151
|
van de Water JAJM, Allemand D, Ferrier‐Pagès C. Bacterial symbionts of the precious coral Corallium rubrum are differentially distributed across colony-specific compartments and differ among colormorphs. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13236. [PMID: 38444282 PMCID: PMC10915489 DOI: 10.1111/1758-2229.13236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/18/2024] [Indexed: 03/07/2024]
Abstract
Corals engage in symbioses with micro-organisms that provide nutrients and protect the host. Where the prokaryotic microbes perform their symbiotic functions within a coral is, however, poorly understood. Here, we studied the tissue-specific microbiota of the coral Corallium rubrum by dissecting its tissues from the skeleton and separating the white polyps from the red-coloured coenenchyme, followed by 16S rRNA gene metabarcoding of the three fractions. Dissection was facilitated by incubating coral fragments in RNAlater, which caused tissues to detach from the skeleton. Our results show compartmentalisation of the microbiota. Specifically, Endozoicomonas, Parcubacteria and a Gammaproteobacteria were primarily located in polyps, whereas Nitrincolaceae and one Spirochaeta phylotype were found mainly in the coenenchyme. The skeleton-associated microbiota was distinct from the microbiota in the tissues. Given the difference in tissue colour and microbiota of the polyps and coenenchyme, we analysed the microbiota of three colormorphs of C. rubrum (red, pink, white), finding that the main difference was a very low abundance of Spirochaeta in white colormorphs. While the functions of C. rubrum's symbionts are unknown, their localisation within the colony suggests that microhabitats exist, and the presence of Spirochaeta appears to be linked to the colour of C. rubrum.
Collapse
Affiliation(s)
- Jeroen A. J. M. van de Water
- Unité de Recherche sur la Biologie des Coraux Précieux CSM – CHANELCentre Scientifique de MonacoMonacoPrincipality of Monaco
- Coral Ecophysiology Team, Department of Marine BiologyCentre Scientifique de MonacoMonacoPrincipality of Monaco
- Department of Estuarine & Delta SystemsRoyal Netherlands Institute for Sea ResearchYersekeThe Netherlands
| | - Denis Allemand
- Centre Scientifique de MonacoMonacoPrincipality of Monaco
| | - Christine Ferrier‐Pagès
- Coral Ecophysiology Team, Department of Marine BiologyCentre Scientifique de MonacoMonacoPrincipality of Monaco
| |
Collapse
|
152
|
Vargas-Gastélum L, Romer AS, Ghotbi M, Dallas JW, Alexander NR, Moe KC, McPhail KL, Neuhaus GF, Shadmani L, Spatafora JW, Stajich JE, Tabima JF, Walker DM. Herptile gut microbiomes: a natural system to study multi-kingdom interactions between filamentous fungi and bacteria. mSphere 2024; 9:e0047523. [PMID: 38349154 PMCID: PMC10964425 DOI: 10.1128/msphere.00475-23] [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: 08/22/2023] [Accepted: 01/10/2024] [Indexed: 03/27/2024] Open
Abstract
Reptiles and amphibians (herptiles) are some of the most endangered and threatened species on the planet and numerous conservation strategies are being implemented with the goal of ensuring species recovery. Little is known, however, about the gut microbiome of wild herptiles and how it relates to the health of these populations. Here, we report results from the gut microbiome characterization of both a broad survey of herptiles, and the correlation between the fungus Basidiobolus, and the bacterial community supported by a deeper, more intensive sampling of Plethodon glutinosus, known as slimy salamanders. We demonstrate that bacterial communities sampled from frogs, lizards, and salamanders are structured by the host taxonomy and that Basidiobolus is a common and natural component of these wild gut microbiomes. Intensive sampling of multiple hosts across the ecoregions of Tennessee revealed that geography and host:geography interactions are strong predictors of distinct Basidiobolus operational taxonomic units present within a given host. Co-occurrence analyses of Basidiobolus and bacterial community diversity support a correlation and interaction between Basidiobolus and bacteria, suggesting that Basidiobolus may play a role in structuring the bacterial community. We further the hypothesis that this interaction is advanced by unique specialized metabolism originating from horizontal gene transfer from bacteria to Basidiobolus and demonstrate that Basidiobolus is capable of producing a diversity of specialized metabolites including small cyclic peptides.IMPORTANCEThis work significantly advances our understanding of biodiversity and microbial interactions in herptile microbiomes, the role that fungi play as a structural and functional members of herptile gut microbiomes, and the chemical functions that structure microbiome phenotypes. We also provide an important observational system of how the gut microbiome represents a unique environment that selects for novel metabolic functions through horizontal gene transfer between fungi and bacteria. Such studies are needed to better understand the complexity of gut microbiomes in nature and will inform conservation strategies for threatened species of herpetofauna.
Collapse
Affiliation(s)
- Lluvia Vargas-Gastélum
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Alexander S. Romer
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Marjan Ghotbi
- Research Division 3, Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - Jason W. Dallas
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - N. Reed Alexander
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kylie C. Moe
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Kerry L. McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - George F. Neuhaus
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, Oregon, USA
| | - Leila Shadmani
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Joseph W. Spatafora
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
- Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Javier F. Tabima
- Department of Biology, Clark University, Worcester, Massachusetts, USA
| | - Donald M. Walker
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| |
Collapse
|
153
|
Alvernaz SA, Wenzel ES, Nagelli U, Pezley LB, LaBomascus B, Gilbert JA, Maki PM, Tussing-Humphreys L, Peñalver Bernabé B. Inflammatory Dietary Potential Is Associated with Vitamin Depletion and Gut Microbial Dysbiosis in Early Pregnancy. Nutrients 2024; 16:935. [PMID: 38612969 PMCID: PMC11013194 DOI: 10.3390/nu16070935] [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: 02/20/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/14/2024] Open
Abstract
Pregnancy alters many physiological systems, including the maternal gut microbiota. Diet is a key regulator of this system and can alter the host immune system to promote inflammation. Multiple perinatal disorders have been associated with inflammation, maternal metabolic alterations, and gut microbial dysbiosis, including gestational diabetes mellitus, pre-eclampsia, preterm birth, and mood disorders. However, the effects of high-inflammatory diets on the gut microbiota during pregnancy have yet to be fully explored. We aimed to address this gap using a system-based approach to characterize associations among dietary inflammatory potential, a measure of diet quality, and the gut microbiome during pregnancy. Forty-seven pregnant persons were recruited prior to 16 weeks of gestation. Participants completed a food frequency questionnaire (FFQ) and provided fecal samples. Dietary inflammatory potential was assessed using the Dietary Inflammatory Index (DII) from the FFQ data. Fecal samples were analyzed using 16S rRNA amplicon sequencing. Differential taxon abundances with respect to the DII score were identified, and the microbial metabolic potential was predicted using PICRUSt2. Inflammatory diets were associated with decreased vitamin and mineral intake and a dysbiotic gut microbiota structure and predicted metabolism. Gut microbial compositional differences revealed a decrease in short-chain fatty acid producers such as Faecalibacterium, and an increase in predicted vitamin B12 synthesis, methylglyoxal detoxification, galactose metabolism, and multidrug efflux systems in pregnant individuals with increased DII scores. Dietary inflammatory potential was associated with a reduction in the consumption of vitamins and minerals and predicted gut microbiota metabolic dysregulation.
Collapse
Affiliation(s)
- Suzanne A. Alvernaz
- Department of Biomedical Engineering, University of Illinois, Chicago, IL 60607, USA; (S.A.A.); (U.N.)
| | - Elizabeth S. Wenzel
- Department of Psychology, University of Illinois, Chicago, IL 60607, USA; (E.S.W.); (P.M.M.)
| | - Unnathi Nagelli
- Department of Biomedical Engineering, University of Illinois, Chicago, IL 60607, USA; (S.A.A.); (U.N.)
| | - Lacey B. Pezley
- Department of Kinesiology and Nutrition, University of Illinois, Chicago, IL 60612, USA; (L.B.P.); (B.L.); (L.T.-H.)
| | - Bazil LaBomascus
- Department of Kinesiology and Nutrition, University of Illinois, Chicago, IL 60612, USA; (L.B.P.); (B.L.); (L.T.-H.)
| | - Jack A. Gilbert
- Department of Pediatrics, University of California, San Diego, CA 92093, USA;
- Scripps Oceanographic Institute, University of California, San Diego, CA 92037, USA
| | - Pauline M. Maki
- Department of Psychology, University of Illinois, Chicago, IL 60607, USA; (E.S.W.); (P.M.M.)
- Department of Psychiatry, University of Illinois, Chicago, IL 60612, USA
- Department of Obstetrics and Gynecology, University of Illinois, Chicago, IL 60612, USA
| | - Lisa Tussing-Humphreys
- Department of Kinesiology and Nutrition, University of Illinois, Chicago, IL 60612, USA; (L.B.P.); (B.L.); (L.T.-H.)
| | - Beatriz Peñalver Bernabé
- Department of Biomedical Engineering, University of Illinois, Chicago, IL 60607, USA; (S.A.A.); (U.N.)
- Center for Bioinformatics and Quantitative Biology, University of Illinois, Chicago, IL 60612, USA
| |
Collapse
|
154
|
Lapidot R, Faits T, Ismail A, Allam M, Khumalo Z, MacLeod W, Kwenda G, Mupila Z, Nakazwe R, Segrè D, Johnson WE, Thea DM, Mwananyanda L, Gill CJ. Nasopharyngeal Dysbiosis Precedes the Development of Lower Respiratory Tract Infections in Young Infants, a Longitudinal Infant Cohort Study. Gates Open Res 2024; 6:48. [PMID: 39050991 PMCID: PMC11266592 DOI: 10.12688/gatesopenres.13561.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/24/2024] [Indexed: 07/27/2024] Open
Abstract
Background Infants suffering from lower respiratory tract infections (LRTIs) have distinct nasopharyngeal (NP) microbiome profiles that correlate with severity of disease. Whether these profiles precede the infection or are a consequence of it, is unknown. In order to answer this question, longitudinal studies are needed. Methods We conducted a retrospective analysis of NP samples collected in a longitudinal birth cohort study of Zambian mother-infant pairs. Samples were collected every two weeks from 1-week through 14-weeks of age. Ten of the infants in the cohort who developed LRTI were matched 1:3 with healthy comparators. We completed 16S rRNA gene sequencing on the samples each of these infants contributed and compared the NP microbiome of the healthy infants to infants who developed LRTI. Results The infant NP microbiome maturation was characterized by transitioning from Staphylococcus dominant to respiratory-genera dominant profiles during the first three months of life, similar to what is described in the literature. Interestingly, infants who developed LRTI had distinct NP microbiome characteristics before infection, in most cases as early as the first week of life. Their NP microbiome was characterized by the presence of Novosphingobium, Delftia, high relative abundance of Anaerobacillus, Bacillus, and low relative abundance of Dolosigranulum, compared to the healthy controls. Mothers of infants with LRTI also had low relative abundance of Dolosigranulum in their baseline samples compared to mothers of infants that did not develop an LRTI. Conclusions Our results suggest that specific characteristics of the NP microbiome precede LRTI in young infants and may be present in their mothers as well. Early dysbiosis may play a role in the causal pathway leading to LRTI or could be a marker of underlying immunological, environmental, or genetic characteristics that predispose to LRTI.
Collapse
Affiliation(s)
- Rotem Lapidot
- Pediatric Infectious Diseases, Boston Medical Center, Boston, MA, 02118, USA
- Pediatrics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Tyler Faits
- Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, 2131, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, 2131, South Africa
| | - Zamantungwak Khumalo
- Sequencing Core Facility, National Institute for Communicable Diseases, Johannesburg, 2131, South Africa
- Department of Veterinary Tropical Diseases, University of Pretoria, Pretoria, 0002, South Africa
| | - William MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | | | - Ruth Nakazwe
- Department of Pathology and Microbiology, University Teaching Hospital, Lusaka, Zambia
| | - Daniel Segrè
- Bioinformatics Program and Biological Design Center, Boston University, Boston, MA, 02118, USA
- Department of Physics, Boston University, Boston, MA, 02118, USA
- Department of Biology, Boston University, Boston, MA, 02118, USA
- Department of Biomedical Engineering, Boston University, Boston, MA, 02118, USA
| | - William Evan Johnson
- Computational Biomedicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Donald M Thea
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | | | - Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, MA, 02118, USA
| |
Collapse
|
155
|
Ribeiro FA, Lau SK, Furbeck RA, Herrera NJ, Henriott ML, Bland NA, Fernando SC, Subbiah J, Pflanzer SB, Dinh TT, Miller RK, Sullivan GA, Calkins CR. Effects of relative humidity on dry-aged beef quality. Meat Sci 2024; 213:109498. [PMID: 38520828 DOI: 10.1016/j.meatsci.2024.109498] [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: 11/02/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
This study was conducted to evaluate the effects of relative humidity (RH) on moisture loss and flavor in dry-aged beef. Sixteen strip loins were assigned to one of the four aging treatments: vacuum (WET), dry-aging at 50% RH, dry-aging at 70% RH, or dry-aging at 85% RH and aged for 42 days at 2 °C. Loins were evaluated for evaporation loss, trim loss, tenderness, sensory, and microbiological characteristics. Results show that lower RH results in accelerated moisture loss during the first 3 days of the aging process without significantly affecting the total amount of moisture loss. Pseudomonadales dominated the aerobically dry-aged loins while Enterobacteriales was the most abundant in the wet-aged samples. Dry-aged samples had increased content of free amino acids in the cooked meat juice compared to the wet-aged counterpart. Dry aging at 50% RH tended to associate with more desirable flavor notes.
Collapse
Affiliation(s)
- Felipe A Ribeiro
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, United States
| | - Soon K Lau
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588-6205, United States; Department of Biological Systems Engineering, University of Nebraska, Lincoln, NE 68583-0726, United States
| | - Rebecca A Furbeck
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, United States
| | - Nicolas J Herrera
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, United States
| | - Morgan L Henriott
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, United States
| | - Nicolas A Bland
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, United States
| | - Samodha C Fernando
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, United States
| | - Jeyamkondan Subbiah
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588-6205, United States; Department of Biological Systems Engineering, University of Nebraska, Lincoln, NE 68583-0726, United States; Department of Food Science, University of Arkansas, Fayetteville, AR 72704, United States
| | - Sérgio B Pflanzer
- College of Food Engineering, Department of Food Technology, University of Campinas, Campinas, São Paulo 13083-862, Brazil
| | - Thu T Dinh
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS 39762, United States
| | - Rhonda K Miller
- Texas A&M University Animal Science Department, 2471 TAMU, College Station, TX 77843, United States
| | - Gary A Sullivan
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, United States
| | - Chris R Calkins
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, United States.
| |
Collapse
|
156
|
Ricci F, Leggat W, Pasella MM, Bridge T, Horowitz J, Girguis PR, Ainsworth T. Deep sea treasures - Insights from museum archives shed light on coral microbial diversity within deepest ocean ecosystems. Heliyon 2024; 10:e27513. [PMID: 38468949 PMCID: PMC10926130 DOI: 10.1016/j.heliyon.2024.e27513] [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: 04/26/2023] [Revised: 02/15/2024] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
Deep sea benthic habitats are low productivity ecosystems that host an abundance of organisms within the Cnidaria phylum. The technical limitations and the high cost of deep sea surveys have made exploring deep sea environments and the biology of the organisms that inhabit them challenging. In spite of the widespread recognition of Cnidaria's environmental importance in these ecosystems, the microbial assemblage and its role in coral functioning have only been studied for a few deep water corals. Here, we explored the microbial diversity of deep sea corals by recovering nucleic acids from museum archive specimens. Firstly, we amplified and sequenced the V1-V3 regions of the 16S rRNA gene of these specimens, then we utilized the generated sequences to shed light on the microbial diversity associated with seven families of corals collected from depth in the Coral Sea (depth range 1309 to 2959 m) and Southern Ocean (depth range 1401 to 2071 m) benthic habitats. Surprisingly, Cyanobacteria sequences were consistently associated with six out of seven coral families from both sampling locations, suggesting that these bacteria are potentially ubiquitous members of the microbiome within these cold and deep sea water corals. Additionally, we show that Cnidaria might benefit from symbiotic associations with a range of chemosynthetic bacteria including nitrite, carbon monoxide and sulfur oxidizers. Consistent with previous studies, we show that sequences associated with the bacterial phyla Proteobacteria, Verrucomicrobia, Planctomycetes and Acidobacteriota dominated the microbial community of corals in the deep sea. We also explored genomes of the bacterial genus Mycoplasma, which we identified as associated with specimens of three deep sea coral families, finding evidence that these bacteria may aid the host immune system. Importantly our results show that museum specimens retain components of host microbiome that can provide new insights into the diversity of deep sea coral microbiomes (and potentially other organisms), as well as the diversity of microbes writ large in deep sea ecosystems.
