings of the colon and caecum revealed a severe necrotising typhlocolitis associated with cyathostomin larvae and bacterial overgrowth in the mucosa of the large intestine. Main limitations The study population in this outbreak is small. There are several confounding factors limiting this to a descriptive case series. Faecal microbiota has been shown to reflect the large intestinal microbiota but do not represent changes directly. Conclusions These findings suggest that acute larval cyathostominosis is associated with dysbiosis of the gut microbiota as well as the inflammatory stimulus of numerous emerging larvae leading to structural and functional pathology of the large intestine.
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Affiliation(s)
- Nicola Walshe
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Grace Mulcahy
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland.,Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, APC Microbiome, Moorepark, Ireland.,APC Microbiome Ireland, Moorepark, Ireland
| | | | - Paul Cotter
- Teagasc Food Research Centre, APC Microbiome, Moorepark, Ireland.,APC Microbiome Ireland, Moorepark, Ireland.,Vistamilk, Moorepark, Ireland
| | - Hanne Jahns
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Vivienne Duggan
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
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13
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Peterson VL, Richards JB, Meyer PJ, Cabrera-Rubio R, Tripi JA, King CP, Polesskaya O, Baud A, Chitre AS, Bastiaanssen TFS, Woods LS, Crispie F, Dinan TG, Cotter PD, Palmer AA, Cryan JF. Sex-dependent associations between addiction-related behaviors and the microbiome in outbred rats. EBioMedicine 2020; 55:102769. [PMID: 32403084 PMCID: PMC7218262 DOI: 10.1016/j.ebiom.2020.102769] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/06/2020] [Accepted: 04/14/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Multiple factors contribute to the etiology of addiction, including genetics, sex, and a number of addiction-related behavioral traits. One behavioral trait where individuals assign incentive salience to food stimuli ("sign-trackers", ST) are more impulsive compared to those that do not ("goal-trackers", GT), as well as more sensitive to drugs and drug stimuli. Furthermore, this GT/ST phenotype predicts differences in other behavioral measures. Recent studies have implicated the gut microbiota as a key regulator of brain and behavior, and have shown that many microbiota-associated changes occur in a sex-dependent manner. However, few studies have examined how the microbiome might influence addiction-related behaviors. To this end, we sought to determine if gut microbiome composition was correlated with addiction-related behaviors determined by the GT/ST phenotype. METHODS Outbred male (N=101) and female (N=101) heterogeneous stock rats underwent a series of behavioral tests measuring impulsivity, attention, reward-learning, incentive salience, and locomotor response. Cecal microbiome composition was estimated using 16S rRNA gene amplicon sequencing. Behavior and microbiome were characterized and correlated with behavioral phenotypes. Robust sex differences were observed in both behavior and microbiome; further analyses were conducted within sex using the pre-established goal/sign-tracking (GT/ST) phenotype and partial least squares differential analysis (PLS-DA) clustered behavioral phenotype. RESULTS Overall microbiome composition was not associated to the GT/ST phenotype. However, microbial alpha diversity was significantly decreased in female STs. On the other hand, a measure of impulsivity had many significant correlations to microbiome in both males and females. Several measures of impulsivity were correlated with the genus Barnesiella in females. Female STs had notable correlations between microbiome and attentional deficient. In both males and females, many measures were correlated with the bacterial families Ruminocococcaceae and Lachnospiraceae. CONCLUSIONS These data demonstrate correlations between several addiction-related behaviors and the microbiome specific to sex.
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Affiliation(s)
- Veronica L Peterson
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland
| | - Jerry B Richards
- Department of Pharmacology and Toxicology, University at Buffalo, Buffalo, NY, USA
| | - Paul J Meyer
- Department of Psychology, University at Buffalo, Buffalo, NY, USA
| | - Raul Cabrera-Rubio
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Jordan A Tripi
- Department of Psychology, University at Buffalo, Buffalo, NY, USA
| | | | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Amelie Baud
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, CA, USA
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland
| | | | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, CA, USA; Center for Microbiome Innovation, University of California San Diego, CA, USA
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland; Department of Anatomy and Neuroscience, University College Cork, Room 2.33, 2nd Floor, Western Gateway Building, Cork, Ireland.
