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Knorr J, Lone Z, Werneburg G, Adler A, Agudelo J, Suryavanshi M, Campbell RA, Ericson K, Qiu H, Bajic P, Haber GP, Weight CJ, Ahern PP, Almassi N, Miller AW, Lee BH. An exploratory study investigating the impact of the bladder tumor microbiome on Bacillus Calmette Guerin (BCG) response in non-muscle invasive bladder cancer. Urol Oncol 2024; 42:291.e1-291.e11. [PMID: 38664180 DOI: 10.1016/j.urolonc.2024.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/29/2024] [Accepted: 04/09/2024] [Indexed: 06/23/2024]
Abstract
PURPOSE Intravesical Bacillus Calmette-Guerin (BCG) is standard of care for intermediate- and high-risk non-muscle invasive bladder cancer (NMIBC). The effect of the bladder microbiome on response to BCG is unclear. We sought to characterize the microbiome of bladder tumors in BCG-responders and non-responders and identify potential mechanisms that drive treatment response. MATERIALS AND METHODS Patients with archival pre-treatment biopsy samples (2012-2018) were identified retrospectively. Prospectively, urine and fresh tumor samples were collected from individuals with high-risk NMIBC (2020-2023). BCG response was defined as tumor-free 2 years from induction therapy. Extracted DNA was sequenced for 16S rRNA and shotgun metagenomics. Primary outcomes were species richness (α-diversity) and microbial composition (β-diversity). Paired t-tests were performed for α-diversity (Observed species/Margalef). Statistical analysis for β-diversity (weighted and unweighted UniFrac distances, weighted Bray-Curtis dissimilarity) were conducted through Permanova, with 999 permutations. RESULTS Microbial species richness (P < 0.001) and composition (P = 0.001) differed between BCG responders and non-responders. Lactobacillus spp. were significantly enriched in BCG-responders. Shotgun metagenomics identified possible mechanistic pathways such as assimilatory sulfate reduction. CONCLUSION A compositional difference exists in the tumor microbiome of BCG responders and non-responders with Lactobacillus having increased abundance in BCG responders.
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Affiliation(s)
- Jacob Knorr
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | - Zaeem Lone
- Cleveland Clinic Lerner College of Medicine, Cleveland, OH
| | - Glenn Werneburg
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | - Ava Adler
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Jose Agudelo
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | | | - Rebecca A Campbell
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | - Kyle Ericson
- Univeristy Hospitals Department of Urology, Cleveland, OH
| | - Hong Qiu
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Petar Bajic
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | | | | | - Philip P Ahern
- Cleveland Clinic Lerner Research Institute, Cleveland, OH
| | - Nima Almassi
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH
| | - Aaron W Miller
- Cleveland Clinic Glickman Urological and Kidney Institute, Cleveland, OH; Cleveland Clinic Lerner Research Institute, Cleveland, OH.
| | - Byron H Lee
- University of Texas MD Anderson Cancer Center, Houston, TX.
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2
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Sjövall A, Mustanoja E, Lyyski A, Auvinen P, Silvola J, Aarnisalo A, Pätäri-Sampo A, Laulajainen-Hongisto A. Microbiome of the External Auditory Canal: Changes After Long-Term Hearing Aid Use. Otol Neurotol 2024; 45:696-702. [PMID: 38769078 DOI: 10.1097/mao.0000000000004198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
OBJECTIVE To investigate the microbial changes of long-term hearing aid use culture independently. STUDY DESIGN Cross-sectional study. PATIENTS Fifty long-term hearing aid users and 80 volunteer controls with asymptomatic ears. INTERVENTION External auditory canal (EAC) sampling with DNA-free swabs. MAIN OUTCOME MEASURES Microbial communities in the samples were investigated with amplicon sequencing of the 16S rRNA gene. RESULTS The final analysis contained 48 hearing aid users, 59 controls. Twenty-four samples were excluded because of low sequence count, recent use of antimicrobials and/or corticosteroids, recent cold, or missing health status. The groups showed significant differences in bacterial diversity (beta div., p = 0.011), and hearing aid users showed lower species richness than the control group (alpha div., p < 0.01). The most frequent findings in both groups were Staphylococcus auricularis , Alloiococcus otitis , Cutibacterium acnes , Corynebacterium otitidis , and Staphylococcus unclassified sp. Hearing aid users' samples presented more Corynebacterium tuberculostearicum than the control samples. Common EAC pathogens, such as Staphylococcus aureus or Pseudomonas aeruginosa were rare. CONCLUSION Long-term hearing aid use lowers bacterial diversity and modulates the EAC microbiome. The changes mostly affect commensals. Lowered diversity may predispose individuals to EAC conditions and needs more research.
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Affiliation(s)
- Atte Sjövall
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
| | - Ella Mustanoja
- Institute of Biotechnology, HiLIFE, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Annina Lyyski
- Institute of Biotechnology, HiLIFE, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, HiLIFE, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | | | - Antti Aarnisalo
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
| | - Anu Pätäri-Sampo
- Department of Clinical Microbiology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anu Laulajainen-Hongisto
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and Helsinki University Hospital
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Brame JE, Warbrick I, Heke D, Liddicoat C, Breed MF. Short-term passive greenspace exposures have little effect on nasal microbiomes: A cross-over exposure study of a Māori cohort. ENVIRONMENTAL RESEARCH 2024; 252:118814. [PMID: 38555095 DOI: 10.1016/j.envres.2024.118814] [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: 01/17/2024] [Revised: 03/14/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024]
Abstract
Indigenous health interventions have emerged in New Zealand aimed at increasing people's interactions with and exposure to macro and microbial diversity. Urban greenspaces provide opportunities for people to gain such exposures. However, the dynamics and pathways of microbial transfer from natural environments onto a person remain poorly understood. Here, we analysed bacterial 16S rRNA amplicons in air samples (n = 7) and pre- and post-exposure nasal samples (n = 238) from 35 participants who had 30-min exposures in an outdoor park. The participants were organised into two groups: over eight days each group had two outdoor park exposures and two indoor office exposures, with a cross-over study design and washout days between exposure days. We investigated the effects of participant group, location (outdoor park vs. indoor office), and exposures (pre vs. post) on the nasal bacterial community composition and three key suspected health-associated bacterial indicators (alpha diversity, generic diversity of Gammaproteobacteria, and read abundances of butyrate-producing bacteria). The participants had distinct nasal bacterial communities, but these communities did not display notable shifts in composition following exposures. The community composition and key health bacterial indicators were stable throughout the trial period, with no clear or consistent effects of group, location, or exposure. We conclude that 30-min exposure periods to urban greenspaces are unlikely to create notable changes in the nasal microbiome of visitors, which contrasts with previous research. Our results suggest that longer exposures or activities that involves closer interaction with microbial rich ecological components (e.g., soil) are required for greenspace exposures to result in noteworthy changes in the nasal microbiome.
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Affiliation(s)
- Joel E Brame
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
| | - Isaac Warbrick
- Taupua Waiora Māori Research Centre, Auckland University of Technology, Auckland, New Zealand.
| | - Deborah Heke
- Taupua Waiora Māori Research Centre, Auckland University of Technology, Auckland, New Zealand.
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia.
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4
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Sommer AJ, Kettner JE, Coon KL. Stable flies are bona fide carriers of mastitis-associated bacteria. mSphere 2024:e0033624. [PMID: 38920390 DOI: 10.1128/msphere.00336-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 06/27/2024] Open
Abstract
Hematophagous Stomoxys (stable) fly populations in dairy barns are sustained by a constant availability of cattle hosts and manure, which serve as major reservoirs of both zoonotic and opportunistic bacterial pathogens. However, the composition of the Stomoxys fly microbiota, the mechanisms by which flies acquire their microbiome, and the ability of potentially pathogenic bacteria to colonize and persist in fly hosts remain to be investigated. Here, we longitudinally collected fly and manure samples from two connected dairy facilities. High throughput 16S rRNA gene amplicon sequencing was then used to characterize and compare bacterial communities present on or within flies and in manure collected from the same facility, while culture-dependent methods were used to verify the viability of clinically relevant bacteria. Bacterial alpha diversity was overall higher in manure samples as compared to fly samples, with manure-associated bacterial communities being dominated by members of the Bacteroidales, Eubacteriales, and Oscillospirales. In contrast, flies harbored relatively low-complexity communities dominated by members of the Enterobacterales, Staphylococcales, and Lactobacillales. Clinically relevant bacterial strains, including Escherichia spp. and other taxa associated with mastitic cows housed in the same facilities, were detected in paired fly and manure samples but exhibited dramatically elevated abundances in fly samples as compared to manure samples. Viable colonies of Escherichia, Klebsiella, and Staphylococcus spp. were also readily isolated from fly samples, confirming that flies harbor culturable mastitis-associated bacteria. This study identifies biting flies as bona fide carriers of opportunistically pathogenic bacterial taxa on dairy farms. IMPORTANCE Disease prevention on dairy farms has significant implications for cattle health, food security, and zoonosis. Of particular importance is the control of bovine mastitis, which can be caused by diverse bacteria, including Klebsiella, Escherichia coli, Streptococcus, and Staphylococcus spp. Despite being one of the most significant and costly cattle diseases worldwide, the epidemiology of bovine mastitis is not well understood. This study provides parallel culture-independent and culture-dependent evidence to support the carriage of opportunistically pathogenic bacteria by Stomoxys flies on dairy farms. We further show that the fly microbiota is enriched in clinically relevant taxa-the vast majority of which can be traced to the manure habitats in which flies breed. Altogether, our results identify biting flies as underrecognized carriers of bacterial taxa associated with environmental bovine mastitis and other opportunistic infections in vertebrates and offer important insights into mechanisms of microbial acquisition by these and other medically important insects.
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Affiliation(s)
- Andrew J Sommer
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Julia E Kettner
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kerri L Coon
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Ziemons J, Hillege LE, Aarnoutse R, de Vos-Geelen J, Valkenburg-van Iersel L, Mastenbroek J, van Geel R, Barnett DJM, Rensen SS, van Helvoort A, Dopheide LHJ, Roeselers G, Penders J, Smidt ML, Venema K. Prebiotic fibre mixtures counteract the manifestation of gut microbial dysbiosis induced by the chemotherapeutic 5-Fluorouracil (5-FU) in a validated in vitro model of the colon. BMC Microbiol 2024; 24:222. [PMID: 38918717 DOI: 10.1186/s12866-024-03384-4] [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: 01/30/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND 5-Fluorouracil (5-FU) is used as an antineoplastic agent in distinct cancer types. Increasing evidence suggests that the gut microbiota might modulate 5-FU efficacy and toxicity, potentially affecting the patient's prognosis. The current experimental study investigated 5-FU-induced microbiota alterations, as well as the potential of prebiotic fibre mixtures (M1-M4) to counteract these shifts. METHODS A pooled microbial consortium was derived from ten healthy donors, inoculated in an in vitro model of the colon, and treated with 5-FU, with or without prebiotic fibre mixtures for 72 h. Four different prebiotic fibre mixtures were tested: M1 containing short-chain galacto-oligosaccharides (sc GOS), long-chain fructo-oligosaccharides (lcFOS), and low viscosity pectin (lvPect), M2 consisting of arabinoxylan, beta-glucan, pectin, and resistant starch, M3 which was a mixture of scGOS and lcFOS, and M4 containing arabinoxylan, beta-glucan, pectin, resistant starch, and inulin. RESULTS We identified 5-FU-induced changes in gut microbiota composition, but not in microbial diversity. Administration of prebiotic fibre mixtures during 5-FU influenced gut microbiota composition and taxa abundance. Amongst others, prebiotic fibre mixtures successfully stimulated potentially beneficial bacteria (Bifidobacterium, Lactobacillus, Anaerostipes, Weissella, Olsenella, Senegalimassilia) and suppressed the growth of potentially pathogenic bacteria (Klebsiella, Enterobacter) in the presence of 5-FU. The short-chain fatty acid (SCFA) acetate increased slightly during 5-FU, but even more during 5-FU with prebiotic fibre mixtures, while propionate was lower due to 5-FU with or without prebiotic fibre mixtures, compared to control. The SCFA butyrate and valerate did not show differences among all conditions. The branched-chain fatty acids (BCFA) iso-butyrate and iso-valerate were higher in 5-FU, but lower in 5-FU + prebiotics, compared to control. CONCLUSIONS These data suggest that prebiotic fibre mixtures represent a promising strategy to modulate 5-FU-induced microbial dysbiosis towards a more favourable microbiota, thereby possibly improving 5-FU efficacy and reducing toxicity, which should be evaluated further in clinical studies.
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Affiliation(s)
- Janine Ziemons
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands.
