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Aizpurua O, Nyholm L, Morris E, Chaverri G, Herrera Montalvo LG, Flores-Martinez JJ, Lin A, Razgour O, Gilbert MTP, Alberdi A. The role of the gut microbiota in the dietary niche expansion of fishing bats. Anim Microbiome 2021; 3:76. [PMID: 34711286 PMCID: PMC8555116 DOI: 10.1186/s42523-021-00137-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 10/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background Due to its central role in animal nutrition, the gut microbiota is likely a relevant factor shaping dietary niche shifts. We analysed both the impact and contribution of the gut microbiota to the dietary niche expansion of the only four bat species that have incorporated fish into their primarily arthropodophage diet. Results We first compared the taxonomic and functional features of the gut microbiota of the four piscivorous bats to that of 11 strictly arthropodophagous species using 16S rRNA targeted amplicon sequencing. Second, we increased the resolution of our analyses for one of the piscivorous bat species, namely Myotis capaccinii, and analysed multiple populations combining targeted approaches with shotgun sequencing. To better understand the origin of gut microorganisms, we also analysed the gut microbiota of their fish prey (Gambusia holbrooki). Our analyses showed that piscivorous bats carry a characteristic gut microbiota that differs from that of their strict arthropodophagous counterparts, in which the most relevant bacteria have been directly acquired from their fish prey. This characteristic microbiota exhibits enrichment of genes involved in vitamin biosynthesis, as well as complex carbohydrate and lipid metabolism, likely providing their hosts with an enhanced capacity to metabolise the glycosphingolipids and long-chain fatty acids that are particularly abundant in fish. Conclusions Our results depict the gut microbiota as a relevant element in facilitating the dietary transition from arthropodophagy to piscivory. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-021-00137-w.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.
| | - Lasse Nyholm
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
| | - Evie Morris
- University of Exeter, Streatham Campus, Biosciences, Exeter, EX4 4PS, UK
| | - Gloriana Chaverri
- Sede del Sur, Universidad de Costa Rica, #4000 Alamedas, Golfito, 60701, Costa Rica.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancón, República de Panamá
| | - L Gerardo Herrera Montalvo
- Estación de Biología Chamela, Instituto de Biología, Universidad Nacional Autónoma de México, Apartado Postal 21, San Patricio, 48980, Jalisco, Mexico
| | - José Juan Flores-Martinez
- Laboratorio de Sistemas de Información Geográfica, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Circuito Exterior s/n, Ciudad Universitaria, 04510, Mexico City, Mexico
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, 130117, China
| | - Orly Razgour
- University of Exeter, Streatham Campus, Biosciences, Exeter, EX4 4PS, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, 1353, Copenhagen, Denmark
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Naya-Català F, do Vale Pereira G, Piazzon MC, Fernandes AM, Calduch-Giner JA, Sitjà-Bobadilla A, Conceição LEC, Pérez-Sánchez J. Cross-Talk Between Intestinal Microbiota and Host Gene Expression in Gilthead Sea Bream ( Sparus aurata) Juveniles: Insights in Fish Feeds for Increased Circularity and Resource Utilization. Front Physiol 2021; 12:748265. [PMID: 34675821 PMCID: PMC8523787 DOI: 10.3389/fphys.2021.748265] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/02/2021] [Indexed: 01/03/2023] Open
Abstract
New types of fish feed based on processed animal proteins (PAPs), insect meal, yeast, and microbial biomasses have been used with success in gilthead sea bream. However, some drawback effects on feed conversion and inflammatory systemic markers were reported in different degrees with PAP- and non-PAP-based feed formulations. Here, we focused on the effects of control and two experimental diets on gut mucosal-adherent microbiota, and how it correlated with host transcriptomics at the local (intestine) and systemic (liver and head kidney) levels. The use of tissue-specific PCR-arrays of 93 genes in total rendered 13, 12, and 9 differentially expressed (DE) genes in the intestine, liver, and head kidney, respectively. Illumina sequencing of gut microbiota yielded a mean of 125,350 reads per sample, assigned to 1,281 operational taxonomic unit (OTUs). Bacterial richness and alpha diversity were lower in fish fed with the PAP diet, and discriminant analysis displayed 135 OTUs driving the separation between groups with 43 taxa correlating with 27 DE genes. The highest expression of intestinal pcna and alpi was achieved in PAP fish with intermediate values in non-PAP, being the pro-inflammatory action of alpi associated with the presence of Psychrobacter piscatorii. The intestinal muc13 gene was down-regulated in non-PAP fish, with this gene being negatively correlated with anaerobic (Chloroflexi and Anoxybacillus) and metal-reducing (Pelosinus and Psychrosinus) bacteria. Other inflammatory markers (igm, il8, tnfα) were up-regulated in PAP fish, positively correlating the intestinal igm gene with the inflammasome activator Escherichia/Shigella, whereas the systemic expression of il8 and tnfα was negatively correlated with the Bacilli class in PAP fish and positively correlated with Paracoccus yeei in non-PAP fish. Overall changes in the expression pattern of il10, galectins (lgals1, lgals8), and toll-like receptors (tlr2, tlr5, tlr9) reinforced the anti-inflammatory profile of fish fed with the non-PAP diet, with these gene markers being associated with a wide range of OTUs. A gut microbiota-liver axis was also established, linking the microbial generation of short chain fatty acids with the fueling of scd1- and elovl6-mediated lipogenesis. In summary, by correlating the microbiome with host gene expression, we offer new insights in the evaluation of fish diets promoting gut and metabolism homeostasis, and ultimately, the health of farmed fish.
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Affiliation(s)
- Fernando Naya-Català
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | | | - M Carla Piazzon
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ana Margarida Fernandes
- SPAROS Lda, Area Empresarial de Marim, Olhăo, Portugal.,Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Josep Alvar Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
| | | | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal (IATS-CSIC), Castellón, Spain
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53
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Effects of Dietary Fishmeal Replacement by Poultry By-Product Meal and Hydrolyzed Feather Meal on Liver and Intestinal Histomorphology and on Intestinal Microbiota of Gilthead Seabream (Sparus aurata). APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11198806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The effects on liver and intestinal histomorphology and on intestinal microbiota in gilthead seabream (Sparus aurata) fed diets that contained poultry by-product meal (PBM) and hydrolyzed feather meal (HFM) as fishmeal replacements were studied. Fish fed on a series of isonitrogenous and isoenergetic diets, where fishmeal protein of the control diet (FM diet) was replaced by either PBM or by HFM at 25%, 50% and 100% without amino acid supplementation (PBM25, PBM50, PBM100, HFM25, HFM50 and HFM100 diets) or supplemented with lysine and methionine (PBM25+, PBM50+, HFM25+ and HFM50+ diets). The use of PBM and HFM at 25% fishmeal replacement generated a similar hepatic histomorphology to FM-fed fish, indicating that both land animal proteins are highly digestible at low FM replacement levels. However, 50% and 100% FM replacement levels by either PBM or HFM resulted in pronounced hepatic alterations in fish with the latter causing more severe degradation of the liver. Dietary amino acid supplementation delivered an improved tissue histology signifying their importance at high FM replacement levels. Intestinal microbiota was dominated by Proteobacteria (58.8%) and Actinobacteria (32.4%) in all dietary groups, but no specific pattern was observed among them at any taxonomic level. This finding was probably driven by the high inter-individual variability observed.
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54
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The effect of benzo[a]pyrene on the gut microbiota of Nile tilapia (Oreochromis niloticus). Appl Microbiol Biotechnol 2021; 105:7935-7947. [PMID: 34542683 DOI: 10.1007/s00253-021-11592-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 09/06/2021] [Accepted: 09/11/2021] [Indexed: 02/07/2023]
Abstract
Benzo[a]pyrene (BaP) is a highly toxic and carcinogenic polycyclic aromatic hydrocarbon (PAH) whose toxicological effects in the gut microbiota of aquatic organisms have not yet been fully revealed. Therefore, in this study, we used high-throughput 16S rRNA gene sequencing to evaluate the effects of BaP in the gut microbiome of Oreochromis niloticus, including its possible participation in the process of detoxification and its ability to recover. The fish were injected with a single intraperitoneal dose of 20 mg kg-1 of BaP, and the effects in the microbiome were evaluated at 24, 72, and 120 h post-injection. The results indicate a clear dysbiosis (in composition, relative abundance, diversity, and interaction networks) of the gut microbiota during 24 h post-injection, dominated by Fusobacteria and Bacteroidetes and a decrease in Proteobacteria and Spirochaetae. Interestingly, a slight recovery of the microbiome begins at 72 h and stabilises at 120 h post-injection. Pathway analysis revealed the participation of the gut microbiome in PAH degradation mainly at 24 h post-injection. This study provides new insights in the toxicology of BaP in O. niloticus and the first evidence of the ability of the gut microbiome to recovery after a chemical disturbance. KEY POINTS: • Benzo[a]pyrene caused a dysbiosis in the gut microbiota of Oreochromis niloticus. • We observed an enrichment of bacteria involved in the metabolism of xenobiotics. • The gut microbiota was recovered after exposure to benzo[a]pyrene.
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55
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Leech T, McDowall L, Hopkins KP, Sait SM, Harrison XA, Bretman A. Social environment drives sex and age-specific variation in Drosophila melanogaster microbiome composition and predicted function. Mol Ecol 2021; 30:5831-5843. [PMID: 34494339 DOI: 10.1111/mec.16149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/05/2021] [Accepted: 08/20/2021] [Indexed: 12/25/2022]
Abstract
Social environments influence multiple traits of individuals including immunity, stress and ageing, often in sex-specific ways. The composition of the microbiome (the assemblage of symbiotic microorganisms within a host) is determined by environmental factors and the host's immune, endocrine and neural systems. The social environment could alter host microbiomes extrinsically by affecting transmission between individuals, probably promoting homogeneity in the microbiome of social partners. Alternatively, intrinsic effects arising from interactions between the microbiome and host physiology (the microbiota-gut-brain axis) could translate social stress into dysbiotic microbiomes, with consequences for host health. We investigated how manipulating social environments during larval and adult life-stages altered the microbiome composition of Drosophila melanogaster fruit flies. We used social contexts that particularly alter the development and lifespan of males, predicting that any intrinsic social effects on the microbiome would therefore be sex-specific. The presence of adult males during the larval stage significantly altered the microbiome of pupae of both sexes. In adults, same-sex grouping increased bacterial diversity in both sexes. Importantly, the microbiome community structure of males was more sensitive to social contact at older ages, an effect partially mitigated by housing focal males with young rather than coaged groups. Functional analyses suggest that these microbiome changes impact ageing and immune responses. This is consistent with the hypothesis that the substantial effects of the social environment on individual health are mediated through intrinsic effects on the microbiome, and provides a model for understanding the mechanistic basis of the microbiota-gut-brain axis.
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Affiliation(s)
- Thomas Leech
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Max Planck Institute for Biology of Ageing, Köln, Germany
| | - Laurin McDowall
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,School of Life Sciences, University of Dundee, Dundee, UK
| | - Kevin P Hopkins
- Institute of Zoology, Zoological Society of London, London, UK
| | - Steven M Sait
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Xavier A Harrison
- Institute of Zoology, Zoological Society of London, London, UK.,Centre for Ecology & Conservation, University of Exeter, Penryn, UK
| | - Amanda Bretman
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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56
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Fei N, Choo-Kang C, Reutrakul S, Crowley SJ, Rae D, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Bovet P, Riesen W, Korte W, Luke A, Layden BT, Gilbert JA, Dugas LR. Gut microbiota alterations in response to sleep length among African-origin adults. PLoS One 2021; 16:e0255323. [PMID: 34495955 PMCID: PMC8425534 DOI: 10.1371/journal.pone.0255323] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
Sleep disorders are increasingly being characterized in modern society as contributing to a host of serious medical problems, including obesity and metabolic syndrome. Changes to the microbial community in the human gut have been reportedly associated with many of these cardiometabolic outcomes. In this study, we investigated the impact of sleep length on the gut microbiota in a large cohort of 655 participants of African descent, aged 25-45, from Ghana, South Africa (SA), Jamaica, and the United States (US). The sleep duration was self-reported via a questionnaire. Participants were classified into 3 sleep groups: short (<7hrs), normal (7-<9hrs), and long (≥9hrs). Forty-seven percent of US participants were classified as short sleepers and 88% of SA participants as long sleepers. Gut microbial composition analysis (16S rRNA gene sequencing) revealed that bacterial alpha diversity negatively correlated with sleep length (p<0.05). Furthermore, sleep length significantly contributed to the inter-individual beta diversity dissimilarity in gut microbial composition (p<0.01). Participants with both short and long-sleep durations exhibited significantly higher abundances of several taxonomic features, compared to normal sleep duration participants. The predicted relative proportion of two genes involved in the butyrate synthesis via lysine pathway were enriched in short sleep duration participants. Finally, co-occurrence relationships revealed by network analysis showed unique interactions among the short, normal and long duration sleepers. These results suggest that sleep length in humans may alter gut microbiota by driving population shifts of the whole microbiota and also specific changes in Exact Sequence Variants abundance, which may have implications for chronic inflammation associated diseases. The current findings suggest a possible relationship between disrupted sleep patterns and the composition of the gut microbiota. Prospective investigations in larger and more prolonged sleep researches and causally experimental studies are needed to confirm these findings, investigate the underlying mechanism and determine whether improving microbial homeostasis may buffer against sleep-related health decline in humans.