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14
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Heras V, Clooney AG, Ryan FJ, Cabrera-Rubio R, Casey PG, Hueston CM, Pinheiro J, Rudkin JK, Melgar S, Cotter P, Hill C, Gahan C. Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection. Access Microbiol 2020. [DOI: 10.1099/acmi.mim2019.po0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Vanessa Heras
- APC Microbiome Ireland, Cork, Ireland
- University College Cork, Cork, Ireland
| | | | | | | | | | | | | | | | | | - Paul Cotter
- Moorepark Food Research Centre, Teagasc, Cork
- APC Microbiome Ireland, Cork, Ireland
| | | | - Cormac Gahan
- APC Microbiome Ireland, Cork, Ireland
- University College Cork, Cork, Ireland
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15
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Cabrera-Rubio R, Patterson AM, Cotter PD, Beraza N. Cholestasis induced by bile duct ligation promotes changes in the intestinal microbiome in mice. Sci Rep 2019; 9:12324. [PMID: 31444478 PMCID: PMC6707139 DOI: 10.1038/s41598-019-48784-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/22/2019] [Indexed: 02/08/2023] Open
Abstract
Increasing evidence point to the relevance of intestinal disfunction and changes in the microbiome composition during chronic liver disease. More specifically, recent studies have highlighted that cholestatic diseases associate with a reduction in the microbiome diversity in patients. Still, the dynamics of the changes in the microbiome composition observed, as well as their implication in contributing to the pathogenesis of this disease remain largely undefined. Hence, experimental mouse models resembling the human pathogenesis are crucial to move forward our understanding on the mechanisms underpinning cholestatic disease and to enable the development of effective therapeutics. Our results show that the bile duct ligation (BDL) experimental model of cholestasis leads to rapid and significant changes in the microbiome diversity, with more than 100 OTUs being significantly different in faecal samples obtained from WT mice at 3 days and 7 days after BDL when compared to control animals. Changes in the microbial composition in mice after BDL included the enrichment of Akkermansia, Prevotella, Bacteroides and unclassified Ruminococcaceae in parallel with a drastic reduction of the presence of Faecalibacterium prausnitzii. In conclusion, our results support that bile duct ligation induces changes in the microbiome that partly resemble the gut microbial changes observed during human cholestatic disease.
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Affiliation(s)
- Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland.,APC Microbiome Institute, University College Cork, Co, Cork, Ireland
| | - Angela M Patterson
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute, Norwich Research Park, Norwich, UK
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland.,APC Microbiome Institute, University College Cork, Co, Cork, Ireland
| | - Naiara Beraza
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute, Norwich Research Park, Norwich, UK.
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16
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Fogarty C, Burgess CM, Cotter PD, Cabrera-Rubio R, Whyte P, Smyth C, Bolton DJ. Diversity and composition of the gut microbiota of Atlantic salmon (Salmo salar) farmed in Irish waters. J Appl Microbiol 2019; 127:648-657. [PMID: 31021487 DOI: 10.1111/jam.14291] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 12/25/2022]
Abstract
AIMS Information on the gut microbiota of salmon is essential for optimizing nutrition while maintaining host health and welfare. This study's objectives were to characterize the microbiota in the GI tract of Atlantic salmon (Salmo salar) farmed in waters off the west coast of Ireland and to investigate whether there is a difference in microbiota diversity between the proximal and distal regions of the intestine. METHODS AND RESULTS The microbiota from the proximal and distal intestine (PI and DI, respectively) of Atlantic salmon was examined using MiSeq Illumina high-throughput sequencing of the 16S ribosomal RNA gene. The PI region had greater bacterial diversity than the DI region. Six phyla were present in the DI samples, dominated by Tenericutes and Firmicutes. These six phyla were also amongst the 12 phyla detected in the PI samples. The PI microbiota was dominated by Tenericutes, Firmicutes, Bacteroidetes and Proteobacteria. A core microbiota of 20 operational taxonomic units (OTUs) common to both regions was observed. CONCLUSIONS It was concluded that Tenericutes were the dominant phylum in both PI and DI samples, and the PI region had greater Shannon and Simpson diversity of bacteria. However, further work is required to identify the functionality of the salmon microbiota. SIGNIFICANCE AND IMPACT OF THE STUDY Our study determined the composition and diversity of the intestinal microbiota in adult salmon from a commercial fishery and provides data to improve our understanding of their contributions to the nutrition, health and welfare of Atlantic salmon farmed in Irish waters.