- Department of Surgery, Maastricht University Medical Center+, Maastricht, The Netherlands.
| | - Lars E Hillege
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Romy Aarnoutse
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Judith de Vos-Geelen
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Liselot Valkenburg-van Iersel
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Internal Medicine, Division of Medical Oncology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Jasper Mastenbroek
- Department of Surgery, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Robin van Geel
- CARIM School for Cardiovascular Disease, Maastricht University, Maastricht, The Netherlands
- Department of Clinical Pharmacy and Toxicology, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - David J M Barnett
- Department of Medical Microbiology, Infectious Diseases, and Infection Prevention, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Sander S Rensen
- Department of Surgery, Maastricht University Medical Center+, Maastricht, The Netherlands
- NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Ardy van Helvoort
- NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
- Danone Nutricia Research, Utrecht, The Netherlands
| | | | | | - John Penders
- Department of Medical Microbiology, Infectious Diseases, and Infection Prevention, Maastricht University Medical Center+, Maastricht, The Netherlands
- NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
- Euregional Microbiome Center, Maastricht, The Netherlands
| | - Marjolein L Smidt
- GROW - School for Oncology and Reproduction, Maastricht University, Maastricht, The Netherlands
- Department of Surgery, Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Koen Venema
- Euregional Microbiome Center, Maastricht, The Netherlands
- Centre for Healthy Eating & Food Innovation, Maastricht University - Campus Venlo, Venlo, The Netherlands
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Hilliam Y, Armbruster CR, Rapsinski GJ, Marshall CW, Moore J, Koirala J, Krainz L, Gaston JR, Cooper VS, Lee SE, Bomberger JM. Cystic fibrosis pathogens persist in the upper respiratory tract following initiation of elexacaftor/tezacaftor/ivacaftor therapy. Microbiol Spectr 2024:e0078724. [PMID: 38916354 DOI: 10.1128/spectrum.00787-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024] Open
Abstract
Elexacaftor/tezacaftor/ivacaftor (ETI) therapy has revolutionized the treatment of cystic fibrosis (CF) for most affected individuals but the effects of treatment on sinus microbiota are still unknown. Changes to the airway microbiota in CF are associated with disease state and alterations to the bacterial community after ETI initiation may require changes to clinical management regimens. We collected sinus swab samples from the middle meatus in an observational study of 38 adults with CF and chronic rhinosinusitis (CRS) from 2017 to 2021 and captured the initiation of ETI therapy. We performed 16S and custom amplicon sequencing to characterize the sinus microbiota pre- and post-ETI. Real-time quantitative PCR (RT-qPCR) was performed to estimate total bacterial abundance. Sinus samples from people with CF (pwCF) clustered into three community types, dependent on the dominant bacterial organism: a Pseudomonas-dominant, Staphylococcus-dominant, and mixed dominance cluster. Shannon's diversity index was low and not significantly altered post-ETI. Total bacterial load was not significantly lowered post-ETI. Pseudomonas spp. abundance was significantly reduced post-ETI, but eradication was not observed. Staphylococcus spp. became the dominant organism in most individuals post-ETI and we showed the presence of methicillin-resistant Staphylococcus aureus (MRSA) in the sinus both pre- and post-ETI. We also demonstrated that the sinus microbiome is predictive of the presence of Pseudomonas spp., Staphylococcus spp., and Serratia spp. in the sputum. Pseudomonas spp. and Staphylococcus spp., including MRSA, persist in the sinuses of pwCF after ETI therapy, indicating that these pathogens will continue to be important in CF airway disease management in the era of highly effective modulator therapies (HEMT).IMPORTANCEHighly effective modulator therapies (HEMT), such as elexacaftor/tezacaftor/ivacaftor (ETI), for cystic fibrosis (CF) have revolutionized patient care and quality of life for most affected individuals. The effects of these therapies on the microbiota of the airways are still unclear, though work has already been published on changes to microbiota in the sputum. Our study presents evidence for reduced relative abundance of Pseudomonas spp. in the sinuses following ETI therapy. We also show that Staphylococcus spp. becomes the dominant organism in the sinus communities of most individuals in this cohort after ETI therapy. We identified methicillin-resistant Staphylococcus aureus (MRSA) in the sinus microbiota both pre- and post-therapy. These findings demonstrate that pathogen monitoring and treatment will remain a vital part of airway disease management for people with cystic fibrosis (pwCF) in the era of HEMT.
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Affiliation(s)
- Yasmin Hilliam
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Catherine R Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Glenn J Rapsinski
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - John Moore
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Junu Koirala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah Krainz
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jordan R Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stella E Lee
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Jennifer M Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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7
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Neumann CJ, Pausan MR, Haid V, Weiss EC, Kolovetsiou-Kreiner V, Amtmann B, Winkler P, Mahnert A, Jantscher-Krenn E, Moissl-Eichinger C. The dynamics of the female microbiome: unveiling abrupt changes of microbial domains across body sites from prepartum to postpartum phases. Microbiol Spectr 2024:e0014724. [PMID: 38917430 DOI: 10.1128/spectrum.00147-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024] Open
Abstract
The microbial ecosystem of women undergoes enormous changes during pregnancy and the perinatal period. Little is known about the extent of changes in the maternal microbiome beyond the vaginal cavity and its recovery after birth. In this study, we followed pregnant women [maternal prepartum (mpre), n = 30] into the postpartum period [1 month postpartum, maternal postpartum (mpost), n = 30]. We profiled their oral, urinary, and vaginal microbiome; archaeome; mycobiome; and urinary metabolome and compared them with those of nonpregnant (np) women (n = 29). Overall, pregnancy status (np, mpre, and mpost) had a smaller effect on the microbiomes than body site, but massive transitions were observed for the oral and urogenital (vaginal and urinary) microbiomes. While the oral microbiome fluctuates during pregnancy but stabilizes rapidly within the first month postpartum, the urogenital microbiome is characterized by a major remodeling caused by a massive loss of Lactobacillus and thus a shift from Vaginal Community State Type (CST) I (40% of women) to CST IV (85% of women). The urinary metabolome rapidly reached an np-like composition after delivery, apart from lactose and oxaloacetic acid, which were elevated during active lactation. Fungal and archaeal profiles were indicative of pregnancy status. Methanobacterium signatures were found mainly in np women, and Methanobrevibacter showed an opposite behavior in the oral cavity (increased) and vagina (decreased) during pregnancy. Our findings suggest that the massive remodeling of the maternal microbiome and metabolome needs more attention and that potential interventions could be envisioned to optimize recovery and avoid long-term effects on maternal health and subsequent pregnancies. IMPORTANCE The perinatal microbiome is of specific interest for the health of the mother and infant. We therefore investigate the dynamics of the female microbiome from nonpregnant over prepartum to the postpartum period in urine and the oral and vaginal cavities. A specific focus of this study is put not only on the bacterial part of the microbiome but also on the underinvestigated contribution of fungi and archaea. To our knowledge, we present the first study highlighting those aspects. Our findings suggest that the massive remodeling of the maternal microbiome and metabolome needs more attention and that potential interventions could be envisioned to optimize recovery and avoid long-term effects on maternal health and subsequent pregnancies.
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Affiliation(s)
- Charlotte J Neumann
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Manuela-Raluca Pausan
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Victoria Haid
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Eva-Christine Weiss
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | | | - Bettina Amtmann
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | - Petra Winkler
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
| | - Evelyn Jantscher-Krenn
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Styria, Austria
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, Graz, Styria, Austria
- BioTechMed, Graz, Styria, Austria
| | - Christine Moissl-Eichinger
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Styria, Austria
- BioTechMed, Graz, Styria, Austria
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8
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Bernardin JR, Gray SM, Bittleston LS. Arthropod prey type drives decomposition rates and microbial community processes. Appl Environ Microbiol 2024:e0039424. [PMID: 38916291 DOI: 10.1128/aem.00394-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/03/2024] [Indexed: 06/26/2024] Open
Abstract
Microbial communities perform various functions, many of which contribute to ecosystem-level nutrient cycling via decomposition. Factors influencing leaf detrital decomposition are well understood in terrestrial and aquatic ecosystems, but much less is known about arthropod detrital inputs. Here, we sought to infer how differences in arthropod detritus affect microbial-driven decomposition and community function in a carnivorous pitcher plant, Sarracenia purpurea. Using sterile mesh bags filled with different types of sterile arthropod prey, we assessed if prey type influenced the rate of decomposition in pitcher plants over 7 weeks. Additionally, we measured microbial community composition and function, including hydrolytic enzyme activity and carbon substrate use. When comparing decomposition rates, we found that ant and beetle prey with higher exoskeleton content lost less mass compared with fly prey. We observed the highest protease activity in the fly treatment, which had the lowest exoskeleton content. Additionally, we saw differences in the pH of the pitcher fluid, driven by the ant treatment which had the lowest pH. According to our results from 16S rRNA gene metabarcoding, prey treatments with the highest bacterial amplicon sequence variant (ASV) richness (ant and beetle) were associated with prey that lost a lower proportion of mass over the 7 weeks. Overall, arthropod detritus provides unique nutrient sources to decomposer communities, with different prey influencing microbial hydrolytic enzyme activity and composition. IMPORTANCE Microbial communities play pivotal roles in nutrient cycling via decomposition and nutrient transformation; however, it is often unclear how different substrates influence microbial activity and community composition. Our study highlights how different types of insects influence decomposition and, in turn, microbial composition and function. We use the aquatic pools found in a carnivorous pitcher plant as small, discrete ecosystems that we can manipulate and study independently. We find that some insect prey (flies) breaks down faster than others (beetles or ants) likely because flies contain more things that are easy for microbes to eat and derive essential nutrients from. This is also reflected in higher enzyme activity in the microbes decomposing the flies. Our work bridges a knowledge gap about how different substrates affect microbial decomposition, contributing to the broader understanding of ecosystem function in a nutrient cycling context.
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Affiliation(s)
- Jessica R Bernardin
- Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - Sarah M Gray
- Department of Biology-Ecology and Evolution, University of Fribourg, Fribourg, Switzerland
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9
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Massier L, Musat N, Stumvoll M, Tremaroli V, Chakaroun R, Kovacs P. Tissue-resident bacteria in metabolic diseases: emerging evidence and challenges. Nat Metab 2024:10.1038/s42255-024-01065-0. [PMID: 38898236 DOI: 10.1038/s42255-024-01065-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024]
Abstract
Although the impact of the gut microbiome on health and disease is well established, there is controversy regarding the presence of microorganisms such as bacteria and their products in organs and tissues. However, recent contamination-aware findings of tissue-resident microbial signatures provide accumulating evidence in support of bacterial translocation in cardiometabolic disease. The latter provides a distinct paradigm for the link between microbial colonizers of mucosal surfaces and host metabolism. In this Perspective, we re-evaluate the concept of tissue-resident bacteria including their role in metabolic low-grade tissue and systemic inflammation. We examine the limitations and challenges associated with studying low bacterial biomass samples and propose experimental and analytical strategies to overcome these issues. Our Perspective aims to encourage further investigation of the mechanisms linking tissue-resident bacteria to host metabolism and their potentially actionable health implications for prevention and treatment.
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Affiliation(s)
- Lucas Massier
- Department of Medicine (H7), Karolinska Institutet, Stockholm, Sweden
| | - Niculina Musat
- Aarhus University, Department of Biology, Section for Microbiology, Århus, Denmark
| | - Michael Stumvoll
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Valentina Tremaroli
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Rima Chakaroun
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany.
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10
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Ullah S, Huyop F, Wahab RA, Huda N, Oyewusi HA, Sujana IGA, Saloko S, Andriani AASPR, Mohamad MAN, Abdul Hamid AA, Mohd Nasir MH, Antara NS, Gunam IBW. The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island. Sci Rep 2024; 14:14122. [PMID: 38898099 PMCID: PMC11187073 DOI: 10.1038/s41598-024-64838-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024] Open
Abstract
Southern Asian flowers offer honeybees a diversity of nectar. Based on its geographical origin, honey quality varies. Traditional methods are less authentic than DNA-based identification. The origin of honey is determined by pollen, polyphenolic, and macro-microorganisms. In this study, amplicon sequencing targets macro-microorganisms in eDNA using the ITS1 region to explore honey's geographical location and authentication. The variety of honey samples was investigated using ITS1 with Illumina sequencing. For all four honey samples, raw sequence reads showed 979,380 raw ITS1 amplicon reads and 375 ASVs up to the phylum level. The highest total number of 202 ASVs up to phylum level identified Bali honey with 211,189 reads, followed by Banggi honey with 309,207 a total number of 111 ASVs, and Lombok represents only 63 ASVs up to phylum level with several read 458,984. Based on Shannon and Chao1, honey samples from Bali (B2) and (B3) exhibited higher diversity than honey from Lombok (B1) and green honey from Sabah (B4), while the Simpson index showed that Banggi honey (B4) had higher diversity. Honey samples had significant variance in mycobiome taxonomic composition and abundance. Zygosaccharomyces and Aspergillus were the main genera found in Lombok honey, with percentages of 68.81% and 29.76% respectively. Bali honey samples (B2 and B3) were identified as having a significant amount of the genus Aureobasidium, accounting for 40.81% and 25% of the readings, respectively. The microbiome composition of Banggi honey (B4) showed a high presence of Zygosaccharomyces 45.17% and Aureobasidium 35.24%. The ITS1 analysis effectively distinguishes between honey samples of different origins and its potential as a discriminatory tool for honey origin and authentication purposes.
