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Pylak M, Oszust K, Panek J, Siegieda D, Cybulska J, Zdunek A, Orzeł A, Frąc M. Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation. Food Chem 2025; 462:140943. [PMID: 39217744 DOI: 10.1016/j.foodchem.2024.140943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 07/27/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024]
Abstract
Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.
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Affiliation(s)
- Michał Pylak
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Karolina Oszust
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Jacek Panek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Dominika Siegieda
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Justyna Cybulska
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
| | - Agnieszka Orzeł
- Dr. Berry Innowacje i Tradycja, Juraszowa 73, 33-386 Podegrodzie, Poland.
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland.
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2
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Mahdavi M, Prévost K, Balthazar P, Hus IFP, Duchesne É, Dumont N, Gagné-Ouellet V, Gagnon C, Laforest-Lapointe I, Massé E. Disturbance of the human gut microbiota in patients with Myotonic Dystrophy type 1. Comput Struct Biotechnol J 2024; 23:2097-2108. [PMID: 38803516 PMCID: PMC11128782 DOI: 10.1016/j.csbj.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a rare autosomal dominant genetic disorder. Although DM1 is primarily characterized by progressive muscular weakness, it exhibits many multisystemic manifestations, such as cognitive deficits, cardiac conduction abnormalities, and cataracts, as well as endocrine and reproductive issues. Additionally, the gastrointestinal (GI) tract is frequently affected, encompassing the entire digestive tract. However, the underlying causes of these GI symptoms remain uncertain, whether it is biomechanical problems of the intestine, involvement of bacterial communities, or both. The primary objective of this study is to investigate the structural changes in the gut microbiome of DM1 patients. To achieve this purpose, 35 patients with DM1 were recruited from the DM-Scope registry of the neuromuscular clinic in the Saguenay-Lac-St-Jean region of the province of Québec, Canada. Stool samples from these 35 patients, including 15 paired samples with family members living with them as controls, were collected. Subsequently, these samples were sequenced by 16S MiSeq and were analyzed with DADA2 to generate taxonomic signatures. Our analysis revealed that the DM1 status correlated with changes in gut bacterial community. Notably, there were differences in the relative abundance of Bacteroidota, Euryarchaeota, Fusobacteriota, and Cyanobacteria Phyla compared to healthy controls. However, no significant shift in gut microbiome community structure was observed between DM1 phenotypes. These findings provide valuable insights into how the gut bacterial community, in conjunction with biomechanical factors, could potentially influence the gastrointestinal tract of DM1 patients.
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Affiliation(s)
- Manijeh Mahdavi
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Karine Prévost
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Philippe Balthazar
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Isabelle Fisette-Paul Hus
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Élise Duchesne
- Physiotherapy teaching unit, Université du Québec à Chicoutimi, Chicoutimi, G7H 2B1, Canada
| | - Nicolas Dumont
- School of Rehabilitation, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Valérie Gagné-Ouellet
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Cynthia Gagnon
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | | | - Eric Massé
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
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3
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Ferreira-Rodríguez N, Nión-Cabeza P, Trigo-Tasende N, Conde-Pérez K, Aja-Macaya P, Nasser-Ali M, Bou G, Poza M, Vallejo J. Native and non-native freshwater bivalves in the bioremediation of bacterial pollution caused by the disposal of sewage. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 360:124648. [PMID: 39095005 DOI: 10.1016/j.envpol.2024.124648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Treated sewage contains a large diversity of pathogens that can be transmitted to the environment and, directly or indirectly, infect humans through water use (i.e., consumption, bathing, or irrigation). In urban environments, wastewater normally flows into wastewater treatment plants (WWTPs), where it is subjected to different processes in order to eliminate the greatest amount of waste. However, there are inequalities among European countries concerning wastewater management. In this context, we evaluate the potential of freshwater mussels to improve water quality (i.e., reduce bacterial abundance) in rivers receiving primary, secondary, or tertiary sewage-treated effluents. Additionally, because freshwater mussels are declining at a global scale and empty niches are progressively occupied by non-native counterparts, we evaluate if depauperate communities and the Asian clams, Corbicula genus, can provide equivalent ecosystem services (i.e., water quality improvement by biofiltration) formerly provided by diverse native communities. For this, an analysis of the bacterial biodiversity of the samples filtered by the different bivalve communities was carried out. The experimental approach was performed by metabarcoding the 16S rRNA gene using Illumina technologies. According to the results obtained, secondary treatment processes were effective in reducing the bacterial diversity. Furthermore, the waters filtered by the bivalves presented a lower bacterial abundance for certain genera. Biofiltration differs, however, among species, with Corbicula reducing a large number of taxa much more efficiently than native freshwater mussels in both diverse and depauperated communities. These results are likely related to Corbicula being a generalist species in front of native mussels, which may be more selective. Considering it is not possible to eradicate Corbicula from European rivers, its filtering capacity should be considered when managing freshwater ecosystems.
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Affiliation(s)
- Noé Ferreira-Rodríguez
- Universidade de Vigo, Departamento de Ecoloxía e Bioloxía Animal, 36310, Vigo, Spain; Faculty of Natural and Agricultural Sciences, Ovidius University Constanța, 900470, Constanța, Romania.
| | - Paula Nión-Cabeza
- Microbiology Research Group, Institute of Biomedical Research (INIBIC), Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC), CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Madrid. Servicio de Microbiología, 3° Planta, Edificio Sur, Hospital Universitario A Coruña, As Xubias, 15006, A Coruña, Spain
| | - Noelia Trigo-Tasende
- Microbiology Research Group, Institute of Biomedical Research (INIBIC), Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC), CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Madrid. Servicio de Microbiología, 3° Planta, Edificio Sur, Hospital Universitario A Coruña, As Xubias, 15006, A Coruña, Spain
| | - Kelly Conde-Pérez
- Microbiology Research Group, Institute of Biomedical Research (INIBIC), Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC), CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Madrid. Servicio de Microbiología, 3° Planta, Edificio Sur, Hospital Universitario A Coruña, As Xubias, 15006, A Coruña, Spain
| | - Pablo Aja-Macaya
- Microbiology Research Group, Institute of Biomedical Research (INIBIC), Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC), CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Madrid. Servicio de Microbiología, 3° Planta, Edificio Sur, Hospital Universitario A Coruña, As Xubias, 15006, A Coruña, Spain
| | - Mohammed Nasser-Ali
- Microbiology Research Group, Institute of Biomedical Research (INIBIC), Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC), CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Madrid. Servicio de Microbiología, 3° Planta, Edificio Sur, Hospital Universitario A Coruña, As Xubias, 15006, A Coruña, Spain
| | - Germán Bou
- Microbiology Research Group, Institute of Biomedical Research (INIBIC), Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC), CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Madrid. Servicio de Microbiología, 3° Planta, Edificio Sur, Hospital Universitario A Coruña, As Xubias, 15006, A Coruña, Spain
| | - Margarita Poza
- Microbiology Research Group, Institute of Biomedical Research (INIBIC), Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC), CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Madrid. Servicio de Microbiología, 3° Planta, Edificio Sur, Hospital Universitario A Coruña, As Xubias, 15006, A Coruña, Spain; Microbiome and Health, Faculty of Sciences, Campus da Zapateira, 15071, A Coruña, Spain
| | - Juan Vallejo
- Microbiology Research Group, Institute of Biomedical Research (INIBIC), Interdisciplinary Center for Chemistry and Biology (CICA), University of A Coruña (UDC), CIBER de Enfermedades Infecciosas (CIBERINFEC-ISCIII), Madrid. Servicio de Microbiología, 3° Planta, Edificio Sur, Hospital Universitario A Coruña, As Xubias, 15006, A Coruña, Spain
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Flores Martinez KE, Bloszies CS, Bolino MJ, Henrick BM, Frese SA. Hemp hull fiber and two constituent compounds , N-trans-caffeoyltyramine and N-trans-feruloyltyramine, shape the human gut microbiome in vitro. Food Chem X 2024; 23:101611. [PMID: 39113742 PMCID: PMC11304861 DOI: 10.1016/j.fochx.2024.101611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 08/10/2024] Open
Abstract
Mounting evidence supports the potential of dietary bioactives to reduce chronic disease risk. N-trans-caffeoyltyramine (NCT) and N-trans-feruloyltyramine (NFT) have been hypothesized to drive regulation of gut permeability, but these components have not yet been studied in the context of the human gut microbiome. This work examined whether purified NCT and NFT, or a hemp hull product containing NCT and NFT (Brightseed® Bio Gut Fiber™), can impact the gut microbiome using an in vitro fermentation assay. Representative human gut microbiomes were treated with Bio Gut Fiber™ or NCT and NFT and compared to starch and methylcellulose, as controls, in vitro. Stronger changes were exerted by Bio Gut Fiber™, NCT, and NFT. Communities treated with Bio Gut Fiber™ saw increased productivity and diversity. We found a dose-dependent effect of NCT and NFT on microbial communities. Here, we describe novel potential for hemp-derived bioactives to shape the gut microbiome.
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Affiliation(s)
| | | | - Matthew J. Bolino
- Department of Nutrition, University of Nevada, Reno, Reno, NV 89557, United States
| | - Bethany M. Henrick
- Brightseed, Inc; South San Francisco, CA 94080, United States
- University of Nebraska, Lincoln, Food Science & Technology; Lincoln, NE 68588, United States
| | - Steven A. Frese
- Department of Nutrition, University of Nevada, Reno, Reno, NV 89557, United States
- University of Nevada, Reno School of Medicine; Reno, NV 89557, United States
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5
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Jarma D, Sacristán-Soriano O, Borrego CM, Hortas F, Peralta-Sánchez JM, Balcázar JL, Green AJ, Alonso E, Sánchez-Melsió A, Sánchez MI. Variability of faecal microbiota and antibiotic resistance genes in flocks of migratory gulls and comparison with the surrounding environment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124563. [PMID: 39019307 DOI: 10.1016/j.envpol.2024.124563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/05/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
Gulls commonly rely on human-generated waste as their primary food source, contributing to the spread of antibiotic-resistant bacteria and their resistance genes, both locally and globally. Our understanding of this process remains incomplete, particularly in relation to its potential interaction with surrounding soil and water. We studied the lesser black-backed gull, Larus fuscus, as a model to examine the spatial variation of faecal bacterial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) and its relationship with the surrounding water and soil. We conducted sampling campaigns within a connectivity network of different flocks of gulls moving across functional units (FUs), each of which represents a module of highly interconnected patches of habitats used for roosting and feeding. The FUs vary in habitat use, with some gulls using more polluted sites (notably landfills), while others prefer more natural environments (e.g., wetlands or beaches). Faecal bacterial communities in gulls from flocks that visit and spend more time in landfills exhibited higher richness and diversity. The faecal microbiota showed a high compositional overlap with bacterial communities in soil. The overlap was greater when compared to landfill (11%) than to wetland soils (6%), and much lower when compared to bacterial communities in surrounding water (2% and 1% for landfill and wetland water, respectively). The relative abundance of ARGs and MGEs were similar between FUs, with variations observed only for specific families of ARGs and MGEs. When exploring the faecal carriage of ARGs and MGEs in bird faeces relative to soil and water compartments, gull faeces were enriched in ARGs classified as High-Risk. Our results shed light on the complex dynamics of antibiotic resistance spread in wild bird populations, providing insights into the interactions among gull movement and feeding behavior, habitat characteristics, and the dissemination of antibiotic resistance determinants across environmental reservoirs.
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Affiliation(s)
- Dayana Jarma
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, Avda. República Árabe Saharaui Democrática 6, 11519, Puerto Real, Cádiz, Spain.
| | - Oriol Sacristán-Soriano
- Institut Català de Recerca de l'Aigua (ICRA-CERCA), Emili Grahit 101, E-17003, Girona, Spain; Universitat de Girona, E-1700, Girona, Spain
| | - Carles M Borrego
- Institut Català de Recerca de l'Aigua (ICRA-CERCA), Emili Grahit 101, E-17003, Girona, Spain; Grup d'Ecologia Microbiana Molecular, Institut d'Ecologia Aquàtica, Universitat de Girona, Campus de Montilivi, E-17003, Girona, Spain
| | - Francisco Hortas
- Departamento de Biología, Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEI·MAR), Universidad de Cádiz, Avda. República Árabe Saharaui Democrática 6, 11519, Puerto Real, Cádiz, Spain
| | - Juan M Peralta-Sánchez
- Departmento de Zoología, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes 6, 41012, Seville, Spain
| | - José L Balcázar
- Institut Català de Recerca de l'Aigua (ICRA-CERCA), Emili Grahit 101, E-17003, Girona, Spain; Universitat de Girona, E-1700, Girona, Spain
| | - Andy J Green
- Department of Conservation Biology and Global Change, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio 26, 41092, Seville, Spain
| | - Esteban Alonso
- Departamento de Química Analítica, Escuela Politécnica Superior, Universidad de Sevilla, C/Virgen de África, 7, 41011, Sevilla, Spain
| | - Alexandre Sánchez-Melsió
- Institut Català de Recerca de l'Aigua (ICRA-CERCA), Emili Grahit 101, E-17003, Girona, Spain; Universitat de Girona, E-1700, Girona, Spain
| | - Marta I Sánchez
- Department of Conservation Biology and Global Change, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio 26, 41092, Seville, Spain
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6
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Cholet F, Agogué H, Ijaz UZ, Lachaussée N, Pineau P, Smith CJ. Low-abundant but highly transcriptionally active uncharacterised Nitrosomonas drive ammonia-oxidation in the Brouage mudflat, France. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 946:174312. [PMID: 38936706 DOI: 10.1016/j.scitotenv.2024.174312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/03/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Exploring differences in nitrification within adjacent sedimentary structures of ridges and runnels on the Brouage mudflat, France, we quantified Potential Nitrification Rates (PNR) alongside amoA genes and transcripts. PNR was lower in ridges (≈1.7 fold-lower) than runnels, despite higher (≈1.8 fold-higher) ammonia-oxidizing bacteria (AOB) abundance. However, AOB were more transcriptionally active in runnels (≈1.9 fold-higher). Sequencing of amoA genes and transcripts revealed starkly contrasting profiles with transcripts from ridges and runnels dominated (≈91 % in ridges and ≈98 % in runnels) by low abundant (≈4.6 % of the DNA community in runnels and ≈0.8 % in ridges) but highly active phylotypes. The higher PNR in runnels was explained by higher abundance of this group, an uncharacterised Nitrosomonas sp. cluster. This cluster is phylogenetically similar to other active ammonia-oxidizers with worldwide distribution in coastal environments indicating its potential, but previously overlooked, contribution to ammonia oxidation globally. In contrast DNA profiles were dominated by highly abundant but low-activity clusters phylogenetically distinct from known Nitrosomonas (Nm) and Nitrosospira (Ns). This cluster is also globally distributed in coastal sediments, primarily detected as DNA, and often classified as Nitrosospira or Nitrosomonas. We therefore propose to classify this cluster as Ns/Nm. Our work indicates that low abundant but highly active AOB could be responsible for the nitrification globally, while the abundant AOB Ns/Nm may not be transcriptionally active, and as such account for the lack of correlation between rate processes and gene abundances often reported in the literature. It also raises the question as to what this seemingly inactive group is doing?
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Affiliation(s)
- Fabien Cholet
- Advanced Research Centre, Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, 11 Chapel Lane G11 6EW, Glasgow, UK..
| | - Hélène Agogué
- LIENSs, UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Umer Z Ijaz
- Advanced Research Centre, Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, 11 Chapel Lane G11 6EW, Glasgow, UK
| | - Nicolas Lachaussée
- LIENSs, UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Philippe Pineau
- LIENSs, UMR 7266, CNRS - La Rochelle Université, 2 Rue Olympe de Gouges, 17000, La Rochelle, France
| | - Cindy J Smith
- Advanced Research Centre, Infrastructure and Environment, James Watt School of Engineering, University of Glasgow, 11 Chapel Lane G11 6EW, Glasgow, UK
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7
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Nanda S, Lamot B, Guarino N, Usler E, Chugani DC, Dutta A, Chow HM. Atypical gut microbiota composition in a mouse model of developmental stuttering. Sci Rep 2024; 14:23457. [PMID: 39379558 DOI: 10.1038/s41598-024-74766-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 09/30/2024] [Indexed: 10/10/2024] Open
Abstract
Developmental stuttering is a complex neurodevelopmental disorder characterized by disfluent speech. It has been associated with mutations in genes involved in lysosomal enzyme trafficking. Mice with mutations in one such gene, Gnptab, exhibit atypical vocalizations analogous to stuttering in humans. This mouse model has enabled the study of various molecular mechanisms related to the disorder. Simultaneously, an increasing number of reports have suggested the role of gut microbiota in altered brain function and development in neurological disorders. In this study, we compared gut microbiota profiles from Gnptab mutant mice to wildtype control mice. Microbiome analysis demonstrated a distinct microbiota profile in Gnptab mutant mice. The most significant alteration was an increased relative abundance of Akkermansia, a genus of mucin degrading bacteria, which has previously been associated with multiple neurological disorders. Moreover, the altered microbiota profile of these mice was predicted to result in differences in abundance of several metabolic pathways, including short chain fatty acid and lipopolysaccharide synthesis. These pathways may play a role in the onset, progression and persistence of developmental stuttering. This is the first study to show a potential link between developmental stuttering and changes in the gut microbiota, laying the groundwork for a new research direction.