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Affiliation(s)
- Na Fei
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Candice Choo-Kang
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
| | - Sirimon Reutrakul
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
| | - Stephanie J. Crowley
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
| | - Dale Rae
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Kweku Bedu-Addo
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Jacob Plange-Rhule
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Terrence E. Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Estelle V. Lambert
- Department of Physiology, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pascal Bovet
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | - Walter Riesen
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | - Wolfgang Korte
- Center for Laboratory Medicine, Canton Hospital, St. Gallen, Switzerland
| | - Amy Luke
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
| | - Brian T. Layden
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America
| | - Jack A. Gilbert
- University of California San Diego, San Diego, California, United States of America
| | - Lara R. Dugas
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
- Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
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57
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Arthur RA, Dos Santos Bezerra R, Ximenez JPB, Merlin BL, de Andrade Morraye R, Neto JV, Fava NMN, Figueiredo DLA, de Biagi CAO, Montibeller MJ, Guimarães JB, Alves EG, Schreiner M, da Costa TS, da Silva CFL, Malheiros JM, da Silva LHB, Ribas GT, Achallma DO, Braga CM, Andrade KFA, do Carmo Alves Martins V, Dos Santos GVN, Granatto CF, Terin UC, Sanches IH, Ramos DE, Garay-Malpartida HM, de Souza GMP, Slavov SN, Silva WA. Microbiome and oral squamous cell carcinoma: a possible interplay on iron metabolism and its impact on tumor microenvironment. Braz J Microbiol 2021; 52:1287-1302. [PMID: 34002353 PMCID: PMC8324744 DOI: 10.1007/s42770-021-00491-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/06/2021] [Indexed: 12/23/2022] Open
Abstract
There is increasing evidence showing positive association between changes in oral microbiome and the occurrence of oral squamous cell carcinoma (OSCC). Alcohol- and nicotine-related products can induce microbial changes but are still unknown if these changes are related to cancerous lesion sites. In an attempt to understand how these changes can influence the OSCC development and maintenance, the aim of this study was to investigate the oral microbiome linked with OSCC as well as to identify functional signatures and associate them with healthy or precancerous and cancerous sites. Our group used data of oral microbiomes available in public repositories. The analysis included data of oral microbiomes from electronic cigarette users, alcohol consumers, and precancerous and OSCC samples. An R-based pipeline was used for taxonomic and functional prediction analysis. The Streptococcus spp. genus was the main class identified in the healthy group. Haemophilus spp. predominated in precancerous lesions. OSCC samples revealed a higher relative abundance compared with the other groups, represented by an increased proportion of Fusobacterium spp., Prevotella spp., Haemophilus spp., and Campylobacter spp. Venn diagram analysis showed 52 genera exclusive of OSCC samples. Both precancerous and OSCC samples seemed to present a specific associated functional pattern. They were menaquinone-dependent protoporphyrinogen oxidase pattern enhanced in the former and both 3',5'-cyclic-nucleotide phosphodiesterase (purine metabolism) and iron(III) transport system ATP-binding protein enhanced in the latter. We conclude that although precancerous and OSCC samples present some differences on microbial profile, both microbiomes act as "iron chelators-like" potentially contributing to tumor growth.
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Affiliation(s)
- Rodrigo Alex Arthur
- Preventive and Community Dentistry Department, Faculty of Dentistry, Federal University of Rio Grande do Sul, Porto Alegre, RS, 90035-003, Brazil
| | - Rafael Dos Santos Bezerra
- Postgraduate Program in Clinical Oncology, Stem Cells and Cell Therapy, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
- Center for Cell-Based Therapy (CEPID/FAPESP), Molecular Genetics and Bioinformatics Laboratory - MGBL, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, 14049-900, Brazil
| | - João Paulo Bianchi Ximenez
- Center for Cell-Based Therapy (CEPID/FAPESP), Molecular Genetics and Bioinformatics Laboratory - MGBL, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Bruna Laís Merlin
- Department of Entomology and Acarology, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Raphael de Andrade Morraye
- Center for Cell-Based Therapy (CEPID/FAPESP), Molecular Genetics and Bioinformatics Laboratory - MGBL, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
- Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, SP, 14049-900, Brazil
| | - João Valentini Neto
- Department of Nutrition, School of Public Health, University of Sao Paulo, São Paulo, SP, 01246-904, Brazil
| | - Natália Melo Nasser Fava
- Department of Hydraulics and Sanitation, São Carlos School of Engineering, University of São Paulo, São Carlos, SP, 13563-120, Brazil
| | - David Livingstone Alves Figueiredo
- Institute for Cancer Research (IPEC), Guarapuava, PR, 85015-430, Brazil
- Department of Medicine, UNICENTRO, Guarapuava, PR, 85015-430, Brazil
| | - Carlos Alberto Oliveira de Biagi
- Center for Cell-Based Therapy (CEPID/FAPESP), Molecular Genetics and Bioinformatics Laboratory - MGBL, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, 14049-900, Brazil
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil
| | - Maria Jara Montibeller
- Department of Food and Nutrition, School of Pharmaceutical Sciences, São Paulo State University, Araraquara, SP, Brazil
| | - Jhefferson Barbosa Guimarães
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, SP, Brazil
| | - Ellen Gomes Alves
- Undergraduate in Biological Sciences, Institute of Health Sciences, Universidade Paulista, Ribeirão Preto, SP, Brazil
| | - Monique Schreiner
- Graduate Program in Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil
| | - Tiago Silva da Costa
- Department of Biological Sciences and Health, Federal University of Amapá, Macapá, AP, Brazil
| | - Charlie Felipe Liberati da Silva
- Graduate Program in Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil
| | | | - Luan Henrique Burda da Silva
- Graduate Program in Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil
| | - Guilherme Taborda Ribas
- Graduate Program in Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil
| | - Daisy Obispo Achallma
- Laboratorios de Investigación y Desarrollo, FARVET, Chincha Alta, Ica, Perú & Centro de Investigación de Genética y Biología Molecular (CIGBM), Universidad de San Martín de Porres, Lima, Perú
| | - Camila Margalho Braga
- Graduate Program in Parasitic Biology in the Amazon, Pará State University, Belém, PA, Brazil
| | - Karen Flaviane Assis Andrade
- Department of Electrical and Biomedical Engineering, Institute of Technology, Federal University of Pará, Belém, PA, Brazil
| | | | | | | | | | - Igor Henrique Sanches
- Institute of Pathology Tropical and Public Health, Federal University of Goiás, Goiânia, GO, Brazil
| | - Diana Estefania Ramos
- Department of Oral; Maxillofacial Surgery, and Periodontology, School of Dentistry of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Gabriela Marcelino Pereira de Souza
- Center for Cell-Based Therapy (CEPID/FAPESP), Molecular Genetics and Bioinformatics Laboratory - MGBL, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, 14049-900, Brazil
| | - Svetoslav Nanev Slavov
- Center for Cell-Based Therapy (CEPID/FAPESP), Molecular Genetics and Bioinformatics Laboratory - MGBL, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, 14049-900, Brazil
| | - Wilson Araújo Silva
- Center for Cell-Based Therapy (CEPID/FAPESP), Molecular Genetics and Bioinformatics Laboratory - MGBL, National Institute of Science and Technology in Stem Cell and Cell Therapy (INCTC/CNPq), Regional Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501, Ribeirão Preto, SP, 14049-900, Brazil.
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, 14049-900, Brazil.
- Center for Cell-Based Therapy (CEPID/FAPESP), Molecular Genetics and Bioinformatics Laboratory - MGBL, Blood Center of Ribeirão Preto, Rua Tenente Catão Roxo, 2501 - 14051-140 Ribeirão Preto, São Paulo, Brasil.
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58
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Identification of Biomolecules Involved in the Adaptation to the Environment of Cold-Loving Microorganisms and Metabolic Pathways for Their Production. Biomolecules 2021; 11:biom11081155. [PMID: 34439820 PMCID: PMC8393263 DOI: 10.3390/biom11081155] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 12/22/2022] Open
Abstract
Cold-loving microorganisms of all three domains of life have unique and special abilities that allow them to live in harsh environments. They have acquired structural and molecular mechanisms of adaptation to the cold that include the production of anti-freeze proteins, carbohydrate-based extracellular polymeric substances and lipids which serve as cryo- and osmoprotectants by maintaining the fluidity of their membranes. They also produce a wide diversity of pigmented molecules to obtain energy, carry out photosynthesis, increase their resistance to stress and provide them with ultraviolet light protection. Recently developed analytical techniques have been applied as high-throughoutput technologies for function discovery and for reconstructing functional networks in psychrophiles. Among them, omics deserve special mention, such as genomics, transcriptomics, proteomics, glycomics, lipidomics and metabolomics. These techniques have allowed the identification of microorganisms and the study of their biogeochemical activities. They have also made it possible to infer their metabolic capacities and identify the biomolecules that are parts of their structures or that they secrete into the environment, which can be useful in various fields of biotechnology. This Review summarizes current knowledge on psychrophiles as sources of biomolecules and the metabolic pathways for their production. New strategies and next-generation approaches are needed to increase the chances of discovering new biomolecules.
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Nakai M, Ribeiro RV, Stevens BR, Gill P, Muralitharan RR, Yiallourou S, Muir J, Carrington M, Head GA, Kaye DM, Marques FZ. Essential Hypertension Is Associated With Changes in Gut Microbial Metabolic Pathways: A Multisite Analysis of Ambulatory Blood Pressure. Hypertension 2021; 78:804-815. [PMID: 34333988 DOI: 10.1161/hypertensionaha.121.17288] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Michael Nakai
- Hypertension Research Laboratory, School of Biological Sciences, Monash University, Melbourne, Australia (M.N., R.R.M., F.Z.M.)
| | - Rosilene V Ribeiro
- Charles Perkins Centre, University of Sydney, Australia (R.V.R.).,School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Australia (R.V.R.)
| | - Bruce R Stevens
- Department of Physiology and Functional Genomics, University of Florida, College of Medicine, Gainesville (B.R.S.)
| | - Paul Gill
- Department of Gastroenterology (P.G., J.M.), Monash University, Melbourne, Australia
| | - Rikeish R Muralitharan
- Hypertension Research Laboratory, School of Biological Sciences, Monash University, Melbourne, Australia (M.N., R.R.M., F.Z.M.).,Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur (R.R.M.)
| | - Stephanie Yiallourou
- Preclinical Disease and Prevention, Baker Heart and Diabetes Institute, Melbourne, Australia (S.Y., M.C.)
| | - Jane Muir
- Department of Gastroenterology (P.G., J.M.), Monash University, Melbourne, Australia
| | - Melinda Carrington
- Preclinical Disease and Prevention, Baker Heart and Diabetes Institute, Melbourne, Australia (S.Y., M.C.)
| | - Geoffrey A Head
- Department of Pharmacology, Faculty of Medicine Nursing and Health Sciences (G.A.H.), Monash University, Melbourne, Australia.,Neuropharmacology Laboratory, Baker Heart and Diabetes Institute, Melbourne, Australia (G.A.H.)
| | - David M Kaye
- Clinical School, Faculty of Medicine Nursing and Health Sciences (D.M.K.), Monash University, Melbourne, Australia.,Heart Failure Research Group, Baker Heart and Diabetes Institute, Melbourne, Australia (D.M.K., F.Z.M.).,Department of Cardiology, Alfred Hospital, Melbourne, Australia (D.M.K.)
| | - Francine Z Marques
- Hypertension Research Laboratory, School of Biological Sciences, Monash University, Melbourne, Australia (M.N., R.R.M., F.Z.M.).,Heart Failure Research Group, Baker Heart and Diabetes Institute, Melbourne, Australia (D.M.K., F.Z.M.)
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60
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Boehme M, Guzzetta KE, Bastiaanssen TFS, van de Wouw M, Moloney GM, Gual-Grau A, Spichak S, Olavarría-Ramírez L, Fitzgerald P, Morillas E, Ritz NL, Jaggar M, Cowan CSM, Crispie F, Donoso F, Halitzki E, Neto MC, Sichetti M, Golubeva AV, Fitzgerald RS, Claesson MJ, Cotter PD, O'Leary OF, Dinan TG, Cryan JF. Microbiota from young mice counteracts selective age-associated behavioral deficits. NATURE AGING 2021; 1:666-676. [PMID: 37117767 DOI: 10.1038/s43587-021-00093-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 06/25/2021] [Indexed: 04/30/2023]
Abstract
The gut microbiota is increasingly recognized as an important regulator of host immunity and brain health. The aging process yields dramatic alterations in the microbiota, which is linked to poorer health and frailty in elderly populations. However, there is limited evidence for a mechanistic role of the gut microbiota in brain health and neuroimmunity during aging processes. Therefore, we conducted fecal microbiota transplantation from either young (3-4 months) or old (19-20 months) donor mice into aged recipient mice (19-20 months). Transplant of a microbiota from young donors reversed aging-associated differences in peripheral and brain immunity, as well as the hippocampal metabolome and transcriptome of aging recipient mice. Finally, the young donor-derived microbiota attenuated selective age-associated impairments in cognitive behavior when transplanted into an aged host. Our results reveal that the microbiome may be a suitable therapeutic target to promote healthy aging.
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Affiliation(s)
- Marcus Boehme
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Katherine E Guzzetta
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | | | - Gerard M Moloney
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | | | - Simon Spichak
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | | | | | | | - Nathaniel L Ritz
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Minal Jaggar
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Fiona Crispie
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Francisco Donoso
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Evelyn Halitzki
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Marta C Neto
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Marzia Sichetti
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Anna V Golubeva
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Rachel S Fitzgerald
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Marcus J Claesson
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Olivia F O'Leary
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland.
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61
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Sung JY, Lee YJ, Cho YJ, Shin MN, Lee SJ, Lee HS, Koh H, Bae JW, Shin JH, Kim HJ, Lee DW. A large-scale metagenomic study for enzyme profiles using the focused identification of the NGS-based definitive enzyme research (FINDER) strategy. Biotechnol Bioeng 2021; 118:4360-4374. [PMID: 34309016 DOI: 10.1002/bit.27904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/23/2021] [Accepted: 07/23/2021] [Indexed: 11/09/2022]
Abstract
Excavating the molecular details of many diverse enzymes from metagenomes remains challenging in agriculture, food, health, and environmental fields. We present a versatile method that accelerates metabolic enzyme discovery for highly selective gene capture in metagenomes using next-generation sequencing. Culture-independent enzyme mining of environmental DNA is based on a set of short identifying degenerate sequences specific for a wide range of enzyme superfamilies, followed by multiplexed DNA barcode sequencing. A strategy of 'focused identification of next-generation sequencing-based definitive enzyme research' enabled us to generate targeted enzyme datasets from metagenomes, resulting in minimal hands-on obtention of high-throughput biological diversity and potential function profiles, without being time-consuming. This method also provided a targeted inventory of predicted proteins and molecular features of metabolic activities from several metagenomic samples. We suggest that the efficiency and sensitivity of this method will accelerate the decryption of microbial diversity and the signature of proteins and their metabolism from environmental samples.