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Affiliation(s)
- Saeed Ullah
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia.
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia.
| | - Roswanira Ab Wahab
- Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
| | - Nurul Huda
- Faculty of Sustainable Agriculture, Universiti Malaysia Sabah, 90509, Sandakan, Sabah, Malaysia
| | - Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Johor Bahru, Malaysia
- Biochemistry Unit, Department of Science Technology, The Federal Polytechnic, P. M. B 5351, Ado Ekiti, Ekiti State, Nigeria
| | - I Gede Arya Sujana
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia
| | - Satrijo Saloko
- Faculty of Food Technology and Agro Industry, University of Mataram, Mataram, Nusa Tenggara Barat, 83126, Indonesia
| | | | - Mohd Azrul Naim Mohamad
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Mohd Hamzah Mohd Nasir
- Research Unit for Bioinformatics and Computational Biology (RUBIC), Kulliyyah of Science, International Islamic University Malaysia, Bandar Indera Mahkota, 25200, Kuantan, Pahang, Malaysia
| | - Nyoman Semadi Antara
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia
| | - Ida Bagus Wayan Gunam
- Bioindustry Laboratory, Department of Agro-Industrial Technology, Udayana University, Denpasar, Indonesia.
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11
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Dagbasi A, Byrne C, Blunt D, Serrano-Contreras JI, Becker GF, Blanco JM, Camuzeaux S, Chambers E, Danckert N, Edwards C, Bernal A, Garcia MV, Hanyaloglu A, Holmes E, Ma Y, Marchesi J, Martinez-Gili L, Mendoza L, Tashkova M, Perez-Moral N, Garcia-Perez I, Robles AC, Sands C, Wist J, Murphy KG, Frost G. Diet shapes the metabolite profile in the intact human ileum, which affects PYY release. Sci Transl Med 2024; 16:eadm8132. [PMID: 38896603 DOI: 10.1126/scitranslmed.adm8132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/24/2024] [Indexed: 06/21/2024]
Abstract
The human ileum contains a high density of enteroendocrine L-cells, which release the appetite-suppressing hormones glucagon-like peptide-1 (GLP-1) and peptide tyrosine tyrosine (PYY) in response to food intake. Recent evidence highlighted the potential role of food structures in PYY release, but the link between food structures, ileal metabolites, and appetite hormone release remains unclear owing to limited access to intact human ileum. In a randomized crossover trial (ISRCTN11327221; isrctn.com), we investigated the role of human ileum in GLP-1 and PYY release by giving healthy volunteers diets differing in fiber and food structure: high-fiber (intact or disrupted food structures) or low-fiber disrupted food structures. We used nasoenteric tubes to sample chyme from the intact distal ileum lumina of humans in the fasted state and every 60 min for 480 min postprandially. We demonstrate the highly dynamic, wide-ranging molecular environment of the ileum over time, with a substantial decrease in ileum bacterial numbers and bacterial metabolites after food intake. We also show that high-fiber diets, independent of food structure, increased PYY release compared with a low-fiber diet during 0 to 240 min postprandially. High-fiber diets also increased ileal stachyose, and a disrupted high-fiber diet increased certain ileal amino acids. Treatment of human ileal organoids with ileal fluids or an amino acid and stachyose mixture stimulated PYY expression in a similar profile to blood PYY concentrations, confirming the role of ileal metabolites in PYY release. Our study demonstrates the diet-induced changes over time in the metabolite environment of intact human ileum, which play a role in PYY release.
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Affiliation(s)
- Aygul Dagbasi
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Claire Byrne
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Dominic Blunt
- Department of Imaging, Charing Cross Hospital, Imperial NHS Trust, London W6 8RF, UK
| | - Jose Ivan Serrano-Contreras
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Georgia Franco Becker
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Jesus Miguens Blanco
- Division of Digestive Diseases, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Stephane Camuzeaux
- National Phenome Centre, Imperial College London, Hammersmith Hospital Campus, London W12 0HS, UK
| | - Edward Chambers
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Nathan Danckert
- Division of Digestive Diseases, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | | | - Andres Bernal
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Maria Valdivia Garcia
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Aylin Hanyaloglu
- Institute of Reproductive and Development Biology (IRDB), Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Hammersmith Hospital, London W12 0NN, UK
| | - Elaine Holmes
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Yue Ma
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Julian Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Laura Martinez-Gili
- Division of Digestive Diseases, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
- Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London W12 0NN, UK
| | - Lilian Mendoza
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Martina Tashkova
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | | | - Isabel Garcia-Perez
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Andres Castillo Robles
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Caroline Sands
- National Phenome Centre, Imperial College London, Hammersmith Hospital Campus, London W12 0HS, UK
| | - Julien Wist
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
- Chemistry Department, Universidad del Valle, Cali 76001, Colombia
| | - Kevin G Murphy
- Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
| | - Gary Frost
- Section of Nutrition, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, 6th Floor Commonwealth Building, Hammersmith Hospital, London W12 0NN, UK
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12
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Dean CJ, Deng Y, Wehri TC, Pena-Mosca F, Ray T, Crooker BA, Godden SM, Caixeta LS, Noyes NR. The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk. mSystems 2024; 9:e0115823. [PMID: 38785438 DOI: 10.1128/msystems.01158-23] [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: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.
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Affiliation(s)
- C J Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Y Deng
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T C Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - F Pena-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B A Crooker
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - S M Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L S Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N R Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
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13
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De Coninck L, Soto A, Wang L, De Wolf K, Smitz N, Deblauwe I, Mbigha Donfack KC, Müller R, Delang L, Matthijnssens J. Lack of abundant core virome in Culex mosquitoes from a temperate climate region despite a mosquito species-specific virome. mSystems 2024; 9:e0001224. [PMID: 38742876 DOI: 10.1128/msystems.00012-24] [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: 01/04/2024] [Accepted: 04/15/2024] [Indexed: 05/16/2024] Open
Abstract
In arthropod-associated microbial communities, insect-specific viruses (ISVs) are prevalent yet understudied due to limited infectivity outside their natural hosts. However, ISVs might play a crucial role in regulating mosquito populations and influencing arthropod-borne virus transmission. Some studies have indicated a core virome in mosquitoes consisting of mostly ISVs. Employing single mosquito metagenomics, we comprehensively profiled the virome of native and invasive mosquito species in Belgium. This approach allowed for accurate host species determination, prevalence assessment of viruses and Wolbachia, and the identification of novel viruses. Contrary to our expectations, no abundant core virome was observed in Culex mosquitoes from Belgium. In that regard, we caution against rigidly defining mosquito core viromes and encourage nuanced interpretations of other studies. Nonetheless, our study identified 45 viruses of which 28 were novel, enriching our understanding of the mosquito virome and ISVs. We showed that the mosquito virome in this study is species-specific and less dependent on the location where mosquitoes from the same species reside. In addition, because Wolbachia has previously been observed to influence arbovirus transmission, we report the prevalence of Wolbachia in Belgian mosquitoes and the detection of several Wolbachia mobile genetic elements. The observed prevalence ranged from 83% to 92% in members from the Culex pipiens complex.IMPORTANCECulex pipiens mosquitoes are important vectors for arboviruses like West Nile virus and Usutu virus. Virome studies on individual Culex pipiens, and on individual mosquitoes in general, have been lacking. To mitigate this, we sequenced the virome of 190 individual Culex and 8 individual Aedes japonicus mosquitoes. We report the lack of a core virome in these mosquitoes from Belgium and caution the interpretation of other studies in this light. The discovery of new viruses in this study will aid our comprehension of insect-specific viruses and the mosquito virome in general in relation to mosquito physiology and mosquito population dynamics.
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Affiliation(s)
- Lander De Coninck
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Alina Soto
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Mosquito Virology Team, Leuven, Belgium
| | - Lanjiao Wang
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Mosquito Virology Team, Leuven, Belgium
| | - Katrien De Wolf
- Department Biomedical Sciences, The Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biology, Terrestrial Ecology Unit, Ghent University, Ghent, Belgium
| | - Nathalie Smitz
- Department of Biology, Royal Museum for Central Africa (Barcoding Facility for Organisms and Tissues of Policy Concern), Tervuren, Belgium
| | - Isra Deblauwe
- Department Biomedical Sciences, The Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Karelle Celes Mbigha Donfack
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Ruth Müller
- Department Biomedical Sciences, The Unit of Entomology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Delang
- KU Leuven, Department of Microbiology, Immunology, & Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy, Mosquito Virology Team, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Division of Clinical and Epidemiological Virology, Laboratory of Viral Metagenomics, Leuven, Belgium
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14
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Pacheco-Sandoval A, Schramm Y, Heckel G, Giffard-Mena I, Lago-Lestón A. Unraveling the gut microbiota of Mexican pinnipeds: the dominance of life histories over phylogeny. Appl Environ Microbiol 2024; 90:e0203023. [PMID: 38771055 DOI: 10.1128/aem.02030-23] [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: 12/01/2023] [Accepted: 03/26/2024] [Indexed: 05/22/2024] Open
Abstract
Studying how phylogeny influences the composition and functions of microbiotas within animal hosts is essential for gaining insights into the connection between genetics, ecology, and health in the animal kingdom. However, due to limited comprehensive studies, this influence remains unclear for many wild mammals, including Mexican pinnipeds. We employed 16S rRNA gene deep-sequencing to investigate the impact of phylogeny on the gut microbiota of four pinniped species inhabiting Mexican shores: the Pacific harbor seal (Phoca vitulina richardii), the northern elephant seal (Mirounga angustirostris), the California sea lion (Zalophus californianus), and the Guadalupe fur seal (Arctocephalus philippii townsendi). Our results indicated that factors such as diets and shared life histories exerted more influence on microbiota composition than phylogeny alone. Notably, otariid species sharing similar life histories displayed greater microbiota similarity than phocids, which have distinct life histories and fewer microbiota similarities. Furthermore, harbor seals have more microbial similarities with the two otariid species than with elephant seals. Of particular concern, we observed a higher abundance of potentially pathogenic bacteria (e.g., Photobacterium damselae and Clostridium perfringens) in harbor seals and Guadalupe fur seals compared to other pinnipeds. This finding could pose health threats to these species and nearby human populations.IMPORTANCEPinnipeds in Mexico host microbial communities that remain understudied. While several factors can influence microbiota composition, the role of phylogenetic relationships among these pinnipeds remains unclear due to limited knowledge of the microbiota in certain species. This study aimed to fill this gap by characterizing the composition and function of the gut microbiota in the four pinniped species that occur in Mexico. Our analysis reveals that shared diets and life histories contribute to similarities in the composition of gut microbial communities. This study also highlights the potential differences in the metabolic capabilities and adaptations within the gut microbiota of pinnipeds. Understanding how phylogeny impacts microbial communities enhances our insights into the evolutionary dynamics of marine mammals.
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Affiliation(s)
- A Pacheco-Sandoval
- Posgrado de Ciencias de la Vida, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - Y Schramm
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - G Heckel
- Departamento de Biología de la Conservación, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
| | - I Giffard-Mena
- Universidad Autónoma de Baja California, Facultad de Ciencias Marinas, Ensenada, Baja California, Mexico
| | - A Lago-Lestón
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Ensenada, Baja California, Mexico
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15
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Fricker AD, Yao T, Lindemann SR, Flores GE. Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage. FEMS Microbiol Ecol 2024; 100:fiae078. [PMID: 38794902 PMCID: PMC11180985 DOI: 10.1093/femsec/fiae078] [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: 10/03/2023] [Revised: 05/03/2024] [Accepted: 05/23/2024] [Indexed: 05/26/2024] Open
Abstract
Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.