Collapse
Affiliation(s)
- Francesco Ricci
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington, NSW, Australia
- University of Melbourne, School of Biosciences, Parkville, VIC, Australia
- Monash University, Department of Microbiology, Biomedicine Discovery Institute, Clayton, VIC, Australia
| | - William Leggat
- University of Newcastle, School of Environmental and Life Sciences, Callaghan, NSW, Australia
| | - Marisa M. Pasella
- University of Melbourne, School of Biosciences, Parkville, VIC, Australia
| | - Tom Bridge
- Biodiversity and Geosciences Program, Museum of Tropical Queensland, Queensland Museum, Townsville, QLD, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
| | - Jeremy Horowitz
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
- Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Peter R. Girguis
- University of Harvard, Department of Organismic and Evolutionary Biology, Cambridge, MA, USA
| | - Tracy Ainsworth
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington, NSW, Australia
| |
Collapse
|
157
|
Stante M, Weiland-Bräuer N, von Hoyningen-Huene AJE, Schmitz RA. Marine bacteriophages disturb the associated microbiota of Aurelia aurita with a recoverable effect on host morphology. Front Microbiol 2024; 15:1356337. [PMID: 38533338 PMCID: PMC10964490 DOI: 10.3389/fmicb.2024.1356337] [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: 12/15/2023] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
The concept of the metaorganism describes a multicellular host and its diverse microbial community, which form one biological unit with a combined genetic repertoire that significantly influences health and survival of the host. The present study delved into the emerging field of bacteriophage research within metaorganisms, focusing on the moon jellyfish Aurelia aurita as a model organism. The previously isolated Pseudomonas phage BSwM KMM1 and Citrobacter phages BSwM KMM2 - KMM4 demonstrated potent infectivity on bacteria present in the A. aurita-associated microbiota. In a host-fitness experiment, Baltic Sea subpopulation polyps were exposed to individual phages and a phage cocktail, monitoring polyp survival and morphology, as well as microbiome changes. The following effects were obtained. First, phage exposure in general led to recoverable malformations in polyps without affecting their survival. Second, analyses of the community structure, using 16S rRNA amplicon sequencing, revealed alterations in the associated microbial community in response to phage exposure. Third, the native microbiota is dominated by an uncultured likely novel Mycoplasma species, potentially specific to A. aurita. Notably, this main colonizer showed resilience through the recovery after initial declines, which aligned with abundance changes in Bacteroidota and Proteobacteria, suggesting a dynamic and adaptable microbial community. Overall, this study demonstrates the resilience of the A. aurita metaorganism facing phage-induced perturbations, emphasizing the importance of understanding host-phage interactions in metaorganism biology. These findings have implications for ecological adaptation and conservation in the rapidly changing marine environment, particularly regarding the regulation of blooming species and the health of marine ecosystems during ongoing environmental changes.
Collapse
Affiliation(s)
| | | | | | - Ruth Anne Schmitz
- Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany
| |
Collapse
|
158
|
Lackner S, Mahnert A, Moissl-Eichinger C, Madl T, Habisch H, Meier-Allard N, Kumpitsch C, Lahousen T, Kohlhammer-Dohr A, Mörkl S, Strobl H, Holasek S. Interindividual differences in aronia juice tolerability linked to gut microbiome and metabolome changes-secondary analysis of a randomized placebo-controlled parallel intervention trial. MICROBIOME 2024; 12:49. [PMID: 38461313 PMCID: PMC10924357 DOI: 10.1186/s40168-024-01774-4] [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: 07/11/2023] [Accepted: 02/05/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Aronia melanocarpa is a berry rich in polyphenols known for health benefits. However, the bioavailability of polyphenols has been questioned, and the individual taste acceptance of the fruit with its specific flavor varies. We recently observed substantial differences in the tolerability of aronia juice among healthy females, with half of the individuals tolerating aronia juice without complaints. Given the importance of the gut microbiome in food digestion, we investigated in this secondary analysis of the randomized placebo-controlled parallel intervention study (ClinicalTrials.gov registration: NCT05432362) if aronia juice tolerability was associated with changes in intestinal microbiota and bacterial metabolites, seeking for potential mechanistic insights into the impact on aronia polyphenol tolerance and metabolic outcomes. RESULTS Forty females were enrolled for this 6-week trial, receiving either 100 ml natural aronia juice (verum, V) twice daily or a polyphenol-free placebo (P) with a similar nutritional profile, followed by a 6-week washout. Within V, individuals were categorized into those who tolerated the juice well (Vt) or reported complaints (Vc). The gut microbiome diversity, as analyzed by 16S rRNA gene-based next-generation sequencing, remained unaltered in Vc but changed significantly in Vt. A MICOM-based flux balance analysis revealed pronounced differences in the 40 most predictive metabolites post-intervention. In Vc carbon-dioxide, ammonium and nine O-glycans were predicted due to a shift in microbial composition, while in Vt six bile acids were the most likely microbiota-derived metabolites. NMR metabolomics of plasma confirmed increased lipoprotein subclasses (LDL, VLDL) post-intervention, reverting after wash out. Stool samples maintained a stable metabolic profile. CONCLUSION In linking aronia polyphenol tolerance to gut microbiota-derived metabolites, our study explores adaptive processes affecting lipoprotein profiles during high polyphenol ingestion in Vt and examines effects on mucosal gut health in response to intolerance to high polyphenol intake in Vc. Our results underpin the importance of individualized hormetic dosing for beneficial polyphenol effects, demonstrate dynamic gut microbiome responses to aronia juice, and emphasize personalized responses in polyphenol interventions.
Collapse
Affiliation(s)
- Sonja Lackner
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Tobias Madl
- Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Hansjörg Habisch
- Division of Medicinal Chemistry, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Nathalie Meier-Allard
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Neue Stiftingtalstraße 6, 8010, Graz, Austria
| | - Theresa Lahousen
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Auenbruggerplatz 31, 8036, Graz, Austria
| | - Alexandra Kohlhammer-Dohr
- Department of Psychiatry and Psychotherapeutic Medicine, Medical University of Graz, Auenbruggerplatz 31, 8036, Graz, Austria
| | - Sabrina Mörkl
- Division of Medical Psychology, Psychosomatics and Psychotherapeutic Medicine, Auenbruggerplatz 3, 8036, Graz, Austria
| | - Herbert Strobl
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria
| | - Sandra Holasek
- Division of Immunology, Otto Loewi Research Center for Vascular Biology, Immunology and Inflammation, Medical University of Graz, Stiftingtalstraße 6, 8010, Graz, Austria.
| |
Collapse
|
159
|
Pearman WS, Duffy GA, Liu XP, Gemmell NJ, Morales SE, Fraser CI. Macroalgal microbiome biogeography is shaped by environmental drivers rather than geographical distance. ANNALS OF BOTANY 2024; 133:169-182. [PMID: 37804485 PMCID: PMC10921836 DOI: 10.1093/aob/mcad151] [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: 07/06/2023] [Accepted: 10/06/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND AND AIMS Contrasting patterns of host and microbiome biogeography can provide insight into the drivers of microbial community assembly. Distance-decay relationships are a classic biogeographical pattern shaped by interactions between selective and non-selective processes. Joint biogeography of microbiomes and their hosts is of increasing interest owing to the potential for microbiome-facilitated adaptation. METHODS In this study, we examine the coupled biogeography of the model macroalga Durvillaea and its microbiome using a combination of genotyping by sequencing (host) and 16S rRNA amplicon sequencing (microbiome). Alongside these approaches, we use environmental data to characterize the relationship between the microbiome, the host, and the environment. KEY RESULTS We show that although the host and microbiome exhibit shared biogeographical structure, these arise from different processes, with host biogeography showing classic signs of geographical distance decay, but with the microbiome showing environmental distance decay. Examination of microbial subcommunities, defined by abundance, revealed that the abundance of microbes is linked to environmental selection. As microbes become less common, the dominant ecological processes shift away from selective processes and towards neutral processes. Contrary to expectations, we found that ecological drift does not promote structuring of the microbiome. CONCLUSIONS Our results suggest that although host macroalgae exhibit a relatively 'typical' biogeographical pattern of declining similarity with increasing geographical distance, the microbiome is more variable and is shaped primarily by environmental conditions. Our findings suggest that the Baas Becking hypothesis of 'everything is everywhere, the environment selects' might be a useful hypothesis to understand the biogeography of macroalgal microbiomes. As environmental conditions change in response to anthropogenic influences, the processes structuring the microbiome of macroalgae might shift, whereas those governing the host biogeography are less likely to change. As a result, increasingly decoupled host-microbe biogeography might be observed in response to such human influences.
Collapse
Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, New Zealand
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, New Zealand
| | - Grant A Duffy
- Department of Marine Science, University of Otago, New Zealand
| | - Xiaoyue P Liu
- Department of Marine Science, University of Otago, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, New Zealand
| | - Sergio E Morales
- Department of Microbiology & Immunology, School of Biomedical Sciences, University of Otago, New Zealand
| | | |
Collapse
|
160
|
Mishra S, Tejesvi MV, Hekkala J, Turunen J, Kandikanti N, Kaisanlahti A, Suokas M, Leppä S, Vihinen P, Kuitunen H, Sunela K, Koivunen J, Jukkola A, Kalashnikov I, Auvinen P, Kääriäinen OS, Peñate Medina T, Peñate Medina O, Saarnio J, Meriläinen S, Rautio T, Aro R, Häivälä R, Suojanen J, Laine M, Erawijattari PP, Lahti L, Karihtala P, Ruuska TS, Reunanen J. Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours. J Adv Res 2024:S2090-1232(24)00090-0. [PMID: 38458256 DOI: 10.1016/j.jare.2024.03.003] [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: 12/21/2023] [Revised: 02/17/2024] [Accepted: 03/06/2024] [Indexed: 03/10/2024] Open
Abstract
INTRODUCTION Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnered interest as promising tools for studying the link between the gut microbiome and human health. The diverse composition of bEVs, including their proteins, mRNAs, metabolites, and lipids, makes them useful for investigating diseases such as cancer. However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbiome communication. In clinical microbiome research, there is a gap in the knowledge on the role of bEVs in solid tumor patients. OBJECTIVES Analyzing the functionality of bEVs using (meta)genomics and proteomics could highlight the unique aspects of host-gut microbiome interactions in solid tumor patients. Therefore, we performed a comparative analysis of the proteome and microbiota composition of gut microbiome-derived bEVs isolated from patients with solid tumors and healthy controls. METHODS After isolating bEVs from the feces of solid tumor patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of feces from patients and controls using 16S sequencing and used machine learning to classify the samples into patients and controls based on their bEVs and fecal microbiomes. RESULTS Solid tumor patients showed decreased microbiota richness and diversity in both the bEVs and feces. However, the bEV proteomes were more diverse in patients than in the controls and were enriched with proteins associated with the metabolism of amino acids and carbohydrates, nucleotide binding, and oxidoreductase activity. Metadata classification of samples was more accurate using fecal bEVs (100%) compared with fecal samples (93%). CONCLUSION Our findings suggest that bEVs are unique functional entities. There is a need to explore bEVs together with conventional gut microbiome analysis in functional cancer research to decipher the potential of bEVs as cancer diagnostic or therapeutic biomarkers.
Collapse
Affiliation(s)
- Surbhi Mishra
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Mysore Vishakantegowda Tejesvi
- Biocenter Oulu, University of Oulu, Oulu, Finland; Ecology and Genetics, Faculty of Science, University of Oulu, Oulu, Finland
| | - Jenni Hekkala
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Jenni Turunen
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Niyati Kandikanti
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
| | - Anna Kaisanlahti
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marko Suokas
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Sirpa Leppä
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Pia Vihinen
- FICAN West Cancer Centre and Department of Oncology, Turku University Hospital and University of Turku, 20521 Turku, Finland
| | - Hanne Kuitunen
- Department of Oncology, Oulu University Hospital, Oulu, Finland
| | | | - Jussi Koivunen
- Department of Medical Oncology and Radiotherapy and Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Arja Jukkola
- Tampere Cancer Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ilja Kalashnikov
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland; Research Program Unit, Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Päivi Auvinen
- Cancer Center, Kuopio University Hospital, Northern Savonia Healthcare Municipality, Kuopio, Finland
| | - Okko-Sakari Kääriäinen
- Cancer Center, Kuopio University Hospital, Northern Savonia Healthcare Municipality, Kuopio, Finland
| | - T Peñate Medina
- Section Biomedical Imaging, Department of Radiology and Neuroradiology and Institute for Experimental Cancer Research, Kiel University, 24105 Kiel, Germany
| | - O Peñate Medina
- Section Biomedical Imaging, Department of Radiology and Neuroradiology and Institute for Experimental Cancer Research, Kiel University, 24105 Kiel, Germany; Lonza Netherlands B.V., 6167 RB Geleen, the Netherlands
| | - Juha Saarnio
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Sanna Meriläinen
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Tero Rautio
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Raila Aro
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Reetta Häivälä
- Translational Medicine Research Unit, Medical Research Center Oulu, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Juho Suojanen
- Päijät-Häme Joint Authority for Health and Wellbeing, Department of Oral and Maxillofacial Surgery, Lahti Central Hospital, 15850 Lahti, Finland; Cleft Palate and Craniofacial Centre, Department of Plastic Surgery, Helsinki University Hospital, 00029 Helsinki, Finland; Clinicum, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland
| | - Mikael Laine
- Department of Abdominal Surgery, Porvoo Hospital, Hospital District of Helsinki and Uusimaa, Porvoo, Finland
| | | | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Peeter Karihtala
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland; Department of Oncology, Oulu University Hospital, Oulu, Finland
| | - Terhi S Ruuska
- Biocenter Oulu, University of Oulu, Oulu, Finland; Research Unit of Clinical Medicine, University of Oulu, Oulu, Finland; Department of Pediatrics and Adolescent Medicine, Oulu University Hospital, Oulu, Finland
| | - Justus Reunanen
- Research Unit of Translational Medicine, University of Oulu, Oulu, Finland; Biocenter Oulu, University of Oulu, Oulu, Finland
| |
Collapse
|
161
|
Rizzello F, Viciani E, Gionchetti P, Filippone E, Imbesi V, Melotti L, Dussias NK, Salice M, Santacroce B, Padella A, Velichevskaya A, Marcante A, Castagnetti A. Signatures of disease outcome severity in the intestinal fungal and bacterial microbiome of COVID-19 patients. Front Cell Infect Microbiol 2024; 14:1352202. [PMID: 38510960 PMCID: PMC10952111 DOI: 10.3389/fcimb.2024.1352202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Background COVID-19, whose causative pathogen is the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic in March 2020. The gastrointestinal tract is one of the targets of this virus, and mounting evidence suggests that gastrointestinal symptoms may contribute to disease severity. The gut-lung axis is involved in the immune response to SARS-CoV-2; therefore, we investigated whether COVID-19 patients' bacterial and fungal gut microbiome composition was linked to disease clinical outcome. Methods In May 2020, we collected stool samples and patient records from 24 hospitalized patients with laboratory-confirmed SARS-CoV-2 infection. Fungal and bacterial gut microbiome was characterized by amplicon sequencing on the MiSeq, Illumina's integrated next generation sequencing instrument. A cohort of 201 age- and sex-matched healthy volunteers from the project PRJNA661289 was used as a control group for the bacterial gut microbiota analysis. Results We observed that female COVID-19 patients had a lower gut bacterial microbiota richness than male patients, which was consistent with a different latency in hospital admittance time between the two groups. Both sexes in the COVID-19 patient study group displayed multiple positive associations with opportunistic bacterial pathogens such as Enterococcus, Streptococcus, and Actinomyces. Of note, the Candida genus dominated the gut mycobiota of COVID-19 patients, and adult patients showed a higher intestinal fungal diversity than elderly patients. We found that Saccharomycetales unassigned fungal genera were positively associated with bacterial short-chain fatty acid (SCFA) producers and negatively associated with the proinflammatory genus Bilophila in COVID-19 patients, and we observed that none of the patients who harbored it were admitted to the high-intensity unit. Conclusions COVID-19 was associated with opportunistic bacterial pathogens, and Candida was the dominant fungal taxon in the intestine. Together, we found an association between commensal SCFA-producers and a fungal genus that was present in the intestines of patients who did not experience the most severe outcome of the disease. We believe that this taxon could have played a role in the disease outcome, and that further studies should be conducted to understand the role of fungi in gastrointestinal and health protection.