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Affiliation(s)
- Jae-Yoon Sung
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Yong-Jik Lee
- Department of Bio-Cosmetics, Seowon University, Chung-Ju, South Korea
| | - Yong-Joon Cho
- Department of Biological Sciences and Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
| | - Myeong-Na Shin
- Department of Central Area Crop Science, NICS, RDA, Suwon, South Korea
| | - Sang-Jae Lee
- Major in Food Biotechnology, Silla University, Busan, South Korea
| | - Han-Seung Lee
- Major in Food Biotechnology, Silla University, Busan, South Korea
| | - Hong Koh
- Department of Pediatrics, Yonsei University, Seoul, South Korea
| | - Jin-Woo Bae
- Department of Biology, Kyung Hee University, Seoul, South Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, South Korea
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Okamura Y, Kinoshita M, Kono T, Sakai M, Hikima JI. Deficiency of interleukin-17 receptor A1 induces microbiota disruption in the intestine of Japanese medaka, Oryzias latipes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100885. [PMID: 34339936 DOI: 10.1016/j.cbd.2021.100885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/11/2021] [Accepted: 07/17/2021] [Indexed: 10/20/2022]
Abstract
The mutual relationship between the intestinal immune system and the gut microbiota has received a great deal of attention. In mammals, interleukin-17A and F (IL-17A/F) are inflammatory cytokines and key regulators of the gut microbiota. However, in teleosts, the function of IL-17A/F in controlling the gut microbiota is poorly understood. We attempted to elucidate the importance of teleost IL-17 signaling in controlling gut microbiota. We previously established a knockout (KO) of IL-17 receptor A (RA) 1, a receptor for IL-17A/F, in the Japanese medaka (Oryzias latipes) using the CRISPR-Cas9 system and performed 16S rRNA-based metagenomic analyses using the anterior and posterior sections of the intestinal tract. The number of observed OTUs in the anterior intestine was significantly decreased in IL-17RA1 KO medaka compared to that in the wild-type (WT). Furthermore, β-diversity analysis (weighted UniFrac) revealed considerably different bacterial composition in the anterior intestine of IL-17RA1 KO compared to WT, with similar findings in α-diversity. Notably, the pathogen Plesiomonas shigelloides was significantly increased in the posterior intestine of IL-17RA1 KO medaka. These findings indicate that signaling via IL-17RA1 is required to maintain a healthy gut microbiota in teleosts and mammals. The involvement of IL-17RA1 in controlling the gut microbiota has been demonstrated, resulting in microbiome dysbiosis in IL-17RA1 KO medaka.
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Affiliation(s)
- Yo Okamura
- Interdisciplinary Graduate School of Agriculture and Engineering, University of Miyazaki, Miyazaki, Japan
| | - Masato Kinoshita
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tomoya Kono
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Masahiro Sakai
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Jun-Ichi Hikima
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan.
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63
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Transcriptome Profiling and Metagenomic Analysis Help to Elucidate Interactions in an Inflammation-Associated Cancer Mouse Model. Cancers (Basel) 2021; 13:cancers13153683. [PMID: 34359585 PMCID: PMC8345192 DOI: 10.3390/cancers13153683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary Colitis-associated colorectal cancer is the third most significant condition that increases the overall risk of developing colorectal cancer. In this study, we examined normal colonic mucosa of tumor-bearing mice in the DSS/AOM mouse model by gene expression profiling and fecal samples by 16s rDNA amplicon sequencing. Gene set enrichment analysis revealed that genes associated with fatty acid metabolism, oxidative phosphorylation, and the PI3K-Akt-mTOR pathways were enriched colonic mucosa of DSS/AOM mice. Additionally, enrichment of the sphingolipid signal and lipoarabinomannan biosynthetic pathways were inferred from fecal microbial composition. Our findings provide insights into altered transcriptome and microbiome in a mouse model of colitis-induced carcinogenesis. Abstract Colitis is a risk factor for colorectal cancer (CRC) and can change the dynamics of gut microbiota, leading to dysbiosis and contributing to carcinogenesis. The functional interactions between colitis-associated CRC and microbiota remain unknown. In this study, colitis and CRC were induced in BALB/c mice by the administration of dextran sodium sulfate (DSS) and/or azoxymethane (AOM). Whole transcriptome profiling of normal colon was then performed, and gene set enrichment analysis (GSEA) revealed enriched fatty acid metabolism, oxidative phosphorylation, and PI3K-Akt-mTOR signaling in the tissues from DSS/AOM mice. Additionally, immunohistochemical staining showed increased expression levels of phosphorylated S6 ribosomal protein, a downstream target of the PI3K-Akt-mTOR pathway in the inflamed mucosa of DSS/AOM mice. Fecal microbes were characterized using 16S rDNA gene sequencing. Redundancy analysis demonstrated a significant dissimilarity between the DSS/AOM group and the others. Functional analysis inferred from microbial composition showed enrichments of the sphingolipid signal and lipoarabinomannan biosynthetic pathways. This study provides additional insights into alterations associated with DSS/AOM-induced colitis and associates PI3K-Akt-mTOR, sphingolipid-signaling and lipoarabinomannan biosynthetic pathways in mouse DSS/AOM-induced colitis.
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64
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Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia). WATER 2021. [DOI: 10.3390/w13141899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hypersaline ecosystems—aquatic environments where concentration of salt exceeds 35 g L−1—host microbial communities that are highly specialised to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages that are characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (total dissolved solids) and alkalinity amongst the most influential parameters driving the community patterns. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.
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65
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Alegbeleye O, Alisoltani A, Abia ALK, Awe AA, Adetunji AT, Rabiu S, Opeolu BO. Investigation into the bacterial diversity of sediment samples obtained from Berg River, Western Cape, South Africa. Folia Microbiol (Praha) 2021; 66:931-947. [PMID: 34224087 DOI: 10.1007/s12223-021-00893-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022]
Abstract
This study used conventional culturing and 16S rRNA metagenomics analyses to assess the diversity of bacterial communities in sediment samples obtained from the Berg River, Western Cape, South Africa. Samples were collected from six points: a residential and recreational area, an industrial area, an informal residential settlement, a point next to a wastewater treatment plant (WWTP), a pumping station, and a residential and agricultural farming area along the river. High bacterial counts recorded on general selective and differential culture media signify substantial microbial contamination along the sampling sites. The most prevalent bacterial phyla detected (through metagenomics analyses) along the sampling sites were Proteobacteria (61%), Planctomycetes (9.5%), Firmicutes (7.8%), Bacteroidetes (5%), Acidobacteria (4.6%), and Actinobacteria (4.6%). Some members of the identified predominant bacterial phyla, genera, and classes are important public health bacteria that have been implicated in human diseases and outbreaks, while some others are metal or hydrocarbon tolerant, indicating possible significant environmental pollution. Notable human pathogenic genera such as Bacillus, Clostridium, Shigella, Legionella, Mycobacterium, and Pseudomonas were identified in varying percentages at five of the six sampling areas. Fecal contamination was particularly rife at all residential areas, with the informal housing area being the most notably polluted. Diverse functional pathways were predicted for identified bacteria, such as those associated with different chronic and infectious human diseases as well as those related to hydrocarbon and metal remediation. The point next to a WWTP contained vastly diverse groups of bacterial contaminants as well as the most abundant pathway identities and titles.
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Affiliation(s)
- Oluwadara Alegbeleye
- Department of Food Science, University of Campinas (UNICAMP), Rua Monteiro Lobato, 80, Campinas, SP, 13083-862, Brazil.
| | | | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Adetunji Ajibola Awe
- Department of Conservation and Marine Sciences, Faculty of Applied Sciences, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Adewole Tomiwa Adetunji
- Department of Agriculture, Faculty of Applied Sciences, Cape Peninsula University of Technology, Western Cape, Wellington, 7654, South Africa
| | - Saidat Rabiu
- Department of Environmental and Occupational Studies, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Beatrice Olutoyin Opeolu
- Extended Curriculum Programmes, Faculty of Applied Sciences, Cape Peninsula University of Technology, Cape Town, 8000, South Africa
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66
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Koch RA, Yoon GM, Aryal UK, Lail K, Amirebrahimi M, LaButti K, Lipzen A, Riley R, Barry K, Henrissat B, Grigoriev IV, Herr JR, Aime MC. Symbiotic nitrogen fixation in the reproductive structures of a basidiomycete fungus. Curr Biol 2021; 31:3905-3914.e6. [PMID: 34245690 DOI: 10.1016/j.cub.2021.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 04/09/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022]
Abstract
Nitrogen (N) fixation is a driving force for the formation of symbiotic associations between N2-fixing bacteria and eukaryotes.1 Limited examples of these associations are known in fungi, and none with sexual structures of non-lichenized species.2-6 The basidiomycete Guyanagaster necrorhizus is a sequestrate fungus endemic to the Guiana Shield.7 Like the root rot-causing species in its sister genera Armillaria and Desarmillaria, G. necrorhizus sporocarps fruit from roots of decaying trees (Figures 1A-1C),8 and genome sequencing is consistent with observations that G. necrorhizus is a white-rotting decomposer. This species also represents the first documentation of an arthropod-dispersed sequestrate fungus. Numerous species of distantly related wood-feeding termites, which scavenge for N-rich food, feed on the mature spore-bearing tissue, or gleba, of G. necrorhizus. During feeding, mature spores adhere to termites for subsequent dispersal.9 Using chemical assays, isotope analysis, and high-throughput sequencing, we show that the sporocarps harbor actively N2-fixing Enterobacteriaceae species and that the N content within fungal tissue increases with maturation. Untargeted proteomic profiling suggests that ATP generation in the gleba is accomplished via fermentation. The use of fermentation-an anaerobic process-indicates that the sporocarp environment is anoxic, likely an adaptation to protect the oxygen-sensitive nitrogenase enzyme. Sporocarps also have a thick outer covering, possibly to limit oxygen diffusion. The enriched N content within mature sporocarps may offer a dietary inducement for termites in exchange for spore dispersal. These results show that the flexible metabolic capacity of fungi may facilitate N2-fixing associations, as well as higher-level organismal associations.
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Affiliation(s)
- Rachel A Koch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA; Department of Plant Pathology, University of Nebraska, Lincoln, NE 68520, USA.
| | - Gyeong Mee Yoon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mojgan Amirebrahimi
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert Riley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille 13288, France; Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, Marseille 13288, France; Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Joshua R Herr
- Department of Plant Pathology, University of Nebraska, Lincoln, NE 68520, USA; Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68520, USA
| | - M Catherine Aime
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA.
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Sasso Pisano Geothermal Field Environment Harbours Diverse Ktedonobacteria Representatives and Illustrates Habitat-Specific Adaptations. Microorganisms 2021; 9:microorganisms9071402. [PMID: 34209727 PMCID: PMC8306680 DOI: 10.3390/microorganisms9071402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 12/26/2022] Open
Abstract
The hydrothermal steam environment of Sasso Pisano (Italy) was selected to investigate the associated microbial community and its metabolic potential. In this context, 16S and 18S rRNA gene partial sequences of thermophilic prokaryotes and eukaryotes inhabiting hot springs and fumaroles as well as mesophilic microbes colonising soil and water were analysed by high-throughput amplicon sequencing. The eukaryotic and prokaryotic communities from hot environments clearly differ from reference microbial communities of colder soil sites, though Ktedonobacteria showed high abundances in various hot spring samples and a few soil samples. This indicates that the hydrothermal steam environments of Sasso Pisano represent not only a vast reservoir of thermophilic but also mesophilic members of this Chloroflexi class. Metabolic functional profiling revealed that the hot spring microbiome exhibits a higher capability to utilise methane and aromatic compounds and is more diverse in its sulphur and nitrogen metabolism than the mesophilic soil microbial consortium. In addition, heavy metal resistance-conferring genes were significantly more abundant in the hot spring microbiome. The eukaryotic diversity at a fumarole indicated high abundances of primary producers (unicellular red algae: Cyanidiales), consumers (Arthropoda: Collembola sp.), and endoparasite Apicomplexa (Gregarina sp.), which helps to hypothesise a simplified food web at this hot and extremely nutrient-deprived acidic environment.