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Affiliation(s)
- Sayan Nanda
- Department of Communication Sciences and Disorders, University of Delaware, Newark, DE, 19716, USA.
| | - Bryan Lamot
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Nicole Guarino
- Department of Communication Sciences and Disorders, University of Delaware, Newark, DE, 19716, USA
| | - Evan Usler
- Department of Communication Sciences and Disorders, University of Delaware, Newark, DE, 19716, USA
| | - Diane C Chugani
- Department of Communication Sciences and Disorders, University of Delaware, Newark, DE, 19716, USA
| | - Aditya Dutta
- Departments of Animal and Food Sciences, Biological Sciences, Medical and Molecular Sciences, Microbiology Graduate Program, University of Delaware, Newark, DE, 19716, USA.
| | - Ho Ming Chow
- Department of Communication Sciences and Disorders, University of Delaware, Newark, DE, 19716, USA.
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8
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Baldi A, Braat S, Hasan MI, Bennett C, Barrios M, Jones N, Abdul Azeez I, Wilcox S, Roy PK, Bhuiyan MSA, Ataide R, Clucas D, Larson LM, Hamadani J, Zimmermann M, Bowden R, Jex A, Biggs BA, Pasricha SR. Effects of iron supplements and iron-containing micronutrient powders on the gut microbiome in Bangladeshi infants: a randomized controlled trial. Nat Commun 2024; 15:8640. [PMID: 39367018 PMCID: PMC11452624 DOI: 10.1038/s41467-024-53013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 09/27/2024] [Indexed: 10/06/2024] Open
Abstract
Anemia is highly prevalent globally, especially in young children in low-income countries, where it often overlaps with a high burden of diarrheal disease. Distribution of iron interventions (as supplements or iron-containing multiple micronutrient powders, MNPs) is a key anemia reduction strategy. Small studies in Africa indicate iron may reprofile the gut microbiome towards pathogenic species. We seek to evaluate the safety of iron and MNPs based on their effects on diversity, composition, and function of the gut microbiome in children in rural Bangladesh as part of a large placebo-controlled randomized controlled trial of iron or MNPs given for 3 months (ACTRN12617000660381). In 923 infants, we evaluate the microbiome before, immediately following, and nine months after interventions, using 16S rRNA gene sequencing and shotgun metagenomics in a subset. We identify no increase in diarrhea with either treatment. In our primary analysis, neither iron nor MNPs alter gut microbiome diversity or composition. However, when not adjusting for multiple comparisons, compared to placebo, children receiving iron and MNPs exhibit reductions in commensal species (e.g., Bifidobacterium, Lactobacillus) and increases in potential pathogens, including Clostridium. These increases are most evident in children with baseline iron repletion and are further supported by trend-based statistical analyses.
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Affiliation(s)
- Andrew Baldi
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
| | - Sabine Braat
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Centre for Epidemiology and Biostatistics, University of Melbourne School of Population and Global Health, Carlton, Carlton, VIC, Australia
- Department of Infectious Diseases at the Peter Doherty Institute of Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Mohammed Imrul Hasan
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- International Center for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Cavan Bennett
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Marilou Barrios
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Naomi Jones
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Imadh Abdul Azeez
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Stephen Wilcox
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Pradip Kumar Roy
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Faculty of Science, University of Melbourne, Melbourne, VIC, Australia
| | | | - Ricardo Ataide
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Infectious Diseases at the Peter Doherty Institute of Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Danielle Clucas
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- Diagnostic Haematology, The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Leila M Larson
- Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Jena Hamadani
- International Center for Diarrheal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Michael Zimmermann
- Medical Research Council Translational Immune Discovery Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, England, UK
| | - Rory Bowden
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Aaron Jex
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- Faculty of Science, University of Melbourne, Melbourne, VIC, Australia
| | - Beverley-Ann Biggs
- Department of Infectious Diseases at the Peter Doherty Institute of Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Sant-Rayn Pasricha
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
- Diagnostic Haematology, The Royal Melbourne Hospital, Parkville, VIC, Australia.
- Clinical Haematology at The Royal Melbourne Hospital and the Peter MacCallum Cancer Centre, Parkville, VIC, Australia.
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9
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Hernandez-Hernandez O, Sabater C, Calvete-Torre I, Doyagüez EG, Muñoz-Labrador AM, Julio-Gonzalez C, de Las Rivas B, Muñoz R, Ruiz L, Margolles A, Mancheño JM, Moreno FJ. Tailoring the natural rare sugars D-tagatose and L-sorbose to produce novel functional carbohydrates. NPJ Sci Food 2024; 8:74. [PMID: 39366963 PMCID: PMC11452612 DOI: 10.1038/s41538-024-00320-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 09/25/2024] [Indexed: 10/06/2024] Open
Abstract
This multidisciplinary study details the biosynthesis of novel non-digestible oligosaccharides derived from rare sugars, achieved through transfructosylation of D-tagatose and L-sorbose by levansucrase from Bacillus subtilis CECT 39 (SacB). The characterization of these carbohydrates using NMR and molecular docking was instrumental in elucidating the catalytic mechanism and substrate preference of SacB. Tagatose-based oligosaccharides were higher in abundance than L-sorbose-based oligosaccharides, with the most representative structures being: β-D-Fru-(2→6)-β-D-Fru-(2→1)-D-Tag and β-D-Fru-(2→1)-D-Tag. In vitro studies demonstrated the resistance of tagatose-based oligosaccharides to intestinal digestion and their prebiotic properties, providing insights into their structure-function relationship. β-D-Fru-(2→1)-D-Tag was the most resistant structure to small-intestinal digestion after three hours (99.8% remained unaltered). This disaccharide and the commercial FOS clustered in similar branches, indicating comparable modulatory properties on human fecal microbiota, and exerted a higher bifidogenic effect than unmodified tagatose. The bioconversion of selected rare sugars into β-fructosylated species with a higher degree of polymerization emerges as an efficient strategy to enhance the bioavailability of these carbohydrates and promote their interaction with the gut microbiota. These findings open up new opportunities for tailoring natural rare sugars, like D-tagatose and L-sorbose, to produce novel biosynthesized carbohydrates with functional and structural properties desirable for use as emerging prebiotics and low-calorie sweeteners.
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Affiliation(s)
| | - Carlos Sabater
- Dairy Research Institute of Asturias (IPLA-CSIC), Paseo Río Linares s/n, 3300, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, 33011, Oviedo, Asturias, Spain
| | - Inés Calvete-Torre
- Dairy Research Institute of Asturias (IPLA-CSIC), Paseo Río Linares s/n, 3300, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, 33011, Oviedo, Asturias, Spain
| | - Elisa G Doyagüez
- Centro de Química Orgánica "Lora Tamayo" (CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Ana M Muñoz-Labrador
- Institute of Food Science Research, CIAL (CSIC-UAM), Nicolas Cabrera 9, 28049, Madrid, Spain
| | - Cristina Julio-Gonzalez
- Institute of Food Science Research, CIAL (CSIC-UAM), Nicolas Cabrera 9, 28049, Madrid, Spain
| | - Blanca de Las Rivas
- Institute of Food Science, Technology and Nutrition, ICTAN (CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Rosario Muñoz
- Institute of Food Science, Technology and Nutrition, ICTAN (CSIC), Juan de la Cierva 3, 28006, Madrid, Spain
| | - Lorena Ruiz
- Dairy Research Institute of Asturias (IPLA-CSIC), Paseo Río Linares s/n, 3300, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, 33011, Oviedo, Asturias, Spain
| | - Abelardo Margolles
- Dairy Research Institute of Asturias (IPLA-CSIC), Paseo Río Linares s/n, 3300, Villaviciosa, Asturias, Spain
- Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, 33011, Oviedo, Asturias, Spain
| | - José M Mancheño
- Institute of Physical Chemistry 'Blas Cabrera' (IQF-CSIC), Serrano 119, 28006, Madrid, Spain
| | - F Javier Moreno
- Institute of Food Science Research, CIAL (CSIC-UAM), Nicolas Cabrera 9, 28049, Madrid, Spain.
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10
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Castells-Nobau A, Moreno-Navarrete JM, de la Vega-Correa L, Puig I, Federici M, Sun J, Burcelin R, Guzylack-Piriou L, Gourdy P, Cazals L, Arnoriaga-Rodríguez M, Frühbeck G, Seoane LM, López-Miranda J, Tinahones FJ, Dieguez C, Dumas ME, Pérez-Brocal V, Moya A, Perakakis N, Mingrone G, Bornstein S, Rodriguez Hermosa JI, Castro E, Fernández-Real JM, Mayneris-Perxachs J. Multiomics of the intestine-liver-adipose axis in multiple studies unveils a consistent link of the gut microbiota and the antiviral response with systemic glucose metabolism. Gut 2024:gutjnl-2024-332602. [PMID: 39358003 DOI: 10.1136/gutjnl-2024-332602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 09/06/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND The microbiota is emerging as a key factor in the predisposition to insulin resistance and obesity. OBJECTIVE To understand the interplay among gut microbiota and insulin sensitivity in multiple tissues. DESIGN Integrative multiomics and multitissue approach across six studies, combining euglycaemic clamp measurements (used in four of the six studies) with other measurements of glucose metabolism and insulin resistance (glycated haemoglobin (HbA1c) and fasting glucose). RESULTS Several genera and species from the Proteobacteria phylum were consistently negatively associated with insulin sensitivity in four studies (ADIPOINST, n=15; IRONMET, n=121, FLORINASH, n=67 and FLOROMIDIA, n=24). Transcriptomic analysis of the jejunum, ileum and colon revealed T cell-related signatures positively linked to insulin sensitivity. Proteobacteria in the ileum and colon were positively associated with HbA1c but negatively with the number of T cells. Jejunal deoxycholic acid was negatively associated with insulin sensitivity. Transcriptomics of subcutaneous adipose tissue (ADIPOMIT, n=740) and visceral adipose tissue (VAT) (ADIPOINST, n=29) revealed T cell-related signatures linked to HbA1c and insulin sensitivity, respectively. VAT Proteobacteria were negatively associated with insulin sensitivity. Multiomics and multitissue integration in the ADIPOINST and FLORINASH studies linked faecal Proteobacteria with jejunal and liver deoxycholic acid, as well as jejunal, VAT and liver transcriptomic signatures involved in the actin cytoskeleton, insulin and T cell signalling. Fasting glucose was consistently linked to interferon-induced genes and antiviral responses in the intestine and VAT. Studies in Drosophila melanogaster validated these human insulin sensitivity-associated changes. CONCLUSION These data provide comprehensive insights into the microbiome-gut-adipose-liver axis and its impact on systemic insulin action, suggesting potential therapeutic targets.Cite Now.
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Affiliation(s)
- Anna Castells-Nobau
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Parc Hospitalari Martí i Julià, Edifici M2, Salt, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - José Maria Moreno-Navarrete
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Lisset de la Vega-Correa
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Irene Puig
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
| | - Massimo Federici
- Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, Rome, Italy
| | - Jiuwen Sun
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Parc Hospitalari Martí i Julià, Edifici M2, Salt, Spain
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
- Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR), Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Team 2: 'Intestinal Risk Factors, Diabetes, Dyslipidemia, and Heart Failure', F-31432, Toulouse, France
| | - Remy Burcelin
- Institut National de la Santé et de la Recherche Médicale (INSERM), Toulouse, France
- Université Paul Sabatier (UPS), Unité Mixte de Recherche (UMR), Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Team 2: 'Intestinal Risk Factors, Diabetes, Dyslipidemia, and Heart Failure', F-31432, Toulouse, France
| | - Laurence Guzylack-Piriou
- Team "Immunité et ALTernatives aux Antibiotiques (IALTA)", Laboratory of host to pathogens Interactions (IHAP), UMR INRAE 1225 / ENVT, Toulouse, France
| | - Pierre Gourdy
- Department of Diabetology, metabolic Diseases and Nutrition, CHU de Toulouse, Toulouse, France
- Institute of Metabolic and Cardiovascular Diseases, UMR1297 I2MC, INSERM, Toulouse 3 University, Toulouse, France
| | - Laurent Cazals
- Department of Diabetology, metabolic Diseases and Nutrition, CHU de Toulouse, Toulouse, France
- Institute of Metabolic and Cardiovascular Diseases, UMR1297 I2MC, INSERM, Toulouse 3 University, Toulouse, France
| | - María Arnoriaga-Rodríguez
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Gema Frühbeck
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Endocrinology & Nutrition, Clínica Universidad de Navarra, IdiSNA, Pamplona, Spain
| | - Luisa Maria Seoane
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Fisiopatología Endocrina Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - José López-Miranda
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Internal Medicine, Hospital Universitario Reina Sofía, Maimonides Institute for Biomedical Research in Cordoba (IMIBIC), Universidad de Córdoba, Córdoba, Spain
| | - Francisco J Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Virgen de la Victoria Hospital, Department of Endocrinology, Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, Málaga, Spain
| | - Carlos Dieguez
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Physiology, CIMUS, University of Santiago de Compostela, Instituto de Investigación Sanitaria, Santiago de Compostela, Spain
| | - Marc-Emmanuel Dumas
- Section of Biomolecular Medicine, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Section of Genomic and Environmental Medicine, National Heart & Lung Institute, Imperial College London, London, UK
- European Genomic Institute for Diabetes, CNRS UMR 8199, INSERM UMR 1283, Institut Pasteur de Lille, Lille University Hospital; University of Lille, Lille, France
- McGill Genome Centre, Mc Gill University, Montréal, Quebec, Canada
| | - Vicente Pérez-Brocal
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Andrés Moya
- Department of Genomics and Health, Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia, Spanish National Research Council (CSIC-UVEG), Valencia, Spain
| | - Nikolaos Perakakis
- Department of Internal Medicine III, University Hospital Carl Gustav Carus, TU Dresden, Paul Langerhans Institute Dresden (PLID), Helmholtz Center Munich, Dresden, Germany
| | - Geltrude Mingrone
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefan Bornstein
- Department of Internal Medicine III, University Hospital Carl Gustav Carus, TU Dresden, Paul Langerhans Institute Dresden (PLID), Helmholtz Center Munich, Dresden, Germany
| | | | - Ernesto Castro
- General and Digestive Surgery Service, Dr. Josep Trueta University Hospital, Girona, Spain
| | - Jose Manuel Fernández-Real
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Nutrition, Eumetabolism and Health Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Girona, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
- Department of Medical Sciences, School of Medicine, University of Girona, Girona, Spain
| | - Jordi Mayneris-Perxachs
- Department of Diabetes, Endocrinology and Nutrition, Dr. Josep Trueta University Hospital, Girona, Spain
- Integrative Systems Medicine and Biology Group, Girona Biomedical Research Institute (IDIBGI-CERCA), Parc Hospitalari Martí i Julià, Edifici M2, Salt, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Instituto de Salud Carlos III, Madrid, Spain
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11
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Jansen VL, Davids M, van Mourik DJ, Levels JH, Coppens M, Middeldorp S, Nieuwdorp M, van Mens TE. Gut microbiome composition and intestinal immunity in antiphospholipid syndrome patients versus healthy controls. Lupus 2024; 33:1373-1378. [PMID: 39152759 PMCID: PMC11443740 DOI: 10.1177/09612033241274515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
Abstract
INTRODUCTION The gut microbiome is recognized as a factor that could potentially contribute to the persistent antibodies of antiphospholipid syndrome (APS). Gut microbial interventions can both induce and mitigate APS in mice. In human APS patients, anti-beta-2-glycoprotein I (β2GP-1) titers correlate with antibody titers against a gut commensal protein homologous to β2GP-1. AIM To investigate the effect of the intestinal microenvironment on human APS. Methods We cross-sectionally compared intestinal microbiota composition quantified by shotgun sequencing; fecal short chain fatty acids (SCFAs), bacterial metabolites known to affect autoimmune processes; and fecal calprotectin, an intestinal inflammatory marker, in APS patients and healthy controls. RESULTS Neither alpha nor beta diversity of the gut microbiota differed between APS patients (n = 15) and controls (n = 16) and no taxa were differentially abundant. Moreover, fecal SCFAs and fecal calprotectin, did not differ between the groups. CONCLUSION Gut microbiome effects on the APS phenotype are likely not driven by bacterial overabundance, SCFA production or intestinal inflammation.