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Affiliation(s)
- Colin Fogarty
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.,School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Ireland, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Ireland, Cork, Ireland
| | - Paul Whyte
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor Smyth
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.,School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland
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17
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Walshe N, Duggan V, Cabrera-Rubio R, Crispie F, Cotter P, Feehan O, Mulcahy G. Removal of adult cyathostomins alters faecal microbiota and promotes an inflammatory phenotype in horses. Int J Parasitol 2019; 49:489-500. [PMID: 30986403 DOI: 10.1016/j.ijpara.2019.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/13/2019] [Accepted: 02/24/2019] [Indexed: 12/19/2022]
Abstract
The interactions between parasitic helminths and gut microbiota are considered to be an important, although as yet incompletely understood, factor in the regulation of immunity, inflammation and a range of diseases. Infection with intestinal helminths is ubiquitous in grazing horses, with cyathostomins (about 50 species of which are recorded) predominating. Consequences of infection include both chronic effects, and an acute inflammatory syndrome, acute larval cyathostominosis, which sometimes follows removal of adult helminths by administration of anthelmintic drugs. The presence of cyathostomins as a resident helminth population of the equine gut (the "helminthome") provides an opportunity to investigate the effect helminth infection, and its perturbation, has on both the immune system and bacterial microbiome of the gut, as well as to determine the specific mechanisms of pathophysiology involved in equine acute larval cyathostominosis. We studied changes in the faecal microbiota of two groups of horses following treatment with anthelmintics (fenbendazole or moxidectin). We found decreases in both alpha diversity and beta diversity of the faecal microbiota at Day 7 post-treatment, which were reversed by Day 14. These changes were accompanied by increases in inflammatory biomarkers. The general pattern of faecal microbiota detected was similar to that seen in the relatively few equine gut microbiome studies reported to date. We conclude that interplay between resident cyathostomin populations and the bacterial microbiota of the equine large intestine is important in maintaining homeostasis and that disturbance of this ecology can lead to gut dysbiosis and play a role in the aetiology of inflammatory conditions in the horse, including acute larval cyathostominosis.
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Affiliation(s)
- Nicola Walshe
- School of Veterinary Medicine, Veterinary Sciences Centre, University College Dublin, Ireland
| | - Vivienne Duggan
- School of Veterinary Medicine, Veterinary Sciences Centre, University College Dublin, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, APC Microbiome, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, APC Microbiome, Ireland
| | - Paul Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, APC Microbiome, Ireland
| | - Orna Feehan
- School of Veterinary Medicine, Veterinary Sciences Centre, University College Dublin, Ireland
| | - Grace Mulcahy
- School of Veterinary Medicine, Veterinary Sciences Centre, University College Dublin, Ireland.
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18
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Cabrera-Rubio R, Kunz C, Rudloff S, García-Mantrana I, Crehuá-Gaudiza E, Martínez-Costa C, Collado MC. Association of Maternal Secretor Status and Human Milk Oligosaccharides With Milk Microbiota: An Observational Pilot Study. J Pediatr Gastroenterol Nutr 2019; 68:256-263. [PMID: 30540710 DOI: 10.1097/mpg.0000000000002216] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
BACKGROUND AND OBJECTIVES Breast milk contains several bioactive factors including human milk oligosaccharides (HMOs) and microbes that shape the infant gut microbiota. HMO profile is determined by secretor status; however, their influence on milk microbiota is still uncovered. This study is aimed to determine the impact of the FUT2 genotype on the milk microbiota during the first month of lactation and the association with HMO. METHODS Milk microbiota from 25 healthy lactating women was determined by quantitative polymerase chain reaction and 16S gene pyrosequencing. Secretor genotype was obtained by polymerase chain reaction-random fragment length polymorphisms and by HMO identification and quantification. RESULTS The most abundant bacteria were Staphylococcus and Streptococcus, followed by Enterobacteriaceae-related bacteria. The predominant HMO in secretor milk samples were 2'FL and lacto-N-fucopentaose I, whereas non-secretor milk was characterized by lacto-N-fucopentaose II and lacto-N-difucohexaose II. Differences in microbiota composition and quantity were found depending on secretor/non-secretor status. Lactobacillus spp, Enterococcus spp, and Streptococcus spp were lower in non-secretor than in secretor samples. Bifidobacterium genus and species were less prevalent in non-secretor samples. Despite no differences on diversity and richness, non-secretor samples had lower Actinobacteria and higher relative abundance of Enterobacteriaceae, Lactobacillaceae, and Staphylococcaceae. CONCLUSIONS Maternal secretor status is associated with the human milk microbiota composition and is maintained during the first 4 weeks. Specific associations between milk microbiota, HMO, and secretor status were observed, although the potential biological impact on the neonate remains elusive. Future studies are needed to reveal the early nutrition influence on the reduction of risk of disease.