Collapse
Affiliation(s)
- Fernando Rizzello
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | | | - Paolo Gionchetti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Eleonora Filippone
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Veronica Imbesi
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
| | - Laura Melotti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Nikolas Konstantine Dussias
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Marco Salice
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
| | | | | | | | | | | |
Collapse
|
162
|
Forsyth CB, Shaikh M, Engen PA, Preuss F, Naqib A, Palmen BA, Green SJ, Zhang L, Bogin ZR, Lawrence K, Sharma D, Swanson GR, Bishehsari F, Voigt RM, Keshavarzian A. Evidence that the loss of colonic anti-microbial peptides may promote dysbiotic Gram-negative inflammaging-associated bacteria in aging mice. FRONTIERS IN AGING 2024; 5:1352299. [PMID: 38501032 PMCID: PMC10945560 DOI: 10.3389/fragi.2024.1352299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/02/2024] [Indexed: 03/20/2024]
Abstract
Introduction: Aging studies in humans and mice have played a key role in understanding the intestinal microbiome and an increased abundance of "inflammaging" Gram-negative (Gn) bacteria. The mechanisms underlying this inflammatory profile in the aging microbiome are unknown. We tested the hypothesis that an aging-related decrease in colonic crypt epithelial cell anti-microbial peptide (AMP) gene expression could promote colonic microbiome inflammatory Gn dysbiosis and inflammaging. Methods: As a model of aging, C57BL/6J mice fecal (colonic) microbiota (16S) and isolated colonic crypt epithelial cell gene expression (RNA-seq) were assessed at 2 months (mth) (human: 18 years old; yo), 15 mth (human: 50 yo), and 25 mth (human: 84 yo). Informatics examined aging-related microbial compositions, differential colonic crypt epithelial cell gene expressions, and correlations between colonic bacteria and colonic crypt epithelial cell gene expressions. Results: Fecal microbiota exhibited significantly increased relative abundances of pro-inflammatory Gn bacteria with aging. Colonic crypt epithelial cell gene expression analysis showed significant age-related downregulation of key AMP genes that repress the growth of Gn bacteria. The aging-related decrease in AMP gene expressions is significantly correlated with an increased abundance in Gn bacteria (dysbiosis), loss of colonic barrier gene expression, and senescence- and inflammation-related gene expression. Conclusion: This study supports the proposed model that aging-related loss of colonic crypt epithelial cell AMP gene expression promotes increased relative abundances of Gn inflammaging-associated bacteria and gene expression markers of colonic inflammaging. These data may support new targets for aging-related therapies based on intestinal genes and microbiomes.
Collapse
Affiliation(s)
- Christopher B. Forsyth
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
| | - Maliha Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Phillip A. Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Fabian Preuss
- Department of Biological Sciences, University of Wisconsin Parkside, Kenosha, WI, United States
| | - Ankur Naqib
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, United States
| | - Breanna A. Palmen
- Department of Biological Sciences, University of Wisconsin Parkside, Kenosha, WI, United States
| | - Stefan J. Green
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, IL, United States
| | - Lijuan Zhang
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Zlata R. Bogin
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Kristi Lawrence
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Deepak Sharma
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Garth R. Swanson
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
| | - Faraz Bishehsari
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
| | - Robin M. Voigt
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
| | - Ali Keshavarzian
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, IL, United States
- Department of Physiology, Rush University Medical Center, Chicago, IL, United States
| |
Collapse
|
163
|
Pearman WS, Morales SE, Vaux F, Gemmell NJ, Fraser CI. Host population crashes disrupt the diversity of associated marine microbiomes. Environ Microbiol 2024; 26:e16611. [PMID: 38519875 DOI: 10.1111/1462-2920.16611] [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: 11/05/2023] [Accepted: 03/01/2024] [Indexed: 03/25/2024]
Abstract
Host-associated microbial communities are shaped by myriad factors ranging from host conditions, environmental conditions and other microbes. Disentangling the ecological impact of each of these factors can be particularly difficult as many variables are correlated. Here, we leveraged earthquake-induced changes in host population structure to assess the influence of population crashes on marine microbial ecosystems. A large (7.8 magnitude) earthquake in New Zealand in 2016 led to widespread coastal uplift of up to ~6 m, sufficient to locally extirpate some intertidal southern bull kelp populations. These uplifted populations are slowly recovering, but remain at much lower densities than at nearby, less-uplifted sites. By comparing the microbial communities of the hosts from disturbed and relatively undisturbed populations using 16S rRNA gene amplicon sequencing, we observed that disturbed host populations supported higher functional, taxonomic and phylogenetic microbial beta diversity than non-disturbed host populations. Our findings shed light on microbiome ecological assembly processes, particularly highlighting that large-scale disturbances that affect host populations can dramatically influence microbiome structure. We suggest that disturbance-induced changes in host density limit the dispersal opportunities of microbes, with host community connectivity declining with the density of host populations.
Collapse
Affiliation(s)
- William S Pearman
- Department of Marine Science, University of Otago, Dunedin, New Zealand
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- National Institute of Water and Atmospheric Research Ltd, Auckland, New Zealand
| | - Sergio E Morales
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Felix Vaux
- National Institute of Water and Atmospheric Research Ltd, Auckland, New Zealand
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ceridwen I Fraser
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| |
Collapse
|
164
|
Balboni A, Franzo G, Bano L, Urbani L, Segatore S, Rizzardi A, Cordioli B, Cornaggia M, Terrusi A, Vasylyeva K, Dondi F, Battilani M. No viable bacterial communities reside in the urinary bladder of cats with feline idiopathic cystitis. Res Vet Sci 2024; 168:105137. [PMID: 38181480 DOI: 10.1016/j.rvsc.2024.105137] [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: 05/24/2023] [Revised: 12/22/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Urinary microbial diversities have been reported in humans according to sex, age and clinical status, including painful bladder syndrome/interstitial cystitis (PBS/IC). To date, the role of the urinary microbiome in the pathogenesis of PBS/IC is debated. Feline idiopathic cystitis (FIC) is a chronic lower urinary tract disorder affecting cats with similarities to PBS/IC in women and represents an important problem in veterinary medicine as its aetiology is currently unknown. In this study, the presence of a bacterial community residing in the urinary bladder of cats with a diagnosis of FIC was investigated. Nineteen cats with clinical signs and history of FIC and without growing bacteria in standard urine culture were included and urine collected with ultrasound-guided cystocentesis. Bacterial community was investigated using a culture-dependent approach consisted of expanded quantitative urine culture techniques and a culture-independent approach consisted of 16S rRNA NGS. Several methodological practices were adopted to both avoid and detect any contamination or bias introduced by means of urine collection and processing which could be relevant due to the low microbial biomass environment of the bladder and urinary tract, including negative controls analysis. All the cats included showed no growing bacteria in the urine analysed. Although few reads were originated using 16S rRNA NGS, a comparable pattern was observed between urine samples and negative controls, and no taxa were confidently classified as non-contaminant. The results obtained suggest the absence of viable bacteria and of bacterial DNA of urinary origin in the urinary bladder of cats with FIC.
Collapse
Affiliation(s)
- Andrea Balboni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padova, Viale dell'Università 16, 35020, Legnaro, Padova, Italy
| | - Luca Bano
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Lorenza Urbani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Sofia Segatore
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Alessia Rizzardi
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Benedetta Cordioli
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Matteo Cornaggia
- Diagnostic and Microbiology Laboratory, Istituto Zooprofilattico Sperimentale delle Venezie, Vicolo Mazzini 4, 31020, Villorba, Treviso, Italy
| | - Alessia Terrusi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Kateryna Vasylyeva
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| | - Francesco Dondi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy.
| | - Mara Battilani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano Emilia, Bologna, Italy
| |
Collapse
|
165
|
Fukumori K, Kondo NI, Kohzu A, Tsuchiya K, Ito H, Kadoya T. Vertical eDNA distribution of cold-water fishes in response to environmental variables in stratified lake. Ecol Evol 2024; 14:e11091. [PMID: 38500853 PMCID: PMC10945234 DOI: 10.1002/ece3.11091] [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: 09/19/2023] [Revised: 01/22/2024] [Accepted: 02/16/2024] [Indexed: 03/20/2024] Open
Abstract
In summer, the survival zones of cold-water species are predicted to narrow by both increasing water temperatures from the surface and by expanding hypoxic zones from the lake bottom. To examine how the abundance of cold-water fishes changes along environmental gradients, we assessed the vertical environmental DNA (eDNA) distributions of three salmonid species which may have different water temperature tolerances during both stratification and turnover periods using quantitative PCR (qPCR). In addition, we examined on the vertical distribution of diverse fish fauna using an eDNA metabarcoding assay. The results suggested that the kokanee salmon (Oncorhynchus nerka) eDNA were abundant in deep, cold waters. On the other hand, rainbow trout (O. mykiss) eDNA were distributed uniformly throughout the water column, suggesting that they may have high water-temperature tolerance compared with kokanee salmon. The eDNA concentrations of masu salmon (O. masou) were below the detection limit (i.e., <10 copies μL-1) at all stations and depths and hence could not be quantified during stratification. Together with the finding that the eDNA distributions of other prey fish species were also constrained vertically in species-specific ways, our results suggest that climate change will result in substantial changes in the vertical distributions of lake fish species and thus affect their populations and interactions.
Collapse
Affiliation(s)
- Kayoko Fukumori
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Natsuko I. Kondo
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Ayato Kohzu
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Kenji Tsuchiya
- Regional Environment Conservation DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Hiroshi Ito
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| | - Taku Kadoya
- Biodiversity DivisionNational Institute for Environmental Studies (NIES)IbarakiJapan
| |
Collapse
|
166
|
Beaver RC, Vachon MA, Tully CS, Engel K, Spasov E, Binns WJ, Noël JJ, Neufeld JD. Impact of dry density and incomplete saturation on microbial growth in bentonite clay for nuclear waste storage. J Appl Microbiol 2024; 135:lxae053. [PMID: 38458234 DOI: 10.1093/jambio/lxae053] [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: 04/28/2023] [Revised: 10/12/2023] [Accepted: 03/07/2024] [Indexed: 03/10/2024]
Abstract
AIMS Many countries are in the process of designing a deep geological repository (DGR) for long-term storage of used nuclear fuel. For several designs, used fuel containers will be placed belowground, with emplacement tunnels being backfilled using a combination of highly compacted powdered bentonite clay buffer boxes surrounded by a granulated "gapfill" bentonite. To limit the potential for microbiologically influenced corrosion of used fuel containers, identifying conditions that suppress microbial growth is critical for sustainable DGR design. This study investigated microbial communities in powdered and gapfill bentonite clay incubated in oxic pressure vessels at dry densities between 1.1 g cm-3 (i.e. below repository target) and 1.6 g cm-3 (i.e. at or above repository target) as a 1-year time series. RESULTS Our results showed an initial (i.e. 1 month) increase in the abundance of culturable heterotrophs associated with all dry densities <1.6 g cm-3, which reveals growth during transient low-pressure conditions associated with the bentonite saturation process. Following saturation, culturable heterotroph abundances decreased to those of starting material by the 6-month time point for all 1.4 and 1.6 g cm-3 pressure vessels, and the most probable numbers of culturable sulfate-reducing bacteria (SRB) remained constant for all vessels and time points. The 16S rRNA gene sequencing results showed a change in microbial community composition from the starting material to the 1-month time point, after which time most samples were dominated by sequences associated with Pseudomonas, Bacillus, Cupriavidus, and Streptomyces. Similar taxa were identified as dominant members of the culture-based community composition, demonstrating that the dominant members of the clay microbial communities are viable. Members of the spore-forming Desulfosporosinus genus were the dominant SRB for both clay and culture profiles. CONCLUSIONS After initial microbial growth while bentonite was below target pressure in the early phases of saturation, microbial growth in pressure vessels with dry densities of at least 1.4 g cm-3 was eventually suppressed as bentonite neared saturation.
Collapse
Affiliation(s)
- Rachel C Beaver
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Melody A Vachon
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Claire S Tully
- Department of Chemistry, Western University, London, Ontario, N6A 3K7, Canada
| | - Katja Engel
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - Emilie Spasov
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| | - W Jeffrey Binns
- Nuclear Waste Management Organization, Toronto, Ontario, M4T 2S3, Canada
| | - James J Noël
- Department of Chemistry, Western University, London, Ontario, N6A 3K7, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada
| |
Collapse
|
167
|
Abe S, Masuda A, Matsumoto T, Inoue J, Toyama H, Sakai A, Kobayashi T, Tanaka T, Tsujimae M, Yamakawa K, Gonda M, Masuda S, Uemura H, Kohashi S, Inomata N, Nagao K, Harada Y, Miki M, Irie Y, Juri N, Ko T, Yokotani Y, Oka Y, Ota S, Kanzawa M, Itoh T, Imai T, Fukumoto T, Hara E, Kodama Y. Impact of intratumoral microbiome on tumor immunity and prognosis in human pancreatic ductal adenocarcinoma. J Gastroenterol 2024; 59:250-262. [PMID: 38242997 PMCID: PMC10904450 DOI: 10.1007/s00535-023-02069-5] [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: 07/23/2023] [Accepted: 12/17/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND Recent evidence suggests that the presence of microbiome within human pancreatic ductal adenocarcinoma (PDAC) tissue potentially influences cancer progression and prognosis. However, the significance of tumor-resident microbiome remains unclear. We aimed to elucidate the impact of intratumoral bacteria on the pathophysiology and prognosis of human PDAC. METHODS The presence of intratumoral bacteria was assessed in 162 surgically resected PDACs using quantitative polymerase chain reaction (qPCR) and in situ hybridization (ISH) targeting 16S rRNA. The intratumoral microbiome was explored by 16S metagenome sequencing using DNA extracted from formalin-fixed paraffin-embedded tissues. The profile of intratumoral bacteria was compared with clinical information, pathological findings including tumor-infiltrating T cells, tumor-associated macrophage, fibrosis, and alterations in four main driver genes (KRAS, TP53, CDKN2A/p16, SMAD4) in tumor genomes. RESULTS The presence of intratumoral bacteria was confirmed in 52 tumors (32%) using both qPCR and ISH. The 16S metagenome sequencing revealed characteristic bacterial profiles within these tumors, including phyla such as Proteobacteria and Firmicutes. Comparison of bacterial profiles between cases with good and poor prognosis revealed a significant positive correlation between a shorter survival time and the presence of anaerobic bacteria such as Bacteroides, Lactobacillus, and Peptoniphilus. The abundance of these bacteria was correlated with a decrease in the number of tumor-infiltrating T cells positive for CD4, CD8, and CD45RO. CONCLUSIONS Intratumoral infection of anaerobic bacteria such as Bacteroides, Lactobacillus, and Peptoniphilus is correlated with the suppressed anti-PDAC immunity and poor prognosis.