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Affiliation(s)
- Valérie Lbi Jansen
- Department of (Experimental) Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Pulmonary Hypertension & Thrombosis, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
| | - Mark Davids
- Department of (Experimental) Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Dagmar Jm van Mourik
- Department of (Experimental) Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Pulmonary Hypertension & Thrombosis, Amsterdam, The Netherlands
- Department of Medicine - Thrombosis and Haemostasis, Leiden University Medical Center, Leiden, The Netherlands
| | - Johannes Hm Levels
- Department of (Experimental) Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Michiel Coppens
- Department of (Experimental) Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Pulmonary Hypertension & Thrombosis, Amsterdam, The Netherlands
| | - Saskia Middeldorp
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Max Nieuwdorp
- Department of (Experimental) Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
| | - Thijs E van Mens
- Department of (Experimental) Vascular Medicine, Amsterdam UMC Location University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Cardiovascular Sciences, Pulmonary Hypertension & Thrombosis, Amsterdam, The Netherlands
- Amsterdam Reproduction & Development Research Institute, Amsterdam, The Netherlands
- Department of Medicine - Thrombosis and Haemostasis, Leiden University Medical Center, Leiden, The Netherlands
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12
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de Carvalho FM, Laux M, Ciapina LP, Gerber AL, Guimarães APC, Kloh VP, Apolinário M, Paes JES, Jonck CR, de Vasconcelos ATR. Finding microbial composition and biological processes as predictive signature to access the ongoing status of mangrove preservation. Int Microbiol 2024; 27:1485-1500. [PMID: 38388811 PMCID: PMC11452435 DOI: 10.1007/s10123-024-00492-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 01/08/2024] [Accepted: 02/13/2024] [Indexed: 02/24/2024]
Abstract
Mangroves are complex land-sea transition ecosystems whose microbiota are essential for their nutrient recycling and conservation. Brazil is the third-largest estuarine area in the world and "Baía de Todos os Santos" (BTS) is one of the largest bays of the country, with wide anthropogenic exploration. Using a metagenomic approach, we investigated composition and functional adaptability as signatures of the microbiome of pristine and anthropized areas of BTS, including those under petroleum refinery influence. The taxonomic analysis showed dominance of sulfate-reducing Desulfobacteraceae, Rhodobacteraceae, and Flavobacteriaceae. Taxa were significantly diverse between pristine and disturbed areas. Disturbed mangroves showed a notary increase in abundance of halophilic, sulfur-related, and hydrocarbon-degrading genera and a decrease in diatoms compared to pristine area. The metabolic profile of BTS mangroves was correlated with the differentially abundant microbiota. Two ecological scenarios were observed: one marked by functions of central metabolism associated with biomass degradation and another by mechanisms of microbial adaptability to pollution conditions and environmental degradation. Part of the microbiome was distinct and not abundant in Brazilian estuarine soils. The microbiome signature observed in each BTS mangrove reflects how human actions impact the diversity of these ecosystems and also emphasize their role in attempting to restore disturbed mangroves. The microbiome may act as a potential biological indicator of the preservation status of these soils, despite the limitation of soil property conditions. Additionally, our data pointed to metagenomics as an additional tool for environmental assessment and reinforced the need for protective measures for the mangroves under study.
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Affiliation(s)
- Fabíola Marques de Carvalho
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Marcele Laux
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Luciane Prioli Ciapina
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Ana Paula C Guimarães
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Vinícius Prata Kloh
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil
| | - Moacir Apolinário
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Jorge Eduardo Santos Paes
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Célio Roberto Jonck
- Petróleo Brasileiro S. A., Centro de Pesquisa Leopoldo Américo Miguez de Mello, Rio de Janeiro, RJ, Brazil
| | - Ana Tereza R de Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Avenida Getúlio Vargas 333, Quitandinha Petrópolis, Rio de Janeiro, 25651-075, Brazil.
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13
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Posada LF, Arteaga-Figueroa LA, Adarve-Rengifo I, Cadavid M, Zapata S, Álvarez JC. Endophytic microbial diversity associated with commercial cultivar and crop wild relative banana variety could provide clues for microbial community management. Microbiol Res 2024; 287:127862. [PMID: 39121704 DOI: 10.1016/j.micres.2024.127862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/09/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
Endophytes, microorganisms inhabiting internal plant tissues, play a pivotal role in plant growth and disease resistance. Moreover, previous studies have established that Musa plants derive disease protective functions from their microbiome. Notably, one of the crop wild relatives of banana, the Calcutta 4 variety, exhibits resistance to various phytopathogens such as Pseudocercospora fijiensis (P. fijiensis), while the Williams commercial cultivar (cv.) is highly susceptible. Therefore, this study aims primarily to characterize and compare the endophytic microbiota composition of Calcutta 4 and Williams banana plants when grown sympatrically. Alongside, differences in endophytic microbiome between plant sections (shoot or roots), growth phases (in vitro or greenhouse) and fitness factors such as the addition of plant growth-promoting bacteria Bacillus subtilis EA-CB0575 (T2 treatment) or infection by P. fijiensis (T3 treatment) were examined. Both culture-dependent and -independent techniques were used to evaluate these differences and assess the culturability of banana endophytes under varying conditions. Microbial cultures resulted in 331 isolates distributed across 54 genera when all treatments were evaluated, whereas 16 S sequencing produced 9510 ASVs assigned in 1456 genera. Alpha and beta diversity exhibited significant differences based on plant section, with an increase in phylogenetic diversity observed in plants with pathogen infection (T3) compared to control plants (T1). Additionally, four differentially abundant genera associated with nitrogen metabolism were identified in T3 plants and seven genera showed differential abundance when comparing varieties. When culture-dependent and -independent methods were compared, it was found that isolates represented 3.7 % of the genera detected by culture-independent methods, accounting for 12-41 % of the total data depending on the treatment. These results are crucial for proposing management strategies derived from crop wild relatives to enhance the resilience of susceptible commercial varieties against fitness factors affecting crop development. Additionally, they help to decipher the pathogenic effects of P. fijiensis in banana plants and advance the understanding of how plant domestication influences the endosphere.
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Affiliation(s)
- Luisa F Posada
- Grupo de Investigación Zentech. Pontificia Universidad Javeriana. Facultad de Ingeniería. Departamento de Ingeniería Industrial, Carrera 7 # 40-62, Bogotá, Colombia
| | - Luis A Arteaga-Figueroa
- Grupo de Investigación CIBIOP. Universidad EAFIT. Biological Sciences Department, Carrera 49 # 7 sur-50, Medellín, Colombia
| | - Isabel Adarve-Rengifo
- Grupo de Investigación CIBIOP. Universidad EAFIT. Biological Sciences Department, Carrera 49 # 7 sur-50, Medellín, Colombia
| | - Maria Cadavid
- Grupo de Investigación CIBIOP. Universidad EAFIT. Biological Sciences Department, Carrera 49 # 7 sur-50, Medellín, Colombia
| | | | - Javier C Álvarez
- Grupo de Investigación CIBIOP. Universidad EAFIT. Biological Sciences Department, Carrera 49 # 7 sur-50, Medellín, Colombia.
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Viteri G, Aranda A, de Mera YD, Rodríguez A, Rodríguez D, Rodríguez-Fariñas N, Valiente N, Seseña S. Air quality in a small city: criteria pollutants, volatile organic compounds, metals, and microbes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:58119-58135. [PMID: 39312116 DOI: 10.1007/s11356-024-35096-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 09/17/2024] [Indexed: 10/11/2024]
Abstract
This work presents a year-long integral study of air quality parameters in Ciudad Real, a small city in the center of Spain, and its influence on the nearby national park, Las Tablas de Daimiel. The study covers meteorological parameters and criteria pollutants such as O3, NO, NO2, SO2, and PM10. Additionally, for each month, a 1-week campaign was performed sampling air in sorbent tubes with 8-h time resolution to analyze anthropogenic volatile organic compounds and the effects of seasons, daytime, and working-weekend days. During these campaigns, 24-h PM2.5 samples were also collected to measure the load of bacteria and fungi, as well as the trace concentrations of elements.The city and the national park NOx profiles showed that emissions from the town had a non-perceivable effect on the protected area. PM10 levels in Ciudad Real were influenced by Saharan intrusions, as was the national park; however, Ciudad Real had a higher contribution from anthropogenic sources. Ozone levels were lower in the city during the cold season due to the higher concentration of NOx and have not changed significantly in the last decade.The VOCs with higher average concentrations were toluene, m,p-xylene, benzene, methylene chloride, and o-xylene, with traffic being the main source of these pollutants in the city. For benzene and carbon tetrachloride levels, weak carcinogenic risks were estimated. In PM2.5, the most abundant metals were Na, Zn, Mg, Ca, Al, Fe, and K. The carcinogenic and non-carcinogenic risks estimated from the levels of the studied metals were negligible. Bacterial and fungal counts positively correlated with the concentration of PM2.5. Microbial community composition showed seasonal variability, with the dominance of human pathogenic bacteria which correlated with certain pollutants such as SO2. Bacillus and Cutibacterium were the most abundant genera.
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Affiliation(s)
- Gabriela Viteri
- Facultad de Ciencias y Tecnologías Químicas, Avenida Camilo José Cela S/N, 13071, Ciudad Real, Spain
| | - Alfonso Aranda
- Facultad de Ciencias y Tecnologías Químicas, Avenida Camilo José Cela S/N, 13071, Ciudad Real, Spain.
| | - Yolanda Díaz de Mera
- Facultad de Ciencias y Tecnologías Químicas, Avenida Camilo José Cela S/N, 13071, Ciudad Real, Spain
| | - Ana Rodríguez
- Facultad de Ciencias Ambientales y Bioquímica, Avenida Carlos III S/N, 45071, Toledo, Spain
| | - Diana Rodríguez
- Facultad de Ciencias Ambientales y Bioquímica, Avenida Carlos III S/N, 45071, Toledo, Spain
| | | | - Nicolas Valiente
- Departamento de Cienciay , Tecnología Agroforestal y Genética, Campus Universitario S/N, 02071, Albacete, Spain
| | - Susana Seseña
- Facultad de Ciencias Ambientales y Bioquímica, Avenida Carlos III S/N, 45071, Toledo, Spain
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15
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Brochu HN, Smith E, Jeong S, Carlson M, Hansen SG, Tisoncik-Go J, Law L, Picker LJ, Gale M, Peng X. Pre-challenge gut microbial signature predicts RhCMV/SIV vaccine efficacy in rhesus macaques. Microbiol Spectr 2024:e0128524. [PMID: 39345211 DOI: 10.1128/spectrum.01285-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/21/2024] [Indexed: 10/01/2024] Open
Abstract
Rhesus cytomegalovirus expressing simian immunodeficiency virus (RhCMV/SIV) vaccines protect ~59% of vaccinated rhesus macaques against repeated limiting-dose intra-rectal exposure with highly pathogenic SIVmac239M, but the exact mechanism responsible for the vaccine efficacy is unknown. It is becoming evident that complex interactions exist between gut microbiota and the host immune system. Here, we aimed to investigate if the rhesus gut microbiome impacts RhCMV/SIV vaccine-induced protection. Three groups of 15 rhesus macaques naturally pre-exposed to RhCMV were vaccinated with RhCMV/SIV vaccines. Rectal swabs were collected longitudinally both before SIV challenge (after vaccination) and post-challenge and were profiled using 16S rRNA based microbiome analysis. We identified ~2,400 16S rRNA amplicon sequence variants (ASVs), representing potential bacterial species/strains. Global gut microbial profiles were strongly associated with each of the three vaccination groups, and all animals tended to maintain consistent profiles throughout the pre-challenge phase. Despite vaccination group differences, by using newly developed compositional data analysis techniques, we identified a common gut microbial signature predictive of vaccine protection outcome across the three vaccination groups. Part of this microbial signature persisted even after SIV challenge. We also observed a strong correlation between this microbial signature and an early signature derived from whole blood transcriptomes in the same animals. Our findings indicate that changes in gut microbiomes are associated with RhCMV/SIV vaccine-induced protection and early host response to vaccination in rhesus macaques.IMPORTANCEThe human immunodeficiency virus (HIV) has infected millions of people worldwide. Unfortunately, still there is no vaccine that can prevent or treat HIV infection. A promising pre-clinical HIV vaccine based on rhesus cytomegalovirus (RhCMV) expressing simian immunodeficiency virus (SIV) antigens (RhCMV/SIV) provides sustained, durable protection against SIV challenge in ~59% of vaccinated rhesus macaques. There is an urgent need to understand the cause of this protection vs non-protection outcome. In this study, we profiled the gut microbiomes of 45 RhCMV/SIV vaccinated rhesus macaques and identified gut microbial signatures that were predictive of RhCMV/SIV vaccination groups and vaccine protection outcomes. These vaccine protection-associated microbial features were significantly correlated with early vaccine-induced host immune signatures in whole blood from the same animals. These findings show that the gut microbiome may be involved in RhCMV/SIV vaccine-induced protection, warranting further research into the impact of the gut microbiome in human vaccine trials.
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Affiliation(s)
- Hayden N Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, North Carolina, USA
| | - Elise Smith
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Sangmi Jeong
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, North Carolina, USA
| | - Michelle Carlson
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Jennifer Tisoncik-Go
- Department of Immunology, University of Washington, Seattle, Washington, USA
- Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, Washington, USA
- Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, Oregon, USA
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, Washington, USA
- Center for Innate Immunity and Immune Disease, University of Washington, Seattle, Washington, USA
- Washington National Primate Research Center, University of Washington, Seattle, Washington, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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16
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Yergaliyev T, Künzel S, Hanauska A, Rees A, Wild KJ, Pétursdóttir ÁH, Gunnlaugsdóttir H, Reynolds CK, Humphries DJ, Rodehutscord M, Camarinha-Silva A. The effect of Asparagopsis taxiformis, Ascophyllum nodosum, and Fucus vesiculosus on ruminal methanogenesis and metagenomic functional profiles in vitro. Microbiol Spectr 2024:e0394223. [PMID: 39347544 DOI: 10.1128/spectrum.03942-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 07/08/2024] [Indexed: 10/01/2024] Open
Abstract
The ruminant-microorganism symbiosis is unique by providing high-quality food from fibrous materials but also contributes to the production of one of the most potent greenhouse gases-methane. Mitigating methanogenesis in ruminants has been a focus of interest in the past decades. One of the promising strategies to combat methane production is the use of feed supplements, such as seaweeds, that might mitigate methanogenesis via microbiome modulation and direct chemical inhibition. We conducted in vitro investigations of the effect of three seaweeds (Ascophyllum nodosum, Asparagopsis taxiformis, and Fucus vesiculosus) harvested at different locations (Iceland, Scotland, and Portugal) on methane production. We applied metataxonomics (16S rRNA gene amplicons) and metagenomics (shotgun) methods to uncover the interplay between the microbiome's taxonomical and functional states, methanogenesis rates, and seaweed supplementations. Methane concentration was reduced by A. nodosum and F. vesiculosus, both harvested in Scotland and A. taxiformis, with the greatest effect of the latter. A. taxiformis acted through the reduction of archaea-to-bacteria ratios but not eukaryotes-to-bacteria. Moreover, A. taxiformis application was accompanied by shifts in both taxonomic and functional profiles of the microbial communities, decreasing not only archaeal ratios but also abundances of methanogenesis-associated functions. Methanobrevibacter "SGMT" (M. smithii, M. gottschalkii, M. millerae or M. thaueri; high methane yield) to "RO" (M. ruminantium and M. olleyae; low methane yield) clades ratios were also decreased, indicating that A. taxiformis application favored Methanobrevibacter species that produce less methane. Most of the functions directly involved in methanogenesis were less abundant, while the abundances of the small subset of functions that participate in methane assimilation were increased. IMPORTANCE The application of A. taxiformis significantly reduced methane production in vitro. We showed that this reduction was linked to changes in microbial function profiles, the decline in the overall archaeal community counts, and shifts in ratios of Methanobrevibacter "SGMT" and "RO" clades. A. nodosum and F. vesiculosus, obtained from Scotland, also decreased methane concentration in the total gas, while the same seaweed species from Iceland did not.