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Affiliation(s)
- Ashwana D Fricker
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330, United States
| | - Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, United States
| | - Gilberto E Flores
- Department of Biology, California State University, 18111 Nordhoff Street, Northridge, CA 91330, United States
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16
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Sintoris S, Binkowska JM, Gillan JL, Zuurbier RP, Twynam-Perkins J, Kristensen M, Melrose L, Parga PL, Rodriguez AR, Chu ML, van Boeckel SR, Wildenbeest JG, Bowdish DME, Currie AJ, Thwaites RS, Schwarze J, van Houten MA, Boardman JP, Cunningham S, Bogaert D, Davidson DJ. Nasal cathelicidin is expressed in early life and is increased during mild, but not severe respiratory syncytial virus infection. Sci Rep 2024; 14:13928. [PMID: 38886476 PMCID: PMC11182768 DOI: 10.1038/s41598-024-64446-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/10/2024] [Indexed: 06/20/2024] Open
Abstract
Respiratory syncytial virus is the major cause of acute lower respiratory tract infections in young children, causing extensive mortality and morbidity globally, with limited therapeutic or preventative options. Cathelicidins are innate immune antimicrobial host defence peptides and have antiviral activity against RSV. However, upper respiratory tract cathelicidin expression and the relationship with host and environment factors in early life, are unknown. Infant cohorts were analysed to characterise early life nasal cathelicidin levels, revealing low expression levels in the first week of life, with increased levels at 9 months which are comparable to 2-year-olds and healthy adults. No impact of prematurity on nasal cathelicidin expression was observed, nor were there effects of sex or birth mode, however, nasal cathelicidin expression was lower in the first week-of-life in winter births. Nasal cathelicidin levels were positively associated with specific inflammatory markers and demonstrated to be associated with microbial community composition. Importantly, levels of nasal cathelicidin expression were elevated in infants with mild RSV infection, but, in contrast, were not upregulated in infants hospitalised with severe RSV infection. These data suggest important relationships between nasal cathelicidin, upper airway microbiota, inflammation, and immunity against RSV infection, with interventional potential.
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Affiliation(s)
- Sofia Sintoris
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Justyna M Binkowska
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Jonathan L Gillan
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Roy P Zuurbier
- Spaarne Gasthuis Academy, Spaarne Gasthuis, 2134 TM, Hoofddorp, The Netherlands
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
- Department of Paediatrics, Emma Children's Hospital, Amsterdam UMC, Amsterdam, the Netherlands
| | - Jonathan Twynam-Perkins
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Maartje Kristensen
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Lauren Melrose
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Paula Lusaretta Parga
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Alicia Ruiz Rodriguez
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Mei Ling Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Sara R van Boeckel
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Joanne G Wildenbeest
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Dawn M E Bowdish
- Firestone Institute for Respiratory Health, St. Joseph's Healthcare, 50 Charlton Avenue East, T2128, Hamilton, ON, L8N 4A6, Canada
| | - Andrew J Currie
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA, Australia
| | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jurgen Schwarze
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | | | - James P Boardman
- Centre for Reproductive Health, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Steve Cunningham
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
| | - Debby Bogaert
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA, Utrecht, The Netherlands
| | - Donald J Davidson
- Centre for Inflammation Research, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh BioQuarter, 4 - 5 Little France Drive, Edinburgh, EH16 4UU, Scotland, UK.
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Perth, WA, Australia.
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17
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Bowden AC, Allbaugh RA, Gall AJ, Costa MDO, Leis M, Sebbag L. Ocular diagnostics, ophthalmic findings, and conjunctival microbiome in the Chilean flamingo (Phoenicopterus chilensis). Vet Ophthalmol 2024. [PMID: 38880760 DOI: 10.1111/vop.13242] [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: 01/12/2024] [Revised: 05/13/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024]
Abstract
OBJECTIVE To establish normative data for selected ocular diagnostic tests and commensal conjunctival microflora and describe the incidence of ocular pathology in Chilean flamingos. ANIMALS STUDIED A total of 41 Chilean flamingos were examined at the Blank Park Zoo in Des Moines, Iowa. PROCEDURES In 20 flamingos, blink rate was assessed undisturbed in their exhibit, then gentle manual restraint was used to assess palpebral fissure length (PFL), aqueous tear production (phenol red thread test [PRTT] in one eye, endodontic absorbent paper point tear test [EAPPTT] in the other), intraocular pressure (IOP; rebound tonometry), and fluorescein staining. Twenty-one other flamingos were brought to a darkened area for neuro-ophthalmic examination, slit lamp biomicroscopy, and indirect ophthalmoscopy. Swabs from seven flamingos were used for ocular microbiome evaluation. RESULTS Results are presented as mean ± standard deviation (range). Flamingos comprised 23 females/18 males, aged 11 ± 9.1 (0.7-40) years. Test results: blink rate, 3.7 ± 2 (1-9) blinks/min; PFL, 11.2 ± 1.2 (9-14) mm; IOP, 14 ± 3.2 (10-22) mmHg; EAPPT, 10.2 ± 2.8 (9-14) mm/min; PRTT, 6.8 ± 2.5 (3-13) mm/15 s. Dazzle reflex was positive in four birds examined. Pathologies included cataracts (n = 7 birds), corneal fibrosis (n = 3), endothelial pigment (n = 2), uveal cysts (n = 1), lens luxation (n = 1), and uveitis (n = 1). Ocular microbiome showed high diversity of taxa. CONCLUSIONS Baseline ocular parameters and incidence of ophthalmic pathology assist veterinarians with disease screening for Chilean flamingos, while the ocular microbiome showed high diversity.
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Affiliation(s)
- Anna Catherine Bowden
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Rachel A Allbaugh
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | | | - Matheus de O Costa
- Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Faculty of Veterinary Medicine, Population Clinical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Marina Leis
- Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lionel Sebbag
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
- Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Rehovot, Israel
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18
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Natalini JG, Wong KK, Nelson NC, Wu BG, Rudym D, Lesko MB, Qayum S, Lewis TC, Wong A, Chang SH, Chan JCY, Geraci TC, Li Y, Wang C, Li H, Pamar P, Schnier J, Mahoney IJ, Malik T, Darawshy F, Sulaiman I, Kugler MC, Singh R, Collazo DE, Chang M, Patel S, Kyeremateng Y, McCormick C, Barnett CR, Tsay JCJ, Brosnahan SB, Singh S, Pass HI, Angel LF, Segal LN. Longitudinal Lower Airway Microbial Signatures of Acute Cellular Rejection in Lung Transplantation. Am J Respir Crit Care Med 2024; 209:1463-1476. [PMID: 38358857 DOI: 10.1164/rccm.202309-1551oc] [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: 09/10/2023] [Accepted: 02/14/2024] [Indexed: 02/17/2024] Open
Abstract
Rationale: Acute cellular rejection (ACR) after lung transplant is a leading risk factor for chronic lung allograft dysfunction. Prior studies have demonstrated dynamic microbial changes occurring within the allograft and gut that influence local adaptive and innate immune responses. However, the lung microbiome's overall impact on ACR risk remains poorly understood. Objectives: To evaluate whether temporal changes in microbial signatures were associated with the development of ACR. Methods: We performed cross-sectional and longitudinal analyses (joint modeling of longitudinal and time-to-event data and trajectory comparisons) of 16S rRNA gene sequencing results derived from lung transplant recipient lower airway samples collected at multiple time points. Measurements and Main Results: Among 103 lung transplant recipients, 25 (24.3%) developed ACR. In comparing samples acquired 1 month after transplant, subjects who never developed ACR demonstrated lower airway enrichment with several oral commensals (e.g., Prevotella and Veillonella spp.) than those with current or future (beyond 1 mo) ACR. However, a subgroup analysis of those who developed ACR beyond 1 month revealed delayed enrichment with oral commensals occurring at the time of ACR diagnosis compared with baseline, when enrichment with more traditionally pathogenic taxa was present. In longitudinal models, dynamic changes in α-diversity (characterized by an initial decrease and a subsequent increase) and in the taxonomic trajectories of numerous oral commensals were more commonly observed in subjects with ACR. Conclusions: Dynamic changes in the lower airway microbiota are associated with the development of ACR, supporting its potential role as a useful biomarker or in ACR pathogenesis.
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Affiliation(s)
- Jake G Natalini
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Kendrew K Wong
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Nathaniel C Nelson
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- Veterans Affairs New York Harbor Healthcare System, New York, New York
| | - Darya Rudym
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Melissa B Lesko
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Seema Qayum
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Tyler C Lewis
- New York University Langone Transplant Institute, New York, New York
| | - Adrian Wong
- New York University Langone Transplant Institute, New York, New York
| | - Stephanie H Chang
- Department of Cardiothoracic Surgery, and
- New York University Langone Transplant Institute, New York, New York
| | - Justin C Y Chan
- Department of Cardiothoracic Surgery, and
- New York University Langone Transplant Institute, New York, New York
| | - Travis C Geraci
- Department of Cardiothoracic Surgery, and
- New York University Langone Transplant Institute, New York, New York
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Chan Wang
- Department of Population Health, New York University Grossman School of Medicine, New York, New York
| | - Huilin Li
- Department of Population Health, New York University Grossman School of Medicine, New York, New York
| | - Prerna Pamar
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Joseph Schnier
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Ian J Mahoney
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Tahir Malik
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Fares Darawshy
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- The Institute of Pulmonology, Hadassah Medical Center, Jerusalem, Israel
- The Faculty of Medicine at the Hebrew University of Jerusalem, Jerusalem, Israel
| | - Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- Department of Respiratory Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland; and
- Department of Respiratory Medicine, Beaumont Hospital, Dublin, Ireland
| | - Matthias C Kugler
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Rajbir Singh
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Destiny E Collazo
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Miao Chang
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Shrey Patel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Yaa Kyeremateng
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Colin McCormick
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Clea R Barnett
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Jun-Chieh J Tsay
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- Veterans Affairs New York Harbor Healthcare System, New York, New York
| | - Shari B Brosnahan
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | - Shivani Singh
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
| | | | - Luis F Angel
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
- New York University Langone Transplant Institute, New York, New York
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine
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19
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Desorcy-Scherer K, Zuniga-Chaves I, Reisner MA, Suen G, Hernandez LL. Investigating the influence of perinatal fluoxetine exposure on murine gut microbial communities during pregnancy and lactation. Sci Rep 2024; 14:13762. [PMID: 38877103 PMCID: PMC11178873 DOI: 10.1038/s41598-024-62224-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 05/15/2024] [Indexed: 06/16/2024] Open
Abstract
Selective Serotonin Reuptake Inhibitor (SSRI) therapy is common among perinatal populations for the treatment of mood disorders. Medications can affect diversity and composition of the gut microbiome, which plays a key role in modulating health. While previous studies have examined the effects of antidepressant exposure on the maternal gut microbiome, whether SSRI exposure affects the offspring gut microbiome is unknown. We investigated the effects of maternal fluoxetine exposure on the gut microbiome of maternal and offspring mice during pregnancy and lactation (embryonic day 10-lactation day 21; E10-L21). Stool samples collected on E17, L11, L15, and L21 were examined using 16S rRNA sequencing. Our results suggest that maternal fluoxetine exposure may result in decreased alpha diversity of the offspring gut microbiome in early life. Furthermore, we observed several genera-specific differences in the gut microbiome based on treatment, specifically of Turicibacter, Parasutterella, and Romboutsia. These findings support our understanding of gut health, as dysbiotic development of the gut microbiome has been associated with local and systemic health problems including gastrointestinal morbidities and interrupted growth patterns in infants. Future research should pursue study in human populations and those at high risk for gut microbial dysbiosis and intestinal injury.
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Affiliation(s)
- Katelyn Desorcy-Scherer
- School of Nursing, University of Wisconsin-Madison, 701 Highland Avenue, Madison, WI, 54705, USA.
| | - Ibrahim Zuniga-Chaves
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Maggie A Reisner
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Laura L Hernandez
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
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20
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Grieneisen L, Hays A, Cook E, Blekhman R, Tecot S. Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats in a novel sample type. Am J Primatol 2024:e23656. [PMID: 38873762 DOI: 10.1002/ajp.23656] [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: 06/01/2023] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
The gut microbiome is a plastic phenotype; gut microbial composition is highly variable across an individual host's lifetime and between host social groups, and this variation has consequences for host health. However, we do not yet fully understand how longitudinal microbial dynamics and their social drivers may be influenced by ecological stressors, such as habitat degradation. Answering these questions is difficult in most wild animal systems, as it requires long-term collections of matched host, microbiome, and environmental trait data. To test if temporal and social influences on microbiome composition differ by the history of human disturbance, we leveraged banked, desiccated fecal samples collected over 5 months in 2004 from two ecologically distinct populations of wild, red-bellied lemurs (Eulemur rubriventer) that are part of a long-term study system. We found that social group explained more variation in microbiome composition than host population membership did, and that temporal variation in common microbial taxa was similar between populations, despite differences in history of human disturbance. Furthermore, we found that social group membership and collection month were both more important than individual lemur identity. Taken together, our results suggest that synchronized environments use can lead to synchronized microbial dynamics over time, even between habitats of varying quality, and that desiccated samples could become a viable approach for studying primate gut microbiota. Our work opens the door for other projects to utilize historic biological sample data sets to answer novel temporal microbiome questions in an ecological context.