Collapse
Affiliation(s)
- Shohei Abe
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Atsuhiro Masuda
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan.
| | - Tomonori Matsumoto
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Jun Inoue
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Hirochika Toyama
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Arata Sakai
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Takashi Kobayashi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Takeshi Tanaka
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Masahiro Tsujimae
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Kohei Yamakawa
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Masanori Gonda
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Shigeto Masuda
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Hisahiro Uemura
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Shinya Kohashi
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Noriko Inomata
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Kae Nagao
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Yoshiyuki Harada
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Mika Miki
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Yosuke Irie
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Noriko Juri
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Testuhisa Ko
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Yusuke Yokotani
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Yuki Oka
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Shogo Ota
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Maki Kanzawa
- Division of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Tomoo Itoh
- Division of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Toshio Imai
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Takumi Fukumoto
- Division of Hepato-Biliary-Pancreatic Surgery, Department of Surgery, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Eiji Hara
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuzo Kodama
- Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| |
Collapse
|
168
|
Lazcano RF, Kelly JJ, Hoellein TJ. Biofilms on plastic litter in an urban river: Community composition and activity vary by substrate type. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e11008. [PMID: 38443318 DOI: 10.1002/wer.11008] [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: 11/05/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 03/07/2024]
Abstract
In aquatic ecosystems, plastic litter is a substrate for biofilms. Biofilms on plastic and natural surfaces share similar composition and activity, with some differences due to factors such as porosity. In freshwaters, most studies have examined biofilms on benthic substrates, while little research has compared the activity and composition of biofilms on buoyant plastic and natural surfaces. Additionally, the influence of substrate size and successional stage on biofilm composition has not been commonly assessed. We incubated three plastics of distinct textures that are buoyant in rivers, low-density polyethylene (rigid; 1.7 mm thick), low-density polyethylene film (flexible; 0.0254 mm thick), and foamed polystyrene (brittle; 6.5 mm thick), as well as wood substrates (untreated oak veneer; 0.6 mm thick) in the Chicago River. Each material was incubated at three sizes (1, 7.5, and 15 cm2 ). Substrates were incubated at 2-10 cm depths and removed weekly for 6 weeks. On each substrate we measured chlorophyll concentration, biofilm biomass, respiration, and flux of nitrogen gas. We sequenced 16S and 23S rRNA genes at Weeks 1, 3, and 6 to capture biofilm community composition across successional stages. Chlorophyll, biomass, and N2 flux were similar across substrates, but respiration was greater on wood than plastics. Bacterial and algal richness and diversity were highest on foam and wood compared to polyethylene substrates. Bacterial biofilm community composition was distinct between wood and plastic substrates, while the algal community was distinct on wood and foam, which were different from each other and polyethylene substrates. These results indicate that polymer properties influence biofilm alpha and beta diversity, which may affect transport and distribution of plastic pollution and associated microbes, as well as biogeochemical processes in urban rivers. This study provides valuable insights into the effects of substrate on biofilm characteristics, and the ecological impacts of plastic pollution on urban rivers. PRACTITIONER POINTS: Plastic physical and chemical properties act as forces of selection for biofilm. Biofilm activity was similar among three different types of plastic. Community composition between plastic and wood was different.
Collapse
Affiliation(s)
- Raúl F Lazcano
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - John J Kelly
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Timothy J Hoellein
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| |
Collapse
|
169
|
Gunjur A, Shao Y, Rozday T, Klein O, Mu A, Haak BW, Markman B, Kee D, Carlino MS, Underhill C, Frentzas S, Michael M, Gao B, Palmer J, Cebon J, Behren A, Adams DJ, Lawley TD. A gut microbial signature for combination immune checkpoint blockade across cancer types. Nat Med 2024; 30:797-809. [PMID: 38429524 PMCID: PMC10957475 DOI: 10.1038/s41591-024-02823-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: 06/23/2023] [Accepted: 01/12/2024] [Indexed: 03/03/2024]
Abstract
Immune checkpoint blockade (ICB) targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte protein 4 (CTLA-4) can induce remarkable, yet unpredictable, responses across a variety of cancers. Studies suggest that there is a relationship between a cancer patient's gut microbiota composition and clinical response to ICB; however, defining microbiome-based biomarkers that generalize across cohorts has been challenging. This may relate to previous efforts quantifying microbiota to species (or higher taxonomic rank) abundances, whereas microbial functions are often strain specific. Here, we performed deep shotgun metagenomic sequencing of baseline fecal samples from a unique, richly annotated phase 2 trial cohort of patients with diverse rare cancers treated with combination ICB (n = 106 discovery cohort). We demonstrate that strain-resolved microbial abundances improve machine learning predictions of ICB response and 12-month progression-free survival relative to models built using species-rank quantifications or comprehensive pretreatment clinical factors. Through a meta-analysis of gut metagenomes from a further six comparable studies (n = 364 validation cohort), we found cross-cancer (and cross-country) validity of strain-response signatures, but only when the training and test cohorts used concordant ICB regimens (anti-PD-1 monotherapy or combination anti-PD-1 plus anti-CTLA-4). This suggests that future development of gut microbiome diagnostics or therapeutics should be tailored according to ICB treatment regimen rather than according to cancer type.
Collapse
Affiliation(s)
- Ashray Gunjur
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK.
| | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Timothy Rozday
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Oliver Klein
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Andre Mu
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Bastiaan W Haak
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Amsterdam, Netherlands
| | - Ben Markman
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Alfred Health, Melbourne, Victoria, Australia
- School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Damien Kee
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Rare Cancer Laboratory, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Matteo S Carlino
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
- Melanoma Institute of Australia, University of Sydney, Sydney, New South Wales, Australia
| | - Craig Underhill
- Border Medical Oncology and Haematology Research Unit, Albury-Wodonga Regional Cancer Centre, Albury-Wodonga, New South Wales, Australia
- Rural Medical School, University of New South Wales, Albury, New South Wales, Australia
| | - Sophia Frentzas
- Department of Medical Oncology, Monash Health, Melbourne, Victoria, Australia
| | - Michael Michael
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Bo Gao
- Department of Medical Oncology, Blacktown and Westmead Hospitals, Sydney, New South Wales, Australia
| | - Jodie Palmer
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - Jonathan Cebon
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
- Department of Medical Oncology, Austin Health, Melbourne, Victoria, Australia
| | - Andreas Behren
- Olivia Newton-John Cancer Research Institute, La Trobe University School of Cancer Medicine, Melbourne, Victoria, Australia
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK.
| |
Collapse
|
170
|
Von Eggers JM, Wisnoski NI, Calder JW, Capo E, Groff DV, Krist AC, Shuman B. Environmental filtering governs consistent vertical zonation in sedimentary microbial communities across disconnected mountain lakes. Environ Microbiol 2024; 26:e16607. [PMID: 38477387 DOI: 10.1111/1462-2920.16607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 02/28/2024] [Indexed: 03/14/2024]
Abstract
Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes-like dispersal limitation-contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.
Collapse
Affiliation(s)
- Jordan M Von Eggers
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
| | - Nathan I Wisnoski
- Wyoming Geographic Information Science Center, University of Wyoming, Laramie, Wyoming, USA
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - John W Calder
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Eric Capo
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden
| | - Dulcinea V Groff
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
| | - Amy C Krist
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming, USA
| | - Bryan Shuman
- Department of Geology and Geophysics, University of Wyoming, Laramie, Wyoming, USA
- Program in Ecology and Evolution, University of Wyoming, Laramie, Wyoming, USA
| |
Collapse
|
171
|
Sweeney CJ, Kaushik R, Bottoms M. Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2024; 20:337-358. [PMID: 37452668 DOI: 10.1002/ieam.4812] [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: 03/28/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
There is increasing interest in further developing the plant protection product (PPP) environmental risk assessment, particularly within the European Union, to include the assessment of soil microbial community composition, as measured by metabarcoding approaches. However, to date, there has been little discussion as to how this could be implemented in a standardized, reliable, and robust manner suitable for regulatory decision-making. Introduction of metabarcoding-based assessments of the soil microbiome into the PPP risk assessment would represent a significant increase in the degree of complexity of the data that needs to be processed and analyzed in comparison to the existing risk assessment on in-soil organisms. The bioinformatics procedures to process DNA sequences into community compositional data sets currently lack standardization, while little information exists on how these data should be used to generate regulatory endpoints and the ways in which these endpoints should be interpreted. Through a thorough and critical review, we explore these challenges. We conclude that currently, we do not have a sufficient degree of standardization or understanding of the required bioinformatics and data analysis procedures to consider their use in an environmental risk assessment context. However, we highlight critical knowledge gaps and the further research required to understand whether metabarcoding-based assessments of the soil microbiome can be utilized in a statistically and ecologically relevant manner within a PPP risk assessment. Only once these challenges are addressed can we consider if and how we should use metabarcoding as a tool for regulatory decision-making to assess and monitor ecotoxicological effects on soil microorganisms within an environmental risk assessment of PPPs. Integr Environ Assess Manag 2024;20:337-358. © 2023 SETAC.
Collapse
Affiliation(s)
- Christopher J Sweeney
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| | - Rishabh Kaushik
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| | - Melanie Bottoms
- Syngenta, Jealott's Hill International Research Centre Bracknell, Bracknell, Berkshire, UK
| |
Collapse
|
172
|
von Hoyningen-Huene AJE, Bang C, Rausch P, Rühlemann M, Fokt H, He J, Jensen N, Knop M, Petersen C, Schmittmann L, Zimmer T, Baines JF, Bosch TCG, Hentschel U, Reusch TBH, Roeder T, Franke A, Schulenburg H, Stukenbrock E, Schmitz RA. The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions. Front Microbiol 2024; 15:1347422. [PMID: 38476944 PMCID: PMC10927989 DOI: 10.3389/fmicb.2024.1347422] [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: 11/30/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.
Collapse
Affiliation(s)
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Philipp Rausch
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Malte Rühlemann
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Hannover Medical School, Institute for Medical Microbiology and Hospital Epidemiology, Hannover, Germany
| | - Hanna Fokt
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jinru He
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Nadin Jensen
- Institute for General Microbiology, Kiel University, Kiel, Germany
| | - Mirjam Knop
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
| | - Carola Petersen
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lara Schmittmann
- Research Unit Ocean Dynamics, GEOMAR Helmholtz Institute for Ocean Research Kiel, Kiel, Germany
| | - Thorsten Zimmer
- Institute for General Microbiology, Kiel University, Kiel, Germany
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Thomas C. G. Bosch
- Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany
| | - Ute Hentschel
- Marine Evolutionary Ecology, GEOMAR Helmholtz Center for Ocean Research, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thorsten B. H. Reusch
- Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Thomas Roeder
- Department of Molecular Physiology, Zoology, Kiel University, Kiel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Antibiotic Resistance Group, Max-Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eva Stukenbrock
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Kiel University, Kiel, Germany
| |
Collapse
|
173
|
Truter M, Koopman JE, Jordaan K, Tsamkxao LO, Cowan DA, Underdown SJ, Ramond JB, Rifkin RF. Documenting the diversity of the Namibian Ju|'hoansi intestinal microbiome. Cell Rep 2024; 43:113690. [PMID: 38244196 DOI: 10.1016/j.celrep.2024.113690] [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: 02/11/2022] [Revised: 10/27/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
We investigate the bacterial and fungal composition and functionality of the Ju|'hoansi intestinal microbiome (IM). The Juǀ'hoansi are a hunter-gatherer community residing in northeastern Namibia. They formerly subsisted by hunting and gathering but have been increasingly exposed to industrial dietary sources, medicines, and lifestyle features. They present an opportunity to study the evolution of the human IM in situ, from a predominantly hunter-gatherer to an increasingly Western urban-forager-farmer lifestyle. Their bacterial IM resembles that of typical hunter-gatherers, being enriched for genera such as Prevotella, Blautia, Faecalibacterium, Succinivibrio, and Treponema. Fungal IM inhabitants include animal pathogens and plant saprotrophs such as Fusarium, Issatchenkia, and Panellus. Our results suggest that diet and culture exert a greater influence on Ju|'hoansi IM composition than age, self-identified biological sex, and medical history. The Ju|'hoansi exhibit a unique core IM composition that diverges from the core IMs of other populations.
Collapse
Affiliation(s)
- Mia Truter
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Scientific Computing Research Unit, Department of Chemistry, University of Cape Town, Rondebosch 7700, South Africa
| | - Jessica E Koopman
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Karen Jordaan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Leon Oma Tsamkxao
- Juǀ'hoan Traditional Authority (JUTA), Tsumkwe, Otjozondjupa Region, Namibia
| | - Don A Cowan
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa
| | - Simon J Underdown
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK
| | - Jean-Baptiste Ramond
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK; Extreme Ecosystem Microbiomics & Ecogenomics (E(2)ME) Lab., Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Riaan F Rifkin
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield 0028, South Africa; Juǀ'hoan Traditional Authority (JUTA), Tsumkwe, Otjozondjupa Region, Namibia; Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford OX3 0BP, UK.
| |
Collapse
|
174
|
Nikitina D, Lukosevicius R, Tilinde D, Muskieta T, Hov JR, Melum E, Klovins J, Org E, Kiudelis G, Kupcinskas J, Skieceviciene J. Cell-Free Microbial DNA Analysis: Effects of Blood Plasma and Serum Quantity, Biobanking Protocols, and Isolation Kits. Biopreserv Biobank 2024. [PMID: 38416864 DOI: 10.1089/bio.2023.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024] Open
Abstract
Recent studies highlight the presence of bacterial sequences in the human blood, suggesting potential clinical significance for circulating microbial signatures. These sequences could presumably serve in the diagnosis, prediction, or monitoring of various health conditions. Ensuring the similarity of samples before bacterial analysis is crucial, especially when combining samples from different biobanks prepared under varying conditions (such as different DNA extraction kits, centrifugation conditions, blood collection tubes, etc.). In this study, we aimed to analyze the impact of different sample collection and nucleic acid extraction criteria (blood collection tube, centrifugation, input volume, and DNA extraction kit) on circulating bacterial composition. Blood samples from four healthy individuals were collected into three different sample collection tubes: K2EDTA plasma tube, sodium citrate plasma tube, and gel tube for blood serum. Tubes were centrifugated at standard and double centrifugation conditions. DNA extraction was performed using 100, 200, and 500 μL plasma/serum input volumes. DNA extraction was performed using three different isolation kits: Norgen plasma/serum cell-free circulating DNA purification micro kit, Applied Biosystems MagMAX cell-free DNA isolation kit, and Qiagen QIAamp MinElute cell-free circulating DNA mini kit. All samples were subjected to 16S rRNA V1-V2 library preparation and sequencing. In total, 216 DNA and 18 water control samples were included in the study. According to PERMANOVA, PCoA, Mann-Whitney, and FDR tests the effect of the DNA extraction kit on the microbiota composition was the greatest, whereas the type of blood collection tube, centrifugation type, and sample input volume for the extraction had minor effects. Samples extracted with the Norgen DNA extraction kit were enriched with Gram-negative bacteria, whereas samples extracted with the Qiagen and MagMAX kits were enriched with Gram-positive bacteria. Bacterial profiles of samples prepared with the Qiagen and MagMAX DNA extraction kits were more similar, whereas samples prepared with the Norgen DNA extraction kit were significantly different from other groups.