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Affiliation(s)
- Raul Cabrera-Rubio
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain
| | | | - Silvia Rudloff
- Institute of Nutritional Science
- Department of Pediatrics, Justus-Liebig-University, Giessen, Germany
| | - Izaskun García-Mantrana
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain
| | | | | | - M Carmen Collado
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain
- Department of Pediatrics, Hospital Clinico Universitario, Nutrition Research Group of INCLIVA, University of Valencia, Spain
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Las Heras V, Clooney AG, Ryan FJ, Cabrera-Rubio R, Casey PG, Hueston CM, Pinheiro J, Rudkin JK, Melgar S, Cotter PD, Hill C, Gahan CGM. Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection. Microbiome 2019; 7:7. [PMID: 30658700 PMCID: PMC6339339 DOI: 10.1186/s40168-019-0621-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/04/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND A westernized diet comprising a high caloric intake from animal fats is known to influence the development of pathological inflammatory conditions. However, there has been relatively little focus upon the implications of such diets for the progression of infectious disease. Here, we investigated the influence of a high-fat (HF) diet upon parameters that influence Listeria monocytogenes infection in mice. RESULTS We determined that short-term administration of a HF diet increases the number of goblet cells, a known binding site for the pathogen, in the gut and also induces profound changes to the microbiota and promotes a pro-inflammatory gene expression profile in the host. Host physiological changes were concordant with significantly increased susceptibility to oral L. monocytogenes infection in mice fed a HF diet relative to low fat (LF)- or chow-fed animals. Prior to Listeria infection, short-term consumption of HF diet elevated levels of Firmicutes including Coprococcus, Butyricicoccus, Turicibacter and Clostridium XIVa species. During active infection with L. monocytogenes, microbiota changes were further exaggerated but host inflammatory responses were significantly downregulated relative to Listeria-infected LF- or chow-fed groups, suggestive of a profound tempering of the host response influenced by infection in the context of a HF diet. The effects of diet were seen beyond the gut, as a HF diet also increased the sensitivity of mice to systemic infection and altered gene expression profiles in the liver. CONCLUSIONS We adopted a systems approach to identify the effects of HF diet upon L. monocytogenes infection through analysis of host responses and microbiota changes (both pre- and post-infection). Overall, the results indicate that short-term consumption of a westernized diet has the capacity to significantly alter host susceptibility to L. monocytogenes infection concomitant with changes to the host physiological landscape. The findings suggest that diet should be a consideration when developing models that reflect human infectious disease.
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Affiliation(s)
- Vanessa Las Heras
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Adam G Clooney
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Feargal J Ryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Pat G Casey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Cara M Hueston
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jorge Pinheiro
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Justine K Rudkin
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Cormac G M Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
- School of Pharmacy, University College Cork, Cork, Ireland.