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Affiliation(s)
- Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan Campus, Kelowna, BC, Canada
| | - Allison Hays
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
| | - Erica Cook
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Stacey Tecot
- Laboratory for the Evolutionary Endocrinology of Primates, University of Arizona, Tucson, AZ, USA
- School of Anthropology, University of Arizona, Tucson, AZ, USA
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21
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Yadegar A, Bar-Yoseph H, Monaghan TM, Pakpour S, Severino A, Kuijper EJ, Smits WK, Terveer EM, Neupane S, Nabavi-Rad A, Sadeghi J, Cammarota G, Ianiro G, Nap-Hill E, Leung D, Wong K, Kao D. Fecal microbiota transplantation: current challenges and future landscapes. Clin Microbiol Rev 2024; 37:e0006022. [PMID: 38717124 DOI: 10.1128/cmr.00060-22] [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] [Indexed: 06/14/2024] Open
Abstract
SUMMARYGiven the importance of gut microbial homeostasis in maintaining health, there has been considerable interest in developing innovative therapeutic strategies for restoring gut microbiota. One such approach, fecal microbiota transplantation (FMT), is the main "whole gut microbiome replacement" strategy and has been integrated into clinical practice guidelines for treating recurrent Clostridioides difficile infection (rCDI). Furthermore, the potential application of FMT in other indications such as inflammatory bowel disease (IBD), metabolic syndrome, and solid tumor malignancies is an area of intense interest and active research. However, the complex and variable nature of FMT makes it challenging to address its precise functionality and to assess clinical efficacy and safety in different disease contexts. In this review, we outline clinical applications, efficacy, durability, and safety of FMT and provide a comprehensive assessment of its procedural and administration aspects. The clinical applications of FMT in children and cancer immunotherapy are also described. We focus on data from human studies in IBD in contrast with rCDI to delineate the putative mechanisms of this treatment in IBD as a model, including colonization resistance and functional restoration through bacterial engraftment, modulating effects of virome/phageome, gut metabolome and host interactions, and immunoregulatory actions of FMT. Furthermore, we comprehensively review omics technologies, metagenomic approaches, and bioinformatics pipelines to characterize complex microbial communities and discuss their limitations. FMT regulatory challenges, ethical considerations, and pharmacomicrobiomics are also highlighted to shed light on future development of tailored microbiome-based therapeutics.
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Affiliation(s)
- Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Haggai Bar-Yoseph
- Department of Gastroenterology, Rambam Health Care Campus, Haifa, Israel
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tanya Marie Monaghan
- National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, United Kingdom
- Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Sepideh Pakpour
- School of Engineering, Faculty of Applied Sciences, UBC, Okanagan Campus, Kelowna, British Columbia, Canada
| | - Andrea Severino
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Ed J Kuijper
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Elisabeth M Terveer
- Center for Microbiota Analysis and Therapeutics (CMAT), Leiden University Center for Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Sukanya Neupane
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Sadeghi
- School of Engineering, Faculty of Applied Sciences, UBC, Okanagan Campus, Kelowna, British Columbia, Canada
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell'Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Gemelli IRCCS, Rome, Italy
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Estello Nap-Hill
- Department of Medicine, Division of Gastroenterology, St Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dickson Leung
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Karen Wong
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Dina Kao
- Division of Gastroenterology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
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22
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Goloshchapov OV, Chukhlovin AB, Bug DS, Polev DE, Kosarev OV, Klementeva RV, Izmailova EA, Kazantsev IV, Khalipskaia MS, Goloshchapova МО, Yudintseva OS, Barkhatov IM, Petukhova NV, Zubarovskaya LS, Kulagin AD, Moiseev IS. Safety, Feasibility, and Advantages of Oral Microbiota Transplantation: The First Clinical Case. J Pediatr Hematol Oncol 2024:00043426-990000000-00438. [PMID: 38875447 DOI: 10.1097/mph.0000000000002896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 04/30/2024] [Indexed: 06/16/2024]
Abstract
The pilot clinical study presented demonstrates the possibility, safety, and effectiveness of oral microbiota transplantation from a healthy donor to a patient with neuroblastoma to prevent chemotherapy-induced oral mucositis. A 6-month-old patient with a diagnosis of retroperitoneal neuroblastoma was treated according to the NB 2004 protocol. Due to the development of severe oral mucositis, it was decided to perform oral microbiota transplantation. During the next 3 chemotherapy cycles and conditioning regimen before autologous hematopoietic cell transplantation (auto-HCT), the patient was repeatedly injected per os with donor saliva from her healthy mother. Oral microbiota transplantation was shown to effectively prevent the development of oral mucositis after chemotherapy, and only grade 1 oral mucositis developed after auto-HCT. In all loci of the oral cavity, there was a decreased abundance of bacteria from the Staphylococcaceae, Micrococcaceae, and Xanthomonadaceae families. Conversely, there was an increase in the relative abundance of Streptococcaceae and certain other bacterial taxa. In conclusion, the transplantation of maternal saliva in this patient prevented severe mucositis and was accompanied by a compositional change of the patient's oral microbiota. No adverse events due to the transplantation of maternal saliva were noted.
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Affiliation(s)
| | | | | | | | - Oleg V Kosarev
- Saint Petersburg Mining University, Saint Petersburg, Russian Federation
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23
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Tierney BT, Kim J, Overbey EG, Ryon KA, Foox J, Sierra MA, Bhattacharya C, Damle N, Najjar D, Park J, Garcia Medina JS, Houerbi N, Meydan C, Wain Hirschberg J, Qiu J, Kleinman AS, Al-Ghalith GA, MacKay M, Afshin EE, Dhir R, Borg J, Gatt C, Brereton N, Readhead BP, Beyaz S, Venkateswaran KJ, Wiseman K, Moreno J, Boddicker AM, Zhao J, Lajoie BR, Scott RT, Altomare A, Kruglyak S, Levy S, Church GM, Mason CE. Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight. Nat Microbiol 2024:10.1038/s41564-024-01635-8. [PMID: 38862604 DOI: 10.1038/s41564-024-01635-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/09/2024] [Indexed: 06/13/2024]
Abstract
Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes. However, documenting microbial shifts during spaceflight has been difficult due to mission constraints that lead to limited sampling and profiling. Here we executed a six-month longitudinal study to quantify the high-resolution human microbiome response to three days in orbit for four individuals. Using paired metagenomics and metatranscriptomics alongside single-nuclei immune cell profiling, we characterized time-dependent, multikingdom microbiome changes across 750 samples and 10 body sites before, during and after spaceflight at eight timepoints. We found that most alterations were transient across body sites; for example, viruses increased in skin sites mostly during flight. However, longer-term shifts were observed in the oral microbiome, including increased plaque-associated bacteria (for example, Fusobacteriota), which correlated with immune cell gene expression. Further, microbial genes associated with phage activity, toxin-antitoxin systems and stress response were enriched across multiple body sites. In total, this study reveals in-depth characterization of microbiome and immune response shifts experienced by astronauts during short-term spaceflight and the associated changes to the living environment, which can help guide future missions, spacecraft design and space habitat planning.
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Affiliation(s)
- Braden T Tierney
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Eliah G Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- BioAstra, Inc., New York, NY, USA
- Center for STEM, University of Austin, Austin, TX, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Maria A Sierra
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA
| | - Chandrima Bhattacharya
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Deena Najjar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jiwoon Park
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - J Sebastian Garcia Medina
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA
| | - Nadia Houerbi
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | | | - Jake Qiu
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ashley S Kleinman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Matthew MacKay
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Raja Dhir
- Seed Health, Inc., Venice, CA, USA
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Christine Gatt
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Nicholas Brereton
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Benjamin P Readhead
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA
| | - Semir Beyaz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | | | | | | | - Ryan T Scott
- KBR; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | | | | | | | - George M Church
- Harvard Medical School and the Wyss Institute, Boston, MA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- BioAstra, Inc., New York, NY, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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Martinez-Villegas L, Lado P, Klompen H, Wang S, Cummings C, Pesapane R, Short SM. The microbiota of Amblyomma americanum reflects known westward expansion. PLoS One 2024; 19:e0304959. [PMID: 38857239 PMCID: PMC11164389 DOI: 10.1371/journal.pone.0304959] [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: 10/17/2023] [Accepted: 05/22/2024] [Indexed: 06/12/2024] Open
Abstract
Amblyomma americanum, a known vector of multiple tick-borne pathogens, has expanded its geographic distribution across the United States in the past decades. Tick microbiomes may play a role shaping their host's life history and vectorial capacity. Bacterial communities associated with A. americanum may reflect, or enable, geographic expansion and studying the microbiota will improve understanding of tick-borne disease ecology. We examined the microbiota structure of 189 adult ticks collected in four regions encompassing their historical and current geographic distribution. Both geographic region of origin and sex were significant predictors of alpha diversity. As in other tick models, within-sample diversity was low and uneven given the presence of dominant endosymbionts. Beta diversity analyses revealed that bacterial profiles of ticks of both sexes collected in the West were significantly different from those of the Historic range. Biomarkers were identified for all regions except the historical range. In addition, Bray-Curtis dissimilarities overall increased with distance between sites. Relative quantification of ecological processes showed that, for females and males, respectively, drift and dispersal limitation were the primary drivers of community assembly. Collectively, our findings highlight how microbiota structural variance discriminates the western-expanded populations of A. americanum ticks from the Historical range. Spatial autocorrelation, and particularly the detection of non-selective ecological processes, are indicative of geographic isolation. We also found that prevalence of Ehrlichia chaffeensis, E. ewingii, and Anaplasma phagocytophilum ranged from 3.40-5.11% and did not significantly differ by region. Rickettsia rickettsii was absent from our samples. Our conclusions demonstrate the value of synergistic analysis of biogeographic and microbial ecology data in investigating range expansion in A. americanum and potentially other tick vectors as well.
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Affiliation(s)
- Luis Martinez-Villegas
- Department of Entomology, The Ohio State University, Columbus, Ohio, United States of America
| | - Paula Lado
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Hans Klompen
- Department of Evolution, Ecology, and Organismal Biology and Museum of Biological Diversity, The Ohio State University, Columbus, Ohio, United States of America
| | - Selena Wang
- Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Caleb Cummings
- Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Risa Pesapane
- Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, United States of America
- School of Environment and Natural Resources, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Sarah M. Short
- Department of Entomology, The Ohio State University, Columbus, Ohio, United States of America
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Paix B, van der Valk E, de Voogd NJ. Dynamics, diversity, and roles of bacterial transmission modes during the first asexual life stages of the freshwater sponge Spongilla lacustris. ENVIRONMENTAL MICROBIOME 2024; 19:37. [PMID: 38851755 PMCID: PMC11162577 DOI: 10.1186/s40793-024-00580-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
BACKGROUND Sponge-associated bacteria play important roles in the physiology of their host, whose recruitment processes are crucial to maintain symbiotic associations. However, the acquisition of bacterial communities within freshwater sponges is still under explored. Spongilla lacustris is a model sponge widely distributed in European rivers and lakes, producing dormant cysts (named gemmules) for their asexual reproduction, before winter. Through an in vitro experiment, this study aims to describe the dynamics of bacterial communities and their transmission modes following the hatching of these gemmules. RESULTS An overall change of bacterial β-diversity was observed through the ontology of the juvenile sponges. These temporal differences were potentially linked, first to the osculum acquisition and the development of a canal system, and then, the increasing colonization of the Chlorella-like photosymbionts. Gemmules hatching with a sterilized surface were found to have a more dispersed and less diverse microbiome, revealing the importance of gemmule epibacteria for the whole holobiont stability. These epibacteria were suggested to be vertically transmitted from the maternal tissues to the gemmule surface. Vertical transmission through the incorporation of bacterial communities inside of the gemmule, was also found as a dominant transmission mode, especially with the nitrogen fixers Terasakiellaceae. Finally, we showed that almost no ASVs were shared between the free-living community and the juveniles, suggesting that horizontal recruitment is unlikely to happen during the first stages of development. However, the free-living bacteria filtered are probably used as a source of nutrients, allowing an enrichment of copiotrophic bacteria already present within its microbiome. CONCLUSIONS This study brings new insight for a better understanding of the microbiome acquisition during the first stages of freshwater sponge development. We showed the importance of epibacterial communities on gemmules for the whole holobiont stability, and demonstrated the near absence of recruitment of free-living bacteria during the first stages.
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Affiliation(s)
- Benoit Paix
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- UMR CARRTEL, INRAE - Université Savoie Mont-Blanc, Thonon-les-Bains, France.
| | - Elodie van der Valk
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Biology (IBL), Leiden University, PO Box 9505, Leiden, 2333BE, The Netherlands
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, Leiden, The Netherlands.
- Institute of Biology (IBL), Leiden University, PO Box 9505, Leiden, 2333BE, The Netherlands.