Collapse
Affiliation(s)
- Darja Nikitina
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rokas Lukosevicius
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Deimante Tilinde
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Tomas Muskieta
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Johannes Roksund Hov
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, Hybrid Technology Hub Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Janis Klovins
- Latvian Biomedical Research and Study Center, Riga, Latvia
| | - Elin Org
- Institute of Genomics, Estonian Genome Centre, University of Tartu, Tartu, Estonia
| | - Gediminas Kiudelis
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Laboratory of Clinical and Molecular Gastroenterology, Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| |
Collapse
|
175
|
Metze D, Schnecker J, de Carlan CLN, Bhattarai B, Verbruggen E, Ostonen I, Janssens IA, Sigurdsson BD, Hausmann B, Kaiser C, Richter A. Soil warming increases the number of growing bacterial taxa but not their growth rates. SCIENCE ADVANCES 2024; 10:eadk6295. [PMID: 38394199 PMCID: PMC10889357 DOI: 10.1126/sciadv.adk6295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Soil microorganisms control the fate of soil organic carbon. Warming may accelerate their activities putting large carbon stocks at risk of decomposition. Existing knowledge about microbial responses to warming is based on community-level measurements, leaving the underlying mechanisms unexplored and hindering predictions. In a long-term soil warming experiment in a Subarctic grassland, we investigated how active populations of bacteria and archaea responded to elevated soil temperatures (+6°C) and the influence of plant roots, by measuring taxon-specific growth rates using quantitative stable isotope probing and 18O water vapor equilibration. Contrary to prior assumptions, increased community growth was associated with a greater number of active bacterial taxa rather than generally faster-growing populations. We also found that root presence enhanced bacterial growth at ambient temperatures but not at elevated temperatures, indicating a shift in plant-microbe interactions. Our results, thus, reveal a mechanism of how soil bacteria respond to warming that cannot be inferred from community-level measurements.
Collapse
Affiliation(s)
- Dennis Metze
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Doctoral School in Microbiology and Environmental Science, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Biplabi Bhattarai
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Erik Verbruggen
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Ivika Ostonen
- Department of Geography, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Ivan A. Janssens
- Research Group Plants and Ecosystems, University of Antwerp, Antwerp, Belgium
| | - Bjarni D. Sigurdsson
- Faculty of Environmental and Forest Sciences, Agricultural University of Iceland, Hvanneyri, Borgarnes, Iceland
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Division of Clinical Microbiology, Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Christina Kaiser
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- International Institute for Applied Systems Analysis, Advancing Systems Analysis Program, Laxenburg, Austria
| |
Collapse
|
176
|
Bornbusch SL, Bamford A, Thacher P, Crosier A, Marinari P, Bortner R, Garelle D, Livieri T, Santymire R, Comizzoli P, Maslanka M, Maldonado JE, Koepfli KP, Muletz-Wolz CR, DeCandia AL. Markers of fertility in reproductive microbiomes of male and female endangered black-footed ferrets (Mustela nigripes). Commun Biol 2024; 7:224. [PMID: 38396133 PMCID: PMC10891159 DOI: 10.1038/s42003-024-05908-0] [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: 09/26/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Reproductive microbiomes contribute to reproductive health and success in humans. Yet data on reproductive microbiomes, and links to fertility, are absent for most animal species. Characterizing these links is pertinent to endangered species, such as black-footed ferrets (Mustela nigripes), whose populations show reproductive dysfunction and rely on ex-situ conservation husbandry. To understand microbial contributions to animal reproductive success, we used 16S rRNA amplicon sequencing to characterize male (prepuce) and female (vaginal) microbiomes of 59 black-footed ferrets at two ex-situ facilities and in the wild. We analyzed variation in microbiome structure according to markers of fertility such as numbers of viable and non-viable offspring (females) and sperm concentration (males). Ferret vaginal microbiomes showed lower inter-individual variation compared to prepuce microbiomes. In both sexes, wild ferrets harbored potential soil bacteria, perhaps reflecting their fossorial behavior and exposure to natural soil microbiomes. Vaginal microbiomes of ex-situ females that produced non-viable litters had greater phylogenetic diversity and distinct composition compared to other females. In males, sperm concentration correlated with varying abundances of bacterial taxa (e.g., Lactobacillus), mirroring results in humans and highlighting intriguing dynamics. Characterizing reproductive microbiomes across host species is foundational for understanding microbial biomarkers of reproductive success and for augmenting conservation husbandry.
Collapse
Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA.
- Department of Nutrition Science, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA.
| | | | - Piper Thacher
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
| | - Adrienne Crosier
- Center for Animal Care Services, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Paul Marinari
- Center for Animal Care Services, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Robyn Bortner
- National Black-Footed Ferret Conservation Center, US Fish and Wildlife Service, Carr, CO, USA
| | - Della Garelle
- National Black-Footed Ferret Conservation Center, US Fish and Wildlife Service, Carr, CO, USA
| | | | | | - Pierre Comizzoli
- Center for Species Survival, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Michael Maslanka
- Department of Nutrition Science, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA, USA
- Center for Species Survival, Smithsonian's National Zoo & Conservation Biology Institute, Front Royal, VA, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
| | - Alexandra L DeCandia
- Center for Conservation Genomics, Smithsonian's National Zoo & Conservation Biology Institute, Washington, DC, USA
- Department of Biology, Georgetown University, Washington, DC, USA
| |
Collapse
|
177
|
Liao Y, Wu YX, Tang M, Chen YW, Xie JR, Du Y, Wang TM, He YQ, Xue WQ, Zheng XH, Liu QY, Zheng MQ, Jia YJ, Tong XT, Zhou T, Li XZ, Yang DW, Diao H, Jia WH. Microbes translocation from oral cavity to nasopharyngeal carcinoma in patients. Nat Commun 2024; 15:1645. [PMID: 38388556 PMCID: PMC10883945 DOI: 10.1038/s41467-024-45518-2] [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: 04/08/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
The presence of oral microbes in extra-oral sites is linked to gastrointestinal cancers. However, their potential ectopically colonization in the nasopharynx and impact on local cancer development remains uncertain. Our study involving paired nasopharyngeal-oral microbial samples from nasopharyngeal carcinoma (NPC) patients and controls unveils an aberrant oral-to-nasopharyngeal microbial translocation associated with increased NPC risk (OR = 4.51, P = 0.012). Thirteen species are classified as oral-translocated and enriched in NPC patients. Among these, Fusobacterium nucleatum and Prevotella intermedia are validated through culturomics and clonal strain identification. Nasopharyngeal biopsy meta-transcriptomes confirm these microbes within tumors, influencing local microenvironment and cytokine response. These microbes correlate significantly with the Epstein-Barr virus (EBV) loads in the nasopharynx, exhibiting an increased dose-response relationship. Collectively, our study identifies oral microbes migrating to the nasopharynx, infiltrating tumors, impacting microenvironments and linking with EBV infection. These results enhance our understanding of abnormal microbial communication and their roles in carcinogenesis.
Collapse
Affiliation(s)
- Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan-Xia Wu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Minzhong Tang
- Key Laboratory of Nasopharyngeal Carcinoma Molecular Epidemiology, Wuzhou Red Cross Hospital, Wuzhou, Guangxi, China
| | - Yi-Wei Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jin-Ru Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Du
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qiao-Yun Liu
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Mei-Qi Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yi-Jing Jia
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xia-Ting Tong
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Da-Wei Yang
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Hua Diao
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.
- School of Public Health, Sun Yat-sen University, Guangzhou, China.
| |
Collapse
|
178
|
Del Rey YC, Schramm A, L. Meyer R, Lund MB, Schlafer S. Combined pH ratiometry and fluorescence lectin-binding analysis (pH-FLBA) for microscopy-based analyses of biofilm pH and matrix carbohydrates. Appl Environ Microbiol 2024; 90:e0200723. [PMID: 38265212 PMCID: PMC10880593 DOI: 10.1128/aem.02007-23] [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: 11/06/2023] [Accepted: 12/08/2023] [Indexed: 01/25/2024] Open
Abstract
Bacterial biofilms have a complex and heterogeneous three-dimensional architecture that is characterized by chemically and structurally distinct microenvironments. Confocal microscopy-based pH ratiometry and fluorescence lectin-binding analysis (FLBA) are well-established methods to characterize pH developments and the carbohydrate matrix architecture of biofilms at the microscale. Here, we developed a combined analysis, pH-FLBA, to concomitantly map biofilm pH and the distribution of matrix carbohydrates in bacterial biofilms while preserving the biofilm microarchitecture. As a proof of principle, the relationship between pH and the presence of galactose- and fucose-containing matrix components was investigated in dental biofilms grown with and without sucrose. The pH response to a sucrose challenge was monitored in different areas at the biofilm base using the ratiometric pH-sensitive dye C-SNARF-4. Thereafter, the fucose- and galactose-specific fluorescently labeled lectins Aleuria aurantia lectin (AAL) and Morus nigra agglutinin G (MNA-G) were used to visualize carbohydrate matrix components in the same biofilm areas and their immediate surroundings. Sucrose during growth significantly decreased biofilm pH (P < 0.05) and increased the amounts of both MNA-G- and AAL-targeted matrix carbohydrates (P < 0.05). Moreover, it modulated the biofilm composition towards a less diverse community dominated by streptococci, as determined by 16S rRNA gene sequencing. Altogether, these results suggest that the production of galactose- and fucose-containing matrix carbohydrates is related to streptococcal metabolism and, thereby, pH profiles in dental biofilms. In conclusion, pH-FLBA using lectins with different carbohydrate specificities is a useful method to investigate the association between biofilm pH and the complex carbohydrate architecture of bacterial biofilms.IMPORTANCEBiofilm pH is a key regulating factor in several biological and biochemical processes in environmental, industrial, and medical biofilms. At the microscale, microbial biofilms are characterized by steep pH gradients and an extracellular matrix rich in carbohydrate components with diffusion-modifying properties that contribute to bacterial acid-base metabolism. Here, we propose a combined analysis of pH ratiometry and fluorescence lectin-binding analysis, pH-FLBA, to concomitantly investigate the matrix architecture and pH developments in microbial biofilms, using complex saliva-derived biofilms as an example. Spatiotemporal changes in biofilm pH are monitored non-invasively over time by pH ratiometry, while FLBA with lectins of different carbohydrate specificities allows mapping the distribution of multiple relevant matrix components in the same biofilm areas. As the biofilm structure is preserved, pH-FLBA can be used to investigate the in situ relationship between the biofilm matrix architecture and biofilm pH in complex multispecies biofilms.
Collapse
Affiliation(s)
- Yumi C. Del Rey
- Section for Oral Ecology, Cariology, Department of Dentistry and Oral Health, Aarhus University, Aarhus, Denmark
| | - Andreas Schramm
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Rikke L. Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Marie Braad Lund
- Section for Microbiology, Department of Biology, Aarhus University, Aarhus, Denmark
| | - Sebastian Schlafer
- Section for Oral Ecology, Cariology, Department of Dentistry and Oral Health, Aarhus University, Aarhus, Denmark
| |
Collapse
|
179
|
Storz L, Schmid B, Bosshard PP, Schmid-Grendelmeier P, Brüggen MC, Lang C. Decreased skin colonization with Malassezia spp. and increased skin colonization with Candida spp. in patients with severe atopic dermatitis. Front Med (Lausanne) 2024; 11:1353784. [PMID: 38444416 PMCID: PMC10912638 DOI: 10.3389/fmed.2024.1353784] [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: 12/11/2023] [Accepted: 02/07/2024] [Indexed: 03/07/2024] Open
Abstract
Background Atopic dermatitis (AD) is a chronic relapsing inflammatory skin disease in which patients are sensitized towards a plethora of allergens. The hosts fungal microbiota, the mycobiota, that is believed to be altered in patients suffering from AD acts as such an allergen. The correlation context of specific sensitization, changes in mycobiota and its impact on disease severity however remains poorly understood. Objectives We aim to enhance the understanding of the specific sensitization towards the mycobiota in AD patients in relation to their fungal skin colonization. Methods Sensitization pattern towards the Malassezia spp. and Candida albicans of 16 AD patients and 14 healthy controls (HC) were analyzed with the newly developed multiplex-assay ALEX2® and the established singleplex-assay ImmunoCAP®. We compared these findings with the fungal skin colonization analyzed by DNA sequencing of the internal transcribed spacer region 1 (ITS1). Results Sensitization in general and towards Malassezia spp. and C. albicans is increased in AD patients compared to HC with a quantitative difference in severe AD when compared to mild to moderate AD. Further we saw an association between sensitization towards and skin colonization with Candida spp. yet a negative correlation between sensitization towards and skin colonization with Malassezia spp. Conclusion We conclude that AD in general and severe AD in particular is associated with increased sensitization towards the hosts own mycobiota. There is positive correlation in Candida spp. skin colonization and negative in Malassezia spp. skin colonization when compared to AD, AD severity as well as to specific sensitization patterns.
Collapse
Affiliation(s)
- Lukas Storz
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Bettina Schmid
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Philipp Peter Bosshard
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Peter Schmid-Grendelmeier
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Medical Campus Davos, Davos, Switzerland
| | - Marie-Charlotte Brüggen
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Medical Campus Davos, Davos, Switzerland
| | - Claudia Lang
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| |
Collapse
|
180
|
Brealey JC, Kodama M, Rasmussen JA, Hansen SB, Santos-Bay L, Lecaudey LA, Hansen M, Fjære E, Myrmel LS, Madsen L, Bernhard A, Sveier H, Kristiansen K, Gilbert MTP, Martin MD, Limborg MT. Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon. mSystems 2024; 9:e0104323. [PMID: 38294254 PMCID: PMC10886447 DOI: 10.1128/msystems.01043-23] [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: 09/27/2023] [Accepted: 12/19/2023] [Indexed: 02/01/2024] Open
Abstract
Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.
Collapse
Affiliation(s)
- Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Miyako Kodama
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - Søren B Hansen
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Luisa Santos-Bay
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Laurène A Lecaudey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Aquaculture Department, SINTEF Ocean, Trondheim, Norway
| | - Martin Hansen
- Department of Environmental Science, Environmental Metabolomics Lab, Aarhus University, Roskilde, Denmark
| | - Even Fjære
- Institute of Marine Research, Bergen, Norway
| | | | - Lise Madsen
- Institute of Marine Research, Bergen, Norway
- Department of Clinical Medicine, University of Bergen, Norway, Bergen, Norway
| | | | | | - Karsten Kristiansen
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, Faculty of Health and Medical Sciences,University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
181
|
Buiatte V, Fonseca A, Alonso Madureira P, Nakashima Vaz AC, Tizioto PC, Centola Vidal AM, Ganda E, de Azevedo Ruiz VL. A comparative study of the bacterial diversity and composition of nursery piglets' oral fluid, feces, and housing environment. Sci Rep 2024; 14:4119. [PMID: 38374338 PMCID: PMC10876639 DOI: 10.1038/s41598-024-54269-5] [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: 10/09/2023] [Accepted: 02/10/2024] [Indexed: 02/21/2024] Open
Abstract
The oral cavity is the portal of entry for many microorganisms that affect swine, and the swine oral fluid has been used as a specimen for the diagnosis of several infectious diseases. The oral microbiota has been shown to play important roles in humans, such as protection against non-indigenous bacteria. In swine, studies that have investigated the microbial composition of the oral cavity of pigs are scarce. This study aimed to characterize the oral fluid microbiota of weaned pigs from five commercial farms in Brazil and compare it to their respective fecal and environmental microbiotas. Bacterial compositions were determined by 16S rRNA gene sequencing and analyzed in R Studio. Oral fluid samples were significantly less diverse (alpha diversity) than pen floor and fecal samples (P < 0.01). Alpha diversity changed among farms in oral fluid and pen floor samples, but no differences were observed in fecal samples. Permutational ANOVA revealed that beta diversity was significantly different among sample types (P = 0.001) and farms (P = 0.001), with separation of sample types (feces, pen floor, and oral fluid) on the principal coordinates analysis. Most counts obtained from oral fluid samples were classified as Firmicutes (80.4%) and Proteobacteria (7.7%). The genera Streptococcus, members of the Pasteurellaceae family, and Veillonella were differentially abundant in oral fluid samples when compared to fecal samples, in which Streptococcus was identified as a core genus that was strongly correlated (SparCC) with other taxa. Firmicutes and Bacteroidota were the most relatively abundant phyla identified in fecal and pen floor samples, and Prevotella_9 was the most classified genus. No differentially abundant taxa were identified when comparing fecal samples and pen floor samples. We concluded that under the conditions of our study, the oral fluid microbiota of weaned piglets is different (beta diversity) and less diverse (alpha diversity) than the fecal and environmental microbiotas. Several differentially abundant taxa were identified in the oral fluid samples, and some have been described as important colonizers of the oral cavity in human microbiome studies. Further understanding of the relationship between the oral fluid microbiota and swine is necessary and would create opportunities for the development of innovative solutions that target the microbiota to improve swine health and production.