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Kiernan MG, Coffey JC, McDermott K, Cotter PD, Cabrera-Rubio R, Kiely PA, Dunne CP. The Human Mesenteric Lymph Node Microbiome Differentiates Between Crohn's Disease and Ulcerative Colitis. J Crohns Colitis 2019; 13:58-66. [PMID: 30239655 PMCID: PMC6302955 DOI: 10.1093/ecco-jcc/jjy136] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
BACKGROUND AND AIMS Mesenteric lymph nodes are sites in which translocated bacteria incite and progress immunological responses. For this reason, understanding the microbiome of mesenteric lymph nodes in inflammatory bowel disease is important. The bacterial profile of Crohn's disease mesenteric lymph nodes has been analysed using culture-independent methods in only one previous study. This study aimed to investigate the mesenteric lymph node microbiota from both Crohn's disease and ulcerative colitis patients. METHODS Mesenteric lymph nodes were collected from Crohn's disease and ulcerative colitis patients undergoing resection. Total DNA was extracted from mesenteric lymph nodes and assessed for the presence of bacterial DNA [16S]. All work was completed in a sterile environment using aseptic techniques. Samples positive for 16S DNA underwent next-generation sequencing, and the identity of bacterial phyla and species were determined. RESULTS Crohn's disease mesenteric lymph nodes had a distinctly different microbial profile to that observed in ulcerative colitis. The relative abundance of Firmicutes was greater in nodes from ulcerative colitis patients, whereas Proteobacteria were more abundant in Crohn's disease. Although species diversity was reduced in the mesenteric lymph nodes of patients with Crohn's disease, these lymph nodes contained greater numbers of less dominant phyla, mainly Fusobacteria. CONCLUSION This study confirms that there are distinct differences between the Crohn's disease and ulcerative colitis mesenteric lymph node microbiomes. Such microbial differences could aid in the diagnosis of Crohn's disease or ulcerative colitis, particularly in cases of indeterminate colitis at time of resection, or help explain their mechanisms of development and progression.
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Affiliation(s)
- Miranda G Kiernan
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland
| | - J Calvin Coffey
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland,Department of Surgery, University Hospital Limerick, Limerick, Ireland
| | - Kieran McDermott
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland
| | - Paul D Cotter
- APC Microbiome Institute, University College Cork, Cork, Ireland,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Raul Cabrera-Rubio
- APC Microbiome Institute, University College Cork, Cork, Ireland,Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Patrick A Kiely
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland
| | - Colum P Dunne
- Graduate Entry Medical School and Centre for Interventions in Infection, Inflammation & Immunity [4i], University of Limerick, Limerick, Ireland,Corresponding author: Professor Colum Dunne, Director of Research, Graduate Entry Medical School, University of Limerick, Limerick V94 T9PX, Ireland. Tel: +353-[0]61-234703;
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Johnston DGW, Williams MA, Thaiss CA, Cabrera-Rubio R, Raverdeau M, McEntee C, Cotter PD, Elinav E, O'Neill LAJ, Corr SC. Loss of MicroRNA-21 Influences the Gut Microbiota, Causing Reduced Susceptibility in a Murine Model of Colitis. J Crohns Colitis 2018; 12:835-848. [PMID: 29608690 DOI: 10.1093/ecco-jcc/jjy038] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 03/27/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS microRNAs regulate gene expression and influence the pathogenesis of human diseases. The present study investigated the role of microRNA-21 [miR-21] in the pathogenesis of intestinal inflammation, because miR-21 is highly expressed in inflammatory bowel disease. Inflammatory bowel disease is associated with intestinal barrier dysfunction and an altered gut microbiota. Recent studies have demonstrated that host microRNAs can shape the microbiota. Thus, we determined the influence of miR-21 on the gut microbiota and observed the subsequent impact in a dextran sodium sulphate [DSS]-induced colitis model. METHODS The influence of miR-21 on the gut microbiota and inflammation was assessed in wild-type [WT] and miR-21-/- mice, in co-housed mice, following antibiotic depletion of the microbiota, or by colonization of germ-free [GF] mice with fecal homogenate, prior to DSS administration. We carried out 16S rRNA sequencing on WT and miR-21-/- mice to dissect potential differences in the gut microbiota. RESULTS miR-21-/- mice have reduced susceptibility to DSS-induced colitis compared with WT mice. Co-housing conferred some protection to WT mice, while GF mice colonized with fecal homogenate from miR-21-/- were protected from DSS colitis compared with those colonized with WT homogenate. Further supporting a role for the microbiota in the observed phenotype, the protection afforded by miR-21 depletion was lost when mice were pre-treated with antibiotics. The 16S rRNA sequencing revealed significant differences in the composition of WT and miR-21-/- intestinal microbiota. CONCLUSIONS These findings suggest that miR-21 influences the pathogenesis of intestinal inflammation by causing propagation of a disrupted gut microbiota.