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Affiliation(s)
- Timur Yergaliyev
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Susanne Künzel
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Anna Hanauska
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Antonia Rees
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Katharina J Wild
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | | | | | - Christopher K Reynolds
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - David J Humphries
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
| | - Markus Rodehutscord
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
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17
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Gonzales G, Malka R, Marinelli LM, Lee CM, Cook S, Miar S, Dion GR, Guda T. Localized delivery of therapeutics impact laryngeal mechanics, local inflammatory response, and respiratory microbiome following upper airway intubation injury in swine. Respir Res 2024; 25:351. [PMID: 39342180 PMCID: PMC11439253 DOI: 10.1186/s12931-024-02973-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 09/09/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Laryngeal injury associated with traumatic or prolonged intubation may lead to voice, swallow, and airway complications. The interplay between inflammation and microbial population shifts induced by intubation may relate to clinical outcomes. The objective of this study was to investigate laryngeal mechanics, tissue inflammatory response, and local microbiome changes with laryngotracheal injury and localized delivery of therapeutics via drug-eluting endotracheal tube. METHODS A simulated traumatic intubation injury was created in Yorkshire crossbreed swine under direct laryngoscopy. Endotracheal tubes electrospun with roxadustat or valacyclovir- loaded polycaprolactone (PCL) fibers were placed in the injured airway for 3, 7, or 14 days (n = 3 per group/time and ETT type). Vocal fold stiffness was then evaluated with normal indentation and laryngeal tissue sections were histologically examined. Immunohistochemistry and inflammatory marker profiling were conducted to evaluate the inflammatory response associated with injury and ETT placement. Additionally, ETT biofilm formation was visualized using scanning electron microscopy and micro-computed tomography, while changes in the airway microbiome were profiled through 16S rRNA sequencing. RESULTS Laryngeal tissue with roxadustat ETT placement had increasing localized stiffness outcomes over time and histological assessment indicated minimal epithelial ulceration and fibrosis, while inflammation remained severe across all timepoints. In contrast, vocal fold tissue with valacyclovir ETT placement showed no significant changes in stiffness over time; histological analysis presented a reduction in epithelial ulceration and inflammation scores along with increased fibrosis observed at 14 days. Immunohistochemistry revealed a decline in M1 and M2 macrophage markers over time for both ETT types. Among the cytokines, IL-8 levels differed significantly between the roxadustat and valacyclovir ETT groups, while no other cytokines showed statistically significant differences. Additionally, increased biofilm formation was observed in the coated ETTs with notable alterations in microbiota distinctive to each ETT type and across time. CONCLUSION The injured and intubated airway resulted in increased laryngeal stiffness. Local inflammation and the type of therapeutic administered impacted the bacterial composition within the upper respiratory microbiome, which in turn mediated local tissue healing and recovery.
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Affiliation(s)
- Gabriela Gonzales
- Department of Biomedical Engineering and Chemical Engineering, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX, 78249, USA
| | - Ronit Malka
- Department of Otolaryngology-Head and Neck Surgery, Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA
| | - Lisa M Marinelli
- Department of Pathology and Area Laboratory Services, Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA
| | - Christine M Lee
- Department of Pathology and Area Laboratory Services, Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA
| | - Stacy Cook
- Department of Otolaryngology-Head and Neck Surgery, Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, TX, USA
| | - Solaleh Miar
- Department of Civil, Environmental, and Biomedical Engineering, University of Hartford, West Hartford, CT, USA
| | - Gregory R Dion
- Department of Otolaryngology-Head and Neck Surgery,, University of Cincinnati, Cincinnati, OH, USA
| | - Teja Guda
- Department of Biomedical Engineering and Chemical Engineering, The University of Texas at San Antonio, 1 UTSA Circle, San Antonio, TX, 78249, USA.
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18
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Nweze JE, Gupta S, Salcher MM, Šustr V, Horváthová T, Angel R. Disruption of millipede-gut microbiota in E. pulchripes and G. connexa highlights the limited role of litter fermentation and the importance of litter-associated microbes for nutrition. Commun Biol 2024; 7:1204. [PMID: 39342029 PMCID: PMC11438867 DOI: 10.1038/s42003-024-06821-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 09/02/2024] [Indexed: 10/01/2024] Open
Abstract
Millipedes are thought to depend on their gut microbiome for processing plant-litter-cellulose through fermentation, similar to many other arthropods. However, this hypothesis lacks sufficient evidence. To investigate this, we used inhibitors to disrupt the gut microbiota of juvenile Epibolus pulchripes (tropical, CH4-emitting) and Glomeris connexa (temperate, non-CH4-emitting) and isotopic labelling. Feeding the millipedes sterile or antibiotics-treated litter reduced faecal production and microbial load without major impacts on survival or weight. Bacterial diversity remained similar, with Bacteroidota dominant in E. pulchripes and Pseudomonadota in G. connexa. Sodium-2-bromoethanesulfonate treatment halted CH4 emissions in E. pulchripes, but it resumed after returning to normal feeding. Employing 13C-labeled leaf litter and RNA-SIP revealed a slow and gradual prokaryote labelling, indicating a significant density shift only by day 21. Surprisingly, labelling of the fungal biomass was somewhat quicker. Our findings suggest that fermentation by the gut microbiota is likely not essential for the millipede's nutrition.
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Affiliation(s)
- Julius Eyiuche Nweze
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Shruti Gupta
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Michaela M Salcher
- Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
| | - Vladimír Šustr
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia
| | - Terézia Horváthová
- Institute of Hydrobiology, Biology Centre CAS, České Budějovice, Czechia
- Department of Aquatic Ecology, EAWAG, Dübendorf, Switzerland
| | - Roey Angel
- Institute of Soil Biology and Biogeochemistry, Biology Centre CAS, České Budějovice, Czechia.
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia.
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19
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Schmartz GP, Rehner J, Gund MP, Keller V, Molano LAG, Rupf S, Hannig M, Berger T, Flockerzi E, Seitz B, Fleser S, Schmitt-Grohé S, Kalefack S, Zemlin M, Kunz M, Götzinger F, Gevaerd C, Vogt T, Reichrath J, Diehl L, Hecksteden A, Meyer T, Herr C, Gurevich A, Krug D, Hegemann J, Bozhueyuek K, Gulder TAM, Fu C, Beemelmanns C, Schattenberg JM, Kalinina OV, Becker A, Unger M, Ludwig N, Seibert M, Stein ML, Hanna NL, Martin MC, Mahfoud F, Krawczyk M, Becker SL, Müller R, Bals R, Keller A. Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics. Nat Commun 2024; 15:8261. [PMID: 39327438 PMCID: PMC11427559 DOI: 10.1038/s41467-024-52598-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.
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Affiliation(s)
- Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
| | - Madline P Gund
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
| | - Verena Keller
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | | | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
- Synoptic Dentistry, Saarland University, 66421, Homburg, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, 66421, Homburg, Germany
| | - Tim Berger
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Elias Flockerzi
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Sara Fleser
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Sabina Schmitt-Grohé
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Sandra Kalefack
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Michael Zemlin
- Department of General Pediatrics and Neonatology, Saarland University, 66421, Homburg, Germany
| | - Michael Kunz
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Felix Götzinger
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Caroline Gevaerd
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Thomas Vogt
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Jörg Reichrath
- Clinic for Dermatology, Venereology, and Allergology, 66421, Homburg, Germany
| | - Lisa Diehl
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Anne Hecksteden
- Institute for Sport and Preventive Medicine, Saarland University, 66123, Saarbrücken, Germany
- Chair of Sports Medicine, Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Tim Meyer
- Institute for Sport and Preventive Medicine, Saarland University, 66123, Saarbrücken, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Center for Bioinformatics Saar and Saarland University, Saarland Informatics Campus, 66123, Saarbrücken, Germany
| | - Daniel Krug
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Julian Hegemann
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Kenan Bozhueyuek
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Tobias A M Gulder
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, 66123, Saarbrücken, Germany
| | - Chengzhang Fu
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Christine Beemelmanns
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Jörn M Schattenberg
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | - Olga V Kalinina
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
| | - Anouck Becker
- Department for Neurology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Marcus Unger
- Department for Neurology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Nicole Ludwig
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Martina Seibert
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Marie-Louise Stein
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Nikolas Loka Hanna
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
| | - Marie-Christin Martin
- Department of Ophthalmology, Saarland University Medical Center, 66421, Homburg, Germany
| | - Felix Mahfoud
- Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine, Saarland University Hospital, 66421, Homburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, 66421, Homburg, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, 66421, Homburg, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany
- PharmaScienceHub, 66123, Saarbrücken, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, Saarbrücken, Germany
- PharmaScienceHub, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, 66123, Saarbrücken, Germany.
- PharmaScienceHub, 66123, Saarbrücken, Germany.
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20
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Schmartz GP, Rehner J, Schuff MJ, Molano LAG, Becker SL, Krawczyk M, Tagirdzhanov A, Gurevich A, Francke R, Müller R, Keller V, Keller A. Exploring microbial diversity and biosynthetic potential in zoo and wildlife animal microbiomes. Nat Commun 2024; 15:8263. [PMID: 39327429 PMCID: PMC11427580 DOI: 10.1038/s41467-024-52669-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 09/13/2024] [Indexed: 09/28/2024] Open
Abstract
Understanding human, animal, and environmental microbiota is essential for advancing global health and combating antimicrobial resistance (AMR). We investigate the oral and gut microbiota of 48 animal species in captivity, comparing them to those of wildlife animals. Specifically, we characterize the microbiota composition, metabolic pathways, AMR genes, and biosynthetic gene clusters (BGCs) encoding the production of specialized metabolites. Our results reveal a high diversity of microbiota, with 585 novel species-level genome bins (SGBs) and 484 complete BGCs identified. Functional gene analysis of microbiomes shows diet-dependent variations. Furthermore, by comparing our findings to wildlife-derived microbiomes, we observe the impact of captivity on the animal microbiome, including examples of converging microbiome compositions. Importantly, our study identifies AMR genes against commonly used veterinary antibiotics, as well as resistance to vancomycin, a critical antibiotic in human medicine. These findings underscore the importance of the 'One Health' approach and the potential for zoonotic transmission of pathogenic bacteria and AMR. Overall, our study contributes to a better understanding of the complexity of the animal microbiome and highlights its BGC diversity relevant to the discovery of novel antimicrobial compounds.
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Affiliation(s)
- Georges P Schmartz
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | - Miriam J Schuff
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | | | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, 66421 Saarland University, Homburg, Germany
| | - Marcin Krawczyk
- Department of Medicine II, 66421 Saarland University, Homburg, Germany
| | - Azat Tagirdzhanov
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
| | - Alexey Gurevich
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
- Department of Computer Science, Saarland University, 66123, Saarbrücken, Germany
| | | | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany
| | - Verena Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Helmholtz Institute for Pharmaceutical Research Saarland, Helmholtz Center for Infection Research, 66123, Saarbrücken, Germany.
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21
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Vettorazzo S, Boscaini A, Cerasino L, Salmaso N. From small water bodies to lakes: Exploring the diversity of freshwater bacteria in an Alpine Biosphere Reserve. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 954:176495. [PMID: 39341249 DOI: 10.1016/j.scitotenv.2024.176495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 09/19/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024]
Abstract
Small water bodies, although supporting high biodiversity, are often understudied in the Alpine region. In this work, we characterized the planktic and benthic bacterial communities, as well as the water chemistry, of a wide physiographic range of 19 freshwater bodies within an Alpine Biosphere Reserve, including ponds, pasture ponds, peat bogs, shallow lakes, and lakes. We collected both water and surface sediment samples, followed by metabarcoding analysis based on the V3-V4 regions of the 16S rRNA gene. We investigated the changes in biodiversity and the distribution of unique and shared amplicon sequence variants (ASVs) between water (11,829 ASVs) and surface sediment (19,145 ASVs) habitats, as well as across different freshwater typologies. The majority of ASVs (78 %) were unique to a single sample, highlighting the variability and uniqueness of bacterial communities in such freshwater bodies. Most freshwater environments showed higher α-diversity in sediment samples (median, 1469 ASVs) compared to water (468 ASVs). We found that water and sediment habitats harboured unique bacterial communities with significant differences in their taxonomic compositions. Benthic bacteria were associated with several biogeochemical and degradative processes occurring in the sediments, with no notable differences among freshwater typologies and with phylogenetically and ecologically similar species. Conversely, planktic communities showed greater heterogeneity: small water bodies and peat bogs were characterized by higher relative abundances of Patescibacteria (up to 33 %), while lakes and shallow lakes were dominated by Actinobacteriota (up to 36 %). Cyanobacteria (426 ASVs) were generally distributed at low abundances in both water and sediment habitats. Overall, our results provided essential insights into the bacterial ecology of understudied environments such as ponds and pasture ponds and highlighted the importance of further exploring their rich pelagic and benthic bacterial biodiversity.
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Affiliation(s)
- Sara Vettorazzo
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy.
| | - Adriano Boscaini
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Leonardo Cerasino
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy
| | - Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098 San Michele all'Adige, Italy; NBFC, National Biodiversity Future Center, Palermo 90133, Italy
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22
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Kwak S, Wang C, Usyk M, Wu F, Freedman ND, Huang WY, McCullough ML, Um CY, Shrubsole MJ, Cai Q, Li H, Ahn J, Hayes RB. Oral Microbiome and Subsequent Risk of Head and Neck Squamous Cell Cancer. JAMA Oncol 2024:2824198. [PMID: 39325441 PMCID: PMC11428028 DOI: 10.1001/jamaoncol.2024.4006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Importance The oral microbiota may be involved in development of head and neck squamous cell cancer (HNSCC), yet current evidence is largely limited to bacterial 16S amplicon sequencing or small retrospective case-control studies. Objective To test whether oral bacterial and fungal microbiomes are associated with subsequent risk of HNSCC development. Design, Setting, and Participants Prospective nested case-control study among participants providing oral samples in 3 epidemiological cohorts, the American Cancer Society Cancer Prevention Study II Nutrition Cohort, the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial, and the Southern Community Cohort Study. Two hundred thirty-six patients who prospectively developed HNSCC were identified during a mean (SD) of 5.1 (3.6) years of follow-up. Control participants who remained HNSCC free were selected by 2:1 frequency matching on cohort, age, sex, race and ethnicity, and time since oral sample collection. Data analysis was conducted in 2023. Exposures Characterization of the oral bacterial microbiome using whole-genome shotgun sequencing and the oral fungal microbiome using internal transcribed spacer sequencing. Association of bacterial and fungal taxa with HNSCC was assessed by analysis of compositions of microbiomes with bias correction. Association with red and orange oral pathogen complexes was tested by logistic regression. A microbial risk score for HNSCC risk was calculated from risk-associated microbiota. Main Outcomes and Measures The primary outcome was HNSCC incidence. Results The study included 236 HNSCC case participants with a mean (SD) age of 60.9 (9.5) years and 24.6% women during a mean of 5.1 (3.6) years of follow-up, and 485 matched control participants. Overall microbiome diversity at baseline was not related to subsequent HNSCC risk; however 13 oral bacterial species were found to be differentially associated with development of HNSCC. The species included the newly identified Prevotella salivae, Streptococcus sanguinis, and Leptotrichia species, as well as several species belonging to beta and gamma Proteobacteria. The red/orange periodontal pathogen complex was moderately associated with HNSCC risk (odds ratio, 1.06 per 1 SD; 95% CI, 1.00-1.12). A 1-SD increase in microbial risk score (created based on 22 bacteria) was associated with a 50% increase in HNSCC risk (multivariate odds ratio, 1.50; 95% CI, 1.21-1.85). No fungal taxa associated with HNSCC risk were identified. Conclusions and Relevance This case-control study yielded compelling evidence that oral bacteria are a risk factor for HNSCC development. The identified bacteria and bacterial complexes hold promise, along with other risk factors, to identify high-risk individuals for personalized prevention of HNSCC.
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Affiliation(s)
- Soyoung Kwak
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- NYU Laura and Isaac Perlmutter Cancer Center, New York, New York
| | - Chan Wang
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- NYU Laura and Isaac Perlmutter Cancer Center, New York, New York
| | - Mykhaylo Usyk
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- NYU Laura and Isaac Perlmutter Cancer Center, New York, New York
| | - Feng Wu
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- NYU Laura and Isaac Perlmutter Cancer Center, New York, New York
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | | | - Caroline Y Um
- Department of Population Science, American Cancer Society, Atlanta, Georgia
| | - Martha J Shrubsole
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Qiuyin Cai
- Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
- Department of Medicine, Division of Epidemiology, Vanderbilt Epidemiology Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Huilin Li
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- NYU Laura and Isaac Perlmutter Cancer Center, New York, New York
| | - Jiyoung Ahn
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- NYU Laura and Isaac Perlmutter Cancer Center, New York, New York
| | - Richard B Hayes
- Department of Population Health, NYU Grossman School of Medicine, New York, New York
- NYU Laura and Isaac Perlmutter Cancer Center, New York, New York
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23
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Wirbel J, Essex M, Forslund SK, Zeller G. A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies. Genome Biol 2024; 25:247. [PMID: 39322959 PMCID: PMC11423519 DOI: 10.1186/s13059-024-03390-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 09/06/2024] [Indexed: 09/27/2024] Open
Abstract
BACKGROUND In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations. RESULTS Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications. CONCLUSIONS Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.
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Affiliation(s)
- Jakob Wirbel
- Structural and Computational Biology Unit (SCB), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Morgan Essex
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max-Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin (a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany
| | - Sofia Kirke Forslund
- Structural and Computational Biology Unit (SCB), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max-Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany.
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.
- Charité-Universitätsmedizin Berlin (a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany.
| | - Georg Zeller
- Structural and Computational Biology Unit (SCB), European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Center for Infectious Diseases (LUCID), Leiden University, Leiden University Medical Center (LUMC), Leiden, Netherlands.