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Pust MM, Rocha Castellanos DM, Rzasa K, Dame A, Pishchany G, Assawasirisin C, Liss A, Fernandez-Del Castillo C, Xavier RJ. Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm. Gut 2024; 73:1131-1141. [PMID: 38429112 PMCID: PMC11187374 DOI: 10.1136/gutjnl-2023-331012] [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: 08/28/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024]
Abstract
OBJECTIVE This study aims to validate the existence of a microbiome within intraductal papillary mucinous neoplasm (IPMN) that can be differentiated from the taxonomically diverse DNA background of next-generation sequencing procedures. DESIGN We generated 16S rRNA amplicon sequencing data to analyse 338 cyst fluid samples from 190 patients and 19 negative controls, the latter collected directly from sterile syringes in the operating room. A subset of samples (n=20) and blanks (n=5) were spiked with known concentrations of bacterial cells alien to the human microbiome to infer absolute abundances of microbial traces. All cyst fluid samples were obtained intraoperatively and included IPMNs with various degrees of dysplasia as well as other cystic neoplasms. Follow-up culturing experiments were conducted to assess bacterial growth for microbiologically significant signals. RESULTS Microbiome signatures of cyst fluid samples were inseparable from those of negative controls, with no difference in taxonomic diversity, and microbial community composition. In a patient subgroup that had recently undergone invasive procedures, a bacterial signal was evident. This outlier signal was not characterised by higher taxonomic diversity but by an increased dominance index of a gut-associated microbe, leading to lower taxonomic evenness compared with the background signal. CONCLUSION The 'microbiome' of IPMNs and other pancreatic cystic neoplasms does not deviate from the background signature of negative controls, supporting the concept of a sterile environment. Outlier signals may appear in a small fraction of patients following recent invasive endoscopic procedures. No associations between microbial patterns and clinical or cyst parameters were apparent.
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Affiliation(s)
- Marie-Madlen Pust
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Kara Rzasa
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrea Dame
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Gleb Pishchany
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
| | - Charnwit Assawasirisin
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrew Liss
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
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27
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Moraes JGN, Gull T, Ericsson AC, Poock SE, Caldeira MO, Lucy MC. Establishment of the uterine microbiome following artificial insemination in virgin heifers. Front Microbiol 2024; 15:1385505. [PMID: 38903779 PMCID: PMC11188424 DOI: 10.3389/fmicb.2024.1385505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction The concept of a sterile uterus was challenged by recent studies that have described the microbiome of the virgin and pregnant uterus for species including humans and cattle. We designed two studies that tested whether the microbiome is introduced into the uterus when the virgin heifer is first inseminated and whether the origin of the microbiome is the vagina/cervix. Methods The uterine microbiome was measured immediately before and after an artificial insemination (AI; Study 1; n = 7 AI and n = 6 control) and 14 d after insemination (Study 2; n = 12 AI and n = 12 control) in AI and non-AI (control) Holstein heifers. A third study (Study 3; n = 5 Holstein heifers) that included additional negative controls was subsequently conducted to support the presence of a unique microbiome within the uterus despite the low microbial biomass and regardless of insemination. Traditional bacteriological culture was performed in addition to 16S rRNA gene sequencing on the same samples to determine whether there were viable organisms in addition to those detected based on DNA sequencing (16S rRNA gene sequence). Results and discussion Inseminating a heifer did not lead to a large change in the microbiome when assessed by traditional methods of bacterial culture or metataxonomic (16S rRNA gene) sequencing (results of Studies 1 and 2). Very few bacteria were cultured from the body or horn of the uterus regardless of whether an AI was or was not (negative control) performed. The cultured bacterial genera (e.g., Bacillus, Corynebacterium, Cutibacterium, Micrococcus, Staphylococcus, and Streptococcus) were typical of those found in the soil, environment, skin, mucous membranes, and urogenital tract of animals. Metataxonomic sequencing of 16S rRNA gene generated a large number of amplicon sequence variants (ASV), but these larger datasets that were based on DNA sequencing did not consistently demonstrate an effect of AI on the abundance of ASVs across all uterine locations compared with the external surface of the tract (e.g., perimetrium; positive control samples for environment contamination during slaughter and collection). Major genera identified by 16S rRNA gene sequencing overlapped with those identified with bacterial culture and included Cutibacterium, Staphylococcus, and Streptococcus.
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Affiliation(s)
- Joao G. N. Moraes
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Tamara Gull
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Aaron C. Ericsson
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Scott E. Poock
- College of Veterinary Medicine, University of Missouri, Columbia, MO, United States
| | - Monica O. Caldeira
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Matthew C. Lucy
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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28
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Thumann TA, Pferschy-Wenzig EM, Kumpitsch C, Duller S, Högenauer C, Kump P, Aziz-Kalbhenn H, Ammar RM, Rabini S, Moissl-Eichinger C, Bauer R. Rapid biotransformation of STW 5 constituents by human gut microbiome from IBS- and non-IBS donors. Microbiol Spectr 2024; 12:e0403123. [PMID: 38738925 DOI: 10.1128/spectrum.04031-23] [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: 11/28/2023] [Accepted: 04/03/2024] [Indexed: 05/14/2024] Open
Abstract
STW 5, a blend of nine medicinal plant extracts, exhibits promising efficacy in treating functional gastrointestinal disorders, notably irritable bowel syndrome (IBS). Nonetheless, its effects on the gastrointestinal microbiome and the role of microbiota on the conversion of its constituents are still largely unexplored. This study employed an experimental ex vivo model to investigate STW 5's differential effects on fecal microbial communities and metabolite production in samples from individuals with and without IBS. Using 560 fecal microcosms (IBS patients, n = 6; healthy controls, n = 10), we evaluated the influence of pre-digested STW 5 and controls on microbial and metabolite composition at time points 0, 0.5, 4, and 24 h. Our findings demonstrate the potential of this ex vivo platform to analyze herbal medicine turnover within 4 h with minimal microbiome shifts due to abiotic factors. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products, such as 18β-glycyrrhetinic acid, davidigenin, herniarin, 3-(3-hydroxyphenyl)propanoic acid, and 3-(2-hydroxy-4-methoxyphenyl)propanoic acid occurred. For davidigenin, 3-(3-hydroxyphenyl)propanoic acid and 18β-glycyrrhetinic acid, anti-inflammatory, cytoprotective, or spasmolytic activities have been previously described. Notably, the microbiome-driven metabolic transformation did not induce a global microbiome shift, and the detected metabolites were minimally linked to specific taxa. Observed biotransformations were independent of IBS diagnosis, suggesting potential benefits for IBS patients from biotransformation products of STW 5. IMPORTANCE STW 5 is an herbal medicinal product with proven clinical efficacy in the treatment of functional gastrointestinal disorders, like functional dyspepsia and irritable bowel syndrome (IBS). The effects of STW 5 on fecal microbial communities and metabolite production effects have been studied in an experimental model with fecal samples from individuals with and without IBS. While only minor taxonomic disparities were noted between IBS- and non-IBS samples and upon treatment with STW 5, rapid metabolic turnover of STW 5 components into specific degradation products with reported anti-inflammatory, cytoprotective, or spasmolytic activities was observed, which may be relevant for the pharmacological activity of STW 5.
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Affiliation(s)
- Timo A Thumann
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Eva-Maria Pferschy-Wenzig
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Christina Kumpitsch
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Stefanie Duller
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | | | - Patrizia Kump
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Heba Aziz-Kalbhenn
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
| | - Ramy M Ammar
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
- Department of Pharmacology, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Sabine Rabini
- Steigerwald Arzneimittelwerk GmbH, Bayer Consumer Health, Darmstadt, Germany
| | - Christine Moissl-Eichinger
- BioTechMed, Graz, Austria
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Rudolf Bauer
- Department of Pharmacognosy, Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- BioTechMed, Graz, Austria
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29
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Camacho-Sanchez M. A new spike-in-based method for quantitative metabarcoding of soil fungi and bacteria. Int Microbiol 2024; 27:719-730. [PMID: 37672116 DOI: 10.1007/s10123-023-00422-5] [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: 05/08/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
Metabarcoding is a powerful tool to characterize biodiversity in biological samples. The interpretation of taxonomic profiles from metabarcoding data has been hindered by their compositional nature. Several strategies have been proposed to transform compositional data into quantitative data, but they have intrinsic limitations. Here, I propose a workflow based on bacterial and fungal cellular internal standards (spike-ins) for absolute quantification of the microbiota in soil samples. These standards were added to the samples before DNA extraction in amounts estimated after qPCRs, to target around 1-2% coverage in the sequencing run. In bacteria, proportions of spike-in reads in the sequencing run were very similar (< 2-fold change) to those predicted by the qPCR assessment, and for fungi they differed up to 40-fold. The low variation among replicates highlights the reproducibility of the method. Estimates based on multiple bacterial spike-ins were highly correlated (r = 0.99). Procrustes analysis evidenced significant biological effects on the community composition when normalizing compositional data. A protocol based on qPCR estimation of input amounts of cellular spikes is proposed as a cheap and reliable strategy for quantitative metabarcoding of biological samples.
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Affiliation(s)
- Miguel Camacho-Sanchez
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA) Centro Las Torres, Alcalá del Río, 41200, Seville, Spain.
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30
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Ballesté E, Liang H, Migliorato L, Sala-Comorera L, Méndez J, Garcia-Aljaro C. Exploring plastic biofilm formation and Escherichia coli colonisation in marine environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13308. [PMID: 38924372 DOI: 10.1111/1758-2229.13308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
Microorganisms, including potential pathogens, can colonise plastic surfaces in aquatic environments. This study investigates the colonisation of plastic pellets by Escherichia coli (E. coli) as a proxy for faecal pathogens in aquatic environments. Plastic pellets from a polluted beach were placed in seawater aquaria spiked with E. coli. Diverse bacteria, primarily from the Proteobacteria phylum, rapidly colonised the pellets within 24 h, with notable species known for plastic or hydrocarbon degradation. Over 26 days, biofilms formed on the plastic surfaces, reaching bacterial populations of up to 6.8·105 gene copies (gc) of the 16S rRNA mm-2. E. coli, was detected in the pellets for up to 7 days using culture methods, exhibiting varying attachment densities regardless of source or environmental factors. The study highlights plastic biofilms as reservoirs for E. coli, contributing to the survival and persistence of faecal bacteria in aquatic systems. These findings deepen our understanding of the risks associated with plastic pollution in marine settings, offering insights into the behaviour of faecal indicators and their implications for water quality assessments, while providing valuable information on potential pathogen dissemination within plastic-associated microbial communities.
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Affiliation(s)
- Elisenda Ballesté
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Hongxia Liang
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Beijing Municipal Ecological and Environmental Monitoring Center, Beijing, China
| | - Laura Migliorato
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Laura Sala-Comorera
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Javier Méndez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Garcia-Aljaro
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
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31
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Mengis T, Zajac N, Bernhard L, Heggli I, Herger N, Devan J, Marcus R, Brunner F, Laux C, Farshad M, Distler O, Dudli S. Intervertebral disc microbiome in Modic changes: Lack of result replication underscores the need for a consensus in low-biomass microbiome analysis. JOR Spine 2024; 7:e1330. [PMID: 38585427 PMCID: PMC10995447 DOI: 10.1002/jsp2.1330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/14/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
Introduction The emerging field of the disc microbiome challenges traditional views of disc sterility, which opens new avenues for novel clinical insights. However, the lack of methodological consensus in disc microbiome studies introduces discrepancies. The aims of this study were to (1) compare the disc microbiome of non-Modic (nonMC), Modic type 1 change (MC1), and MC2 discs to findings from prior disc microbiome studies, and (2) investigate if discrepancies to prior studies can be explained with bioinformatic variations. Methods Sequencing of 16S rRNA in 70 discs (24 nonMC, 25 MC1, and 21 MC2) for microbiome profiling. The experimental setup included buffer contamination controls and was performed under aseptic conditions. Methodology and results were contrasted with previous disc microbiome studies. Critical bioinformatic steps that were different in our best-practice approach and previous disc microbiome studies (taxonomic lineage assignment, prevalence cut-off) were varied and their effect on results were compared. Results There was limited overlap of results with a previous study on MC disc microbiome. No bacterial genera were shared using the same bioinformatic parameters. Taxonomic lineage assignment using "amplicon sequencing variants" was more sensitive and detected 48 genera compared to 22 with "operational taxonomic units" (previous study). Increasing filter cut-off from 4% to 50% (previous study) reduced genera from 48 to 4 genera. Despite these differences, both studies observed dysbiosis with an increased abundance of gram-negative bacteria in MC discs as well as a lower beta-diversity. Cutibacterium was persistently detected in all groups independent of the bioinformatic approach, emphasizing its prevalence. Conclusion There is dysbiosis in MC discs. Bioinformatic parameters impact results yet cannot explain the different findings from this and a previous study. Therefore, discrepancies are likely caused by different sample preparations or true biologic differences. Harmonized protocols are required to advance understanding of the disc microbiome and its clinical implications.