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68
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Vargas O, Gutiérrez MS, Caruffo M, Valderrama B, Medina DA, García K, Reyes-Jara A, Toro M, Feijóo CG, Navarrete P. Probiotic Yeasts and Vibrio anguillarum Infection Modify the Microbiome of Zebrafish Larvae. Front Microbiol 2021; 12:647977. [PMID: 34248866 PMCID: PMC8260990 DOI: 10.3389/fmicb.2021.647977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 05/28/2021] [Indexed: 12/12/2022] Open
Abstract
The host microbiome plays an essential role in health and disease. Microbiome modification by pathogens or probiotics has been poorly explored especially in the case of probiotic yeasts. Next-generation sequencing currently provides the best tools for their characterization. Debaryomyces hansenii 97 (D. hansenii 97) and Yarrowia lipolytica 242 (Y. lipolytica 242) are yeasts that protect wildtype zebrafish (Danio rerio) larvae against a Vibrio anguillarum (V. anguillarum) infection, increasing their survival rate. We investigate the effect of these microorganisms on the microbiome and neutrophil response (inflammation) in zebrafish larvae line Tg(Bacmpx:GFP)i114. We postulated that preinoculation of larvae with yeasts would attenuate the intestinal neutrophil response and prevent modification of the larval microbiome induced by the pathogen. Microbiome study was performed by sequencing the V3-V4 region of the 16S rRNA gene and prediction of metabolic pathways by Piphillin in conventionally raised larvae. Survival and the neutrophil response were both evaluated in conventional and germ-free conditions. V. anguillarum infection resulted in higher neutrophil number in the intestinal area compared to non-infected larvae in both conditions. In germ-free conditions, infected larvae pre-inoculated with yeasts showed fewer neutrophil numbers than infected larvae. In both conditions, only D. hansenii 97 increased the survival of infected larvae. Beta diversity of the microbiota was modified by V. anguillarum and both yeasts, compared to non-inoculated larvae. At 3 days post-infection, V. anguillarum modified the relative abundance of 10 genera, and pre-inoculation with D. hansenii 97 and Y. lipolytica 242 prevented the modification of 5 and 6 of these genera, respectively. Both yeasts prevent the increase of Ensifer and Vogesella identified as negative predictors for larval survival (accounting for 40 and 27 of the variance, respectively). In addition, yeast pre-inoculation prevents changes in some metabolic pathways altered by V. anguillarum’s infection. These results suggest that both yeasts and V. anguillarum can shape the larval microbiota configuration in the early developmental stage of D. rerio. Moreover, modulation of key taxa or metabolic pathways of the larval microbiome by yeasts can be associated with the survival of infected larvae. This study contributes to the understanding of yeast–pathogen–microbiome interactions, although further studies are needed to elucidate the mechanisms involved.
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Affiliation(s)
- Orlando Vargas
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - María Soledad Gutiérrez
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
| | - Mario Caruffo
- Laboratorio Inmunologia en Peces, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Benjamín Valderrama
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Daniel A Medina
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile.,Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterinaria, Universidad San Sebastián, Puerto Montt, Chile
| | - Katherine García
- Facultad de Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Santiago, Chile
| | - Angélica Reyes-Jara
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Magaly Toro
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Carmen G Feijóo
- ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile.,Laboratorio Inmunologia en Peces, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile.,ANID - Millennium Science Initiative Program - Millennium Nucleus in the Biology of the Intestinal Microbiota, Santiago, Chile
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69
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Li C, Tang D, Wang Y, Fan Q, Zhang X, Cui X, Yu H. Endogenous bacteria inhabiting the Ophiocordyceps highlandensis during fruiting body development. BMC Microbiol 2021; 21:178. [PMID: 34116633 PMCID: PMC8196446 DOI: 10.1186/s12866-021-02227-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 05/10/2021] [Indexed: 01/04/2023] Open
Abstract
Background The genus Ophiocordyceps, which includes Ophiocordyceps sinensis, has been demonstrated to be one of the most valuable medicinal taxa. The low rate of larval infection and slow development that characterize the cultivation of this genus should be urgently addressed. To identify potential bioinoculants that stimulate the growth of Ophiocordyceps, O. highlandensis was selected as a model system, and a total of 72 samples were collected to systematically compare the microbial communities present during fruiting body development. By applying high-throughput 16S and ITS2 amplicon sequencing technology, the bacterial and fungal communities were identified in O. highlandensis and its surrounding soil, and the functional dynamics of the bacteria were explored. Results The results indicate that the most abundant bacteria across all the samples from O. highlandensis were Proteobacteria, Firmicutes and Bacteroidetes, while members of Ascomycota were detected among the fungi. The pathways enriched in the developmental stages were associated with carbohydrate degradation, nucleotides and pyridoxal biosynthesis, and the TCA cycle. Compared with that in the fungal community, an unexpectedly high taxonomic and functional fluctuation was discovered in the bacterial community during the maturation of O. highlandensis. Furthermore, bipartite network analysis identified four potential supercore OTUs associated with O. highlandensis growth. Conclusions All the findings of this study suggest unexpectedly high taxonomic and functional fluctuations in the bacterial community of O. highlandensis during its maturation. O. highlandensis may recruit different endogenous bacteria across its life cycle to enhance growth and support rapid infection. These results may facilitate Ophiocordyceps cultivation and improve the development of strategies for the identification of potential bioinoculant resources. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02227-w.
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Affiliation(s)
- Chengpeng Li
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Dexiang Tang
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Yuanbing Wang
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd, Kunming, 650106, China
| | - Qi Fan
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China
| | - Xiaomei Zhang
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.,Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.,The Research Center of Cordyceps Development and Utilization of Kunming, Yunnan Herbal Biotech Co. Ltd, Kunming, 650106, China.,College of Basic Medicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Xiaolong Cui
- Yunnan Institute of Microbiology, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650091, People's Republic of China.
| | - Hong Yu
- Yunnan Herbal Laboratory, School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China.
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70
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Horinaka A, Kim YH, Kimura A, Iwamoto E, Masaki T, Ichijo T, Sato S. Changes in the predicted function of the rumen bacterial community of Japanese Black beef cattle during the fattening stages according to Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. J Vet Med Sci 2021; 83:1098-1106. [PMID: 34108339 PMCID: PMC8349811 DOI: 10.1292/jvms.21-0121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We investigated changes in the predicted functions of the rumen bacterial community in Japanese Black beef cattle during fattening. Nine cattle were fed a
high-concentrate diet during the early, middle, and late fattening stages consecutively (10–14, 15–22, and 23–30 months of age, respectively). The rumen fluid
and solid samples collected at each stage were subjected to sequencing analyses. The sequencing results were clustered and classified into operational taxonomic
units (OTUs). Representative sequences and a raw counting table for each OTU were submitted to the Piphillin website. The predicted functions were revealed by
the Kyoto Encyclopedia of Genes and Genomes database as the ratio of the total sequence. In the early stage, “Biosynthesis of secondary metabolites” was
significantly higher in the fluid fraction than in the solid fraction. “Two-component system” in the middle stage was significantly lower and “Purine
metabolism” in the late stage was significantly higher in the fluid fraction than those in the solid fraction. The fluid fraction was significantly correlated
with acetic acid, propionic acid, and bacterial metabolism, such as “Biosynthesis of secondary metabolites” and “Sugar metabolism.” Moreover, the solid fraction
was correlated with “Purine metabolism” and “Biosynthesis of secondary metabolism”. These results suggest that the rumen bacterial community in Japanese Black
beef cattle adapts to changes in rumen conditions by altering their functions in response to a long-term high-grain diet.
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Affiliation(s)
- Asahi Horinaka
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Iwate 020-8550, Japan
| | - Yo-Han Kim
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Iwate 020-8550, Japan.,Department of Animal Resources Science, Dankook University, 119 Dandae-ro, Cheonan 31116, Republic of Korea
| | - Atsushi Kimura
- Veterinary Teaching Hospital of Iwate University, Iwate 020-8550, Japan
| | - Eiji Iwamoto
- Hyogo Prefectural Technology Center of Agriculture, Forestry and Fisheries, Hyogo 679-0198, Japan
| | - Tatsunori Masaki
- Hyogo Prefectural Technology Center of Agriculture, Forestry and Fisheries, Hyogo 679-0198, Japan
| | - Toshihiro Ichijo
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Iwate 020-8550, Japan
| | - Shigeru Sato
- Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Iwate University, Iwate 020-8550, Japan
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71
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Ibekwe AM, Ors S, Ferreira JFS, Liu X, Suarez DL. Influence of seasonal changes and salinity on spinach phyllosphere bacterial functional assemblage. PLoS One 2021; 16:e0252242. [PMID: 34061881 PMCID: PMC8168849 DOI: 10.1371/journal.pone.0252242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/11/2021] [Indexed: 11/18/2022] Open
Abstract
The phyllosphere is the aerial part of plants that is exposed to different environmental conditions and is also known to harbor a wide variety of bacteria including both plant and human pathogens. However, studies on phyllosphere bacterial communities have focused on bacterial composition at different stages of plant growth without correlating their functional capabilities to bacterial communities. In this study, we examined the seasonal effects and temporal variabilities driving bacterial community composition and function in spinach phyllosphere due to increasing salinity and season and estimated the functional capacity of bacterial community16S V4 rRNA gene profiles by indirectly inferring the abundance of functional genes based on metagenomics inference tool Piphillin. The experimental design involved three sets of spinach (Spinacia oleracea L., cv. Racoon) grown with saline water during different seasons. Total bacteria DNA from leaf surfaces were sequenced using MiSeq® Illumina platform. About 66.35% of bacteria detected in the phyllosphere were dominated by four phyla- Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. Permutational analysis of variance (PERMANOVA) showed that phyllosphere microbiomes were significantly (P < 0.003) affected by season, but not salinity (P = 0.501). The most abundant inferred functional pathways in leaf samples were the amino acids biosynthesis, ABC transporters, ribosome, aminoacyl-tRNA biosynthesis, two-component system, carbon metabolism, purine metabolism, and pyrimidine metabolism. The photosynthesis antenna proteins pathway was significantly enriched in June leaf samples, when compared to March and May. Several genes related to toxin co-regulated pilus biosynthesis proteins were also significantly enriched in June leaf samples, when compared to March and May leaf samples. Therefore, planting and harvesting times must be considered during leafy green production due to the influence of seasons in growth and proliferation of phyllosphere microbial communities.
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Affiliation(s)
| | - Selda Ors
- Ataturk University, Department of Agricultural Structures and Irrigation, Erzurum, Turkey
| | | | - Xuan Liu
- US Salinity Laboratory, USDA-ARS, Riverside, CA, United States of America
| | - Donald L. Suarez
- US Salinity Laboratory, USDA-ARS, Riverside, CA, United States of America
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72
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Murovec B, Deutsch L, Stres B. General Unified Microbiome Profiling Pipeline (GUMPP) for Large Scale, Streamlined and Reproducible Analysis of Bacterial 16S rRNA Data to Predicted Microbial Metagenomes, Enzymatic Reactions and Metabolic Pathways. Metabolites 2021; 11:336. [PMID: 34074026 PMCID: PMC8225202 DOI: 10.3390/metabo11060336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/14/2021] [Accepted: 05/23/2021] [Indexed: 11/23/2022] Open
Abstract
General Unified Microbiome Profiling Pipeline (GUMPP) was developed for large scale, streamlined and reproducible analysis of bacterial 16S rRNA data and prediction of microbial metagenomes, enzymatic reactions and metabolic pathways from amplicon data. GUMPP workflow introduces reproducible data analyses at each of the three levels of resolution (genus; operational taxonomic units (OTUs); amplicon sequence variants (ASVs)). The ability to support reproducible analyses enables production of datasets that ultimately identify the biochemical pathways characteristic of disease pathology. These datasets coupled to biostatistics and mathematical approaches of machine learning can play a significant role in extraction of truly significant and meaningful information from a wide set of 16S rRNA datasets. The adoption of GUMPP in the gut-microbiota related research enables focusing on the generation of novel biomarkers that can lead to the development of mechanistic hypotheses applicable to the development of novel therapies in personalized medicine.
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Affiliation(s)
- Boštjan Murovec
- Faculty of Electrical Engineering, University of Ljubljana, Tržaška 25, SI-1000 Ljubljana, Slovenia;
| | - Leon Deutsch
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
| | - Blaž Stres
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia;
- Faculty of Civil and Geodetic Engineering, University of Ljubljana, Jamova 2, SI-1000 Ljubljana, Slovenia
- Department of Automation, Jožef Stefan Institute, Biocybernetics and Robotics, Jamova 39, SI-1000 Ljubljana, Slovenia
- Department of Microbiology, University of Innsbruck, Technikerstrasse 25d, A-6020 Innsbruck, Austria
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73
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Laroche O, Pochon X, Wood SA, Keeley N. Beyond taxonomy: Validating functional inference approaches in the context of fish-farm impact assessments. Mol Ecol Resour 2021; 21:2264-2277. [PMID: 33971078 DOI: 10.1111/1755-0998.13426] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/31/2021] [Accepted: 05/04/2021] [Indexed: 11/29/2022]
Abstract
Characterization of microbial assemblages via environmental DNA metabarcoding is increasingly being used in routine monitoring programs due to its sensitivity and cost-effectiveness. Several programs have recently been developed which infer functional profiles from 16S rRNA gene data using hidden-state prediction (HSP) algorithms. These might offer an economic and scalable alternative to shotgun metagenomics. To date, HSP-based methods have seen limited use for benthic marine surveys and their performance in these environments remains unevaluated. In this study, 16S rRNA metabarcoding was applied to sediment samples collected at 0 and ≥1,200 m from Norwegian salmon farms, and three metabolic inference approaches (Paprica, Picrust2 and Tax4Fun2) evaluated against metagenomics and environmental data. While metabarcoding and metagenomics recovered a comparable functional diversity, the taxonomic composition differed between approaches, with genera richness up to 20× higher for metabarcoding. Comparisons between the sensitivity (highest true positive rates) and specificity (lowest true negative rates) of HSP-based programs in detecting functions found in metagenomic data ranged from 0.52 and 0.60 to 0.76 and 0.79, respectively. However, little correlation was observed between the relative abundance of their specific functions. Functional beta-diversity of HSP-based data was strongly associated with that of metagenomics (r ≥ 0.86 for Paprica and Tax4Fun2) and responded similarly to the impact of fish farm activities. Our results demonstrate that although HSP-based metabarcoding approaches provide a slightly different functional profile than metagenomics, partly due to recovering a distinct community, they represent a cost-effective and valuable tool for characterizing and assessing the effects of fish farming on benthic ecosystems.