- Center for Microbiome Analyses and Therapeutics (CMAT), Leiden University Medical Center, Leiden, Netherlands.
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24
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Burcham ZM, Tweedie JL, Farfán-García AE, Nolan VG, Donohoe D, Gómez-Duarte OG, Johnson JG. Campylobacter infection of young children in Colombia and its impact on the gastrointestinal environment. mSphere 2024:e0034224. [PMID: 39320095 DOI: 10.1128/msphere.00342-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 08/26/2024] [Indexed: 09/26/2024] Open
Abstract
Campylobacter infections are a leading cause of bacterial-derived gastroenteritis worldwide with particularly profound impacts on pediatric patients in low- and middle-income countries. It remains unclear how Campylobacter impacts these hosts, though it is becoming increasingly evident that it is a multifactorial process that depends on the host immune response, the gastrointestinal microbiota, various bacterial factors, and host nutritional status. Since these factors likely vary between adult and pediatric patients in different regions of the world, it is important that studies define these attributes in well-characterized clinical cohorts in diverse settings. In this study, we analyzed the fecal microbiota and the metabolomic and micronutrient profiles of asymptomatic and symptomatic pediatric patients in Colombia who were either infected or uninfected with Campylobacter during a case-controlled study on acute diarrheal disease. Here, we report that the microbiome of Campylobacter-infected children only changed in their abundance of Campylobacter spp. despite the inclusion of children with or without diarrhea. In addition to increased Campylobacter, computational models were used to identify fecal metabolites that were associated with Campylobacter infection and found that glucose-6-phosphate and homovanillic acid were the strongest predictors of infection in these pediatric patients, which suggests that colonocyte metabolism is impacted during infection. Despite changes to the fecal metabolome, the concentrations of intestinal minerals and trace elements were not significantly impacted by Campylobacter infection but were elevated in uninfected children with diarrhea.IMPORTANCEGastrointestinal infection with pathogenic Campylobacter species has long been recognized as a significant cause of human morbidity. Recently, it has been observed that pediatric populations in low- and middle-income countries are uniquely impacted by these organisms in that infected children can be persistently colonized, develop enteric dysfunction, and exhibit reduced development and growth. While the association of Campylobacter species with these long-term effects continues to emerge, the impact of infection on the gastrointestinal environment of these children remains uncharacterized. To address this knowledge gap, our group leveraged clinical samples collected during a previous study on gastrointestinal infections in pediatric patients to examine the fecal microbiota, metabolome, and micronutrient profiles of those infected with Campylobacter species and found that the metabolome was impacted in a way that suggests gastrointestinal cell metabolism is affected during infection, which is some of the first data indicating how gastrointestinal health in these patients may be affected.
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Affiliation(s)
- Zachary M Burcham
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jessie L Tweedie
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - A E Farfán-García
- Grupo de Investigación en Manejo Clínico-CliniUDES, Facultad de Ciencias de la Salud, Universidad de Santander, Bucaramanga, Colombia
| | - Vikki G Nolan
- School of Public Health, The University of Memphis, Memphis, Tennessee, USA
| | - Dallas Donohoe
- Department of Nutrition, University of Tennessee, Knoxville, Tennessee, USA
| | - Oscar G Gómez-Duarte
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Jeremiah G Johnson
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
- Department of Microbiology and Immunology, University of Iowa Carver College of Medicine, Iowa, lowa, USA
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25
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Chelliah DS, Ray AE, Zhang E, Terauds A, Ferrari BC. The Vestfold Hills are alive: characterising microbial and environmental dynamics in Old Wallow, eastern Antarctica. Front Microbiol 2024; 15:1443491. [PMID: 39376700 PMCID: PMC11457671 DOI: 10.3389/fmicb.2024.1443491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/09/2024] [Indexed: 10/09/2024] Open
Abstract
Old Wallow is an underexplored, hyper-arid coastal desert in Antarctica's Vestfold Hills. Situated near an elephant seal wallow, we examined how stochastic nutrient inputs from the seal wallow affect soil communities amid environmental changes along a spatially explicit sampling transect. We hypothesized that nutrient levels would be elevated due to proximity to the seal wallow, influencing community distributions. While the soil bacterial and eukaryotic communities at the phylum level were similar to other terrestrial environments, analysis at class and family levels revealed a dominance of unclassified taxa that are often linked to marine environments. Elevated nutrient concentrations (NO3 -, SO4 2-, SO3) were found at Old Wallow, with conductivity and Cl- levels up to 10-fold higher at the lowest elevation soils, correlating with significantly (p < 0.05) higher abundances of halophilic (Halomonadaceace) and uncultivated lineages (Ca Actinomarinales, unclassified Bacillariophyta and unclassified Opisthonkonta). An improved Gradient Forest model was used to quantify microbial responses to 26 soil gradients at OW, revealing variable responses to environmental predictors and identifying critical environmental thresholds or drivers of community turnover. Major tipping points were projected for eukaryotes with SO4 2-, pH, and SO3, and for bacteria with moisture, Na2O, and Cl-. Thus, the Old Wallow ecosystem is primarily shaped by salt, sulphate, and moisture and is dominated by uncultivated taxa, which may be sensitive to environmental changes once critical tipping points are reached. This study provides critical baseline data for future regional monitoring under threats of environmental change.
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Affiliation(s)
- Devan S. Chelliah
- School of Biotechnology and Biomolecular Sciences, The University of NSW, Kensington, NSW, Australia
| | - Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, The University of NSW, Kensington, NSW, Australia
| | - Eden Zhang
- School of Biotechnology and Biomolecular Sciences, The University of NSW, Kensington, NSW, Australia
- Sydney Informatics Hub, Core Research Facility, University of Sydney, Sydney, NSW, Australia
| | - Aleks Terauds
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, TAS, Australia
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, The University of NSW, Kensington, NSW, Australia
- Evolution and Ecology Research Centre, The University of NSW, Kensington, NSW, Australia
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26
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Lutsiv T, Neil ES, McGinley JN, Didinger C, Fitzgerald VK, Weir TL, Hussan H, Hartman TJ, Thompson HJ. Impact of a Pulse-Enriched Human Cuisine on Functional Attributes of the Gut Microbiome Using a Preclinical Model of Dietary-Induced Chronic Diseases. Nutrients 2024; 16:3178. [PMID: 39339778 PMCID: PMC11434987 DOI: 10.3390/nu16183178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Revised: 09/12/2024] [Accepted: 09/16/2024] [Indexed: 09/30/2024] Open
Abstract
Introducing grain legumes, i.e., pulses, into any food pattern effectively increases dietary fiber and other bioactive food components of public health concern; however, the impact depends on the amount consumed. Given the convergence of preclinical and clinical data indicating that intake of at least 300 g (1.5 cup) of cooked pulse per day has clinically observable benefit, the feasibility for a typical consumer was demonstrated by creation of a fourteen-day menu plan that met this criterion. This menu plan, named Bean Cuisine, was comprised of a combination of five cooked pulses: dry beans, chickpeas, cowpeas, dry peas, and lentils. As reported herein, the impact of each menu day of the fourteen-day plan on gut microbial composition and predicted function was evaluated in female C57BL/6J mice, a strain commonly used in studies of metabolic dysfunction-associated chronic diseases. We report that pulse-related effects were observed across a wide variety of food item combinations. In comparison to a pulse-free human cuisine, all pulse menu days enriched for a gut ecosystem were associated with changes in predicted metabolic pathways involving amino acids (lysine, tryptophan, cysteine), short-chain fatty acids (butyrate, acetate), and vitamins (B1, B6, B9, B12, K2) albeit via different combinations of microbiota, according to the PICRUSt2 estimates. The predicted metabolic functions correlating with the various pulses in the menus, indicate the value of a food pattern comprised of all pulse types consumed on a regular basis. This type of multi-pulse food pattern has the potential to enhance the taxonomic and functional diversity of the gut microbiome as a means of strengthening the resilience of the gut ecosystem to the challenges associated with the daily activities of living.
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Affiliation(s)
- Tymofiy Lutsiv
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Elizabeth S Neil
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - John N McGinley
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Chelsea Didinger
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO 80523, USA
| | - Vanessa K Fitzgerald
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA
| | - Tiffany L Weir
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
- Department of Food Science and Human Nutrition, Colorado State University, Fort Collins, CO 80523, USA
| | - Hisham Hussan
- Department of Internal Medicine, University of California, Davis, Sacramento, CA 95817, USA
| | - Terryl J Hartman
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Henry J Thompson
- Cancer Prevention Laboratory, Colorado State University, Fort Collins, CO 80523, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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27
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Tolotti M, Brighenti S, Bruno MC, Cerasino L, Pindo M, Tirler W, Albanese D. Ecological "Windows of opportunity" influence biofilm prokaryotic diversity differently in glacial and non-glacial Alpine streams. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 944:173826. [PMID: 38866149 DOI: 10.1016/j.scitotenv.2024.173826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/04/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024]
Abstract
In glacier-fed streams, the Windows of Opportunity (WOs) are periods of mild environmental conditions supporting the seasonal development of benthic microorganisms. WOs have been defined based on changes in biofilm biomass, but the responses of microbial diversity to WOs in Alpine streams have been overlooked. A two year (2017-2018) metabarcoding of epilithic and epipsammic biofilm prokaryotes was conducted in Alpine streams fed by glaciers (kryal), rock glaciers (rock glacial), or groundwater/precipitation (krenal) in two catchments of the Central-Eastern European Alps (Italy), aiming at testing the hypothesis that: 1) environmental WOs enhance not only the biomass but also the α-diversity of the prokaryotic biofilm in all stream types, 2) diversity and phenology of prokaryotic biofilm are mainly influenced by the physical habitat in glacial streams, and by water chemistry in the other two stream types. The study confirmed kryal and krenal streams as endmembers of epilithic and sediment prokaryotic α- and β-diversity, with rock glacial streams sharing a large proportion of taxa with the two other stream types. Alpha-diversity appeared to respond to ecological WOs, but, contrary to expectations, seasonality was less pronounced in the turbid kryal than in the clear streams. This was attributed to the small size of the glaciers feeding the studied kryal streams, whose discharge dynamics were those typical of the late phase of deglaciation. Prokaryotic α-diversity of non-glacial streams tended to be higher in early summer than in early autumn. Our findings, while confirming that high altitude streams are heavily threatened by climate change, underscore the still neglected role of rock glacier runoffs as climate refugia for the most stenothermic benthic aquatic microorganism. This advocates the need to define and test strategies for protecting these ecosystems for preserving, restoring, and connecting cold Alpine aquatic biodiversity in the context of the progressing global warming.
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Affiliation(s)
- Monica Tolotti
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy; National Biodiversity Future Center (NBFC), Università di Palermo, Palermo, Italy.
| | - Stefano Brighenti
- Competence Centre for Mountain Innovation Ecosystems, Free University of Bolzano, Bolzano/Bozen, Italy
| | - Maria Cristina Bruno
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy; National Biodiversity Future Center (NBFC), Università di Palermo, Palermo, Italy
| | - Leonardo Cerasino
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | - Massimo Pindo
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
| | | | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige, Italy
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28
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Ramakodi MP, Palanivishwanath S. Analysis of 16S rRNA amplicon data illuminates the major role of environment in determining the marine plastisphere microbial communities. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:939. [PMID: 39287716 DOI: 10.1007/s10661-024-13109-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 09/06/2024] [Indexed: 09/19/2024]
Abstract
Microplastics (MPs) are a potential threat to the marine environment and its associated ecosystem functions. Earlier investigations revealed that the microbiome plays a crucial role in deciding the fate of MPs in the environment. Further studies also highlighted the influences of environment and polymer types on the plastisphere microbiome. Nevertheless, the major factor that determines the plastisphere microbiome remains elusive. Thus, we examined the publicly available marine plastisphere data generated from polyethylene (PE), polypropylene (PP), and polystyrene (PS), collected from three different locations to identify the importance of environment and/or polymer types in shaping the microbiome. The beta diversity analyses showed a clear distinction between samples collected from different locations. The PERMANOVA results illustrated a significant influence of environment and sample type (control/PE/PP/PS) on the microbial communities. However, the influence of sample type on microbial diversity was not significant (P-value > 0.05) when the control samples were removed from the dataset but the environment remained a significant factor (P-value < 0.05). Further, the differential abundance analyses explicitly showed the abundance of many bacterial taxa to be significantly influenced (adjusted P-value < 0.05) by the locations rather than the polymer types. The validation analysis also supports the findings. Thus, this study suggests that both the surrounding environment and polymer types determine the microbial communities on marine MPs, but the role of the environment in shaping the microbial composition is greater than that of polymer types.
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Affiliation(s)
- Meganathan P Ramakodi
- CSIR-National Environmental Engineering Research Institute (NEERI), Hyderabad Zonal Centre, IICT Campus, Tarnaka, Hyderabad, Telangana, 500007, India.
| | - Saravanan Palanivishwanath
- CSIR-National Environmental Engineering Research Institute (NEERI), Hyderabad Zonal Centre, IICT Campus, Tarnaka, Hyderabad, Telangana, 500007, India
- Indian Institute of Technology, Jammu & Kashmir, Jammu, 181221, India
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29
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Wang Z, Lloyd D, Zhao S, Motsinger-Reif A. Taxanorm: a novel taxa-specific normalization approach for microbiome data. BMC Bioinformatics 2024; 25:304. [PMID: 39285319 PMCID: PMC11406911 DOI: 10.1186/s12859-024-05918-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/28/2024] [Indexed: 09/19/2024] Open
Abstract
BACKGROUND In high-throughput sequencing studies, sequencing depth, which quantifies the total number of reads, varies across samples. Unequal sequencing depth can obscure true biological signals of interest and prevent direct comparisons between samples. To remove variability due to differential sequencing depth, taxa counts are usually normalized before downstream analysis. However, most existing normalization methods scale counts using size factors that are sample specific but not taxa specific, which can result in over- or under-correction for some taxa. RESULTS We developed TaxaNorm, a novel normalization method based on a zero-inflated negative binomial model. This method assumes the effects of sequencing depth on mean and dispersion vary across taxa. Incorporating the zero-inflation part can better capture the nature of microbiome data. We also propose two corresponding diagnosis tests on the varying sequencing depth effect for validation. We find that TaxaNorm achieves comparable performance to existing methods in most simulation scenarios in downstream analysis and reaches a higher power for some cases. Specifically, it balances power and false discovery control well. When applying the method in a real dataset, TaxaNorm has improved performance when correcting technical bias. CONCLUSION TaxaNorm both sample- and taxon- specific bias by introducing an appropriate regression framework in the microbiome data, which aids in data interpretation and visualization. The 'TaxaNorm' R package is freely available through the CRAN repository https://CRAN.R-project.org/package=TaxaNorm and the source code can be downloaded at https://github.com/wangziyue57/TaxaNorm .
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Affiliation(s)
- Ziyue Wang
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
- Department of Population Health, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Dillon Lloyd
- Department of Biological Sciences and Statistics, North Carolina State University, Raleigh, NC, 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Shanshan Zhao
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, NC, 27709, USA.
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Leino LI, Vesterinen EJ, Sánchez-Virosta P, Puigbò P, Eeva T, Rainio MJ. Pollution-related changes in nest microbiota: Implications for growth and fledging in three passerine birds. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 357:124434. [PMID: 38936789 DOI: 10.1016/j.envpol.2024.124434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/12/2024] [Accepted: 06/23/2024] [Indexed: 06/29/2024]
Abstract
Non-ferrous smelters emit toxic metals into the environment, posing a threat to wildlife health. Despite the acknowledged role of microbes in host health, the impact of such emissions on host-associated microbiota, especially in wild birds, remains largely unexplored. This study investigates the associations of metal pollution, fitness, and nest microbiota (serving as a proxy for early-life microbial environment) which may influence the nestling health and development. Our study focuses on three passerine birds, the great tit (Parus major), blue tit (Cyanistes caeruleus), and pied flycatcher (Ficedula hypoleuca), within control and metal-polluted sites around a Finnish copper-nickel smelter. The polluted sites had been contaminated with arsenic (As), cadmium (Cd), copper (Cu), nickel (Ni), and zinc (Zn). We performed bacterial 16S rRNA sequencing and metal analyses on 90 nests and monitored nestling body mass, fledging success, and various biotic and abiotic factors. Our findings revealed species-specific responses to metal exposure in terms of both fitness and nest microbiota. P. major and C. caeruleus showed sensitivity to pollution, with decreased nestling growth and fledging in the polluted zone. This was accompanied by a shift in the bacterial community composition, which was characterized by an increase in some pathogenic bacteria (in P. major and C. caeruleus nests) and by a decrease in plant-associated bacteria (within C. caeruleus nests). Conversely, F. hypoleuca and their nest microbiota showed limited responses to pollution, indicating greater tolerance to pollution-induced environmental changes. Although pollution did not correlate with nest alpha diversity or the most abundant bacterial taxa across all species, certain potential pathogens within the nests were enriched in polluted environments and negatively correlated with nestling fitness parameters. Our results suggest that metal pollution may alter the nest bacterial composition in some bird species, either directly or indirectly through environmental changes, promoting pathogenic bacteria and potentially impacting bird survival.