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Affiliation(s)
- Tamara Mengis
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Natalia Zajac
- Functional Genomics Center ZurichUniversity and ETH ZurichZurichSwitzerland
| | - Laura Bernhard
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Irina Heggli
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Nick Herger
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Jan Devan
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Roy Marcus
- Department of Radiology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Florian Brunner
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Christoph Laux
- Department of Orthopedics, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Mazda Farshad
- Department of Orthopedics, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
| | - Stefan Dudli
- Center of Experimental Rheumatology, Department of RheumatologyUniversity Hospital, University of ZurichZurichSwitzerland
- Department of Physical Medicine and Rheumatology, Balgrist University HospitalUniversity of ZurichZurichSwitzerland
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32
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Vinayamohan PG, Poelstra J, Cheng TY, Goetz H, Renaud DL, Gomez DE, Habing G. Exploring the effects of transport duration on the fecal microbial communities of surplus dairy calves. J Dairy Sci 2024; 107:3863-3884. [PMID: 38216047 DOI: 10.3168/jds.2023-24002] [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: 07/23/2023] [Accepted: 12/03/2023] [Indexed: 01/14/2024]
Abstract
Transportation significantly affects the health and welfare of surplus dairy calves, largely due to the various stressors and pathogen exposures encountered during the process. Concurrently, an animal's microbiome is known to correlate with its health status, with stress-induced alterations in the microbiota potentially precipitating various diseases. This study aimed to compare the effects of transportation durations of 6, 12, or 16 h on the fecal microbiota in young surplus dairy calves. We used a randomized controlled design in which surplus dairy calves aged 1 to 19 d from 5 commercial dairy farms in Ontario were allocated into 1 of 3 transportation groups (6, 12, and 16 h of continuous transportation). Health assessments were conducted before, immediately after, and for 2 wk following transportation. Fecal samples were collected before, immediately after, and at 24 and 72 h after transportation and subjected to 16S rRNA sequencing. Alpha diversity metrics showed no significant differences between the 3 transportation groups at any of the sampling time points. Although β diversity metrics revealed no clustering by transportation groups, they indicated significant differences across sampling time points within each group. The overall analysis revealed a total of 22 phyla and 353 genera, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria being the most abundant phyla. Bacteroides, Escherichia/Shigella, Lactobacillus, Collinsella, and Bifidobacterium were the most abundant genera. The reduction in Fusobacteria abundance before and after transport was significantly larger in the 16-h transportation group when compared with the 6-h transportation group. We also identified several genus-level and amplicon sequence variation-level taxa that displayed significant differences in their abundances across various transportation groups, observed at all sampling time points investigated. This research identifies microbiota changes due to varying transportation durations in surplus dairy calves, providing a broad understanding of the microbial shifts in surplus dairy calves after transportation across varying durations. Although these variations may not directly correlate with overall calf health or indicate dysbiosis, these results emphasize the importance of further investigating transportation practices to enhance calf health and well-being. Further studies are warranted to elucidate the relationship between microbiota and calf health.
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Affiliation(s)
| | - Jelmer Poelstra
- Molecular and Cellular Imaging Center (MCIC), The Ohio State University, Wooster, OH 44691
| | - Ting-Yu Cheng
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Hanne Goetz
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - David L Renaud
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - Diego E Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada, NIG 2W1
| | - Greg Habing
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210.
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Bornbusch SL, Shinnerl HE, Gentry L, Keady MM, Glick V, Muletz-Wolz CR, Power ML. Local environment shapes milk microbiomes while evolutionary history constrains milk macronutrients in captive cercopithecine primates. Environ Microbiol 2024; 26:e16664. [PMID: 38830671 DOI: 10.1111/1462-2920.16664] [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: 02/09/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024]
Abstract
Milk is a complex biochemical fluid that includes macronutrients and microbiota, which, together, are known to facilitate infant growth, mediate the colonization of infant microbiomes, and promote immune development. Examining factors that shape milk microbiomes and milk-nutrient interplay across host taxa is critical to resolving the evolution of the milk environment. Using a comparative approach across four cercopithecine primate species housed at three facilities under similar management conditions, we test for the respective influences of the local environment (housing facility) and host species on milk (a) macronutrients (fat, sugar, and protein), (b) microbiomes (16S rRNA), and (c) predicted microbial functions. We found that milk macronutrients were structured according to host species, while milk microbiomes and predicted function were strongly shaped by the local environment and, to a lesser extent, host species. The milk microbiomes of rhesus macaques (Macaca mulatta) at two different facilities more closely resembled those of heterospecific facility-mates compared to conspecifics at a different facility. We found similar, facility-driven patterns of microbial functions linked to physiology and immune modulation, suggesting that milk microbiomes may influence infant health and development. These results provide novel insight into the complexity of milk and its potential impact on infants across species and environments.
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Affiliation(s)
- Sally L Bornbusch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Hannah E Shinnerl
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Lindsey Gentry
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Mia M Keady
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Virginia Glick
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
- Department of Immunology and Infectious Disease, Harvard University, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Carly R Muletz-Wolz
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
| | - Michael L Power
- Department of Nutrition Science, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, USA
- Center for Species Survival, Smithsonian National Zoo and Conservation Biology Institute, Washington, DC, USA
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Wong S, Kaur J, Kumar P, Karremans AP, Sharma J. Distinct orchid mycorrhizal fungal communities among co-occurring Vanilla species in Costa Rica: root substrate and population-based segregation. MYCORRHIZA 2024; 34:229-250. [PMID: 38664239 DOI: 10.1007/s00572-024-01147-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/15/2024] [Indexed: 06/12/2024]
Abstract
Despite being the second largest family of flowering plants, orchids represent community structure variation in plant-microbial associations, contributes to niche partitioning in metacommunity assemblages. Yet, mycorrhizal communities and interactions remain unknown for orchids that are highly specialized or even obligated in their associations with their mycorrhizal partners. In this study, we sought to compare orchid mycorrhizal fungal (OMF) communities of three co-occurring hemiepiphytic Vanilla species (V. hartii, V. pompona, and V. trigonocarpa) in tropical forests of Costa Rica by addressing the identity of their OMF communities across species, root types, and populations, using high-throughput sequencing. Sequencing the nuclear ribosomal internal transcribed spacer (nrITS) yielded 299 fungal Operational Taxonomic Units (OTUs) from 193 root samples. We showed distinct segregation in the putative OMF (pOMF) communities of the three coexisting Vanilla hosts. We also found that mycorrhizal communities associated with the rare V. hartii varied among populations. Furthermore, we identified Tulasnellaceae and Ceratobasidiaceae as dominant pOMF families in terrestrial roots of the three Vanilla species. In contrast, the epiphytic roots were mainly dominated by OTUs belonging to the Atractiellales and Serendipitaceae. Furthermore, the pOMF communities differed significantly across populations of the widespread V. trigonocarpa and showed patterns of distance decay in similarity. This is the first report of different pOMF communities detected in roots of wild co-occurring Vanilla species using high-throughput sequencing, which provides evidence that three coexisting Vanilla species and their root types exhibited pOMF niche partitioning, and that the rare and widespread Vanilla hosts displayed diverse mycorrhizal preferences.
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Affiliation(s)
- Shan Wong
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Jaspreet Kaur
- Department of Biology, University of Wisconsin-La Crosse, 1725 State Street, La Crosse, WI, 54601, USA
| | - Pankaj Kumar
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
| | - Adam P Karremans
- Lankester Botanical Garden, University of Costa Rica, P.O. Box 302-7050, Cartago, Costa Rica
| | - Jyotsna Sharma
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA
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Surmacz B, Stec D, Prus-Frankowska M, Buczek M, Michalczyk Ł, Łukasik P. Pinpointing the microbiota of tardigrades: What is really there? Environ Microbiol 2024; 26:e16659. [PMID: 38899728 DOI: 10.1111/1462-2920.16659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024]
Abstract
Microbiota are considered significant in the biology of tardigrades, yet their diversity and distribution remain largely unexplored. This is partly due to the methodological challenges associated with studying the microbiota of small organisms that inhabit microbe-rich environments. In our study, we characterized the microbiota of 31 species of cultured tardigrades using 16S rRNA amplicon sequencing. We employed various sample preparation strategies and multiple types of controls and estimated the number of microbes in samples using synthetic DNA spike-ins. We also reanalysed data from previous tardigrade microbiome studies. Our findings suggest that the microbial communities of cultured tardigrades are predominantly composed of bacterial genotypes originating from food, medium, or reagents. Despite numerous experiments, we found it challenging to identify strains that were enriched in certain tardigrades, which would have indicated likely symbiotic associations. Putative tardigrade-associated microbes rarely constituted more than 20% of the datasets, although some matched symbionts identified in other studies. We also uncovered serious contamination issues in previous tardigrade microbiome studies, casting doubt on some of their conclusions. We concluded that tardigrades are not universally dependent on specialized microbes. Our work underscores the need for rigorous safeguards in studies of the microbiota of microscopic organisms and serves as a cautionary tale for studies involving samples with low microbiome abundance.
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Affiliation(s)
- Bartłomiej Surmacz
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Daniel Stec
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Monika Prus-Frankowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Łukasz Michalczyk
- Department of Invertebrate Evolution, Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
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Nguyen PN, Samad-Zada F, Chau KD, Rehan SM. Microbiome and floral associations of a wild bee using biodiversity survey collections. Environ Microbiol 2024; 26:e16657. [PMID: 38817079 DOI: 10.1111/1462-2920.16657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 05/07/2024] [Indexed: 06/01/2024]
Abstract
The health of bees can be assessed through their microbiome, which serves as a biomarker indicating the presence of both beneficial and harmful microorganisms within a bee community. This study presents the characterisation of the bacterial, fungal, and plant composition on the cuticle of adult bicoloured sweat bees (Agapostemon virescens). These bees were collected using various methods such as pan traps, blue vane traps and sweep netting across the northern extent of their habitat range. Non-destructive methods were employed to extract DNA from the whole pinned specimens of these wild bees. Metabarcoding of the 16S rRNA, ITS and rbcL regions was then performed. The study found that the method of collection influenced the detection of certain microbial and plant taxa. Among the collection methods, sweep net samples showed the lowest fungal alpha diversity. However, minor differences in bacterial or fungal beta diversity suggest that no single method is significantly superior to others. Therefore, a combination of techniques can cater to a broader spectrum of microbial detection. The study also revealed regional variations in bacterial, fungal and plant diversity. The core microbiome of A. virescens comprises two bacteria, three fungi and a plant association, all of which are commonly detected in other wild bees. These core microbes remained consistent across different collection methods and locations. Further extensive studies of wild bee microbiomes across various species and landscapes will help uncover crucial relationships between pollinator health and their environment.
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Affiliation(s)
- Phuong N Nguyen
- Department of Biology, York University, Toronto, Ontario, Canada
| | | | - Katherine D Chau
- Department of Biology, York University, Toronto, Ontario, Canada
| | - Sandra M Rehan
- Department of Biology, York University, Toronto, Ontario, Canada
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37
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Panzer JJ, Maples C, Meyer MP, Tillotson G, Theis KR, Chopra T. Gut microbiome alpha diversity decreases in relation to body weight, antibiotic exposure, and infection with multidrug-resistant organisms. Am J Infect Control 2024; 52:707-711. [PMID: 38176539 DOI: 10.1016/j.ajic.2023.12.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND The human gastrointestinal tract is home to a dense and diverse microbiome, predominated by bacteria. Despite the conservation of critical functionality across most individuals, the composition of the gut microbiome is highly individualized, leading to differential responses to perturbations such as oral antibiotics or multidrug-resistant organism (MDRO) infection. Herein, subject responses to these perturbations based on their body weight were evaluated. METHODS Fecal samples were collected from 45 subjects at the Detroit Medical Center to evaluate the effects of perturbations on subjects' gut microbiome composition. Bacterial profiling was completed using 16S rRNA gene sequencing. RESULTS Subjects with multiple MDROs, subjects weighing greater than 80 kg infected with MDRO E coli, and subjects weighing less than 80 kg with exposure to vancomycin and carbapenem antibiotics during hospitalization had significantly decreased gut microbiome richness. CONCLUSIONS Both administration of oral antibiotics and MDRO infections decreased gut microbiome alpha diversity, but the magnitude of these gut microbiome perturbations was body weight dependent.
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Affiliation(s)
- Jonathan J Panzer
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI
| | - Catherine Maples
- Department of Infectious Diseases, Wayne State University, Detroit, MI
| | | | | | - Kevin R Theis
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI.
| | - Teena Chopra
- Department of Infectious Diseases, Wayne State University, Detroit, MI.
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Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangen TJ, Sedlazeck FJ. Unveiling microbial diversity: harnessing long-read sequencing technology. Nat Methods 2024; 21:954-966. [PMID: 38689099 DOI: 10.1038/s41592-024-02262-1] [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: 09/08/2022] [Accepted: 03/29/2024] [Indexed: 05/02/2024]
Abstract
Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.