Collapse
Affiliation(s)
- Vinicius Buiatte
- Department of Animal Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ana Fonseca
- Department of Animal Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Paloma Alonso Madureira
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Andréia Cristina Nakashima Vaz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, Universidade de São Paulo, Pirassununga, SP, Brazil
| | | | - Ana Maria Centola Vidal
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, Universidade de São Paulo, Pirassununga, SP, Brazil
| | - Erika Ganda
- Department of Animal Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Vera Letticie de Azevedo Ruiz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, Universidade de São Paulo, Pirassununga, SP, Brazil.
| |
Collapse
|
182
|
Lau CHF, Capitani S, Tien YC, Verellen LA, Kithama M, Kang H, Kiarie EG, Topp E, Diarra MS, Fruci M. Dynamic effects of black soldier fly larvae meal on the cecal bacterial microbiota and prevalence of selected antimicrobial resistant determinants in broiler chickens. Anim Microbiome 2024; 6:6. [PMID: 38360706 PMCID: PMC10868003 DOI: 10.1186/s42523-024-00293-9] [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: 08/08/2023] [Accepted: 01/26/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND We had earlier described the growth-promoting and -depressive effects of replacing soybean meal (SBM) with low (12.5% and 25%) and high (50% and 100%) inclusion levels of black soldier fly larvae meal (BSFLM), respectively, in Ross x Ross 708 broiler chicken diets. Herein, using 16S rRNA gene amplicon sequencing, we investigated the effects of replacing SBM with increasing inclusion levels (0-100%) of BSFLM in broiler diets on the cecal bacterial community composition at each growth phase compared to broilers fed a basal corn-SBM diet with or without the in-feed antibiotic, bacitracin methylene disalicylate (BMD). We also evaluated the impact of low (12.5% and 25%) inclusion levels of BSFLM (LIL-BSFLM) on the prevalence of selected antimicrobial resistance genes (ARGs) in litter and cecal samples from 35-day-old birds. RESULTS Compared to a conventional SBM-based broiler chicken diet, high (50 to100%) inclusion levels of BSFLM (HIL-BSFLM) significantly altered the cecal bacterial composition and structure, whereas LIL-BSFLM had a minimal effect. Differential abundance analysis further revealed that the ceca of birds fed 100% BSFLM consistently harbored a ~ 3 log-fold higher abundance of Romboutsia and a ~ 2 log-fold lower abundance of Shuttleworthia relative to those fed a BMD-supplemented control diet at all growth phases. Transient changes in the abundance of several potentially significant bacterial genera, primarily belonging to the class Clostridia, were also observed for birds fed HIL-BSFLM. At the finisher phase, Enterococci bacteria were enriched in the ceca of chickens raised without antibiotic, regardless of the level of dietary BSFLM. Additionally, bacitracin (bcrR) and macrolide (ermB) resistance genes were found to be less abundant in the ceca of chickens fed antibiotic-free diets, including either a corn-SBM or LIL-BSFLM diet. CONCLUSIONS Chickens fed a HIL-BSFLM presented with an imbalanced gut bacterial microbiota profile, which may be linked to the previously reported growth-depressing effects of a BSFLM diet. In contrast, LIL-BSFLM had a minimal effect on the composition of the cecal bacterial microbiota and did not enrich for selected ARGs. Thus, substitution of SBM with low levels of BSFLM in broiler diets could be a promising alternative to the antibiotic growth promoter, BMD, with the added-value of not enriching for bacitracin- and macrolide-associated ARGs.
Collapse
Affiliation(s)
- Calvin Ho-Fung Lau
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.
| | - Sabrina Capitani
- Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Yuan-Ching Tien
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Lou Ann Verellen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Munene Kithama
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Hellen Kang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- School of Medicine, Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Elijah G Kiarie
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Edward Topp
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Agroécologie research unit, INRAE, Université de Bourgogne, Dijon, France
| | - Moussa S Diarra
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, Guelph, ON, Canada
| | - Michael Fruci
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
- Department of Microbiology and Immunology, University of Western Ontario, London, ON, Canada.
| |
Collapse
|
183
|
Cassas MS, Jonas LC, Anderson CJ, Schmitz-Esser S, Youngs CR. Temporal changes in ewe vaginal microbiota throughout gestation. Front Microbiol 2024; 15:1359678. [PMID: 38426061 PMCID: PMC10901984 DOI: 10.3389/fmicb.2024.1359678] [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: 12/21/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction Numerous factors are known to influence reproductive efficiency in ewes, but few studies have investigated the potential role of vaginal microbiota in sheep reproductive success. The objective of this study was to thoroughly characterize the ewe vaginal microbiota throughout the course of pregnancy. Methods Vaginal samples were collected from 31 pregnant Hampshire and Hampshire X Suffolk crossbred ewes on a weekly basis from pre-breeding to pregnancy testing and then biweekly until just after lambing. To characterize the vaginal microbial communities, DNA was extracted and 16S rRNA gene Illumina MiSeq amplicon sequencing was performed. Results and Discussion Alpha diversity metrics indicated an increase in species richness, evenness, and overall diversity throughout gestation. Distinct shifts in the bacterial communities were observed during gestation and were segregated into three periods: early gestation, a transitional period and mid/late gestation. During early gestation, Actinobacillus, Histophilus, and unclassified Leptotrichiaceae were found in greater relative abundance. During the transitional period, a population shift occurred characterized by increasing relative abundance of Streptococcus and Staphylococcus. During mid/late gestation, Staphylococcus, Streptococcus, and Ureaplasma had the greatest relative abundance. These shifts in the microbial population throughout the ewe's gestation are likely related to hormonal changes triggered by the growing conceptus, specifically increasing blood concentration of progesterone. The transitional period shift in vaginal microbial communities potentially aligns with the placental take-over of progesterone production from the corpus luteum at approximately day 50 after conception (gestational week 7). Understanding the observed variability of the vaginal microbiota throughout pregnancy will allow for future comparison of ewes that did not become pregnant or had abnormal pregnancies, which could lead to the discovery of potential bacterial biomarkers for pregnancy outcome; this understanding could also lead to development of probiotics to improve sheep reproductive success.
Collapse
Affiliation(s)
- Mackenzie S. Cassas
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Lucille C. Jonas
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Chiron J. Anderson
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Stephan Schmitz-Esser
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, United States
| | - Curtis R. Youngs
- Department of Animal Science, Iowa State University, Ames, IA, United States
| |
Collapse
|
184
|
Bell AG, McMurtrie J, Bolaños LM, Cable J, Temperton B, Tyler CR. Influence of host phylogeny and water physicochemistry on microbial assemblages of the fish skin microbiome. FEMS Microbiol Ecol 2024; 100:fiae021. [PMID: 38366921 PMCID: PMC10903987 DOI: 10.1093/femsec/fiae021] [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: 12/05/2023] [Revised: 01/10/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024] Open
Abstract
The skin of fish contains a diverse microbiota that has symbiotic functions with the host, facilitating pathogen exclusion, immune system priming, and nutrient degradation. The composition of fish skin microbiomes varies across species and in response to a variety of stressors, however, there has been no systematic analysis across these studies to evaluate how these factors shape fish skin microbiomes. Here, we examined 1922 fish skin microbiomes from 36 studies that included 98 species and nine rearing conditions to investigate associations between fish skin microbiome, fish species, and water physiochemical factors. Proteobacteria, particularly the class Gammaproteobacteria, were present in all marine and freshwater fish skin microbiomes. Acinetobacter, Aeromonas, Ralstonia, Sphingomonas and Flavobacterium were the most abundant genera within freshwater fish skin microbiomes, and Alteromonas, Photobacterium, Pseudoalteromonas, Psychrobacter and Vibrio were the most abundant in saltwater fish. Our results show that different culturing (rearing) environments have a small but significant effect on the skin bacterial community compositions. Water temperature, pH, dissolved oxygen concentration, and salinity significantly correlated with differences in beta-diversity but not necessarily alpha-diversity. To improve study comparability on fish skin microbiomes, we provide recommendations for approaches to the analyses of sequencing data and improve study reproducibility.
Collapse
Affiliation(s)
- Ashley G Bell
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Jamie McMurtrie
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Luis M Bolaños
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff CF10 3AX, United Kingdom
| | - Ben Temperton
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| | - Charles R Tyler
- College of Life and Environmental Sciences, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
- Sustainable Aquaculture Futures, The University of Exeter, Exter, Devon EX4 4QD, United Kingdom
| |
Collapse
|
185
|
Bunker ME, Weiss SL. The reproductive microbiome and maternal transmission of microbiota via eggs in Sceloporus virgatus. FEMS Microbiol Ecol 2024; 100:fiae011. [PMID: 38308517 PMCID: PMC10873522 DOI: 10.1093/femsec/fiae011] [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: 10/05/2023] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024] Open
Abstract
Maternal transmission of microbes occurs across the animal kingdom and is vital for offspring development and long-term health. The mechanisms of this transfer are most well-studied in humans and other mammals but are less well-understood in egg-laying animals, especially those with no parental care. Here, we investigate the transfer of maternal microbes in the oviparous phrynosomatid lizard, Sceloporus virgatus. We compared the microbiota of three maternal tissues-oviduct, cloaca, and intestine-to three offspring sample types: egg contents and eggshells on the day of oviposition, and hatchling intestinal tissue on the day of hatching. We found that maternal identity is an important factor in hatchling microbiome composition, indicating that maternal transmission is occurring. The maternal cloacal and oviductal communities contribute to offspring microbiota in all three sample types, with minimal microbes sourced from maternal intestines. This indicates that the maternal reproductive microbiome is more important for microbial inheritance than the gut microbiome, and the tissue-level variation of the adult S. virgatus microbiota must develop as the hatchling matures. Despite differences between adult and hatchling communities, offspring microbiota were primarily members of the Enterobacteriaceae and Yersiniaceae families (Phylum Proteobacteria), consistent with this and past studies of adult S. virgatus microbiomes.
Collapse
Affiliation(s)
- Marie E Bunker
- Department of Biology, University of Puget Sound, 1500 N. Warner Street, Tacoma, WA 98416, United States
| | - Stacey L Weiss
- Department of Biology, University of Puget Sound, 1500 N. Warner Street, Tacoma, WA 98416, United States
| |
Collapse
|
186
|
Vlasselaer L, Crauwels S, Lievens B, De Coninck B. Unveiling the microbiome of hydroponically cultivated lettuce: impact of Phytophthora cryptogea infection on plant-associated microorganisms. FEMS Microbiol Ecol 2024; 100:fiae010. [PMID: 38317643 PMCID: PMC10872686 DOI: 10.1093/femsec/fiae010] [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: 08/18/2023] [Revised: 12/08/2023] [Accepted: 02/02/2024] [Indexed: 02/07/2024] Open
Abstract
Understanding the complex interactions between plants and their associated microorganisms is crucial for optimizing plant health and productivity. While microbiomes of soil-bound cultivated crops are extensively studied, microbiomes of hydroponically cultivated crops have received limited attention. To address this knowledge gap, we investigated the rhizosphere and root endosphere of hydroponically cultivated lettuce. Additionally, we sought to explore the potential impact of the oomycete pathogen Phytophthora cryptogea on these microbiomes. Root samples were collected from symptomatic and nonsymptomatic plants in three different greenhouses. Amplicon sequencing of the bacterial 16S rRNA gene revealed significant alterations in the bacterial community upon P. cryptogea infection, particularly in the rhizosphere. Permutational multivariate analysis of variance (perMANOVA) revealed significant differences in microbial communities between plants from the three greenhouses, and between symptomatic and nonsymptomatic plants. Further analysis uncovered differentially abundant zero-radius operational taxonomic units (zOTUs) between symptomatic and nonsymptomatic plants. Interestingly, members of Pseudomonas and Flavobacterium were positively associated with symptomatic plants. Overall, this study provides valuable insights into the microbiome of hydroponically cultivated plants and highlights the influence of pathogen invasion on plant-associated microbial communities. Further research is required to elucidate the potential role of Pseudomonas and Flavobacterium spp. in controlling P. cryptogea infections within hydroponically cultivated lettuce greenhouses.
Collapse
Affiliation(s)
- Liese Vlasselaer
- Plant Health and Protection Laboratory, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| | - Sam Crauwels
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
| | - Bart Lievens
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
- Laboratory for Process Microbial Ecology and Bioinspirational Management, Center of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven, Willem de Croylaan 46, B-3001 Leuven, Belgium
| | - Barbara De Coninck
- Plant Health and Protection Laboratory, Division of Crop Biotechnics, Department of Biosystems, KU Leuven, Willem de Croylaan 42, B-3001 Leuven, Belgium
- KU Leuven Plant Institute, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium
| |
Collapse
|
187
|
Kosmeri C, Giapros V, Serbis A, Baltogianni M. Application of Advanced Molecular Methods to Study Early-Onset Neonatal Sepsis. Int J Mol Sci 2024; 25:2258. [PMID: 38396935 PMCID: PMC10889541 DOI: 10.3390/ijms25042258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/10/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Early-onset sepsis (EOS) is a global health issue, considered one of the primary causes of neonatal mortality. Diagnosis of EOS is challenging because its clinical signs are nonspecific, and blood culture, which is the current gold-standard diagnostic tool, has low sensitivity. Commonly used biomarkers for sepsis diagnosis, including C-reactive protein, procalcitonin, and interleukin-6, lack specificity for infection. Due to the disadvantages of blood culture and other common biomarkers, ongoing efforts are directed towards identifying innovative molecular approaches to diagnose neonates at risk of sepsis. This review aims to gather knowledge and recent research on these emerging molecular methods. PCR-based techniques and unrestricted techniques based on 16S rRNA sequencing and 16S-23S rRNA gene interspace region sequencing offer several advantages. Despite their potential, these approaches are not able to replace blood cultures due to several limitations; however, they may prove valuable as complementary tests in neonatal sepsis diagnosis. Several microRNAs have been evaluated and have been proposed as diagnostic biomarkers in EOS. T2 magnetic resonance and bioinformatic analysis have proposed potential biomarkers of neonatal sepsis, though further studies are essential to validate these findings.
Collapse
Affiliation(s)
- Chrysoula Kosmeri
- Department of Pediatrics, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Vasileios Giapros
- Neonatal Intensive Care Unit, School of Medicine, University of Ioannina, 45500 Ioannina, Greece
| | - Anastasios Serbis
- Department of Pediatrics, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Maria Baltogianni
- Neonatal Intensive Care Unit, School of Medicine, University of Ioannina, 45500 Ioannina, Greece
| |
Collapse
|
188
|
Egyirifa RK, Akorli J. Two promising candidates for paratransgenesis, Elizabethkingia and Asaia, increase in both sexes of Anopheles gambiae mosquitoes after feeding. Malar J 2024; 23:45. [PMID: 38347591 PMCID: PMC10863137 DOI: 10.1186/s12936-024-04870-w] [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: 11/27/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The male mosquito microbiome may be important for identifying ideal candidates for disease control. Among other criteria, mosquito-associated symbionts that have high localization in both male and female mosquitoes and are transmissible through both vertical and sexual routes are desirable. However, mosquito microbiome studies have mainly been female-focused. In this study, the microbiota of male and female Anopheles gambiae sensu lato (s.l.) were compared to identify shared or unique bacteria. METHODS Late larval instars of Anopheles mosquitoes were collected from the field and raised to adults. Equal numbers of males and females of 1-day-old non-sugar-fed, 4-5-day-old sugar-fed and post-blood-fed females were randomly selected for whole-body analyses of bacteria 16S rRNA. RESULTS Results revealed that male and female mosquitoes generally share similar microbiota except when females were blood-fed. Compared to newly emerged unfed mosquitoes, feeding on sugar and/or blood increased variability in microbial composition (⍺-diversity), with a higher disparity among females (39% P = 0.01) than in males (29% P = 0.03). Elizabethkingia meningoseptica and Asaia siamensis were common discriminants between feeding statuses in both males and females. While E. meningoseptica was particularly associated with sugar-fed mosquitoes of both sexes and sustained after blood feeding in females, A. siamensis was also increased in sugar-fed mosquitoes but decreased significantly in blood-fed females (LDA score > 4.0, P < 0.05). Among males, A. siamensis did not differ significantly after sugar meals. CONCLUSIONS Results indicate the opportunities for stable infection in mosquitoes should these species be used in bacteria-mediated disease control. Further studies are recommended to investigate possible host-specific tissue tropism of bacteria species which will inform selection of the most appropriate microbes for effective transmission-blocking strategies.