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Affiliation(s)
- Daniel G W Johnston
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland.,School of Genetics and Microbiology, Moyne Institute of Preventative Medicine, Trinity College Dublin, Dublin, Ireland
| | - Michelle A Williams
- School of Genetics and Microbiology, Moyne Institute of Preventative Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Institute, Cork, Ireland
| | - Mathilde Raverdeau
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Craig McEntee
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, and APC Microbiome Institute, Cork, Ireland
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Luke A J O'Neill
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Sinéad C Corr
- School of Genetics and Microbiology, Moyne Institute of Preventative Medicine, Trinity College Dublin, Dublin, Ireland
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Nilaweera KN, Cabrera-Rubio R, Speakman JR, O'Connor PM, McAuliffe A, Guinane CM, Lawton EM, Crispie F, Aguilera M, Stanley M, Boscaini S, Joyce S, Melgar S, Cryan JF, Cotter PD. Whey protein effects on energy balance link the intestinal mechanisms of energy absorption with adiposity and hypothalamic neuropeptide gene expression. Am J Physiol Endocrinol Metab 2017; 313:E1-E11. [PMID: 28325732 DOI: 10.1152/ajpendo.00356.2016] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 03/17/2017] [Accepted: 03/17/2017] [Indexed: 02/08/2023]
Abstract
We tested the hypothesis that dietary whey protein isolate (WPI) affects the intestinal mechanisms related to energy absorption and that the resulting energy deficit is compensated by changes in energy balance to support growth. C57BL/6 mice were provided a diet enriched with WPI with varied sucrose content, and the impact on energy balance-related parameters was investigated. As part of a high-sucrose diet, WPI reduced the hypothalamic expression of pro-opiomelanocortin gene expression and increased energy intake. The energy expenditure was unaffected, but epididymal weight was reduced, indicating an energy loss. Notably, there was a reduction in the ileum gene expression for amino acid transporter SLC6a19, glucose transporter 2, and fatty acid transporter 4. The composition of the gut microbiota also changed, where Firmicutes were reduced. The above changes indicated reduced energy absorption through the intestine. We propose that this mobilized energy in the adipose tissue and caused hypothalamic changes that increased energy intake, acting to counteract the energy deficit arising in the intestine. Lowering the sucrose content in the WPI diet increased energy expenditure. This further reduced epididymal weight and plasma leptin, whereupon hypothalamic ghrelin gene expression and the intestinal weight were both increased. These data suggest that when the intestine-adipose-hypothalamic pathway is subjected to an additional energy loss (now in the adipose tissue), compensatory changes attempt to assimilate more energy. Notably, WPI and sucrose content interact to enable the component mechanisms of this pathway.
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Affiliation(s)
- Kanishka N Nilaweera
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland;
| | - Raul Cabrera-Rubio
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - John R Speakman
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, Scotland
| | - Paula M O'Connor
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - AnneMarie McAuliffe
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Caitriona M Guinane
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Elaine M Lawton
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Fiona Crispie
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Mònica Aguilera
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maurice Stanley
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Serena Boscaini
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- Department of Anatomy and Neurosciences, University College Cork, Cork, Ireland; and
| | - Susan Joyce
- APC Microbiome Institute, University College Cork, Cork, Ireland
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Silvia Melgar
- APC Microbiome Institute, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Department of Anatomy and Neurosciences, University College Cork, Cork, Ireland; and
| | - Paul D Cotter
- Food Biosciences Department, Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
- APC Microbiome Institute, University College Cork, Cork, Ireland
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Mira-Pascual L, Cabrera-Rubio R, Ocon S, Costales P, Parra A, Suarez A, Moris F, Rodrigo L, Mira A, Collado MC. Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers. J Gastroenterol 2015; 50:167-79. [PMID: 24811328 DOI: 10.1007/s00535-014-0963-x] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 04/11/2014] [Indexed: 02/04/2023]
Abstract
BACKGROUND Epidemiological studies demonstrate a link between gastrointestinal cancers and environmental factors such as diet. It has been suggested that environmental cancer risk is determined by the interaction between diet and microbes. Thus, the purpose of this study was to examine the hypothesis that microbiota composition during colorectal cancer (CRC) progression might differ depending on the stage of the disease. METHODS A total of 28 age-matched and sex-matched subjects, seven with CRC adenocarcinoma, 11 with tubular adenomas and ten healthy subjects with intact colon, were included into the study. Microbiomes from mucosal and fecal samples were analyzed with 16S ribosomal RNA gene pyrosequencing, together with quantitative PCR of specific bacteria and archaea. RESULTS The principal coordinates analysis clearly separated healthy tissue samples from polyps and tumors, supporting the presence of specific bacterial consortia that are associated with affected sites and that can serve as potential biomarkers of CRC progression. A higher presence of Fusobacterium nucleatum and Enterobacteriaceae was found by qPCR in samples from CRC compared to healthy controls. We observed a correlation between CRC process development and levels of Methanobacteriales (R = 0.537, P = 0.007) and Methanobrevibacterium (R = 0.574, P = 0.03) in fecal samples. CONCLUSION Differences in microbial and archaeal composition between mucosal samples from healthy and disease tissues were observed in tubular adenoma and adenocarcinoma. In addition, microbiota from mucosal samples represented the underlying dysbiosis, whereas fecal samples seem not to be appropriate to detect shifts in microbial composition. CRC risk is influenced by microbial composition, showing differences according to disease progression step and tumor severity.