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Affiliation(s)
- Olivier Laroche
- Institute of Marine Research, Tromsø, Norway.,Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Nigel Keeley
- Institute of Marine Research, Tromsø, Norway.,Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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74
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O'Connor BRW, Fernández-Martínez MÁ, Léveillé RJ, Whyte LG. Taxonomic Characterization and Microbial Activity Determination of Cold-Adapted Microbial Communities in Lava Tube Ice Caves from Lava Beds National Monument, a High-Fidelity Mars Analogue Environment. ASTROBIOLOGY 2021; 21:613-627. [PMID: 33794669 DOI: 10.1089/ast.2020.2327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Martian lava tube caves resulting from a time when the planet was still volcanically active are proposed to contain deposits of water ice, a feature that may increase microbial habitability. In this study, we taxonomically characterized and directly measured metabolic activity of the microbial communities that inhabit lava tube ice from Lava Beds National Monument, an analogue environment to martian lava tubes. We investigated whether this environment was habitable to microorganisms by determining their taxonomic diversity, metabolic activity, and viability using both culture-dependent and culture-independent techniques. With 16S rRNA gene sequencing, we recovered 27 distinct phyla from both ice and ice-rock interface samples, primarily consisting of Actinobacteria, Proteobacteria, Bacteroidetes, Firmicutes, and Chloroflexi. Radiorespiration and Biolog EcoPlate assays found these microbial communities to be metabolically active at both 5°C and -5°C and able to metabolize diverse sets of heterotrophic carbon substrates at each temperature. Viable cells were predominantly cold adapted and capable of growth at 5°C (1.3 × 104 to 2.9 × 107 cells/mL), and 24 of 38 cultured isolates were capable of growth at -5°C. Furthermore, 14 of these cultured isolates, and 16 of the 20 most numerous amplicon sequences we recovered were most closely related to isolates and sequences obtained from other cryophilic environments. Given these results, lava tube ice appears to be a habitable environment, and considering the protections martian lava tubes offer to microbial communities from harsh surface conditions, similar martian caves containing ice may be capable of supporting extant, active microbial communities.
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Affiliation(s)
- Brady R W O'Connor
- Department of Natural Resource Sciences, McGill Space Institute, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | | | - Richard J Léveillé
- Department of Earth and Planetary Sciences, McGill Space Institute, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill Space Institute, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
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75
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Abstract
OBJECTIVES The aim of the study was to compare the intestinal microbiome in very low birth weight (VLBW) infants who received different enteral iron supplementation (EIS) doses. STUDY DESIGN Longitudinal stool collection in 80 VLBW infants were conducted up to 2 months postnatally in a prospective study. The 16S rRNA regions V4 was used to calculate microbiome compositions and the Piphillin software was used for bacterial functional prediction. Linear mixed effect models and Wilcoxon rank-sum tests were performed to examine the relationships between initial EIS dosage and stool microbiome and bacterial functional potential. RESULTS There were 105 samples collected before and 237 collected after EIS started from infants with birth gestational age and weight of 28.1 ± 2.4 weeks and 1103 ± 210 g, respectively. The average postnatal age at start of EIS was 17.9 ± 6.9 days and the average initial EIS dose was 4.8 ± 1.1 mg · kg-1 · day-1. Infants who were started on ≥6 mg · kg-1 · day-1 had higher abundances of Proteus and Bifidobacterium and a lower alpha diversity than those started on lower doses (P < 0.05). Infants given higher EIS doses had higher bacterial predicted functional potentials for ferroptosis and epithelial invasion after 2 weeks post EIS. CONCLUSIONS Higher EIS dosage is linked to higher abundances of Proteus and Bifidobacterium, and a less diverse microbiome and higher predicted potential of bacterial epithelial invasion. These observational findings should be further studied in a randomized study to elucidate the optimal dosage of EIS in VLBW infants.
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76
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Romero PE, Calla-Quispe E, Castillo-Vilcahuaman C, Yokoo M, Fuentes-Rivera HL, Ramirez JL, Ampuero A, Ibáñez AJ, Wong P. From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru. PLoS One 2021; 16:e0250401. [PMID: 33886647 PMCID: PMC8061919 DOI: 10.1371/journal.pone.0250401] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/06/2021] [Indexed: 01/04/2023] Open
Abstract
The Rimac river is the main source of water for Lima, Peru's capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. In this work, we aim to produce the first characterization of aquatic bacterial communities in the Rimac river using a 16S rRNA metabarcoding approach which would be useful to identify bacterial diversity and potential understudied pathogens. We report a lower diversity in bacterial communities from the Lower Rimac (Metropolitan zone) in comparison to other sub-basins. Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility and quorum sensing. Additional metabolomic analyses showed the presence of some insecticides and herbicides in the Parac-Upper Rimac and Santa Eulalia-Parac sub-basins. The dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.
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Affiliation(s)
- Pedro E Romero
- Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Erika Calla-Quispe
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Camila Castillo-Vilcahuaman
- Departamento de Ciencias Biológicas y Fisiológicas, Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mateo Yokoo
- Departamento de Ciencias de la Medicina, Facultad de Medicina Humana, Universidad de Piura, Lima, Peru
| | - Hammerly Lino Fuentes-Rivera
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Jorge L Ramirez
- Departamento de Biología Celular y Genética, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - André Ampuero
- Departamento de Malacología y Carcinología, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Alfredo J Ibáñez
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Peru, Lima, Peru
| | - Paolo Wong
- Departamento de Ciencias de la Medicina, Facultad de Medicina Humana, Universidad de Piura, Lima, Peru
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77
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Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes. mSystems 2021; 6:6/2/e00193-20. [PMID: 33824194 PMCID: PMC8561662 DOI: 10.1128/msystems.00193-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The existence of a link between the gut microbiome and autism spectrum disorder (ASD) is well established in mice, but in human populations, efforts to identify microbial biomarkers have been limited due to a lack of appropriately matched controls, stratification of participants within the autism spectrum, and sample size. To overcome these limitations, we crowdsourced the recruitment of families with age-matched sibling pairs between 2 and 7 years old (within 2 years of each other), where one child had a diagnosis of ASD and the other did not. Parents collected stool samples, provided a home video of their ASD child's natural social behavior, and responded online to diet and behavioral questionnaires. 16S rRNA V4 amplicon sequencing of 117 samples (60 ASD and 57 controls) identified 21 amplicon sequence variants (ASVs) that differed significantly between the two cohorts: 11 were found to be enriched in neurotypical children (six ASVs belonging to the Lachnospiraceae family), while 10 were enriched in children with ASD (including Ruminococcaceae and Bacteroidaceae families). Summarizing the expected KEGG orthologs of each predicted genome, the taxonomic biomarkers associated with children with ASD can use amino acids as precursors for butyragenic pathways, potentially altering the availability of neurotransmitters like glutamate and gamma aminobutyric acid (GABA).IMPORTANCE Autism spectrum disorder (ASD), which now affects 1 in 54 children in the United States, is known to have comorbidity with gut disorders of a variety of types; however, the link to the microbiome remains poorly characterized. Recent work has provided compelling evidence to link the gut microbiome to the autism phenotype in mouse models, but identification of specific taxa associated with autism has suffered replicability issues in humans. This has been due in part to sample size that sufficiently covers the spectrum of phenotypes known to autism (which range from subtle to severe) and a lack of appropriately matched controls. Our original study proposes to overcome these limitations by collecting stool-associated microbiome on 60 sibling pairs of children, one with autism and one neurotypically developing, both 2 to 7 years old and no more than 2 years apart in age. We use exact sequence variant analysis and both permutation and differential abundance procedures to identify 21 taxa with significant enrichment or depletion in the autism cohort compared to their matched sibling controls. Several of these 21 biomarkers have been identified in previous smaller studies; however, some are new to autism and known to be important in gut-brain interactions and/or are associated with specific fatty acid biosynthesis pathways.
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78
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Gao B, Chi L, Zhu Y, Shi X, Tu P, Li B, Yin J, Gao N, Shen W, Schnabl B. An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. Biomolecules 2021; 11:530. [PMID: 33918473 PMCID: PMC8066849 DOI: 10.3390/biom11040530] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.
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Affiliation(s)
- Bei Gao
- Department of Marine Science, School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Yixin Zhu
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
| | - Xiaochun Shi
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
| | - Pengcheng Tu
- Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China;
| | - Bing Li
- Suzhou Industrial Park Environmental Law Enforcement Brigade (Environmental Monitoring Station), Suzhou 215021, China;
| | - Jun Yin
- Department of Hydrometeorology, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China;
| | - Nan Gao
- Department of Biotechnology, School of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China;
| | - Weishou Shen
- Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; (X.S.); (W.S.)
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Nanjing 210044, China
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA;
- Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA
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79
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Wu Y, Zhou X, Zhang X, Niu H, Lyu L, Liang C, Chen S, Gong P, Pan J, Li Y, Jiang S, Han X, Zhang L. Breast milk flora plays an important role in infantile eczema: cohort study in Northeast China. J Appl Microbiol 2021; 131:2981-2993. [PMID: 33735474 DOI: 10.1111/jam.15076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/17/2021] [Accepted: 03/08/2021] [Indexed: 12/26/2022]
Abstract
AIMS Infantile eczema, usually coupled with a range of hypersensitive phenotypes, has come into notice with its rising prevalence and unclear pathogenesis. Recent studies show close ties between eczema and an infant's intestinal flora. To gain a further understanding of the interactions between microbiota and eczema, we studied the breast milk flora as a new factor and present the links among breast milk flora, infant intestinal flora and infantile eczema through a cohort study in Northeast China. METHODS AND RESULTS Fifty-two families were recruited with either an eczema or healthy infant younger than 6 months. Analysis and predictions using amplicon sequencing of microbiota found that Bifidobacterium and Bacteroidetes were enriched in healthy and eczema infant stools, respectively, consistent with previous reports. For breast milk flora, more 'positive' bacteria such as Akkermansia were enriched in breast milk from healthy infants' mothers. Further, higher bacterial delivery efficiencies were found in pairs of breast milk flora and infants' stool flora of families with eczema infants compared with families with healthy infants. Bacteroidetes, a widely known indicator of eczema, was found delivered more in eczema pairs. Further metagenomic predictions revealed that the breast milk microbiota participated significantly less in metabolism and immune system pathways, particularly in antigen processing and presentation and in Th17 cell-related pathways. CONCLUSIONS In conclusion, as with other components of breast milk, the breast milk microbiota closely associates with infants' health via mother-infant bacterial delivery and metabolic functions. SIGNIFICANCE AND IMPACT OF THE STUDY Our research aimed to fill the gap between the eczema and breast milk flora and describe the connections among breast milk and intestinal flora and eczema.
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Affiliation(s)
- Y Wu
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - X Zhou
- Department of Adolescent Medical Clinic, Qingdao Central Hospital, Qingdao, China
| | - X Zhang
- Child Healthcare Department, Harbin Children's Hospital, Harbin, China
| | - H Niu
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - L Lyu
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - C Liang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - S Chen
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - P Gong
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - J Pan
- Feihe Innovation Center, Heilongjiang Feihe Dairy Co Ltd, Beijing, China
| | - Y Li
- Feihe Innovation Center, Heilongjiang Feihe Dairy Co Ltd, Beijing, China
| | - S Jiang
- Feihe Innovation Center, Heilongjiang Feihe Dairy Co Ltd, Beijing, China
| | - X Han
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - L Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
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80
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Spichak S, Bastiaanssen TFS, Berding K, Vlckova K, Clarke G, Dinan TG, Cryan JF. Mining microbes for mental health: Determining the role of microbial metabolic pathways in human brain health and disease. Neurosci Biobehav Rev 2021; 125:698-761. [PMID: 33675857 DOI: 10.1016/j.neubiorev.2021.02.044] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022]
Abstract
There is increasing knowledge regarding the role of the microbiome in modulating the brain and behaviour. Indeed, the actions of microbial metabolites are key for appropriate gut-brain communication in humans. Among these metabolites, short-chain fatty acids, tryptophan, and bile acid metabolites/pathways show strong preclinical evidence for involvement in various aspects of brain function and behaviour. With the identification of neuroactive gut-brain modules, new predictive tools can be applied to existing datasets. We identified 278 studies relating to the human microbiota-gut-brain axis which included sequencing data. This spanned across psychiatric and neurological disorders with a small number also focused on normal behavioural development. With a consistent bioinformatics pipeline, thirty-five of these datasets were reanalysed from publicly available raw sequencing files and the remainder summarised and collated. Among the reanalysed studies, we uncovered evidence of disease-related alterations in microbial metabolic pathways in Alzheimer's Disease, schizophrenia, anxiety and depression. Amongst studies that could not be reanalysed, many sequencing and technical limitations hindered the discovery of specific biomarkers of microbes or metabolites conserved across studies. Future studies are warranted to confirm our findings. We also propose guidelines for future human microbiome analysis to increase reproducibility and consistency within the field.
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Affiliation(s)
- Simon Spichak
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Kirsten Berding
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Klara Vlckova
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland.
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Almeida AR, Domingues I, Henriques I. Zebrafish and water microbiome recovery after oxytetracycline exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 272:116371. [PMID: 33433346 DOI: 10.1016/j.envpol.2020.116371] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/14/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Oxytetracycline (OTC) is a broad-spectrum antibiotic widely used in aquaculture, resulting in contamination of aquatic environments. In a previous study, we observed significant effects of OTC sublethal concentrations in zebrafish, its microbiome and the water bacterial community. Here we assessed the extent to which these effects are reversible after a recovery period. Zebrafish adults were exposed to OTC (10,000 μg/L) via water exposure. Effects were analyzed at 5 days (5 dE) and 2 months (2 mE) of exposure and recovery was assessed at 5 days (5dPE) and 1 month (1mPE) after exposure Impacts were observed in fish energetic reserves and in fish and water microbiomes structure, being significant even at 5 dE. At energetic reserves level, the effect in cellular energy allocation (CEA) was dependent on the exposure time: initially CEA increased while after 2 mE CEA decreased. At microbiome level, diversity was not affected but the richness of the water microbiome significantly decreased at 2 mE. Regarding the post-exposure period, at CEA level, organisms seem to recover. In water and gut microbiomes OTC effects were also attenuated after exposure ceases, indicating a recovery. Even so, the structure of water exposed community remained significantly different towards the control, while richness of this community significantly increased at 1mPE. During exposure the relative abundance of 11 and 16 genera was significantly affected in the gut and water microbiomes, respectively, though these numbers decreased to 4 and 8 genera in the post-exposure period. At functional level during exposure 12 and 13 pathways were predicted to be affected in zebrafish gut and water microbiomes respectively, while post-exposure few pathways remained significantly affected. Hence, our results suggest a recovery of the fish fitness as well as of the water and intestine microbiomes after exposure ceases. Even so, some of the effects caused by OTC remain significant after this recovery period.