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Affiliation(s)
- Lyydia I Leino
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Eero J Vesterinen
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Pablo Sánchez-Virosta
- Department of Biology, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
| | - Pere Puigbò
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland; Eurecat, Technology Centre of Catalonia, Reus, Catalonia, Spain; Department of Biochemistry and Biotechnology, Rovira I Virgili University, Tarragona, Catalonia, Spain.
| | - Tapio Eeva
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
| | - Miia J Rainio
- Department of Biology, University of Turku, Henrikinkatu 2, 20014, Turku, Finland.
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Xiong R, Qian D, Qiu Z, Hou Y, Li Q, Shen W. Land-use intensification exerts a greater influence on soil microbial communities than seasonal variations in the Taihu Lake region, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 943:173630. [PMID: 38823709 DOI: 10.1016/j.scitotenv.2024.173630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/13/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
The Taihu Lake region has undergone intensive land-use conversions from natural wetlands (NW) to conventional rice-wheat rotation fields (RW) and further to greenhouse vegetable fields (GH). Nevertheless, the effects of these conversions on soil microbes, particularly in wetland ecosystem, are not well explicit. To explore the impact of land-use intensification on soil microbial communities, monthly soil samples were obtained from replicate plots representing three land-use types (NW, RW, and GH) in subtropical wetlands and then subjected to amplicon sequencing. Land-use intensification had direct effects on bacterial and fungal community composition, with a more pronounced impact on bacteria than on fungi. These changes in bacterial communities were closely correlated with variations in soil environmental variables, such as NO3--N, pH, and electrical conductivity. Land-use intensification led to a decrease in bacterial deterministic processes, with an opposing trend observed in the fungal community. In addition, arable lands (RW and GH), which are affected by anthropogenic activities, exhibited more complex networks. Potential metabolic functional groups in GH had higher absolute abundance. Seasonal variations significantly influenced microbial diversity, composition, and potential metabolic functional groups within each land-use type, particularly in summer, although the magnitude of this impact was much smaller than the impact of land-use intensification. Our findings emphasize the importance of comprehending the ecological consequences of land-use intensification in wetlands for sustainable resource management and biodiversity conservation.
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Affiliation(s)
- Ruonan Xiong
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Dong Qian
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Zijian Qiu
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Yixin Hou
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Qing Li
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Weishou Shen
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China.
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Cruells A, Cabrera-Rubio R, Bustamante M, Pelegrí D, Cirach M, Jimenez-Arenas P, Samarra A, Martínez-Costa C, Collado MC, Gascon M. The influence of pre- and postnatal exposure to air pollution and green spaces on infant's gut microbiota: Results from the MAMI birth cohort study. ENVIRONMENTAL RESEARCH 2024; 257:119283. [PMID: 38830395 DOI: 10.1016/j.envres.2024.119283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 05/14/2024] [Accepted: 05/29/2024] [Indexed: 06/05/2024]
Abstract
BACKGROUND Animal and human studies indicate that exposure to air pollution and natural environments might modulate the gut microbiota, but epidemiological evidence is very scarce. OBJECTIVES To assess the potential impact of pre- and postnatal exposure to air pollution and green spaces on infant gut microbiota assembly and trajectories during the first year of life. METHODS MAMI ("MAternal MIcrobes") birth cohort (Valencia, Spain, N = 162) was used to study the impact of environmental exposure (acute and chronic) on infant gut microbiota during the first year of life (amplicon-based 16S rRNA sequencing). At 7 days and at 1, 6 and 12 months, residential pre- and postnatal exposure to air pollutants (NO2, black carbon -BC-, PM2.5 and O3) and green spaces indicators (NDVI and area of green spaces at 300, 500 and 1000 m buffers) were obtained. For the association between exposures and alpha diversity indicators linear regression models (cross-sectional analyses) and mixed models, including individual as a random effect (longitudinal analyses), were applied. For the differential taxon analysis, the ANCOM-BC package with a log count transformation and multiple-testing corrections were used. RESULTS Acute exposure in the first week of life and chronic postnatal exposure to NO2 were associated with a reduction in microbial alpha diversity, while the effects of green space exposure were not evident. Acute and chronic (prenatal or postnatal) exposure to NO2 resulted in increased abundance of Haemophilus, Akkermansia, Alistipes, Eggerthella, and Tyzerella populations, while increasing green space exposure associated with increased Negativicoccus, Senegalimassilia and Anaerococcus and decreased Tyzzerella and Lachnoclostridium populations. DISCUSSION We observed a decrease in the diversity of the gut microbiota and signs of alteration in its composition among infants exposed to higher levels of NO2. Increasing green space exposure was also associated with changes in gut microbial composition. Further research is needed to confirm these findings.
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Affiliation(s)
- Adrià Cruells
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Raúl Cabrera-Rubio
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Dolors Pelegrí
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Marta Cirach
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Pol Jimenez-Arenas
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain
| | - Anna Samarra
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Cecilia Martínez-Costa
- Department of Pediatrics, University of Valencia, INCLIVA Biomedical Research Institute, Valencia, Spain
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Mireia Gascon
- ISGlobal, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Spain.
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Gonzalez-Soltero R, Tabone M, Larrosa M, Bailen M, Bressa C. VDR gene TaqI (rs731236) polymorphism affects gut microbiota diversity and composition in a Caucasian population. Front Nutr 2024; 11:1423472. [PMID: 39328465 PMCID: PMC11425793 DOI: 10.3389/fnut.2024.1423472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 08/19/2024] [Indexed: 09/28/2024] Open
Abstract
Background The VDR gene is identified as a crucial host factor, influencing the gut microbiota. The current research focuses on an observational study that compares gut microbiota composition among individuals with different VDR gene TaqI polymorphisms in a Caucasian Spanish population. This study aims to elucidate the interplay between genetic variations in the VDR gene and the gut microbial composition. Methods 87 healthy participants (57 men, 30 women), aged 18 to 48 years, were examined. Anthropometric measures, body composition, and dietary habits were assessed. VDR gene polymorphism TaqI rs731236 was determined using TaqMan assays. The V3 and V4 regions of the 16S rRNA gene were sequenced to study bacterial composition, which was analyzed using QIIME2, DADA2 plugin, and PICRUSt2. Statistical analyses included tests for normal distribution, alpha/beta diversity, ADONIS, LEfSe, and DESeq2, with established significance thresholds. Results No significant differences in body composition or dietary habits were observed based on VDR genotypes. Dietary intake analysis revealed no variations in energy, macronutrients, or fiber among the different VDR genotypes. Fecal microbiota analysis indicated significant differences in alpha diversity as measured by Faith's Phylogenetic Diversity index. Differential abundance analysis identified taxonomic disparities, notably in the genera Parabacteroides and Butyricimonas. Conclusion Overall, this study suggests potential associations between genetic variations in the VDR gene and the composition and function of gut microbiota.
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Affiliation(s)
- Rocío Gonzalez-Soltero
- Masmicrobiota Group, Madrid, Spain
- Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - Mariangela Tabone
- Masmicrobiota Group, Madrid, Spain
- Faculty of Biomedical and Health Sciences, Universidad Europea de Madrid, Madrid, Spain
| | - Mar Larrosa
- Masmicrobiota Group, Madrid, Spain
- Department of Nutrition and Food Science, Faculty of Pharmacy, Universidad Complutense de Madrid, Madrid, Spain
| | - Maria Bailen
- Masmicrobiota Group, Madrid, Spain
- Department of Preventive Medicine, Public Health and Microbiology, Faculty of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlo Bressa
- Masmicrobiota Group, Madrid, Spain
- Faculty of Experimental Sciences, Universidad Francisco de Vitoria, Madrid, Spain
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Byers AK, Waipara N, Condron L, Black A. The impacts of ecological disturbances on the diversity of biosynthetic gene clusters in kauri (Agathis australis) soil. ENVIRONMENTAL MICROBIOME 2024; 19:69. [PMID: 39261912 PMCID: PMC11391841 DOI: 10.1186/s40793-024-00613-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
BACKGROUND The ancient kauri (Agathis australis) dominated forests of Aotearoa New Zealand are under threat from a multitude of ecological disturbances such as forest fragmentation, biodiversity loss, climate change, and the spread of the virulent soil pathogen Phytophthora agathidicida. Taking a wider ecosystem-level approach, our research aimed to explore the impacts of forest disturbance and disease outbreaks on the biosynthetic potential and taxonomic diversity of the kauri soil microbiome. We explored the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in soils from a range of kauri forests that varied according to historical disturbance and dieback expression. To characterise the diversity of microbial BGCs, we targeted the non-ribosomal peptide synthetase (NRPS) and polyketide synthetase (PKS) gene regions for sequencing using long-read PacBio® HiFi sequencing. Furthermore, the soil bacterial and fungal communities of each forest were characterized using 16 S rRNA and ITS gene region sequencing. RESULTS We identified a diverse array of naturally occurring microbial BGCs in the kauri forest soils, which may offer promising targets for the exploration of secondary metabolites with anti-microbial activity against P. agathidicida. We detected differences in the number and diversity of microbial BGCs according to forest disturbance history. Notably, soils associated with the most undisturbed kauri forest had a higher number and diversity of microbial NRPS-type BGCs, which may serve as a potential indicator of natural levels of microbiome resistance to pathogen invasion. CONCLUSIONS By linking patterns in microbial biosynthetic diversity to forest disturbance history, this research highlights the need for us to consider the influence of ecological disturbances in potentially predisposing forests to disease by impacting the wider health of forest soil ecosystems. Furthermore, by identifying the range of microbial BGCs present at a naturally high abundance in kauri soils, this research contributes to the future discovery of natural microbial compounds that may potentially enhance the disease resilience of kauri forests. The methodological approaches used in this study highlight the value of moving beyond a taxonomic lens when examining the response of microbial communities to ecosystem disturbance and the need to develop more functional measures of microbial community resilience to invasive plant pathogens.
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Affiliation(s)
- Alexa K Byers
- Bioprotection Aotearoa, Lincoln University, P.O. Box 85084, Lincoln, 7647, New Zealand.
| | - Nick Waipara
- Plant and Food Research, Sandringham, Auckland, 1025, New Zealand
| | - Leo Condron
- Faculty of Agriculture and Life Sciences, Lincoln University, P.O. Box 85084, Lincoln, 7647, New Zealand
| | - Amanda Black
- Bioprotection Aotearoa, Lincoln University, P.O. Box 85084, Lincoln, 7647, New Zealand
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Pereira H, Hoffman JI, Krüger O, Czirják GÁ, Rinaud T, Ottensmann M, Gladow KP, Caspers BA, Maraci Ö, Kaiser S, Chakarov N. The gut microbiota-immune-brain axis in a wild vertebrate: dynamic interactions and health impacts. Front Microbiol 2024; 15:1413976. [PMID: 39318435 PMCID: PMC11420037 DOI: 10.3389/fmicb.2024.1413976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/20/2024] [Indexed: 09/26/2024] Open
Abstract
The gut microbiota-immune-brain axis is a feedback network which influences diverse physiological processes and plays a pivotal role in overall health and wellbeing. Although research in humans and laboratory mice has shed light into the associations and mechanisms governing this communication network, evidence of such interactions in wild, especially in young animals, is lacking. We therefore investigated these interactions during early development in a population of common buzzards (Buteo buteo) and their effects on individual condition. In a longitudinal study, we used a multi-marker approach to establish potential links between the bacterial and eukaryotic gut microbiota, a panel of immune assays and feather corticosterone measurements as a proxy for long-term stress. Using Bayesian structural equation modeling, we found no support for feedback between gut microbial diversity and immune or stress parameters. However, we did find strong relationships in the feedback network. Immunity was negatively correlated with corticosterone levels, and microbial diversity was positively associated with nestling body condition. Furthermore, corticosterone levels and eukaryotic microbiota diversity decreased with age while immune activity increased. The absence of conclusive support for the microbiota-immune-brain axis in common buzzard nestlings, coupled with the evidence for stress mediated immunosuppression, suggests a dominating role of stress-dominated maturation of the immune system during early development. Confounding factors inherent to wild systems and developing animals might override associations known from adult laboratory model subjects. The positive association between microbial diversity and body condition indicates the potential health benefits of possessing a diverse and stable microbiota.
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Affiliation(s)
- Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Joseph I. Hoffman
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Department of Evolutionary Population Genetics, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment, Bielefeld University and University of Münster, Bielefeld, Germany
- British Antarctic Survey, Cambridge, United Kingdom
- Center for Biotechnology (CeBiTec), Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment, Bielefeld University and University of Münster, Bielefeld, Germany
| | - Gábor Á. Czirják
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Kai-Philipp Gladow
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
| | - Barbara A. Caspers
- Joint Institute for Individualisation in a Changing Environment, Bielefeld University and University of Münster, Bielefeld, Germany
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Öncü Maraci
- Joint Institute for Individualisation in a Changing Environment, Bielefeld University and University of Münster, Bielefeld, Germany
- Department of Behavioural Ecology, Bielefeld University, Bielefeld, Germany
| | - Sylvia Kaiser
- Joint Institute for Individualisation in a Changing Environment, Bielefeld University and University of Münster, Bielefeld, Germany
- Department of Behavioural Biology, University of Münster, Münster, Germany
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
- Joint Institute for Individualisation in a Changing Environment, Bielefeld University and University of Münster, Bielefeld, Germany
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do Rosario V, Lorzadeh E, Brodaty H, Anstey KJ, Chan K, Roodenrys S, Kent K, Bliokas V, Phillipson L, Weston-Green K, Francois ME, Jiang X, George J, Potter J, Batterham MJ, Charlton K. Assessing the effect of anthocyanins through diet and supplementation on cognitive function in older adults at risk for dementia: protocol for a randomised controlled trial. BMJ Open 2024; 14:e086435. [PMID: 39260845 PMCID: PMC11409387 DOI: 10.1136/bmjopen-2024-086435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/13/2024] Open
Abstract
INTRODUCTION Promising evidence is emerging for the procognitive, anti-inflammatory and neuroprotective properties of dietary flavonoids, particularly anthocyanins that provide red, purple and blue plant pigments. METHODS AND ANALYSIS The 'Food for Thought' study is a multicentre, 6-month randomised, parallel 3-arm clinical trial. Its primary aim is to investigate whether anthocyanin consumption, either through diet or supplementation, can prevent memory loss progression and improve inflammatory and cardiovascular health in older adults at risk for dementia. Eligible participants will include those aged 60-85 years with a diagnosis of amnestic mild cognitive impairment or with a self-referral of memory concerns and scoring ≤13 on the Memory Index Score within the Telephone Montreal Cognitive Assessment screening test. Participants will be randomised to one of three arms: High anthocyanin ('purple foods') diet (aiming for a target of 250 mg anthocyanins/day); freeze-dried product derived from blackcurrants (250 mg anthocyanins/day); or control (coloured maltose powder). The primary outcome is auditory anterograde memory functioning assessed by the Buschke and Grober Free and Cued Selective Reminding Test-Immediate Recall. Secondary outcomes are additional cognitive functions including processing speed, working memory, aspects of executive functioning (attentional shifting and word generativity) and premorbid estimate as well as subjective memory problems and self-reported depression symptoms. Additional secondary outcomes are blood pressure, inflammatory biomarkers, brain-derived neurotrophic factor, fatty acid profile, apolipoprotein E and polyphenol metabolites, gut microbiota composition and function and vascular and microvascular endothelial function tests. Repeated measures analysis of variance and/or mixed linear modelling will evaluate changes over time, with the inclusion of covariates. ETHICS AND DISSEMINATION Ethics approval has been obtained from the Greater Western Human Research Ethics Committee (2021/ETH12083). A Consumer Advisory Group was established to guide and review the protocol and dissemination strategy. The results of this trial are intended to be published in a peer-reviewed journal. TRIAL SPONSOR National Health and Medical Research Centre Dementia Collaborative Research Centre.Start date of clinical trial: 02 September 2022.Expected end date: 11 October 2024. TRIAL REGISTRATION NUMBER ACTRN12622000065796.