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Affiliation(s)
- L Mira-Pascual
- Department of Biotechnology, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Av. Agustin Escardino 7, 49860, Paterna, Valencia, Spain
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Gomar-Vercher S, Cabrera-Rubio R, Mira A, Montiel-Company JM, Almerich-Silla JM. Relationship of children's salivary microbiota with their caries status: a pyrosequencing study. Clin Oral Investig 2014; 18:2087-94. [PMID: 24532386 DOI: 10.1007/s00784-014-1200-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 01/30/2014] [Indexed: 02/08/2023]
Abstract
PURPOSE Different dental caries status could be related with alterations in oral microbiota. Previous studies have collected saliva as a representative medium of the oral ecosystem. The purpose of this study was to assess the composition of oral microbiota and its relation to the presence of dental caries at different degrees of severity. MATERIALS AND METHODS One hundred ten saliva samples from 12-year-old children were taken and divided into six groups defined in strict accordance with their dental caries prevalence according to the International Caries Detection and Assessment System II criteria. These samples were studied by pyrosequencing PCR products of the 16S ribosomal RNA gene. RESULTS The results showed statistically significant intergroup differences at the class and genus taxonomic levels. Streptococcus is the most frequent genus in all groups; although it did not show intergroup statistical differences. In patients with cavities, Porphyromonas and Prevotella showed an increasing percentage compared to healthy individuals. Bacterial diversity diminished as the severity of the disease increased, so those patients with more advanced stages of caries presented less bacterial diversity than healthy subjects. CONCLUSION Although microbial composition tended to be different, the intragroup variation is large, as evidenced by the lack of clear intragroup clustering in principal component analyses. Thus, no clear differences were found, indicating that using bacterial composition as the sole source of biomarkers for dental caries may not be reliable in the unstimulated saliva samples used in the current study.
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Affiliation(s)
- S Gomar-Vercher
- Stomatology Department, University of Valencia, C/Gascó Oliag 1, 46010, Valencia, Spain
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Simón-Soro A, Belda-Ferre P, Cabrera-Rubio R, Alcaraz LD, Mira A. A tissue-dependent hypothesis of dental caries. Caries Res 2013; 47:591-600. [PMID: 24080530 DOI: 10.1159/000351663] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/18/2013] [Indexed: 11/19/2022] Open
Abstract
Current understanding of dental caries considers this disease a demineralization of the tooth tissues due to the acid produced by sugar-fermenting microorganisms. Thus, caries is considered a diet- and pH-dependent process. We present here the first metagenomic analysis of the bacterial communities present at different stages of caries development, with the aim of determining whether the bacterial composition and biochemical profile are specific to the tissue affected. The data show that microbial composition at the initial, enamel-affecting stage of caries is significantly different from that found at subsequent stages, as well as from dental plaque of sound tooth surfaces. Although the relative proportion of Streptococcus mutans increased from 0.12% in dental plaque to 0.72% in enamel caries, Streptococcus mitis and Streptococcus sanguinis were the dominant streptococci in these lesions. The functional profile of caries-associated bacterial communities indicates that genes involved in acid stress tolerance and dietary sugar fermentation are overrepresented only at the initial stage (enamel caries), whereas other genes coding for osmotic stress tolerance as well as collagenases and other proteases enabling dentin degradation are significantly overrepresented in dentin cavities. The results support a scenario in which pH and diet are determinants of the disease during the degradation of enamel, but in dentin caries lesions not only acidogenic but also proteolytic bacteria are involved. We propose that caries disease is a process of varying etiology, in which acid-producing bacteria are the vehicle to penetrate enamel and allow dentin degrading microorganisms to expand the cavity.