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Affiliation(s)
- Ana Rita Almeida
- CESAM & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal
| | - Inês Domingues
- CESAM & Department of Biology, University of Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal.
| | - Isabel Henriques
- University of Coimbra, CESAM & Department of Life Sciences, Faculty of Science and Technology, Calçada Martim de Freitas, 3000-456, Coimbra, Portugal
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Volatility as a Concept to Understand the Impact of Stress on the Microbiome. Psychoneuroendocrinology 2021; 124:105047. [PMID: 33307493 DOI: 10.1016/j.psyneuen.2020.105047] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 10/29/2020] [Accepted: 11/03/2020] [Indexed: 12/14/2022]
Abstract
The microbiome-gut-brain-axis is a complex phenomenon spanning several dynamic systems in the body which can be parsed at a molecular, cellular, physiological and ecological level. A growing body of evidence indicates that this axis is particularly sensitive to the effects of stress and that it may be relevant to stress resilience and susceptibility. Although stress-induced changes in the composition of the microbiome have been reported, the degree of compositional change over time, which we define as volatility, has not been the subject of in-depth scrutiny. Using a chronic psychosocial stress paradigm in male mice, we report that the volatility of the microbiome significantly correlated with several readouts of the stress response, including behaviour and corticosterone response. We then validated these findings in a second independent group of stressed mice. Additionally, we assessed the relationship between volatility and stress parameters in a cohort of health volunteers who were undergoing academic exams and report similar observations. Finally, we found inter-species similarities in the microbiome stress response on a functional level. Our research highlights the effects of stress on the dynamic microbiome and underscores the informative value of volatility as a parameter that should be considered in all future analyses of the microbiome.
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83
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Cortes-Macías E, Selma-Royo M, García-Mantrana I, Calatayud M, González S, Martínez-Costa C, Collado MC. Maternal Diet Shapes the Breast Milk Microbiota Composition and Diversity: Impact of Mode of Delivery and Antibiotic Exposure. J Nutr 2021; 151:330-340. [PMID: 33188413 PMCID: PMC7850106 DOI: 10.1093/jn/nxaa310] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/21/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Breast milk is a complex biofluid that provides nutrients and bioactive agents, including bacteria, for the development of the infant gut microbiota. However, the impact of maternal diet and other factors, such as mode of delivery and antibiotic exposure, on the breast milk microbiota has yet to be understood. OBJECTIVES This study aimed to examine the association between maternal diet and breast milk microbiota and to ascertain the potential role of mode of delivery and antibiotic exposure. METHODS In a cross-sectional study of the MAMI cohort, breast milk microbiota profiling was assessed in 120 samples from healthy mothers by 16S rRNA gene sequencing. Maternal dietary information was recorded through an FFQ, and clinical characteristics, including mode of delivery, antibiotic exposure, and exclusive breastfeeding, were collected. RESULTS Maternal diet was grouped into 2 clusters: Cluster I (high intake of plant protein, fiber, and carbohydrates), and Cluster II (high intake of animal protein and lipids). Breast milk microbiota was shaped by maternal dietary clusters. Staphylococcus and Bifidobacterium were associated with carbohydrate intake whereas the Streptococcus genus was associated with intakes of the n-3 PUFAs [EPA and docosapentaenoic acid (22:5ω-3)]. Mode of delivery and antibiotic exposure influenced breast milk microbiota in a diet cluster-dependent manner. Differences between/among the maternal dietary clusters were found in the milk microbiota of the cesarean-section (C-section)/antibiotic group, whereas no differences were observed in vaginal births. Lower abundances of Lactobacillus, Bacteroides, and Sediminibacterium genera were observed in Cluster II/C-section/antibiotic exposure compared with the other groups. CONCLUSIONS Maternal diet shapes the composition and diversity of breast milk microbiota, with the most important contributions coming from dietary fiber and both plant and animal protein intakes. The relation between the maternal diet and the milk microbiota needs further research because it has a key impact on infant microbiota development and contributes to infant health outcomes in the short and long term.This trial was registered at clinicaltrials.gov as NCT03552939.
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Affiliation(s)
- Erika Cortes-Macías
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Valencia, Spain
| | - Marta Selma-Royo
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Valencia, Spain
| | - Izaskun García-Mantrana
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Valencia, Spain
| | - Marta Calatayud
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Valencia, Spain
| | - Sonia González
- 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
| | - Cecilia Martínez-Costa
- Department of Pediatrics, School of Medicine, University of Valencia, Valencia, Spain
- Pediatric Gastroenterology and Nutrition Section, Hospital Clínico Universitario Valencia, INCLIVA, Valencia, Spain
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology (IATA-CSIC), National Research Council, Valencia, Spain
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84
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Wang Z, Yu Y, Li X, Xiao H, Zhang P, Shen W, Wan F, He J, Tang S, Tan Z, Wu D, Yao H. Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal Microflora. Front Microbiol 2021; 12:625857. [PMID: 33584627 PMCID: PMC7879537 DOI: 10.3389/fmicb.2021.625857] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/07/2021] [Indexed: 12/20/2022] Open
Abstract
This study was conducted to examine the influences of replacing soybean meal (SBM) with fermented soybean meal (FSBM) in the diet of lactating Holstein cattle on rumen fermentation and ruminal bacterial microbiome. Twenty-four lactating Chinese Holstein dairy cattle were assigned to each of the two treatments in a completely randomized design: the SBM group [the basal total mixed ration (TMR) diet containing 5.77% SBM] and the FSBM group (the experimental TMR diet containing 5.55% FSBM). This trial lasted for 54 days (14 days for adjustment and 40 days for data and sample collection), and samples of rumen liquid were collected on 34 d and 54 d, respectively. The results showed that replacing SBM with FSBM significantly increased the molar percentages of propionate (P < 0.01) and valerate (P < 0.05), but reduced the total volatile fatty acid (TVFA) concentration (P < 0.05), butyrate molar proportion (P < 0.05), and the acetate to propionate ratio (P < 0.01). The copy numbers of total bacteria (P < 0.05), Fibrobacter succinogenes (P < 0.01), Selenomonas ruminantium (P < 0.01), and Prevotella spp. (P < 0.05) in the FSBM group were greater, while the density of Prevotella ruminicola (P < 0.05) was lower than those in the SBM treatment. Additionally, Succiniclasticum ruminis and Saccharofermentans acetigenes were significantly enriched (P < 0.05) in the rumen fluid of FSBM-fed cows, despite the fact that there was no remarkable difference in the Alpha diversity indexes, structure and KEGG pathway abundances of the bacterial community across the two treatments. It could hence be concluded that the substitution of FSBM for SBM modulated rumen fermentation and rumen bacterial microbiota in lactating Holstein dairy cows. Further research is required to elucidate the relevant mechanisms of FSBM, and provide more insights into the application of FSBM in dairy cattle.
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Affiliation(s)
- Zuo Wang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yuannian Yu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Xinyao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Hongyan Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Peihua Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Weijun Shen
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Fachun Wan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Shaoxun Tang
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition & Physiology and Metabolism, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Zhiliang Tan
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Key Laboratory of Animal Nutrition & Physiology and Metabolism, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Duanqin Wu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Hui Yao
- Nanshan Dairy Co., Ltd., Shaoyang, China
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Prem EM, Mutschlechner M, Stres B, Illmer P, Wagner AO. Lignin intermediates lead to phenyl acid formation and microbial community shifts in meso- and thermophilic batch reactors. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:27. [PMID: 33472684 PMCID: PMC7816434 DOI: 10.1186/s13068-020-01855-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/09/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lignin intermediates resulting from lignocellulose degradation have been suspected to hinder anaerobic mineralisation of organic materials to biogas. Phenyl acids like phenylacetate (PAA) are early detectable intermediates during anaerobic digestion (AD) of aromatic compounds. Studying the phenyl acid formation dynamics and concomitant microbial community shifts can help to understand the microbial interdependencies during AD of aromatic compounds and may be beneficial to counteract disturbances. RESULTS The length of the aliphatic side chain and chemical structure of the benzene side group(s) had an influence on the methanogenic system. PAA, phenylpropionate (PPA), and phenylbutyrate (PBA) accumulations showed that the respective lignin intermediate was degraded but that there were metabolic restrictions as the phenyl acids were not effectively processed. Metagenomic analyses confirmed that mesophilic genera like Fastidiosipila or Syntrophomonas and thermophilic genera like Lactobacillus, Bacillus, Geobacillus, and Tissierella are associated with phenyl acid formation. Acetoclastic methanogenesis was prevalent in mesophilic samples at low and medium overload conditions, whereas Methanoculleus spp. dominated at high overload conditions when methane production was restricted. In medium carbon load reactors under thermophilic conditions, syntrophic acetate oxidation (SAO)-induced hydrogenotrophic methanogenesis was the most important process despite the fact that acetoclastic methanogenesis would thermodynamically be more favourable. As acetoclastic methanogens were restricted at medium and high overload conditions, syntrophic acetate oxidising bacteria and their hydrogenotrophic partners could step in for acetate consumption. CONCLUSIONS PAA, PPA, and PBA were early indicators for upcoming process failures. Acetoclastic methanogens were one of the first microorganisms to be impaired by aromatic compounds, and shifts to syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis occurred in thermophilic reactors. Previously assumed associations of specific meso- and thermophilic genera with anaerobic phenyl acid formation could be confirmed.
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Affiliation(s)
- Eva Maria Prem
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria.
| | - Mira Mutschlechner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
| | - Blaz Stres
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000, Ljubljana, Slovenia
- Institute of Sanitary Engineering, Faculty of Civil and Geodetic Engineering, University of Ljubljana, Jamova 2, 1000, Ljubljana, Slovenia
- Department of Automation, Biocybernetics and Robotics, Jozef Štefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Paul Illmer
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
| | - Andreas Otto Wagner
- Department of Microbiology, Universität Innsbruck, Technikerstraße 25d, 6020, Innsbruck, Austria
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86
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Hano T, Ito M, Ito K, Uchida M. Alterations of stool metabolome, phenome, and microbiome of the marine fish, red sea bream, Pagrus major, following exposure to phenanthrene: A non-invasive approach for exposure assessment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:141796. [PMID: 32898801 DOI: 10.1016/j.scitotenv.2020.141796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/12/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
The present study aimed to assess the impact of phenanthrene (Phe) on fish health by addressing the alteration of fecal characteristics, in lieu of collecting biomarkers that often involves injurious or even fatal sampling of organisms. The marine fish red sea bream, Pagrus major, was exposed to Phe at a concentration of 18 μg/L for 16 days followed by depuration for 13 days. We collected feces from Phe-exposed or control (Phe-free) fish and then analyzed the fecal metabolite profile (metabolome), carbon utilization of microbiota (phenome), and bacterial 16s rRNA gene sequence (microbiome). Along with the increase in physiological stress markers (SOD and EROD) in serum and liver, we noted the possible role of intestine as a Phe reservoir. Furthermore, abnormal fecal appearance (green coloration) and remarkable changes in fecal characteristics were observed. These changes include alterations of cholesterol and putrescine metabolism and the enhanced utilization of putrescine as a carbon source. Phe also altered the microbial community, with an increase in Phe-degrading bacteria such as Pseudomonas. Interestingly, these enteric impairments were ameliorated by depuration. Taken together, our findings suggest that these alterations in feces were associated with adaptive responses to environmentally relevant Phe exposure scenarios, and that stool samples are potential candidates for exposure assessment in fish.
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Affiliation(s)
- Takeshi Hano
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan.
| | - Mana Ito
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Katsutoshi Ito
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Motoharu Uchida
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
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Patumcharoenpol P, Nakphaichit M, Panagiotou G, Senavonge A, Suratannon N, Vongsangnak W. MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome. PLoS Comput Biol 2021; 17:e1008487. [PMID: 33406089 PMCID: PMC7787440 DOI: 10.1371/journal.pcbi.1008487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/03/2020] [Indexed: 12/20/2022] Open
Abstract
Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.