Collapse
Affiliation(s)
- Richardson K Egyirifa
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana
| | - Jewelna Akorli
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Legon, Accra, Ghana.
| |
Collapse
|
189
|
Barko P, Nguyen-Edquilang J, Williams DA, Gal A. Fecal microbiome composition and diversity of cryopreserved canine stool at different duration and storage conditions. PLoS One 2024; 19:e0294730. [PMID: 38324560 PMCID: PMC10849402 DOI: 10.1371/journal.pone.0294730] [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: 05/07/2023] [Accepted: 11/07/2023] [Indexed: 02/09/2024] Open
Abstract
Fresh-frozen stool banks intended for humans with gastrointestinal and metabolic disorders have been recently established and there are ongoing efforts to establish the first veterinary fresh-frozen stool bank. Fresh frozen stored feces provide an advantage of increased availability and accessibility to high-quality optimal donor fecal material. The stability of frozen canine feces regarding fecal microbiome composition and diversity has not been reported in dogs, providing the basis for this study. We hypothesized that fecal microbial composition and diversity of healthy dogs would remain stable when stored at -20°C and -80°C for up to 12 months compared to baseline samples evaluated before freezing. Stool samples were collected from 20 apparently healthy dogs, manually homogenized, cryopreserved in 20% glycerol and aliquoted, frozen in liquid nitrogen and stored at -20°C or -80°C for 3, 6, 9, and 12 months. At baseline and after period of storage, aliquots were thawed and treated with propidium monoazide before fecal DNA extraction. Following long-read 16S-rRNA amplicon sequencing, bacterial community composition and diversity were compared among treatment groups. We demonstrated that fresh-frozen canine stools collected from 20 apparently healthy dogs could be stored for up to 12 months at -80°C with minimal change in microbial community composition and diversity and that storage at -80°C is superior to storage at -20°C. We also found that differences between dogs had the largest effect on community composition and diversity. Relative abundances of certain bacterial taxa, including those known to be short-chain fatty acid producers, varied significantly with specific storage temperatures and duration. Further work is required to ascertain whether fecal donor material that differs in bacterial community composition and diversity across storage conditions and duration could lead to differences in clinical efficacy for specific clinical indications of fecal microbiota transplantation.
Collapse
Affiliation(s)
- Patrick Barko
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Julie Nguyen-Edquilang
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - David A. Williams
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Arnon Gal
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| |
Collapse
|
190
|
Kumpitsch C, Fischmeister FPS, Lackner S, Holasek S, Madl T, Habisch H, Wolf A, Schöpf V, Moissl-Eichinger C. Reduced olfactory performance is associated with changed microbial diversity, oralization, and accumulation of dead biomaterial in the nasal olfactory area. Microbiol Spectr 2024; 12:e0154923. [PMID: 38193689 PMCID: PMC10846256 DOI: 10.1128/spectrum.01549-23] [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: 04/17/2023] [Accepted: 12/09/2023] [Indexed: 01/10/2024] Open
Abstract
The partial or complete loss of the sense of smell, which affects about 20% of the population, impairs the quality of life in many ways. Dysosmia and anosmia are mainly caused by aging, trauma, infections, or even neurodegenerative disease. Recently, the olfactory area-a site containing the olfactory receptor cells responsible for odor perception-was shown to harbor a complex microbiome that reflects the state of olfactory function. This initially observed correlation between microbiome composition and olfactory performance needed to be confirmed using a larger study cohort and additional analyses. A total of 120 participants (middle-aged, no neurodegenerative disease) were enrolled in the study to further analyze the microbial role in human olfactory function. Olfactory performance was assessed using the Sniffin' Stick battery, and participants were grouped accordingly (normosmia: n = 93, dysosmia: n = 27). The olfactory microbiome was analyzed by 16S rRNA gene amplicon sequencing and supplemented by metatranscriptomics in a subset (Nose 2.0). Propidium monoazide (PMA) treatment was performed to distinguish between intact and non-intact microbiome components. The gastrointestinal microbiome of these participants was also characterized by amplicon sequencing and metabolomics and then correlated with food intake. Our results confirm that normosmics and dysosmics indeed possess a distinguishable olfactory microbiome. Alpha diversity (i.e., richness) was significantly increased in dysosmics, reflected by an increase in the number of specific taxa (e.g., Rickettsia, Spiroplasma, and Brachybacterium). Lower olfactory performance was associated with microbial signatures from the oral cavity and periodontitis (Fusobacterium, Porphyromonas, and Selenomonas). However, PMA treatment revealed a higher accumulation of dead microbial material in dysosmic subjects. The gastrointestinal microbiome partially overlapped with the nasal microbiome but did not show substantial variation with respect to olfactory performance, although the diet of dysosmic individuals was shifted toward a higher meat intake. Dysosmia is associated with a higher burden of dead microbial material in the olfactory area, indicating an impaired clearance mechanism. As the microbial community of dysosmics (hyposmics and anosmics) appears to be influenced by the oral microbiome, further studies should investigate the microbial oral-nasal interplay in individuals with partial or complete olfactory loss.IMPORTANCEThe loss of the sense of smell is an incisive event that is becoming increasingly common in today's world due to infections such as COVID-19. Although this loss usually recovers a few weeks after infection, in some cases, it becomes permanent-why is yet to be answered. Since this condition often represents a psychological burden in the long term, there is a need for therapeutic approaches. However, treatment options are limited or even not existing. Understanding the role of the microbiome in the impairment of olfaction may enable the prediction of olfactory disorders and/or could serve as a possible target for therapeutic interventions.
Collapse
Affiliation(s)
- Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Florian Ph. S. Fischmeister
- Department of Psychology, University of Graz, Graz, Austria
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
- BioTechMed, Graz, Austria
| | - Sonja Lackner
- Otto Loewi Research Center, Division of Immunology, Medical University of Graz, Graz, Austria
| | - Sandra Holasek
- Otto Loewi Research Center, Division of Immunology, Medical University of Graz, Graz, Austria
| | - Tobias Madl
- BioTechMed, Graz, Austria
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, Graz, Austria
| | - Hansjörg Habisch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, Graz, Austria
| | - Axel Wolf
- Department of Otorhinolaryngology, Medical University of Graz, Graz, Austria
| | - Veronika Schöpf
- Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Vienna, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| |
Collapse
|
191
|
Matějková T, Dodoková A, Kreisinger J, Stopka P, Stopková R. Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice. Microbiol Spectr 2024; 12:e0203723. [PMID: 38171017 PMCID: PMC10846187 DOI: 10.1128/spectrum.02037-23] [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: 05/15/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024] Open
Abstract
Symbiotic microbial communities affect the host immune system and produce molecules contributing to the odor of an individual. In many mammalian species, saliva and vaginal fluids are important sources of chemical signals that originate from bacterial metabolism and may act as honest signals of health and reproductive status. In this study, we aimed to define oral and vaginal microbiomes and their dynamics throughout the estrous cycle in wild house mice. In addition, we analyzed a subset of vaginal proteomes and metabolomes to detect potential interactions with microbiomes. 16S rRNA sequencing revealed that both saliva and vagina are dominated by Firmicutes and Proteobacteria but differ at the genus level. The oral microbiome is more stable during the estrous cycle and most abundant bacteria belong to the genera Gemella and Streptococcus, while the vaginal microbiome shows higher bacterial diversity and dynamics during the reproductive cycle and is characterized by the dominance of Muribacter and Rodentibacter. These two genera cover around 50% of the bacterial community during estrus. Proteomic profiling of vaginal fluids revealed specific protein patterns associated with different estrous phases. Highly expressed proteins in estrus involve the keratinization process thus providing estrus markers (e.g., Hrnr) while some proteins are downregulated such as immune-related proteins that limit bacterial growth (Camp, Clu, Elane, Lyz2, and Ngp). The vaginal metabolome contains volatile compounds potentially involved in chemical communication, for example, ketones, aldehydes, and esters of carboxylic acids. Data integration of all three OMICs data sets revealed high correlations, thus providing evidence that microbiomes, host proteomes, and metabolomes may interact.IMPORTANCEOur data revealed dynamic changes in vaginal, but not salivary, microbiome composition during the reproductive cycle of wild mice. With multiple OMICs platforms, we provide evidence that changes in microbiota in the vaginal environment are accompanied by changes in the proteomic and metabolomics profiles of the host. This study describes the natural microbiota of wild mice and may contribute to a better understanding of microbiome-host immune system interactions during the hormonal and cellular changes in the female reproductive tract. Moreover, analysis of volatiles in the vaginal fluid shows particular substances that can be involved in chemical communication and reproductive behavior.
Collapse
Affiliation(s)
- Tereza Matějková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Alica Dodoková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Pavel Stopka
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Romana Stopková
- Department of Zoology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| |
Collapse
|
192
|
Iwase SC, Osawe S, Happel AU, Gray CM, Holmes SP, Blackburn JM, Abimiku A, Jaspan HB. Longitudinal gut microbiota composition of South African and Nigerian infants in relation to tetanus vaccine responses. Microbiol Spectr 2024; 12:e0319023. [PMID: 38230936 PMCID: PMC10846250 DOI: 10.1128/spectrum.03190-23] [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: 08/29/2023] [Accepted: 12/20/2023] [Indexed: 01/18/2024] Open
Abstract
Infants who are exposed to HIV but uninfected (iHEU) have higher risk of infectious morbidity than infants who are HIV-unexposed and uninfected (iHUU), possibly due to altered immunity. As infant gut microbiota may influence immune development, we evaluated the effects of HIV exposure on infant gut microbiota and its association with tetanus toxoid vaccine responses. We evaluated the gut microbiota of 82 South African (61 iHEU and 21 iHUU) and 196 Nigerian (141 iHEU and 55 iHUU) infants at <1 and 15 weeks of life by 16S rRNA gene sequencing. Anti-tetanus antibodies were measured by enzyme-linked immunosorbent assay at matched time points. Gut microbiota in the 278 included infants and its succession were more strongly influenced by geographical location and age than by HIV exposure. Microbiota of Nigerian infants, who were exclusively breastfed, drastically changed over 15 weeks, becoming dominated by Bifidobacterium longum subspecies infantis. This change was not observed among South African infants, even when limiting the analysis to exclusively breastfed infants. The Least Absolute Shrinkage and Selection Operator regression suggested that HIV exposure and gut microbiota were independently associated with tetanus titers at week 15, and that high passively transferred antibody levels, as seen in the Nigerian cohort, may mitigate these effects. In conclusion, in two African cohorts, HIV exposure minimally altered the infant gut microbiota compared to age and setting, but both specific gut microbes and HIV exposure independently predicted humoral tetanus vaccine responses.IMPORTANCEGut microbiota plays an essential role in immune system development. Since infants HIV-exposed and uninfected (iHEU) are more vulnerable to infectious diseases than unexposed infants, we explored the impact of HIV exposure on gut microbiota and its association with vaccine responses. This study was conducted in two African countries with rapidly increasing numbers of iHEU. Infant HIV exposure did not substantially affect gut microbial succession, but geographic location had a strong effect. However, both the relative abundance of specific gut microbes and HIV exposure were independently associated with tetanus titers, which were also influenced by baseline tetanus titers (maternal transfer). Our findings provide insight into the effect of HIV exposure, passive maternal antibody, and gut microbiota on infant humoral vaccine responses.
Collapse
Affiliation(s)
- Saori C. Iwase
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Sophia Osawe
- Institute of Human Virology-Nigeria, Abuja, Nigeria
| | - Anna-Ursula Happel
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Clive M. Gray
- Division of Molecular Biology and Human Genetics, Biomedical Research Institute, Stellenbosch University, Cape Town, South Africa
| | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, California, USA
| | - Jonathan M. Blackburn
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Chemical and Systems Biology, University of Cape Town, Cape Town, South Africa
| | - Alash'le Abimiku
- Institute of Human Virology-Nigeria, Abuja, Nigeria
- Institute of Human Virology, University of Maryland, School of Medicine, Baltimore, Maryland, USA
| | - Heather B. Jaspan
- Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, Washington, USA
| |
Collapse
|
193
|
Muzny CA, Elnaggar JH, Sousa LGV, Lima Â, Aaron KJ, Eastlund IC, Graves KJ, Dong C, Van Gerwen OT, Luo M, Tamhane A, Long D, Cerca N, Taylor CM. Microbial interactions among Gardnerella, Prevotella and Fannyhessea prior to incident bacterial vaginosis: protocol for a prospective, observational study. BMJ Open 2024; 14:e083516. [PMID: 38316599 PMCID: PMC10859992 DOI: 10.1136/bmjopen-2023-083516] [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: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024] Open
Abstract
INTRODUCTION The aetiology of bacterial vaginosis (BV), a biofilm-associated vaginal infection, remains unknown. Epidemiologic data suggest that it is sexually transmitted. BV is characterised by loss of lactic acid-producing lactobacilli and an increase in facultative and strict anaerobic bacteria. Gardnerella spp are present in 95%-100% of cases; Gardnerella vaginalis has been found to be more virulent than other BV-associated bacteria (BVAB) in vitro. However, G. vaginalis is found in women with normal vaginal microbiota and colonisation is not sufficient for BV development. We hypothesise that Gardnerella spp initiate BV biofilm formation, but incident BV (iBV) requires incorporation of other key BVAB (ie, Prevotella bivia, Fannyhessea vaginae) into the biofilm that alter the transcriptome of the polymicrobial consortium. This study will investigate the sequence of microbiologic events preceding iBV. METHODS AND ANALYSIS This study will enrol 150 women aged 18-45 years with normal vaginal microbiota and no sexually transmitted infections at a sexual health research clinic in Birmingham, Alabama. Women will self-collect twice daily vaginal specimens up to 60 days. A combination of 16S rRNA gene sequencing, qPCR for Gardnerella spp, P. bivia and F. vaginae, and broad range 16S rRNA gene qPCR will be performed on twice daily vaginal specimens from women with iBV (Nugent score 7-10 on at least 2 consecutive days) and controls (with comparable age, race, contraceptive method and menstrual cycle days) maintaining normal vaginal microbiota to investigate changes in the vaginal microbiota over time for women with iBV. Participants will complete daily diaries on multiple factors including sexual activity. ETHICS AND DISSEMINATION This protocol is approved by the University of Alabama at Birmingham Institutional Review Board (IRB-300004547) and written informed consent will be obtained from all participants. Findings will be presented at scientific conferences and published in peer-reviewed journals as well as disseminated to providers and patients in communities of interest.