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Affiliation(s)
- A Simón-Soro
- Department of Genomics and Health, Center for Advanced Research in Public Health, Valencia, Spain
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Abstract
We aimed to determine the bacterial diversity of different oral micro-niches and to assess whether saliva and plaque samples are representative of oral microbial composition. We took minute samples from each surface of the individual teeth and gingival crevices of two healthy volunteers (112 samples per donor), as well as samples from the tongue dorsum and non-stimulated and stimulated saliva. DNA was extracted from 67 selected samples of each donor, and the 16S rRNA gene was amplified by PCR and pyrosequenced to obtain, on average, over 2,700 reads per sample, which were taxonomically assigned to obtain a geographic map of bacterial diversity at each tooth and sulcus location. Analysis of the data shows considerable differences in bacterial composition between teeth at different intra-oral locations and between surfaces of the same tooth. The most pronounced differences were observed in incisors and canines, where genera like Streptococcus were found at 40% to 70% on the vestibular surfaces but were almost absent on the lingual sides. Saliva samples, especially non-stimulated saliva, were not representative of supra-and subgingival plaque in the two individuals tested. We suggest that more precise sampling is required for the proper determination of oral microbial composition and to relate that diversity to epidemiological, clinical, and etiological parameters.
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Affiliation(s)
- A Simón-Soro
- Center for Advanced Research in Public Health (CSISP), Valencia, Spain
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28
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Cabrera-Rubio R, Collado MC, Laitinen K, Salminen S, Isolauri E, Mira A. The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. Am J Clin Nutr 2012; 96:544-51. [PMID: 22836031 DOI: 10.3945/ajcn.112.037382] [Citation(s) in RCA: 517] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Breast milk is recognized as the most important postpartum element in metabolic and immunologic programming of health of neonates. The factors influencing the milk microbiome and the potential impact of microbes on infant health have not yet been uncovered. OBJECTIVE Our objective was to identify pre- and postnatal factors that can potentially influence the bacterial communities inhabiting human milk. DESIGN We characterized the milk microbial community at 3 different time points by pyrosequencing and quantitative polymerase chain reaction in mothers (n = 18) who varied in BMI, weight gain, and mode of delivery. RESULTS We found that the human milk microbiome changes over lactation. Weisella, Leuconostoc, Staphylococcus, Streptococcus, and Lactococcus were predominant in colostrum samples, whereas in 1- and 6-mo milk samples the typical inhabitants of the oral cavity (eg, Veillonella, Leptotrichia, and Prevotella) increased significantly. Milk from obese mothers tended to contain a different and less diverse bacterial community compared with milk from normal-weight mothers. Milk samples from elective but not from nonelective mothers who underwent cesarean delivery contained a different bacterial community than did milk samples from individuals giving birth by vaginal delivery, suggesting that it is not the operation per se but rather the absence of physiological stress or hormonal signals that could influence the microbial transmission process to milk. CONCLUSIONS Our results indicate that milk bacteria are not contaminants and suggest that the milk microbiome is influenced by several factors that significantly skew its composition. Because bacteria present in breast milk are among the very first microbes entering the human body, our data emphasize the necessity to understand the biological role that the milk microbiome could potentially play for human health.
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Affiliation(s)
- Raul Cabrera-Rubio
- Joint Unit of Research in Genomics and Health, Centre for Public Health Research (CSISP)-Cavanilles Institute for Biodiversity and Evolutionary Biology, University of Valencia, Valencia, Spain
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Alcaraz L, Belda-Ferre P, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, Mira A. Identifying a healthy oral microbiome through metagenomics. Clin Microbiol Infect 2012; 18 Suppl 4:54-7. [DOI: 10.1111/j.1469-0691.2012.03857.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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