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Grants
- Kasetsart University Research and Development Institute (KURDI) at Kasetsart University
- Department of Zoology, Faculty of Science, Kasetsart University
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU)
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University
- International Affairs Division (IAD), Kasetsart University
- National Science and Technology Development Agency
- Ratchadapisek Research Funds
- Chulalongkorn University
- Deutsche Forschungsgemeinschaft (DFG) CRC/Transregio 124 “Pathogenic fungi and their human host: Networks of interaction”, subprojects B5 and INF
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Affiliation(s)
- Preecha Patumcharoenpol
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Massalin Nakphaichit
- Department of Biotechnology, Faculty of Agro-Industry, Kasetsart University, Bangkok, Thailand
| | - Gianni Panagiotou
- Systems Biology & Bioinformatics Group, School of Biological Sciences, The University of Hong Kong, Hong Kong S.A.R., China
- Department of Medicine and State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong S.A.R., China
- Systems Biology & Bioinformatics Unit, Leibniz Institute for Natural Product Research and Infection Biology–Hans Knöll Institute, Jena, Germany
| | - Anchalee Senavonge
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Narissara Suratannon
- Pediatric Allergy & Clinical Immunology Research Unit, Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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Lin YF, Sung CM, Ke HM, Kuo CJ, Liu WA, Tsai WS, Lin CY, Cheng HT, Lu MJ, Tsai IJ, Hsieh SY. The rectal mucosal but not fecal microbiota detects subclinical ulcerative colitis. Gut Microbes 2021; 13:1-10. [PMID: 33525983 PMCID: PMC7872041 DOI: 10.1080/19490976.2020.1832856] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/16/2020] [Accepted: 09/24/2020] [Indexed: 02/08/2023] Open
Abstract
Ulcerative colitis (UC), a subtype of inflammatory bowel disease, is characterized by repetitive remission and relapse. Gut microbiome is critically involved in pathogenesis of UC. The shifts in microbiome profile during disease remission remain under-investigated. Recent studies revealed that UC pathogenesis is likely to originate in the mucosal barrier. Therefore, we investigated the effectiveness of mucosal tissue microbiomes to differentiate patients with subclinical UC from healthy individuals. The microbiomes of cecal and rectal biopsies and feces were characterized from 13 healthy individuals and 45 patients with subclinical UC. Total genomic DNA was extracted from the samples, and their microbial communities determined using next-generation sequencing. We found that changes in relative abundance of subclinical UC were marked by a decrease in Proteobacteria and an increase in Bacteroidetes phyla in microbiome derived from rectal tissues but not cecal tissue nor feces. Only in the microbiome of rectal tissue had significantly higher community richness and evenness in subclinical UC patients than controls. Twenty-seven operational taxonomic units were enriched in subclinical UC cohort with majority of the taxa from the Firmicutes phylum. Inference of putative microbial functional pathways from rectal biopsy microbiome suggested a differential increase in interleukin-17 signaling and T-helper cell differentiation pathways. Rectal biopsy tissue was suggested to be more suitable than fecal samples for microbiome assays to distinguish patients with subclinical UC from healthy adults. Assessment of the rectal biopsy microbiome may offer clinical insight into UC disease progression and predict relapse of the diseases.
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Affiliation(s)
- Yu-Fei Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chang Mu Sung
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Graduate Institute of Clinical Medical Science, Chang Gung University, Taoyuan, Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chia-Jung Kuo
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Wei-an Liu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Sy Tsai
- Division of Colorectal Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Yu Lin
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hao-Tsai Cheng
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Meiyeh J Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Isheng. J. Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Sen-Yung Hsieh
- Department of Gastroenterology and Hepatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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89
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Faddetta T, Ardizzone F, Faillaci F, Reina C, Palazzotto E, Strati F, De Filippo C, Spinelli G, Puglia AM, Gallo G, Cavalieri V. Composition and geographic variation of the bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus. Sci Rep 2020; 10:21443. [PMID: 33293569 PMCID: PMC7723044 DOI: 10.1038/s41598-020-78534-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 11/19/2020] [Indexed: 12/26/2022] Open
Abstract
In the present work, culture-based and culture-independent investigations were performed to determine the microbiota structure of the coelomic fluid of Mediterranean sea urchin Paracentrotus lividus individuals collected from two distinct geographical sites neighboring a high-density population bay and a nature reserve, respectively. Next Generation Sequencing analysis of 16S rRNA gene (rDNA) showed that members of the Proteobacteria, Bacteroidetes and Fusobacteria phyla, which have been previously reported to be commonly retrieved from marine invertebrates, dominate the overall population of microorganisms colonizing this liquid tissue, with minority bacterial genera exhibiting remarkable differences among individuals. Our results showed that there is a correlation between microbiota structure and geographical location of the echinoderm collection site, highlighting over-representation of metagenomic functions related to amino acid and bioactive peptides metabolism in specimens inhabiting the nature reserve. Finally, we also described the developmental delay and aberrations exhibited by sea urchin embryos exposed to distinct bacterial isolates, and showed that these defects rely upon hydrophilic compound(s) synthesized by the bacterial strains assayed. Altogether, our findings lay the groundwork to decipher the relationships of bacteria with sea urchins in their aquatic environment, also providing an additional layer of information to understand the biological roles of the coelomic fluid.
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Affiliation(s)
- Teresa Faddetta
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Francesco Ardizzone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Francesca Faillaci
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Chiara Reina
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Piazza Delle Cliniche 2, 90127, Palermo, Italy
| | - Emilia Palazzotto
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Francesco Strati
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello, 16, 20139, Milano, Italy
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council, Via Moruzzi, 1, 56124, Pisa, Italy
| | - Giovanni Spinelli
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Anna Maria Puglia
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Giuseppe Gallo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, viale delle Scienze, ed. 16, 90128, Palermo, Italy.
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90
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Yin X, Altman T, Rutherford E, West KA, Wu Y, Choi J, Beck PL, Kaplan GG, Dabbagh K, DeSantis TZ, Iwai S. A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data. Front Microbiol 2020; 11:595910. [PMID: 33343536 PMCID: PMC7746778 DOI: 10.3389/fmicb.2020.595910] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Metabolomic analyses of human gut microbiome samples can unveil the metabolic potential of host tissues and the numerous microorganisms they support, concurrently. As such, metabolomic information bears immense potential to improve disease diagnosis and therapeutic drug discovery. Unfortunately, as cohort sizes increase, comprehensive metabolomic profiling becomes costly and logistically difficult to perform at a large scale. To address these difficulties, we tested the feasibility of predicting the metabolites of a microbial community based solely on microbiome sequencing data. Paired microbiome sequencing (16S rRNA gene amplicons, shotgun metagenomics, and metatranscriptomics) and metabolome (mass spectrometry and nuclear magnetic resonance spectroscopy) datasets were collected from six independent studies spanning multiple diseases. We used these datasets to evaluate two reference-based gene-to-metabolite prediction pipelines and a machine-learning (ML) based metabolic profile prediction approach. With the pre-trained model on over 900 microbiome-metabolome paired samples, the ML approach yielded the most accurate predictions (i.e., highest F1 scores) of metabolite occurrences in the human gut and outperformed reference-based pipelines in predicting differential metabolites between case and control subjects. Our findings demonstrate the possibility of predicting metabolites from microbiome sequencing data, while highlighting certain limitations in detecting differential metabolites, and provide a framework to evaluate metabolite prediction pipelines, which will ultimately facilitate future investigations on microbial metabolites and human health.
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Affiliation(s)
| | - Tomer Altman
- Altman Analytics LLC, San Francisco, CA, United States
| | | | | | - Yonggan Wu
- Second Genome Inc., Brisbane, CA, United States
| | | | - Paul L. Beck
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Gilaad G. Kaplan
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | | | | | - Shoko Iwai
- Second Genome Inc., Brisbane, CA, United States
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91
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Hupfauf S, Etemadi M, Fernández-Delgado Juárez M, Gómez-Brandón M, Insam H, Podmirseg SM. CoMA - an intuitive and user-friendly pipeline for amplicon-sequencing data analysis. PLoS One 2020; 15:e0243241. [PMID: 33264369 PMCID: PMC7710066 DOI: 10.1371/journal.pone.0243241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022] Open
Abstract
In recent years, there has been a veritable boost in next-generation sequencing (NGS) of gene amplicons in biological and medical studies. Huge amounts of data are produced and need to be analyzed adequately. Various online and offline analysis tools are available; however, most of them require extensive expertise in computer science or bioinformatics, and often a Linux-based operating system. Here, we introduce "CoMA-Comparative Microbiome Analysis" as a free and intuitive analysis pipeline for amplicon-sequencing data, compatible with any common operating system. Moreover, the tool offers various useful services including data pre-processing, quality checking, clustering to operational taxonomic units (OTUs), taxonomic assignment, data post-processing, data visualization, and statistical appraisal. The workflow results in highly esthetic and publication-ready graphics, as well as output files in standardized formats (e.g. tab-delimited OTU-table, BIOM, NEWICK tree) that can be used for more sophisticated analyses. The CoMA output was validated by a benchmark test, using three mock communities with different sample characteristics (primer set, amplicon length, diversity). The performance was compared with that of Mothur, QIIME and QIIME2-DADA2, popular packages for NGS data analysis. Furthermore, the functionality of CoMA is demonstrated on a practical example, investigating microbial communities from three different soils (grassland, forest, swamp). All tools performed well in the benchmark test and were able to reveal the majority of all genera in the mock communities. Also for the soil samples, the results of CoMA were congruent to those of the other pipelines, in particular when looking at the key microbial players.
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Affiliation(s)
- Sebastian Hupfauf
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
| | - Mohammad Etemadi
- Department of Horticultural Science, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - María Gómez-Brandón
- Department of Ecology and Animal Biology, GEA Group, University of Vigo, Vigo, Spain
| | - Heribert Insam
- Department of Microbiology, University of Innsbruck, Innsbruck, Austria
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92
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Piazzon MC, Naya-Català F, Perera E, Palenzuela O, Sitjà-Bobadilla A, Pérez-Sánchez J. Genetic selection for growth drives differences in intestinal microbiota composition and parasite disease resistance in gilthead sea bream. MICROBIOME 2020; 8:168. [PMID: 33228779 PMCID: PMC7686744 DOI: 10.1186/s40168-020-00922-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/09/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND The key effects of intestinal microbiota in animal health have led to an increasing interest in manipulating these bacterial populations to improve animal welfare. The aquaculture sector is no exception and in the last years, many studies have described these populations in different fish species. However, this is not an easy task, as intestinal microbiota is composed of very dynamic populations that are influenced by different factors, such as diet, environment, host age, and genetics. In the current study, we aimed to determine whether the genetic background of gilthead sea bream (Sparus aurata) influences the intestinal microbial composition, how these bacterial populations are modulated by dietary changes, and the effect of selection by growth on intestinal disease resistance. To that aim, three different groups of five families of gilthead sea bream that were selected during two generations for fast, intermediate, or slow growth (F3 generation) were kept together in the same open-flow tanks and fed a control or a well-balanced plant-based diet during 9 months. Six animals per family and dietary treatment were sacrificed and the adherent bacteria from the anterior intestinal portion were sequenced. In parallel, fish of the fast- and slow-growth groups were infected with the intestinal parasite Enteromyxum leei and the disease signs, prevalence, intensity, and parasite abundance were evaluated. RESULTS No differences were detected in alpha diversity indexes among families, and the core bacterial architecture was the prototypical composition of gilthead sea bream intestinal microbiota, indicating no dysbiosis in any of the groups. The plant-based diet significantly changed the microbiota in the intermediate- and slow-growth families, with a much lower effect on the fast-growth group. Interestingly, the smaller changes detected in the fast-growth families potentially accounted for more changes at the metabolic level when compared with the other families. Upon parasitic infection, the fast-growth group showed significantly lower disease signs and parasite intensity and abundance than the slow-growth animals. CONCLUSIONS These results show a clear genome-metagenome interaction indicating that the fast-growth families harbor a microbiota that is more flexible upon dietary changes. These animals also showed a better ability to cope with intestinal infections. Video Abstract.
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Affiliation(s)
- M. Carla Piazzon
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Fernando Naya-Català
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Erick Perera
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Oswaldo Palenzuela
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Ariadna Sitjà-Bobadilla
- Fish Pathology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Endocrinology Group, Instituto de Acuicultura Torre de la Sal (IATS-CSIC), Castellón, Spain
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93
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PROVIT: Supplementary Probiotic Treatment and Vitamin B7 in Depression-A Randomized Controlled Trial. Nutrients 2020; 12:nu12113422. [PMID: 33171595 PMCID: PMC7695208 DOI: 10.3390/nu12113422] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
Gut microbiota are suspected to affect brain functions and behavior as well as lowering inflammation status. Therefore, an effect on depression has already been suggested by recent research. The aim of this randomized double-blind controlled trial was to evaluate the effect of probiotic treatment in depressed individuals. Within inpatient care, 82 currently depressed individuals were randomly assigned to either receive a multistrain probiotic plus biotin treatment or biotin plus placebo for 28 days. Clinical symptoms as well as gut microbiome were analyzed at the begin of the study, after one and after four weeks. After 16S rRNA analysis, microbiome samples were bioinformatically explored using QIIME, SPSS, R and Piphillin. Both groups improved significantly regarding psychiatric symptoms. Ruminococcus gauvreauii and Coprococcus 3 were more abundant and β-diversity was higher in the probiotics group after 28 days. KEGG-analysis showed elevated inflammation-regulatory and metabolic pathways in the intervention group. The elevated abundance of potentially beneficial bacteria after probiotic treatment allows speculations on the functionality of probiotic treatment in depressed individuals. Furthermore, the finding of upregulated vitamin B6 and B7 synthesis underlines the connection between the quality of diet, gut microbiota and mental health through the regulation of metabolic functions, anti-inflammatory and anti-apoptotic properties. Concluding, four-week probiotic plus biotin supplementation, in inpatient individuals with a major depressive disorder diagnosis, showed an overall beneficial effect of clinical treatment. However, probiotic intervention compared to placebo only differed in microbial diversity profile, not in clinical outcome measures.
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94
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Structure and predictive metabolic contribution of intestinal microbiota of Longfin yellowtail (Seriola rivoliana) juveniles in aquaculture systems. Mol Biol Rep 2020; 47:9627-9636. [PMID: 33159677 DOI: 10.1007/s11033-020-05970-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/02/2020] [Indexed: 12/11/2022]
Abstract
Seriola rivoliana intestinal microbiota (IM) was characterised under aquaculture conditions through 16S rRNA amplicon sequencing. Specimens of 30 days after hatching (DAH) were maintained in three tanks and fed under the same environmental conditions for characterisation 15 days prior to sampling. Three fish were randomly taken from each tank; total DNA extraction of the gut microbiota was performed to characterise microbial composition and its metabolic prediction. The V3 hypervariable region of the 16S rRNA was amplified and sequenced with Illumina pair-end technology. The prokaryotic components in the S. rivoliana intestine were dominated mainly by the phyla Proteobacteria, Firmicutes, Bacteroidetes, Cyanobacteria and Actinobacteria. No significant differences in beta diversity were detected in the three samples (tanks). However in alpha diversity, they were detected in juveniles of the same cohort within the same group, as exemplified by enrichment of certain bacterial groups, mainly of the Clostridia class, which were specific in each fish within the same tank. The metabolic prediction analyses suggested that S. rivoliana IM contribute to the metabolism of amino acids, carbohydrates, lipids, and immune system. This study provides the first IM characterisation under rearing conditions of S. rivoliana-a species with broad economic potential-and contributes to novel information for potential use of probiotics in future trials.