Collapse
Affiliation(s)
- Christina A Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jacob H Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Lúcia G V Sousa
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
| | - Ângela Lima
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
| | - Kristal J Aaron
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Isaac C Eastlund
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Keonte J Graves
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Chaoling Dong
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Olivia T Van Gerwen
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Meng Luo
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
- Microbial Genomics Resource Group, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| | - Ashutosh Tamhane
- Division of Nephrology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Dustin Long
- Department of Biostatistics, University of Alabama at Birmingham, School of Public Health, Birmingham, Alabama, USA
| | - Nuno Cerca
- Centre of Biological Engineering, Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), University of Minho-Gualtar Campus, Braga, Portugal
- LABBELS-Associate Laboratory, Braga, Guimarães, Portugal
| | - Christopher M Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, USA
| |
Collapse
|
194
|
Taillieu E, Taelman S, De Bruyckere S, Goossens E, Chantziaras I, Van Steenkiste C, Yde P, Hanssens S, De Meyer D, Van Criekinge W, Stock M, Maes D, Chiers K, Haesebrouck F. The role of Helicobacter suis, Fusobacterium gastrosuis, and the pars oesophageal microbiota in gastric ulceration in slaughter pigs receiving meal or pelleted feed. Vet Res 2024; 55:15. [PMID: 38317242 PMCID: PMC10845778 DOI: 10.1186/s13567-024-01274-1] [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: 10/16/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
This study investigated the role of causative infectious agents in ulceration of the non-glandular part of the porcine stomach (pars oesophagea). In total, 150 stomachs from slaughter pigs were included, 75 from pigs that received a meal feed, 75 from pigs that received an equivalent pelleted feed with a smaller particle size. The pars oesophagea was macroscopically examined after slaughter. (q)PCR assays for H. suis, F. gastrosuis and H. pylori-like organisms were performed, as well as 16S rRNA sequencing for pars oesophagea microbiome analyses. All 150 pig stomachs showed lesions. F. gastrosuis was detected in 115 cases (77%) and H. suis in 117 cases (78%), with 92 cases (61%) of co-infection; H. pylori-like organisms were detected in one case. Higher infectious loads of H. suis increased the odds of severe gastric lesions (OR = 1.14, p = 0.038), while the presence of H. suis infection in the pyloric gland zone increased the probability of pars oesophageal erosions [16.4% (95% CI 0.6-32.2%)]. The causal effect of H. suis was mediated by decreased pars oesophageal microbiome diversity [-1.9% (95% CI - 5.0-1.2%)], increased abundances of Veillonella and Campylobacter spp., and decreased abundances of Lactobacillus, Escherichia-Shigella, and Enterobacteriaceae spp. Higher infectious loads of F. gastrosuis in the pars oesophagea decreased the odds of severe gastric lesions (OR = 0.8, p = 0.0014). Feed pelleting had no significant impact on the prevalence of severe gastric lesions (OR = 1.72, p = 0.28). H. suis infections are a risk factor for ulceration of the porcine pars oesophagea, probably mediated through alterations in pars oesophageal microbiome diversity and composition.
Collapse
Affiliation(s)
- Emily Taillieu
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Steff Taelman
- Department of Data Analysis and Mathematical Modelling, BIOBIX, Ghent University, 9000, Ghent, Belgium
- Department of Data Analysis and Mathematical Modelling, KERMIT, Ghent University, 9000, Ghent, Belgium
- BioLizard Nv, Ghent, Belgium
| | - Sofie De Bruyckere
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evy Goossens
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ilias Chantziaras
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Christophe Van Steenkiste
- Department of Gastroenterology and Hepatology, University Hospital Antwerp, Antwerp University, Edegem, Belgium
- Department of Gastroenterology and Hepatology, General Hospital Maria Middelares, Ghent, Belgium
| | | | | | | | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modelling, BIOBIX, Ghent University, 9000, Ghent, Belgium
| | - Michiel Stock
- Department of Data Analysis and Mathematical Modelling, BIOBIX, Ghent University, 9000, Ghent, Belgium
- Department of Data Analysis and Mathematical Modelling, KERMIT, Ghent University, 9000, Ghent, Belgium
| | - Dominiek Maes
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Koen Chiers
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| |
Collapse
|
195
|
Mercado-Evans V, Mejia ME, Zulk JJ, Ottinger S, Hameed ZA, Serchejian C, Marunde MG, Robertson CM, Ballard MB, Ruano SH, Korotkova N, Flores AR, Pennington KA, Patras KA. Gestational diabetes augments group B Streptococcus infection by disrupting maternal immunity and the vaginal microbiota. Nat Commun 2024; 15:1035. [PMID: 38310089 PMCID: PMC10838280 DOI: 10.1038/s41467-024-45336-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 01/19/2024] [Indexed: 02/05/2024] Open
Abstract
Group B Streptococcus (GBS) is a pervasive perinatal pathogen, yet factors driving GBS dissemination in utero are poorly defined. Gestational diabetes mellitus (GDM), a complication marked by dysregulated immunity and maternal microbial dysbiosis, increases risk for GBS perinatal disease. Using a murine GDM model of GBS colonization and perinatal transmission, we find that GDM mice display greater GBS in utero dissemination and subsequently worse neonatal outcomes. Dual-RNA sequencing reveals differential GBS adaptation to the GDM reproductive tract, including a putative glycosyltransferase (yfhO), and altered host responses. GDM immune disruptions include reduced uterine natural killer cell activation, impaired recruitment to placentae, and altered maternofetal cytokines. Lastly, we observe distinct vaginal microbial taxa associated with GDM status and GBS invasive disease status. Here, we show a model of GBS dissemination in GDM hosts that recapitulates several clinical aspects and identifies multiple host and bacterial drivers of GBS perinatal disease.
Collapse
Affiliation(s)
- Vicki Mercado-Evans
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Marlyd E Mejia
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jacob J Zulk
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Samantha Ottinger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zainab A Hameed
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Camille Serchejian
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Madelynn G Marunde
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Clare M Robertson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mallory B Ballard
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Simone H Ruano
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Natalia Korotkova
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, Lexington, KY, USA
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Anthony R Flores
- Division of Infectious Diseases, Department of Pediatrics, McGovern Medical School, UTHealth Houston, Children's Memorial Hermann Hospital, Houston, TX, USA
| | - Kathleen A Pennington
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kathryn A Patras
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
196
|
Schmiedová L, Černá K, Li T, Těšický M, Kreisinger J, Vinkler M. Bacterial communities along parrot digestive and respiratory tracts: the effects of sample type, species and time. Int Microbiol 2024; 27:127-142. [PMID: 37222909 PMCID: PMC10830831 DOI: 10.1007/s10123-023-00372-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/26/2023] [Accepted: 05/03/2023] [Indexed: 05/25/2023]
Abstract
Digestive and respiratory tracts are inhabited by rich bacterial communities that can vary between their different segments. In comparison with other bird taxa with developed caeca, parrots that lack caeca have relatively lower variability in intestinal morphology. Here, based on 16S rRNA metabarcoding, we describe variation in microbiota across different parts of parrot digestive and respiratory tracts both at interspecies and intraspecies levels. In domesticated budgerigar (Melopsittacus undulatus), we describe the bacterial variation across eight selected sections of respiratory and digestive tracts, and three non-destructively collected sample types (faeces, and cloacal and oral swabs). Our results show important microbiota divergence between the upper and lower digestive tract, but similarities between respiratory tract and crop, and also between different intestinal segments. Faecal samples appear to provide a better proxy for intestinal microbiota composition than the cloacal swabs. Oral swabs had a similar bacterial composition as the crop and trachea. For a subset of tissues, we confirmed the same pattern also in six different parrot species. Finally, using the faeces and oral swabs in budgerigars, we revealed high oral, but low faecal microbiota stability during a 3-week period mimicking pre-experiment acclimation. Our findings provide a basis essential for microbiota-related experimental planning and result generalisation in non-poultry birds.
Collapse
Affiliation(s)
- Lucie Schmiedová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic.
| | - Kateřina Černá
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tao Li
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Těšický
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jakub Kreisinger
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| |
Collapse
|
197
|
McKay JA, Crown M, Bashton M, Pearce D, Entwistle JA, Sangal V. Environmental microbiome in the home and daycare settings during the COVID-19 pandemic, and potential risk of non-communicable disease in children. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13233. [PMID: 38217304 PMCID: PMC10866607 DOI: 10.1111/1758-2229.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/27/2023] [Indexed: 01/15/2024]
Abstract
An exposure to diverse microbial population early in life is important for the development of immunity against various non-communicable diseases including asthma, childhood leukaemia and other cancers. Social mixing in daycare settings helps with exposure to a variety of microbes. However, social isolation and a high emphasis on workplace hygiene during the COVID pandemic may have affected children's exposure to diverse microbiota. The structure of microbial communities and their role in developing immunity to various diseases are not well understood. In this study, we investigated the structure of microbial communities in daycare and home settings during the pandemic. Interestingly, microbial diversity was relatively higher in dust samples collected from homes, with human-associated taxa being more prevalent compared to those from daycare settings. Environmental microbes were more abundant in dust samples from daycare providers. These results potentially suggest that cleaning practices during the pandemic may have influenced the diversity and microbial abundance of the daycare samples. Several bacterial taxa detected in both the environments are known to induce anti-inflammatory and immunomodulatory responses, conferring protection from various diseases. Therefore, exposure to diverse microbial population in early childhood may play an important role in developing immunity against various non-communicable and infectious diseases.
Collapse
Affiliation(s)
- Jill A. McKay
- Faculty of Health and Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Matthew Crown
- Faculty of Health and Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Matthew Bashton
- Faculty of Health and Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - David Pearce
- Faculty of Health and Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| | - Jane A. Entwistle
- Faculty of Environment and EngineeringNorthumbria UniversityNewcastle upon TyneUK
| | - Vartul Sangal
- Faculty of Health and Life SciencesNorthumbria UniversityNewcastle upon TyneUK
| |
Collapse
|
198
|
Andersson AM, Ingham AC, Edslev SM, Sølberg J, Skov L, Koch A, Ghauharali-van der Vlugt K, Stet FS, Brüggen CM, Jakasa I, Kezic S, Thyssen JP. Ethnic endotypes in paediatric atopic dermatitis depend on immunotype, lipid composition and microbiota of the skin. J Eur Acad Dermatol Venereol 2024; 38:365-374. [PMID: 37822011 DOI: 10.1111/jdv.19565] [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: 06/19/2023] [Accepted: 08/21/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) endotypes differ with ethnicity. We examined the skin microbiota, cytokine and lipid profiles in Greenlandic Inuit and Danish children with AD. METHODS Twenty-five Inuit children with AD and 25 Inuit control children were clinically examined and compared to previously collected data from 25 Danish children with AD. Skin tape strips and skin swabs were collected from lesional and non-lesional skin. Levels of cutaneous immune biomarkers, free sphingoid bases and their (glycosyl)ceramides were analysed. Skin swabs were analysed with 16S rRNA and tuf gene for characterization of bacterial species communities. RESULTS Bacterial β-diversity was significantly different between Inuit and Danish AD skin, in both lesional (p < 0.001) and non-lesional (p < 0.001) AD skin, and there was a higher relative abundance of Staphylococcus aureus in Danish compared to Inuit lesional (53% vs. 8%, p < 0.01) and non-lesional skin (55% vs. 5%, p < 0.001). Danish AD children had a higher α-diversity than Inuit children in non-lesional (p < 0.05) but not in lesional skin. Significantly higher levels of type 2 immunity cytokine interleukin (IL)-4 (p < 0.05) and IL-5 (p < 0.01) were identified in Inuit compared to Danish AD children. In contrast, IL-33 (p < 0.01) was higher in Danish lesional and non-lesional AD skin. Higher levels of long-chain glucosylceramide (GlcCER)[S](d26:1) were found in lesional (p < 0.001) and non-lesional (p < 0.001) Inuit skin compared with Danish AD skin. NMF levels were similar in Inuit and Danish AD skin. CONCLUSION Skin microbiota, cytokine and lipid composition differed significantly between Inuit and Danish children with AD and showed a stronger type 2 immune signature in Inuit children.
Collapse
Affiliation(s)
- A M Andersson
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Ilisimatusarfik, University of Greenland, Nuuk, Greenland
- Copenhagen Research Group for Inflammatory Skin (CORGIS), Hellerup, Denmark
| | - A C Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - S M Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - J Sølberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - L Skov
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Copenhagen Research Group for Inflammatory Skin (CORGIS), Hellerup, Denmark
| | - A Koch
- Ilisimatusarfik, University of Greenland, Nuuk, Greenland
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - K Ghauharali-van der Vlugt
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - F S Stet
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - C M Brüggen
- Faculty of Medicine, University Zurich, Zurich, Switzerland
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
| | - I Jakasa
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - S Kezic
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - J P Thyssen
- Department of Dermatology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
199
|
Pasciullo Boychuck S, Brenner LJ, Gagorik CN, Schamel JT, Baker S, Tran E, vonHoldt BM, Koepfli K, Maldonado JE, DeCandia AL. The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations. Ecol Evol 2024; 14:e11017. [PMID: 38362164 PMCID: PMC10867392 DOI: 10.1002/ece3.11017] [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: 10/25/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 02/17/2024] Open
Abstract
California's Channel Islands are home to two endemic mammalian carnivores: island foxes (Urocyon littoralis) and island spotted skunks (Spilogale gracilis amphiala). Although it is rare for two insular terrestrial carnivores to coexist, these known competitors persist on both Santa Cruz Island and Santa Rosa Island. We hypothesized that examination of their gut microbial communities would provide insight into the factors that enable this coexistence, as microbial symbionts often reflect host evolutionary history and contemporary ecology. Using rectal swabs collected from island foxes and island spotted skunks sampled across both islands, we generated 16S rRNA amplicon sequencing data to characterize their gut microbiomes. While island foxes and island spotted skunks both harbored the core mammalian microbiome, host species explained the largest proportion of variation in the dataset. We further identified intraspecific variation between island populations, with greater differentiation observed between more specialist island spotted skunk populations compared to more generalist island fox populations. This pattern may reflect differences in resource utilization following fine-scale niche differentiation. It may further reflect evolutionary differences regarding the timing of intraspecific separation. Considered together, this study contributes to the growing catalog of wildlife microbiome studies, with important implications for understanding how eco-evolutionary processes enable the coexistence of terrestrial carnivores-and their microbiomes-in island environments.
Collapse
Affiliation(s)
| | | | | | | | | | - Elton Tran
- Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNew JerseyUSA
| | | | - Klaus‐Peter Koepfli
- Center for Species SurvivalSmithsonian's National Zoo & Conservation Biology InstituteFront RoyalVirginiaUSA
- Smithsonian‐Mason School of ConservationGeorge Mason UniversityFront RoyalVirginiaUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian's National Zoo & Conservation Biology InstituteWashingtonDCUSA
| | - Alexandra L. DeCandia
- Biology, Georgetown UniversityWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian's National Zoo & Conservation Biology InstituteWashingtonDCUSA
| |
Collapse
|
200
|
Hoffbeck C, Middleton DMRL, Lamar SK, Keall SN, Nelson NJ, Taylor MW. Gut microbiome of the sole surviving member of reptile order Rhynchocephalia reveals biogeographic variation, influence of host body condition and a substantial core microbiota in tuatara across New Zealand. Ecol Evol 2024; 14:e11073. [PMID: 38405409 PMCID: PMC10884523 DOI: 10.1002/ece3.11073] [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: 09/28/2023] [Revised: 01/12/2024] [Accepted: 02/09/2024] [Indexed: 02/27/2024] Open
Abstract
Tuatara are the sole extant species in the reptile order Rhynchocephalia. They are ecologically and evolutionarily unique, having been isolated geographically for ~84 million years and evolutionarily from their closest living relatives for ~250 million years. Here we report the tuatara gut bacterial community for the first time. We sampled the gut microbiota of translocated tuatara at five sanctuaries spanning a latitudinal range of ~1000 km within Aotearoa New Zealand, as well as individuals from the source population on Takapourewa (Stephens Island). This represents a first look at the bacterial community of the order Rhynchocephalia and provides the opportunity to address several key hypotheses, namely that the tuatara gut microbiota: (1) differs from those of other reptile orders; (2) varies among geographic locations but is more similar at sites with more similar temperatures and (3) is shaped by tuatara body condition, parasitism and ambient temperature. We found significant drivers of the microbiota in sampling site, tuatara body condition, parasitism and ambient temperature, suggesting the importance of these factors when considering tuatara conservation. We also derived a 'core' community of shared bacteria across tuatara at many sites, despite their geographic range and isolation. Remarkably, >70% of amplicon sequence variants could not be assigned to known genera, suggesting a largely undescribed gut bacterial community for this ancient host species.
Collapse
Affiliation(s)
- Carmen Hoffbeck
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| | | | - Sarah K. Lamar
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Susan N. Keall
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Nicola J. Nelson
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Michael W. Taylor
- School of Biological SciencesUniversity of AucklandAucklandNew Zealand
| |
Collapse
|