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Affiliation(s)
- Vinicius do Rosario
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
| | - Elnaz Lorzadeh
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
| | - Henry Brodaty
- Centre for Healthy Brain Ageing, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Kaarin J Anstey
- Neuroscience Research Australia, University of New South Wales, Sydney, New South Wales, Australia
- UNSW Ageing Futures Institute, Sydney, New South Wales, Australia
| | - Karina Chan
- Centre for Healthy Brain Ageing, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
| | - Steven Roodenrys
- School of Psychology, Faculty of Arts and Social Science, University of Wollongong, Wollongong, New South Wales, Australia
| | - Katherine Kent
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
- School of Health Sciences, Western Sydney University, Sydney, New South Wales, Australia
| | - Vida Bliokas
- School of Psychology, Faculty of Arts and Social Science, University of Wollongong, Wollongong, New South Wales, Australia
| | - Lyn Phillipson
- School of Health and Society, Faculty of Arts and Social Science, University of Wollongong, Wollongong, New South Wales, Australia
| | - Katrina Weston-Green
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
- Molecular Horizons Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
| | - Monique E Francois
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
| | - Xiaotao Jiang
- Microbiome Research Centre (MRC), University of New South Wales, Sydney, New South Wales, Australia
| | - Jenson George
- Department of Agriculture and Fisheries, Queensland Government, Brisbane, Queensland, Australia
| | - Jan Potter
- Division of Aged Care, Rehabilitation and Palliative Care, Illawarra Shoalhaven Local Health District, Wollongong, New South Wales, Australia
| | - Marijka J Batterham
- National Institute for Applied Statistical Research Australia and the Statistical Consulting Centre, School of Mathematics and Applied Statistics, University of Wollongong, Wollongong, New South Wales, Australia
| | - Karen Charlton
- School of Medical, Indigenous and Health Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
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Del Pinto R, Ferri C, Giannoni M, Cominelli F, Pizarro TT, Pietropaoli D. Meta-analysis of oral microbiome reveals sex-based diversity in biofilms during periodontitis. JCI Insight 2024; 9:e171311. [PMID: 39253976 PMCID: PMC11385077 DOI: 10.1172/jci.insight.171311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/25/2024] [Indexed: 09/11/2024] Open
Abstract
Sex is an often overlooked, yet compulsory, biological variable when performing biomedical research. Periodontitis is a common yet progressively debilitating chronic inflammatory disorder affecting the tissues supporting teeth that ultimately leads to tooth loss if left untreated. The incidence of periodontitis is sex biased, with increased prevalence in males compared with females but with unknown etiology. We performed a sex-specific meta-analysis using publicly available oral microbiome data from different sampling sites of patients with periodontitis and periodontally healthy controls; sex balance was established for each periodontal health condition. Our results show sex-based diversity in oral biofilms of individuals with periodontitis but not in their saliva, with increased abundance of several periodontal pathogens in subgingival plaques from females compared with males. We devised a quantitative measure, uniquely defined as the Microsexome Index (MSI), which indicates that sexual dimorphism in subgingival bacterial composition is a distinct feature of reduced microbial diversity during periodontitis but not under healthy conditions. In addition, we found that smoking exacerbates microsexome diversity in supragingival biofilms, particularly during periodontitis. Taken together, we provide insights regarding sex-based diversity in periodontitis, a disease with multiorgan associations, and provide the rationale for further mechanistic, diagnostic, and therapeutic studies.
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Affiliation(s)
- Rita Del Pinto
- San Salvatore Hospital, Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Oral DISeases and SYstemic interactions study group (ODISSY group), L’Aquila, Italy (detailed in Supplemental Acknowledgments)
| | - Claudio Ferri
- San Salvatore Hospital, Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- Oral DISeases and SYstemic interactions study group (ODISSY group), L’Aquila, Italy (detailed in Supplemental Acknowledgments)
| | - Mario Giannoni
- Oral DISeases and SYstemic interactions study group (ODISSY group), L’Aquila, Italy (detailed in Supplemental Acknowledgments)
- Center of Oral Diseases, Prevention and Translational Research, Dental Clinic, Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Fabio Cominelli
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Theresa T. Pizarro
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Davide Pietropaoli
- Oral DISeases and SYstemic interactions study group (ODISSY group), L’Aquila, Italy (detailed in Supplemental Acknowledgments)
- Center of Oral Diseases, Prevention and Translational Research, Dental Clinic, Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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Lyng M, Þórisdóttir B, Sveinsdóttir SH, Hansen ML, Jelsbak L, Maróti G, Kovács ÁT. Taxonomy of Pseudomonas spp. determines interactions with Bacillus subtilis. mSystems 2024:e0021224. [PMID: 39254334 DOI: 10.1128/msystems.00212-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/16/2024] [Indexed: 09/11/2024] Open
Abstract
Bacilli and pseudomonads are among the most well-studied microorganisms commonly found in soil and frequently co-isolated. Isolates from these two genera are frequently used as plant beneficial microorganisms; therefore, their interaction in the plant rhizosphere is relevant for agricultural applications. Despite this, no systematic approach has been employed to assess the coexistence of members from these genera. Here, we screened 720 fluorescent soil isolates for their effects on Bacillus subtilis pellicle formation in two types of media and found a predictor for interaction outcome in Pseudomonas taxonomy. Interactions were context-dependent, and both medium composition and culture conditions strongly influenced interactions. Negative interactions were associated with Pseudomonas capeferrum, Pseudomonas entomophila, and Pseudomonas protegens, and 2,4-diacetylphloroglucinol was confirmed as a strong (but not exclusive) inhibitor of B. subtilis. Non-inhibiting strains were closely related to Pseudomonas trivialis and Pseudomonas lini. Using such a non-inhibiting isolate, Pseudomonas P9_31, which increased B. subtilis pellicle formation demonstrated that the two species were spatially segregated in cocultures. Our study is the first one to propose an overall negative outcome from pairwise interactions between B. subtilis and fluorescent pseudomonads; hence, cocultures comprising members from these groups are likely to require additional microorganisms for coexistence. IMPORTANCE There is a strong interest in the microbial ecology field to predict interaction among microorganisms, whether two microbial isolates will promote each other's growth or compete for resources. Numerous studies have been performed based on surveying the available literature or testing phylogenetically diverse sets of species in synthetic communities. Here, a high throughput screening has been performed using 720 Pseudomonas isolates, and their impact on the biofilm formation of Bacillus subtilis was tested. The aim was to determine whether a majority of Pseudomonas will promote or inhibit the biofilms of B. subtilis in the co-cultures. This study reports that Pseudomonas taxonomy is a good predictor of interaction outcome, and only a minority of Pseudomonas isolates promote Bacillus biofilm establishment.
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Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Birta Þórisdóttir
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sigrún H Sveinsdóttir
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Morten L Hansen
- Microbiome Interactions and Engineering, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Jelsbak
- Microbiome Interactions and Engineering, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Center, ELKH, Szeged, Hungary
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
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Zhang M, Li X, Oladeinde A, Rothrock M, Pokoo-Aikins A, Zock G. A Novel Slope-Matrix-Graph Algorithm to Analyze Compositional Microbiome Data. Microorganisms 2024; 12:1866. [PMID: 39338540 PMCID: PMC11434172 DOI: 10.3390/microorganisms12091866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Revised: 09/06/2024] [Accepted: 09/07/2024] [Indexed: 09/30/2024] Open
Abstract
Networks are widely used to represent relationships between objects, including microorganisms within ecosystems, based on high-throughput sequencing data. However, challenges arise with appropriate statistical algorithms, handling of rare taxa, excess zeros in compositional data, and interpretation. This work introduces a novel Slope-Matrix-Graph (SMG) algorithm to identify microbiome correlations primarily based on slope-based distance calculations. SMG effectively handles any proportion of zeros in compositional data and involves: (1) searching for correlated relationships (e.g., positive and negative directions of changes) based on a "target of interest" within a setting, and (2) quantifying graph changes via slope-based distances between objects. Evaluations on simulated datasets demonstrated SMG's ability to accurately cluster microbes into distinct positive/negative correlation groups, outperforming methods like Bray-Curtis and SparCC in both sensitivity and specificity. Moreover, SMG demonstrated superior accuracy in detecting differential abundance (DA) compared to ZicoSeq and ANCOM-BC2, making it a robust tool for microbiome analysis. A key advantage is SMG's natural capacity to analyze zero-inflated compositional data without transformations. Overall, this simple yet powerful algorithm holds promise for diverse microbiome analysis applications.
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Affiliation(s)
- Meng Zhang
- Department of Mathematics, University of North Georgia, 82 College Cir, Dahlonega, GA 30597, USA;
| | - Xiang Li
- U.S. National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 950 College Station Road, Athens, GA 30605, USA; (A.O.); (M.R.J.); (G.Z.)
| | - Adelumola Oladeinde
- U.S. National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 950 College Station Road, Athens, GA 30605, USA; (A.O.); (M.R.J.); (G.Z.)
| | - Michael Rothrock
- U.S. National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 950 College Station Road, Athens, GA 30605, USA; (A.O.); (M.R.J.); (G.Z.)
| | - Anthony Pokoo-Aikins
- U.S. National Poultry Research Center, Toxicology & Mycotoxin Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 950 College Station Road, Athens, GA 30605, USA;
| | - Gregory Zock
- U.S. National Poultry Research Center, Egg & Poultry Production Safety Research Unit, Agricultural Research Service, U.S. Department of Agriculture, 950 College Station Road, Athens, GA 30605, USA; (A.O.); (M.R.J.); (G.Z.)
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Tsunematsu R, Mariya T, Umemoto M, Ogawa S, Arai W, Tanaka SE, Ashikawa K, Kubo T, Sakuraba Y, Baba T, Ishioka S, Endo T, Saito T. Microbiological investigation of pregnancies following vaginal radical trachelectomy using 16S rRNA sequencing of FFPE placental specimens. FEBS Open Bio 2024. [PMID: 39245884 DOI: 10.1002/2211-5463.13892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 08/15/2024] [Accepted: 08/24/2024] [Indexed: 09/10/2024] Open
Abstract
This study examined the risk of intrauterine infection associated with radical trachelectomy (RT) in early-stage cervical cancer patients. This procedure preserves fertility but is linked to increased risk of intrauterine infection due to cervical defects during pregnancy. DNA was extracted from the formalin-fixed paraffin-embedded (FFPE) placental specimens of 23 pregnant post-RT patients and 16S rRNA gene sequencing was used for bacterial identification. The prevalence of Lactobacillus crispatus and Burkholderia stabilis was significantly higher in the non-chorioamnionitis group. In contrast, alpha diversity analysis using the PD index showed significantly higher diversity in the chorioamnionitis group (P = 0.04). The demonstrated relationship between chorioamnionitis and microbial diversity affirms the importance of controlling the genital bacterial flora in pregnancies following RT.
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Affiliation(s)
- Risa Tsunematsu
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tasuku Mariya
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mina Umemoto
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shiori Ogawa
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | | | | | - Terufumi Kubo
- Department of Pathology 1st, Sapporo Medical University School of Medicine, Sapporo, Japan
| | | | - Tsuyoshi Baba
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Shinichi Ishioka
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Toshiaki Endo
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tsuyoshi Saito
- Department of Obstetrics and Gynecology, Sapporo Medical University School of Medicine, Sapporo, Japan
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Ravikrishnan A, Wijaya I, Png E, Chng KR, Ho EXP, Ng AHQ, Mohamed Naim AN, Gounot JS, Guan SP, Hanqing JL, Guan L, Li C, Koh JY, de Sessions PF, Koh WP, Feng L, Ng TP, Larbi A, Maier AB, Kennedy BK, Nagarajan N. Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes. Nat Commun 2024; 15:7751. [PMID: 39237540 PMCID: PMC11377447 DOI: 10.1038/s41467-024-52097-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 08/23/2024] [Indexed: 09/07/2024] Open
Abstract
While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun-metagenomic sequencing for high-resolution taxonomic and functional characterization of their gut microbiomes (n = 234). Joint species-level analysis with other Asian cohorts identified distinct age-associated shifts characterized by reduction in microbial richness, and specific Alistipes and Bacteroides species enrichment (e.g., Alistipes shahii and Bacteroides xylanisolvens). Functional analysis confirmed these changes correspond to metabolic potential expansion in aging towards alternate pathways synthesizing and utilizing amino-acid precursors, vis-à-vis dominant microbial guilds producing butyrate in gut from pyruvate (e.g., Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species (e.g., Parabacteroides goldsteinii) and pathobionts (e.g., Klebsiella pneumoniae), highlighting the microbiome's role as biomarkers and potential targets for promoting healthy aging.
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Affiliation(s)
- Aarthi Ravikrishnan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Indrik Wijaya
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Eileen Png
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Kern Rei Chng
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Eliza Xin Pei Ho
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Amanda Hui Qi Ng
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Ahmad Nazri Mohamed Naim
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Jean-Sebastien Gounot
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Shou Ping Guan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Jasinda Lee Hanqing
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Lihuan Guan
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Chenhao Li
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Jia Yu Koh
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Paola Florez de Sessions
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Woon-Puay Koh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Singapore Institute for Clinical Sciences (SICS), Agency for Science Technology and Research (A*STAR), 30 Medical Drive, Brenner Centre for Molecular Medicine, Singapore, 117609, Republic of Singapore
| | - Lei Feng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Tze Pin Ng
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Anis Larbi
- Singapore Immunology Network (SigN), Agency for Science Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore, 138648, Republic of Singapore
| | - Andrea B Maier
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
- Department of Human Movement Sciences, @AgeAmsterdam, Faculty of Behavioural and Movement Sciences, Vrije Universiteit Amsterdam, Amsterdam Movement Sciences, Amsterdam, The Netherlands
| | - Brian K Kennedy
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore
| | - Niranjan Nagarajan
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.
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Bonacolta AM, Visscher PT, Del Campo J, White Iii RA. The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems. NPJ Biofilms Microbiomes 2024; 10:78. [PMID: 39227595 PMCID: PMC11372052 DOI: 10.1038/s41522-024-00547-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 08/12/2024] [Indexed: 09/05/2024] Open
Abstract
Protists are less studied for their role and diversity in ecosystems. Notably, protists have played and still play an important role in microbialites. Microbialites, or lithified microbial mats, represent the oldest evidence of fossil biofilms (~3.5 Gyr). Modern microbialites may offer a unique proxy to study the potential role of protists within a geological context. We examined protist diversity in freshwater (Kelly and Pavilion Lake in British Columbia, Canada) and marine (Highborne Cay, Bahamas) to hypersaline (Shark Bay, Australia) microbialites to decipher their geomicrobiological role. The freshwater microbialite communities were clearly distinct from their marine and hypersaline counterparts. Chlorophytes had higher numerical abundance in freshwater microbialites; whereas pennate diatoms dominated numerically in marine microbialites. Despite the differences, protists across ecosystems may have adopted similar roles and functions. We suggest a consistent biogeochemical role of protists across microbialites globally; but that salinity may shape protist composition and evolution in these ecosystems.
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Affiliation(s)
- Anthony M Bonacolta
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Pieter T Visscher
- Department of Marine Sciences and Earth Sciences, University of Connecticut, Storrs, CT, USA
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia
| | - Javier Del Campo
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, USA.
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.
| | - Richard Allen White Iii
- Australian Centre for Astrobiology, University of New South Wales, Sydney, NSW, Australia.
- North Carolina Research Center (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC, USA.
- Computational Intelligence to Predict Health and Environmental Risks (CIPHER), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC, USA.
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Manus MB, Lucore J, Kuthyar S, Moy M, Savo Sardaro ML, Amato KR. Technical note: A biological anthropologist's guide for applying microbiome science to studies of human and non-human primates. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024:e25020. [PMID: 39222382 DOI: 10.1002/ajpa.25020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/28/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
A central goal of biological anthropology is connecting environmental variation to differences in host physiology, biology, health, and evolution. The microbiome represents a valuable pathway for studying how variation in host environments impacts health outcomes. While there are many resources for learning about methods related to microbiome sample collection, laboratory analyses, and genetic sequencing, there are fewer dedicated to helping researchers navigate the dense portfolio of bioinformatics and statistical approaches for analyzing microbiome data. Those that do exist are rarely related to questions in biological anthropology and instead are often focused on human biomedicine. To address this gap, we expand on existing tutorials and provide a "road map" to aid biological anthropologists in understanding, selecting, and deploying the data analysis and visualization methods that are most appropriate for their specific research questions. Leveraging an existing dataset of fecal samples and survey data collected from wild geladas living in Simien Mountains National Park in Ethiopia (Baniel et al., 2021), this paper guides researchers toward answering three questions related to variation in the gut microbiome across host and environmental factors. By providing explanations, examples, and a reproducible workflow for different analytic methods, we move beyond the theoretical benefits of considering the microbiome within anthropological research and instead present researchers with a guide for applying microbiome science to their work. This paper makes microbiome science more accessible to biological anthropologists and paves the way for continued research into the microbiome's role in the ecology, evolution, and health of human and non-human primates.