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95
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Taylor H, Serrano-Contreras JI, McDonald JAK, Epstein J, Fell JM, Seoane RC, Li JV, Marchesi JR, Hart AL. Multiomic features associated with mucosal healing and inflammation in paediatric Crohn's disease. Aliment Pharmacol Ther 2020; 52:1491-1502. [PMID: 32929796 DOI: 10.1111/apt.16086] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/23/2020] [Accepted: 08/24/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND The gastrointestinal microbiota has an important role in mucosal immune homoeostasis and may contribute to maintaining mucosal healing in Crohn's disease (CD). AIM To identify changes in the microbiota, metabolome and protease activity associated with mucosal healing in established paediatric CD METHODS: Twenty-five participants aged 3-18 years with CD, disease duration of over 6 months, and maintenance treatment with biological therapy were recruited. They were divided into a low calprotectin group (faecal calprotectin <100 μg/g, "mucosal healing," n = 11), and a high calprotectin group (faecal calprotectin >100 μg/g, "mucosal inflammation," n = 11). 16S gene-based metataxonomics, 1 H-NMR spectroscopy-based metabolic profiling and protease activity assays were performed on stool samples. RESULTS Relative abundance of Dialister species was six-times greater in the low calprotectin group (q = 0.00999). Alpha and beta diversity, total protease activity and inferred metagenomic profiles did not differ between groups. Pentanoate (valerate) and lysine were principal discriminators in a machine-learning model which differentiated high and low calprotectin samples using NMR spectra (R2 0.87, Q2 0.41). Mean relative concentration of pentanoate was 1.35-times greater in the low calprotectin group (95% CI 1.03-1.68, P = 0.036) and was positively correlated with Dialister. Mean relative concentration of lysine was 1.54-times greater in the high calprotectin group (95% CI 1.05-2.03, P = 0.028). CONCLUSIONS This multiomic study identified an increase in Dialister species and pentanoate, and a decrease in lysine, in patients with "mucosal healing." It supports further investigation of these as potential novel therapeutic targets in CD.
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Affiliation(s)
- Henry Taylor
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jose Ivan Serrano-Contreras
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Julie A K McDonald
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Jenny Epstein
- Paediatric Gastroenterology Department, Chelsea and Westminster Hospital, London, UK
| | - J M Fell
- Paediatric Gastroenterology Department, Chelsea and Westminster Hospital, London, UK
| | - Rocio C Seoane
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Jia V Li
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.,School of Biosciences, University of Cardiff, Cardiff, UK
| | - Ailsa L Hart
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.,IBD Unit, St. Mark's Hospital, Harrow, UK
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96
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Mitchell K, Ronas J, Dao C, Freise AC, Mangul S, Shapiro C, Moberg Parker J. PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom. Front Microbiol 2020; 11:584699. [PMID: 33123113 PMCID: PMC7573227 DOI: 10.3389/fmicb.2020.584699] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022] Open
Abstract
Improvements in high-throughput sequencing makes targeted amplicon analysis an ideal method for the study of human and environmental microbiomes by undergraduates. Multiple bioinformatics programs are available to process and interpret raw microbial diversity datasets, and the choice of programs to use in curricula is largely determined by student learning goals. Many of the most commonly used microbiome bioinformatics platforms offer end-to-end data processing and data analysis using a command line interface (CLI), but the downside for novice microbiome researchers is the steep learning curve often required. Alternatively, some sequencing providers include processing of raw data and taxonomy assignments as part of their pipelines. This, when coupled with available web-based or graphical user interface (GUI) analysis and visualization tools, eliminates the need for students or instructors to have extensive CLI experience. However, lack of universal data formats can make integration of these tools challenging. For example, tools for upstream and downstream analyses frequently use multiple different data formats which then require writing custom scripts or hours of manual work to make the files compatible. Here, we describe a microbial ecology bioinformatics curriculum that focuses on data analysis, visualization, and statistical reasoning by taking advantage of existing web-based and GUI tools. We created the Program for Unifying Microbiome Analysis Applications (PUMAA), which solves the problem of inconsistent files by formatting the output files from several raw data processing programs to seamlessly transition to a suite of GUI programs for analysis and visualization of microbiome taxonomic and inferred functional profiles. Additionally, we created a series of tutorials to accompany each of the microbiome analysis curricular modules. From pre- and post-course surveys, students in this curriculum self-reported conceptual and confidence gains in bioinformatics and data analysis skills. Students also demonstrated gains in biologically relevant statistical reasoning based on rubric-guided evaluations of open-ended survey questions and the Statistical Reasoning in Biology Concept Inventory. The PUMAA program and associated analysis tutorials enable students and researchers with no computational experience to effectively analyze real microbiome datasets to investigate real-world research questions.
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Affiliation(s)
- Keith Mitchell
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jiem Ronas
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Christopher Dao
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Amanda C Freise
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Casey Shapiro
- Center for Educational Assessment, Center for the Advancement of Teaching, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jordan Moberg Parker
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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97
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Roberts C, Allen R, Bird KE, Cunliffe M. Chytrid fungi shape bacterial communities on model particulate organic matter. Biol Lett 2020; 16:20200368. [PMID: 32991826 PMCID: PMC7532721 DOI: 10.1098/rsbl.2020.0368] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microbial colonization and degradation of particulate organic matter (POM) are important processes that influence the structure and function of aquatic ecosystems. Although POM is readily used by aquatic fungi and bacteria, there is a limited understanding of POM-associated interactions between these taxa, particularly for early-diverging fungal lineages. Using a model ecological system with the chitin-degrading freshwater chytrid fungus Rhizoclosmatium globosum and chitin microbeads, we assessed the impacts of chytrid fungi on POM-associated bacteria. We show that the presence of chytrids on POM alters concomitant bacterial community diversity and structure, including differing responses between chytrid life stages. We propose that chytrids can act as ecosystem facilitators through saprotrophic feeding by producing ‘public goods’ from POM degradation that modify bacterial POM communities. This study suggests that chytrid fungi have complex ecological roles in aquatic POM degradation not previously considered, including the regulation of bacterial colonization, community succession and subsequent biogeochemical potential.
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Affiliation(s)
- Cordelia Roberts
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
| | - Ro Allen
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Kimberley E Bird
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK
| | - Michael Cunliffe
- Marine Biological Association of the UK, The Laboratory, Citadel Hill, Plymouth, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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98
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Moraes LC, Lang PM, Arcanjo RA, Rampelotto PH, Fatturi-Parolo CC, Ferreira MBC, Montagner F. Microbial ecology and predicted metabolic pathways in various oral environments from patients with acute endodontic infections. Int Endod J 2020; 53:1603-1617. [PMID: 33448446 DOI: 10.1111/iej.13389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/11/2020] [Indexed: 01/17/2023]
Abstract
AIM To assess in a cross-sectional clinical study the effect of antibiotics on the diversity, structure and metabolic pathways of bacterial communities in various oral environments in patients with acute primary infections. METHODOLOGY Samples of saliva (SA), supragingival biofilm (SB) and from the pulp cavity (PC) were collected from teeth with acute primary infections and then grouped according to previous use of antibiotics (NoAtb = no antibiotics [n = 6]; Atb = antibiotics [n = 6]). DNA sequencing was conducted using MiSeq (Illumina, San Diego, CA, USA). The V1-V3 hyper-variable region of the 16S rRNA gene was amplified. A custom Mothur pipeline was used for 16S rRNA processing. Subsequent analyses of the sequence dataset were performed in R (using vegan, phyloseq and ggplot2 packages) or QIIME. RESULTS Twelve patients aged from 22 to 56 years were recruited. Participants in the Atb group had taken the beta-lactamics amoxicillin (5/6) or cephalexin (1/6) for 2-3 days. A total of 332 bacterial taxa (OTUs) were identified, belonging to 120 genera, 60 families and nine phyla. Firmicutes (41%) and Bacteroidetes (38%) were the most abundant phyla in all samples. Taxa clustered significantly by oral site (PCoA analysis; P < 0.05, ANOSIM). Use of antibiotics had little effect on this clustering. However, SA, SB and PC had different degrees of richness, diversity and evenness. The greatest diversity was observed in SB samples and the least diversity was observed in PC samples. Metabolic prediction identified 163 pathways and previous use of antibiotics had a major effect on the estimated functional clustering in SA and PC samples. CONCLUSION The ecological niche had a strong influence on the bacterial content of samples from various oral sites. Previous exposure to antibiotics may exert an effect on the phylogenetic composition of SA. Metabolic pathways appear to be modulated by antimicrobial agents in SA and PC samples. The dynamics of host/microbial interactions in the apical region and the functional ecology of the infected pulp cavity should be revisited.
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Affiliation(s)
- L C Moraes
- Programa de Pós-graduação em Odontologia, Faculdade de Odontologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - P M Lang
- Programa de Pós-graduação em Odontologia, Faculdade de Odontologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Curso de Odontologia, Universidade Regional Integrada do Alto Uruguai e das Missões, Erechim, Brazil
| | - R A Arcanjo
- Programa de Pós-graduação em Ciências Biológicas: Farmacologia e Terapêutica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - P H Rampelotto
- Laboratório Experimental de Hepatologia e Gastroenterologia (LEHG), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - C C Fatturi-Parolo
- Programa de Pós-graduação em Odontologia, Faculdade de Odontologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - M B C Ferreira
- Departamento de Odontologia Conservadora, Faculdade de Odontologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - F Montagner
- Programa de Pós-graduação em Odontologia, Faculdade de Odontologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Curso de Odontologia, Universidade Regional Integrada do Alto Uruguai e das Missões, Erechim, Brazil
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Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study. Genomics 2020; 112:4968-4979. [PMID: 32911024 DOI: 10.1016/j.ygeno.2020.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/15/2020] [Accepted: 09/03/2020] [Indexed: 11/22/2022]
Abstract
Meta-omics approaches such as high-throughput sequencing of 16S hypervariable region(s) [HVR(s)] is extensively applied for profiling microbial community. Several studies have deciphered the influence of HVR(s) on bacterial diversity; most of these were devoted to human body habitats. Extent to which targeted HVR(s) influences the diversity estimates of environmental samples is rather unclear. Here, we evaluated the performance of five widely used universal primer pairs spanning V1-V3, V3-V4, V4, V5-V6 and V7-V9 HVRs to characterize bacterial diversity and predictive functionality of complex marine sediments. Obtained results revealed that the HVR(s) V4 and V5-V6 represented the higher species richness than others while, V1-V3 and V7-V9 were unsuccessful to detect Bacteroidetes and Planctomycetes. Further, PICRUSt analysis showed that the selected HVR(s) also had significant impact on the predictive functional profile. Conclusively, this study proved that HVR selection has a profound effect on overall results and thus should be selected with utmost caution.
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100
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LeMay-Nedjelski L, Asbury MR, Butcher J, Ley SH, Hanley AJ, Kiss A, Unger S, Copeland JK, Wang PW, Stintzi A, O'Connor DL. Maternal Diet and Infant Feeding Practices Are Associated with Variation in the Human Milk Microbiota at 3 Months Postpartum in a Cohort of Women with High Rates of Gestational Glucose Intolerance. J Nutr 2020; 151:320-329. [PMID: 32886107 PMCID: PMC7850034 DOI: 10.1093/jn/nxaa248] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/11/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Human milk contains a diverse community of bacteria believed to play a role in breast health and inoculation of the infant's gastrointestinal tract. The role of maternal nutrition and infant feeding practices on the human milk microbiota remains poorly understood. OBJECTIVE Our aim was to explore the associations between maternal diet (delivery to 3 mo postpartum), infant feeding practices, and the microbial composition and predicted function in milk from women with varied metabolic status. METHODS This was an exploratory analysis of a previously completed prospective cohort study of women with varying degrees of gestational glucose intolerance (NCT01405547). Milk samples (n = 93 mothers) were collected at 3 mo postpartum. Maternal dietary information (validated food-frequency questionnaire) and infant feeding practices (human milk exclusivity, frequency of direct breastfeeding per day) were collected. V4-16S ribosomal RNA gene sequencing (Illumina MiSeq) was conducted to determine microbiota composition. RESULTS Intake of polyunsaturated fat [β estimate (SE): 0.036 (0.018), P = 0.047] and fiber from grains [0.027 (0.013), P = 0.048] were positively associated with ɑ-diversity (Shannon index) of human milk. Overall microbial composition of human milk clustered based on human milk exclusivity (weighted UniFrac R2 = 0.034, P = 0.015; Bray-Curtis R2 = 0.041, P = 0.007), frequency of direct breastfeeding per day (Bray-Curtis R2 = 0.057, P = 0.026), and maternal fiber intake from grains (Bray-Curtis R2 = 0.055, P = 0.040). Total fiber, fiber from grains, dietary fat, and infant feeding practices were also associated with a number of differentially abundant taxa. The overall composition of predicted microbial functions was associated with total fiber consumption (Bray-Curtis R2 = 0.067, P = 0.036) and human milk exclusivity (Bray-Curtis R2 = 0.041, P = 0.013). CONCLUSIONS Maternal consumption of fiber and fat, as well as mother's infant feeding practices, are important determinants of the human milk microbiota. Understanding whether these microbial changes impact an infant's overall health and development requires future study.
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Affiliation(s)
- Lauren LeMay-Nedjelski
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada,Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle R Asbury
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada,Translational Medicine Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Sylvia H Ley
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Anthony J Hanley
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Alex Kiss
- Department of Research Design and Biostatistics, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Sharon Unger
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada,Department of Pediatrics, Mount Sinai Hospital, Toronto, Ontario, Canada,Division of Neonatology, The Hospital for Sick Children, Toronto, Ontario, Canada,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Julia K Copeland
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Pauline W Wang
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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