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Affiliation(s)
- Melissa B Manus
- Department of Anthropology, University of Texas at San Antonio, San Antonio, Texas, USA
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Jordan Lucore
- Department of Anthropology, University of Michigan, Ann Arbor, Michigan, USA
| | - Sahana Kuthyar
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Madelyn Moy
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Maria Luisa Savo Sardaro
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
- Department of Human Science and Promotion of the Quality of Life, University of San Raffaele, Rome, Italy
| | - Katherine R Amato
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
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Versi A, Azim A, Ivan FX, Abdel‐Aziz MI, Bates S, Riley J, Uddin M, Zounemat Kermani N, Maitland‐Van Der Zee A, Dahlen S, Djukanovic R, Chotirmall SH, Howarth P, Adcock IM, Chung KF. A severe asthma phenotype of excessive airway Haemophilus influenzae relative abundance associated with sputum neutrophilia. Clin Transl Med 2024; 14:e70007. [PMID: 39187935 PMCID: PMC11347389 DOI: 10.1002/ctm2.70007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND Severe asthma (SA) encompasses several clinical phenotypes with a heterogeneous airway microbiome. We determined the phenotypes associated with a low α-diversity microbiome. METHODS Metagenomic sequencing was performed on sputum samples from SA participants. A threshold of 2 standard deviations below the mean of α-diversity of mild-moderate asthma and healthy control subjects was used to define those with an abnormal abundance threshold as relative dominant species (RDS). FINDINGS Fifty-one out of 97 SA samples were classified as RDSs with Haemophilus influenzae RDS being most common (n = 16), followed by Actinobacillus unclassified (n = 10), Veillonella unclassified (n = 9), Haemophilus aegyptius (n = 9), Streptococcus pseudopneumoniae (n = 7), Propionibacterium acnes (n = 5), Moraxella catarrhalis (n = 5) and Tropheryma whipplei (n = 5). Haemophilus influenzae RDS had the highest duration of disease, more exacerbations in previous year and greatest number on daily oral corticosteroids. Hierarchical clustering of RDSs revealed a C2 cluster (n = 9) of highest relative abundance of exclusively Haemophilus influenzae RDSs with longer duration of disease and higher sputum neutrophil counts associated with enrichment pathways of MAPK, NF-κB, TNF, mTOR and necroptosis, compared to the only other cluster, C1, which consisted of 7 Haemophilus influenzae RDSs out of 42. Sputum transcriptomics of C2 cluster compared to C1 RDSs revealed higher expression of neutrophil extracellular trap pathway (NETosis), IL6-transignalling signature and neutrophil activation. CONCLUSION We describe a Haemophilus influenzae cluster of the highest relative abundance associated with neutrophilic inflammation and NETosis indicating a host response to the bacteria. This phenotype of severe asthma may respond to specific antibiotics.
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Affiliation(s)
- Ali Versi
- National Heart & Lung InstituteImperial College LondonLondonUK
| | - Adnan Azim
- Respiratory Department, Faculty of MedicineSouthampton UniversitySouthamptonUK
| | | | - Mahmoud I Abdel‐Aziz
- Department of Pulmonary MedicineAmsterdam University Medical CentersUniversity of AmsterdamAmsterdamNetherlands
| | | | - John Riley
- Respiratory Therapeutic UnitGSKStockley ParkUK
| | - Mohib Uddin
- AstraZeneca BioPharmaceuticals R&DGothenburgSweden
| | | | - Anke‐H Maitland‐Van Der Zee
- Department of Pulmonary MedicineAmsterdam University Medical CentersUniversity of AmsterdamAmsterdamNetherlands
| | - Sven‐Eric Dahlen
- Department of Medicine HuddingeKarolinska InstituteStockholmSweden
| | - Ratko Djukanovic
- Respiratory Department, Faculty of MedicineSouthampton UniversitySouthamptonUK
| | - Sanjay H Chotirmall
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
- Department of Respiratory and Critical Care MedicineTan Tock Seng HospitalSingaporeSingapore
| | - Peter Howarth
- Respiratory Department, Faculty of MedicineSouthampton UniversitySouthamptonUK
| | - Ian M Adcock
- National Heart & Lung InstituteImperial College LondonLondonUK
| | - Kian Fan Chung
- National Heart & Lung InstituteImperial College LondonLondonUK
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Sanville J, O'Toole GA, Madan J, Coker M. Premodulator microbiome alterations associated with postmodulator growth outcomes in pediatric cystic fibrosis: Can we predict outcomes? J Pediatr Gastroenterol Nutr 2024; 79:695-704. [PMID: 39118488 DOI: 10.1002/jpn3.12350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 08/10/2024]
Abstract
OBJECTIVES The gut microbiota plays an important role in childhood growth. Our longitudinal cohort includes children with cystic fibrosis (CwCF) treated with highly effective modulator therapy. We aimed to elucidate early premodulator microbial signatures associated with postmodulator weight for CwCF later in childhood. METHODS Stool samples were collected from CwCF at 13 days to 60 months. Metagenomic sequencing determined differentially abundant taxa. Children with body mass index or weight for length Z-scores within 1 standard deviation of the mean (SD) were considered normal weight, those >1 SD were classified as risk of overweight while children <1 SD were considered undernourished, although no CwCF met this latter criterion here. Multivariate regression models were applied to identify significant associations between metadata and microbial taxonomic relative abundances. RESULTS One hundred and eighty-nine stool samples were analyzed from 39 CwCF. We identified statistically significant differences in early microbiome patterns among those at risk of being overweight compared to those who were normal weight when adjusted for age, sex, CF mutation, and early feeding method. Early microbiome was a stronger driver of growth status than current modulator use. Among those at risk of overweight, several taxa that were consistently in lower abundance included Eggerthella lentha, Ruminococcus, Bacteroides, with increase in abundance of Bacteroides stercoris. CONCLUSIONS The early microbiome strongly predicts growth in the setting of modulator use for CwCF and we identify microbiome signatures associated with risk of being overweight. We highlight the possibility for interventions or early alternations to nutritional guidance for prevention of comorbid complications.
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Affiliation(s)
- Julie Sanville
- Department of Pediatrics, Division of Pediatric Gastroenterology, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Juliette Madan
- Departments of Pediatrics and Psychiatry, Division of Child and Adolescent Psychiatry, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- Department of Quantitative Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Modupe Coker
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- Department of Quantitative Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
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46
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Xu X, Pioppi A, Kiesewalter HT, Strube ML, Kovács ÁT. Disentangling the factors defining Bacillus subtilis group species abundance in natural soils. Environ Microbiol 2024; 26:e16693. [PMID: 39324517 DOI: 10.1111/1462-2920.16693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 08/14/2024] [Indexed: 09/27/2024]
Abstract
Bacillus subtilis is ubiquitously and broadly distributed in various environments but is mostly isolated from soil. Given that B. subtilis is known as a plant growth-promoting rhizobacterium in agriculture, we aimed to describe the natural distribution of this species and uncover how biotic and abiotic factors affect its distribution. When comparing different soils, we discovered that B. subtilis group species are most abundant in grasslands but can rarely be isolated from forest soil, even if the soil sample sites are situated in proximity. Differential analysis revealed that spore-forming bacteria exhibited enrichments in the grassland, suggesting niche overlap or synergistic interactions leading to the proliferation of certain Bacillus species in grassland environments. Network analysis further revealed that Bacillus and other Bacillota established a densely interconnected hub module in the grassland, characterised by positive associations indicating co-occurrence, a pattern not observed in the forest soil. Speculating that this difference was driven by abiotic factors, we combined amplicon sequencing with physico-chemical analysis of soil samples and found multiple chemical variables, mainly pH, to affect microbial composition. Our study pinpoints the factors that influence B. subtilis abundance in natural soils and, therefore, offers insights for designing B. subtilis-based biocontrol products in agricultural settings.
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Affiliation(s)
- Xinming Xu
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Adele Pioppi
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Heiko T Kiesewalter
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Mikael Lenz Strube
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Ákos T Kovács
- DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
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47
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Ebrahimi H, Dizman N, Meza L, Malhotra J, Li X, Dorff T, Frankel P, Llamas-Quitiquit M, Hsu J, Zengin ZB, Alcantara M, Castro D, Mercier B, Chawla N, Chehrazi-Raffle A, Barragan-Carrillo R, Jaime-Casas S, Govindarajan A, Gillece J, Trent J, Lee PP, Parks TP, Takahashi M, Hayashi A, Kortylewski M, Caporaso JG, Lee K, Tripathi A, Pal SK. Cabozantinib and nivolumab with or without live bacterial supplementation in metastatic renal cell carcinoma: a randomized phase 1 trial. Nat Med 2024; 30:2576-2585. [PMID: 38942995 PMCID: PMC11405272 DOI: 10.1038/s41591-024-03086-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/23/2024] [Indexed: 06/30/2024]
Abstract
Supplementation with CBM588, a bifidogenic live bacterial product, has been associated with improved clinical outcomes in persons with metastatic renal cell carcinoma (mRCC) receiving nivolumab and ipilimumab. However, its effect on those receiving tyrosine kinase inhibitor-based combinations is unknown. In this open-label, randomized, investigator-initiated, phase 1 study, 30 participants with locally advanced or mRCC with histological confirmation of clear cell, papillary or sarcomatoid component were randomized in a 2:1 fashion to receive cabozantinib (an inhibitor of vascular endothelial growth factor receptor, MET and AXL) and nivolumab (anti-programmed cell death protein 1) with or without CBM588 as first-line treatment. Metagenomic sequencing was performed on stool samples to characterize their gut microbiome at baseline and 13 weeks into treatment. The primary endpoint was a change in the relative abundance of Bifidobacterium spp.; secondary endpoints included objective response rate (ORR), progression-free survival (PFS) and toxicity profile. The primary endpoint of the study was not met and the addition of CBM588 to cabozantinib and nivolumab did not result in a difference in the relative abundance of Bifidobacterium spp. or alpha diversity (as measured by the Shannon index). However, ORR was significantly higher in participants treated with CBM588 compared to those in the control arm (14 of 19, 74% versus 2 of 10, 20%; P = 0.01). PFS at 6 months was 84% (16 of 19) and 60% (6 of 10) in the experimental and control arms, respectively. No significant difference in toxicity profile was seen between the study arms. Our results provide a preliminary signal of improved clinical activity with CBM588 in treatment-naive participants with mRCC receiving cabozantinib and nivolumab. Further investigation is needed to confirm these findings and better characterize the underlying mechanism driving this effect.ClinicalTrials.gov identifier: NCT05122546.
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Affiliation(s)
- Hedyeh Ebrahimi
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Nazli Dizman
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- MD Anderson Cancer Center, Houston, TX, USA
| | - Luis Meza
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Jasnoor Malhotra
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Xiaochen Li
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Tanya Dorff
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Paul Frankel
- Department of Biostatistics, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Joann Hsu
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Zeynep B Zengin
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Marice Alcantara
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Daniela Castro
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Benjamin Mercier
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Neal Chawla
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Alex Chehrazi-Raffle
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Salvador Jaime-Casas
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ameish Govindarajan
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - John Gillece
- Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Jeffrey Trent
- Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Peter P Lee
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | | | | | - Marcin Kortylewski
- Department of Immuno-Oncology, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | | | - Keehoon Lee
- Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
| | - Abhishek Tripathi
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
| | - Sumanta K Pal
- Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
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48
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Glendinning L, Wu Z, Vervelde L, Watson M, Balic A. Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota. Microb Genom 2024; 10. [PMID: 39222347 DOI: 10.1099/mgen.0.001289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
The chicken immune system and microbiota play vital roles in maintaining gut homeostasis and protecting against pathogens. In mammals, XCR1+ conventional dendritic cells (cDCs) are located in the gut-draining lymph nodes and play a major role in gut homeostasis. These cDCs sample antigens in the gut luminal contents and limit the inflammatory response to gut commensal microbes by generating appropriate regulatory and effector T-cell responses. We hypothesized that these cells play similar roles in sustaining gut homeostasis in chickens, and that chickens lacking XCR1 were likely to contain a dysbiotic caecal microbiota. Here we compare the caecal microbiota of chickens that were either heterozygous or homozygous XCR1 knockouts, that had or had not been vaccinated for infectious bronchitis virus (IBV). We used short-read (Illumina) and long-read (PacBio HiFi) metagenomic sequencing to reconstruct 670 high-quality, strain-level metagenome assembled genomes. We found no significant differences between alpha diversity or the abundance of specific microbial taxa between genotypes. However, IBV vaccination was found to correlate with significant differences in the richness and beta diversity of the microbiota, and to the abundance of 40 bacterial genera. In conclusion, we found that a lack of XCR1 was not correlated with significant changes in the chicken microbiota, but IBV vaccination was.
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Affiliation(s)
| | - Zhiguang Wu
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Lonneke Vervelde
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Royal GD Animal Health, Deventer, Netherlands
| | - Mick Watson
- Centre for Digital Innovation, DSM Biotechnology Centre, Delft, Netherlands
- Scotland's Rural College, Peter Wilson Building, King's Buildings, Edinburgh, UK
| | - Adam Balic
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
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49
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Eterovick PC, Schmidt R, Sabino-Pinto J, Yang C, Künzel S, Ruthsatz K. The microbiome at the interface between environmental stress and animal health: an example from the most threatened vertebrate group. Proc Biol Sci 2024; 291:20240917. [PMID: 39291456 PMCID: PMC11409201 DOI: 10.1098/rspb.2024.0917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 06/05/2024] [Accepted: 07/25/2024] [Indexed: 09/19/2024] Open
Abstract
Nitrate pollution and global warming are ubiquitous stressors likely to interact and affect the health and survival of wildlife, particularly aquatic ectotherms. Animal health is largely influenced by its microbiome (commensal/symbiotic microorganisms), which responds to such stressors. We used a crossed experimental design including three nitrate levels and five temperature regimes to investigate their interactive and individual effects on an aquatic ectotherm, the European common frog. We associated health biomarkers in larvae with changes in gut bacteria diversity and composition. Larvae experienced higher stress levels and lower body condition under high temperatures and nitrate exposure. Developmental rate increased with temperature but decreased with nitrate pollution. Alterations in bacteria composition but not diversity are likely to correlate with the observed outcomes in larvae health. Leucine degradation decreased at higher temperatures corroborating accelerated development, nitrate degradation increased with nitrate level corroborating reduced body condition and an increase in lysine biosynthesis may have helped larvae deal with the combined effects of both stressors. These results reinforce the importance of associating traditional health biomarkers with underlying microbiome changes. Therefore, we urge studies to investigate the effects of environmental stressors on microbiome composition and consequences for host health in a world threatened by biodiversity loss.
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Affiliation(s)
- Paula Cabral Eterovick
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106, Braunschweig, Germany
| | - Robin Schmidt
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106, Braunschweig, Germany
| | - Joana Sabino-Pinto
- GELIFES—Groningen Institute for Evolutionary Life Sciences, University of Groningen, 9747, AG Groningen, The Netherlands
| | - Chen Yang
- Department of Biostatistics, Southern Medical University, 510515, Guangzhou, People’s Republic of China
| | - Sven Künzel
- Max-Planck-Institut für Evolutionsbiologie, 24306, Plön, Germany
| | - Katharina Ruthsatz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstraße 4, 38106, Braunschweig, Germany
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50
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Blasco-Lavilla N, López-López A, De la Rúa P, Barribeau SM. Infection by Crithidia bombi increases relative abundance of Lactobacillus spp. in the gut of Bombus terrestris. Mol Ecol 2024; 33:e17478. [PMID: 39075965 DOI: 10.1111/mec.17478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/31/2024]
Abstract
Gut microbial communities confer protection against natural pathogens in important pollinators from the genera Bombus and Apis. In commercial species B. terrestris and B. impatiens, the microbiota increases their resistance to the common and virulent trypanosomatid parasite Crithidia bombi. However, the mechanisms by which gut microorganisms protect the host are still unknown. Here, we test two hypotheses: microbiota protect the host (1) through stimulation of its immune response or protection of the gut epithelium and (2) by competing for resources with the parasite inside the gut. To test them, we reduced the microbiota of workers and then rescued the microbial community by feeding them with microbiota supplements. We then exposed them to an infectious dose of C. bombi and characterised gene expression and gut microbiota composition. We examined the expression of three antimicrobial peptide genes and Mucin-5AC, a gene with a putative role in gut epithelium protection, using qPCR. Although a protective effect against C. bombi was observed in bumblebees with supplemented microbiota, we did not observe an effect of the microbiota on gene expression that could explain alone the protective effect observed. On the other hand, we found an increased relative abundance of Lactobacillus bacteria within the gut of infected workers and a negative correlation of this genus with Gilliamella and Snodgrassella genera. Therefore, our results point to a displacement of bumblebee endosymbionts by C. bombi that might be caused by competition for space and nutrients between the parasite and the microbiota within the gut.
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Affiliation(s)
- Nuria Blasco-Lavilla
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, Murcia, Spain
- Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Alejandro López-López
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, Murcia, Spain
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Pilar De la Rúa
- Department of Zoology and Physical Anthropology, Faculty of Veterinary, University of Murcia, Murcia, Spain
| | - Seth Michael Barribeau
- Department of Ecology, Evolution and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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