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Affiliation(s)
- Daniel P Agustinho
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Yilei Fu
- Department of Computer Science, Rice University, Houston, TX, USA
| | - Vipin K Menon
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
- Senior research project manager, Human Genetics, Genentech, South San Francisco, CA, USA
| | - Ginger A Metcalf
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA
| | - Todd J Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
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Wang T, Li P, Bai X, Tian S, Yang M, Leng D, Kui H, Zhang S, Yan X, Zheng Q, Luo P, He C, Jia Y, Wu Z, Qiu H, Li J, Wan F, Ali MA, Mao R, Liu Y, Li D. Vaginal microbiota are associated with in vitro fertilization during female infertility. IMETA 2024; 3:e185. [PMID: 38898981 PMCID: PMC11183179 DOI: 10.1002/imt2.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/02/2024] [Accepted: 03/02/2024] [Indexed: 06/21/2024]
Abstract
The vaginal microbiome plays an essential role in the reproductive health of human females. As infertility increases worldwide, understanding the roles that the vaginal microbiome may have in infertility and in vitro fertilization (IVF) treatment outcomes is critical. To determine the vaginal microbiome composition of 1411 individuals (1255 undergoing embryo transplantation) and their associations with reproductive outcomes, clinical and biochemical features are measured, and vaginal samples are 16S rRNA sequenced. Our results suggest that both too high and too low abundance of Lactobacillus is not beneficial for pregnancy; a moderate abundance is more beneficial. A moderate abundance of Lactobacillus crispatus and Lactobacillus iners (~80%) (with a pregnancy rate of I-B: 54.35% and III-B: 57.73%) is found beneficial for pregnancy outcomes compared with a higher abundance (>90%) of Lactobacillus (I-A: 44.81% and III-A: 51.06%, respectively). The community state type (CST) IV-B (contains a high to moderate relative abundance of Gardnerella vaginalis) shows a similar pregnant ratio (48.09%) with I-A and III-A, and the pregnant women in this CST have a higher abundance of Lactobacillus species. Metagenome analysis of 71 samples shows that nonpregnant women are detected with more antibiotic-resistance genes, and Proteobacteria and Firmicutes are the main hosts. The inherent differences within and between women in different infertility groups suggest that vaginal microbes might be used to detect infertility and potentially improve IVF outcomes.
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Affiliation(s)
- Tao Wang
- Antibiotics Research and Re‐evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of PharmacyChengdu UniversityChengduChina
| | - Penghao Li
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Xue Bai
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Shilin Tian
- College of Life SciencesWuhan UniversityWuhanChina
| | - Maosen Yang
- Antibiotics Research and Re‐evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of PharmacyChengdu UniversityChengduChina
| | - Dong Leng
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Hua Kui
- College of Animal Science and TechnologySichuan Agricultural UniversityChengduChina
| | - Sujuan Zhang
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Xiaomiao Yan
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Qu Zheng
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Pulin Luo
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Changming He
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Yan Jia
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Zhoulin Wu
- College of Food and Biological EngineeringChengdu UniversityChengduChina
| | - Huimin Qiu
- College of AgricultureKunming UniversityKunmingChina
| | - Jing Li
- College of AgricultureKunming UniversityKunmingChina
| | - Feng Wan
- State Key Laboratory of Southwestern Chinese Medicine ResourcesChengdu University of Traditional Chinese MedicineChengduChina
| | - Muhammad A. Ali
- School of Biological SciencesUniversity of the PunjabLahorePakistan
| | - Rurong Mao
- Jinxin Research Institute for Reproductive Medicine and Genetics, Sichuan Jinxin Xi'nan Women's and Children's HospitalChengduChina
| | - Yong‐Xin Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Diyan Li
- Antibiotics Research and Re‐evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of PharmacyChengdu UniversityChengduChina
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Bosch J, Lebre PH, Marais E, Maggs-Kölling G, Cowan DA. Kinetics and pathways of sub-lithic microbial community (hypolithon) development. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13290. [PMID: 38923208 DOI: 10.1111/1758-2229.13290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/03/2024] [Indexed: 06/28/2024]
Abstract
Type I hypolithons are microbial communities dominated by Cyanobacteria. They adhere to the underside of semi-translucent rocks in desert pavements, providing them with a refuge from the harsh abiotic stresses found on the desert soil surface. Despite their crucial role in soil nutrient cycling, our understanding of their growth rates and community development pathways remains limited. This study aimed to quantify the dynamics of hypolithon formation in the pavements of the Namib Desert. We established replicate arrays of sterile rock tiles with varying light transmission in two areas of the Namib Desert, each with different annual precipitation regimes. These were sampled annually over 7 years, and the samples were analysed using eDNA extraction and 16S rRNA gene amplicon sequencing. Our findings revealed that in the zone with higher precipitation, hypolithon formation became evident in semi-translucent rocks 3 years after the arrays were set up. This coincided with a Cyanobacterial 'bloom' in the adherent microbial community in the third year. In contrast, no visible hypolithon formation was observed at the array set up in the hyper-arid zone. This study provides the first quantitative evidence of the kinetics of hypolithon development in hot desert environments, suggesting that development rates are strongly influenced by precipitation regimes.
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Affiliation(s)
- Jason Bosch
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
- Institute of Microbiology of the Czech Academy of Sciences, Czech Academy of Sciences, Praha, Czech Republic
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Eugene Marais
- Gobabeb-Namib Research Institute, Walvis Bay, Namibia
| | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Wu-Chuang A, Mateos-Hernandez L, Abuin-Denis L, Maitre A, Avellanet J, García A, Fuentes D, Cabezas-Cruz A. Exploring the impact of breast cancer on colonization resistance of mouse microbiota using network node manipulation. Heliyon 2024; 10:e30914. [PMID: 38784541 PMCID: PMC11112314 DOI: 10.1016/j.heliyon.2024.e30914] [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: 11/20/2023] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Breast cancer, a global health concern affecting women, has been linked to alterations in the gut microbiota, impacting various aspects of human health. This study investigates the interplay between breast cancer and the gut microbiome, particularly focusing on colonization resistance-an essential feature of the microbiota's ability to prevent pathogenic overgrowth. Using a mouse model of breast cancer, we employ diversity analysis, co-occurrence network analysis, and robustness tests to elucidate the impact of breast cancer on microbiome dynamics. Our results reveal that breast cancer exposure affects the bacterial community's composition and structure, with temporal dynamics playing a role. Network analysis demonstrates that breast cancer disrupts microbial interactions and decreases network complexity, potentially compromising colonization resistance. Moreover, network robustness analysis shows the susceptibility of the microbiota to node removal, indicating potential vulnerability to pathogenic colonization. Additionally, predicted metabolic profiling of the microbiome highlights the significance of the enzyme EC 6.2.1.2 - Butyrate--CoA ligase, potentially increasing butyrate, and balancing the reduction of colonization resistance. The identification of Rubrobacter as a key contributor to this enzyme suggests its role in shaping the microbiota's response to breast cancer. This study uncovers the intricate relationship between breast cancer, the gut microbiome, and colonization resistance, providing insights into potential therapeutic strategies and diagnostic approaches for breast cancer patients.
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Affiliation(s)
- Alejandra Wu-Chuang
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Lourdes Mateos-Hernandez
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Lianet Abuin-Denis
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
- Animal Biotechnology Department, Center for Genetic Engineering and Biotechnology, Avenue 31 between 158 and 190, P.O. Box 6162, 10600, Havana, Cuba
| | - Apolline Maitre
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
- INRAE, UR 0045 Laboratoire de Recherches Sur Le Développement de L'Elevage (SELMET-LRDE), Corte, France
- EA 7310, Laboratoire de Virologie, Université de Corse, Corte, France
| | - Janet Avellanet
- Center of Molecular Immunology (CIM), Calle 15 esq. 216, Atabey, Playa, Havana, Cuba
| | - Arlem García
- Center of Molecular Immunology (CIM), Calle 15 esq. 216, Atabey, Playa, Havana, Cuba
| | - Dasha Fuentes
- National Center for Laboratory Animal Breeding (CENPALAB), Calle 3ra # 40759 entre 6ta y carretera de Tirabeque, Rpto La Unión, Boyeros, Havana, Cuba
| | - Alejandro Cabezas-Cruz
- Anses, INRAE, Ecole Nationale Vétérinaire d’Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
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Teixeira M, Silva F, Ferreira RM, Pereira T, Figueiredo C, Oliveira HP. A review of machine learning methods for cancer characterization from microbiome data. NPJ Precis Oncol 2024; 8:123. [PMID: 38816569 PMCID: PMC11139966 DOI: 10.1038/s41698-024-00617-7] [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: 01/15/2024] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Recent studies have shown that the microbiome can impact cancer development, progression, and response to therapies suggesting microbiome-based approaches for cancer characterization. As cancer-related signatures are complex and implicate many taxa, their discovery often requires Machine Learning approaches. This review discusses Machine Learning methods for cancer characterization from microbiome data. It focuses on the implications of choices undertaken during sample collection, feature selection and pre-processing. It also discusses ML model selection, guiding how to choose an ML model, and model validation. Finally, it enumerates current limitations and how these may be surpassed. Proposed methods, often based on Random Forests, show promising results, however insufficient for widespread clinical usage. Studies often report conflicting results mainly due to ML models with poor generalizability. We expect that evaluating models with expanded, hold-out datasets, removing technical artifacts, exploring representations of the microbiome other than taxonomical profiles, leveraging advances in deep learning, and developing ML models better adapted to the characteristics of microbiome data will improve the performance and generalizability of models and enable their usage in the clinic.
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Affiliation(s)
- Marco Teixeira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal.
- Faculty of Engineering, University of Porto, Porto, Portugal.
| | - Francisco Silva
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
| | - Rui M Ferreira
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
| | - Tania Pereira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Ceu Figueiredo
- Ipatimup - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Faculty of Medicine, University of Porto, Porto, Portugal
| | - Hélder P Oliveira
- Institute for Systems and Computer Engineering, Technology and Science, Porto, Portugal
- Faculty of Science, University of Porto, Porto, Portugal
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Sierra AM, Meléndez O, Bethancourt R, Bethancourt A, Rodríguez-Castro L, López CA, Sedio BE, Saltonstall K, Villarreal A JC. Leaf Endophytes Relationship with Host Metabolome Expression in Tropical Gymnosperms. J Chem Ecol 2024:10.1007/s10886-024-01511-z. [PMID: 38809282 DOI: 10.1007/s10886-024-01511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Plant-microbe interactions play a pivotal role in shaping host fitness, especially concerning chemical defense mechanisms. In cycads, establishing direct correlations between specific endophytic microbes and the synthesis of highly toxic defensive phytochemicals has been challenging. Our research delves into the intricate relationship between plant-microbe associations and the variation of secondary metabolite production in two closely related Zamia species that grow in distinct habitats; terrestrial and epiphytic. Employing an integrated approach, we combined microbial metabarcoding, which characterize the leaf endophytic bacterial and fungal communities, with untargeted metabolomics to test if the relative abundances of specific microbial taxa in these two Zamia species were associated with different metabolome profiles. The two species studied shared approximately 90% of the metabolites spanning diverse biosynthetic pathways: alkaloids, amino acids, carbohydrates, fatty acids, polyketides, shikimates, phenylpropanoids, and terpenoids. Co-occurrence networks revealed positive associations among metabolites from different pathways, underscoring the complexity of their interactions. Our integrated analysis demonstrated to some degree that the intraspecific variation in metabolome profiles of the two host species was associated with the abundance of bacterial orders Acidobacteriales and Frankiales, as well as the fungal endophytes belonging to the orders Chaetothyriales, Glomerellales, Heliotiales, Hypocreales, and Sordariales. We further associate individual metabolic similarity with four specific fungal endophyte members of the core microbiota, but no specific bacterial taxa associations were identified. This study represents a pioneering investigation to characterize leaf endophytes and their association with metabolomes in tropical gymnosperms, laying the groundwork for deeper inquiries into this complex domain.
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Affiliation(s)
- Adriel M Sierra
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
| | - Omayra Meléndez
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Rita Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Ariadna Bethancourt
- Departamento de Microbiología y Parasitología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
| | - Lilisbeth Rodríguez-Castro
- Departamento de Microbiología, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Panamá, Panamá
- Smithsonian Tropical Research Institute, Ancón, Panamá
| | - Christian A López
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Brian E Sedio
- Smithsonian Tropical Research Institute, Ancón, Panamá
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Juan Carlos Villarreal A
- Département de Biologie, Université Laval, Québec, (QC), G1V 0A6, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, (QC), G1V 0A6, Canada.
- Smithsonian Tropical Research Institute, Ancón, Panamá.
- Canada Research Chair in Genomics of Tropical Symbioses, Department of Biology, Université Laval, Québec, G1V 0A6, Canadá.
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Leoni C, Vinci L, Marzano M, D'Erchia AM, Dellino M, Cox SN, Vitagliano A, Visci G, Notario E, Filomena E, Cicinelli E, Pesole G, Ceci LR. Endometrial Cancer: A Pilot Study of the Tissue Microbiota. Microorganisms 2024; 12:1090. [PMID: 38930472 DOI: 10.3390/microorganisms12061090] [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: 04/26/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND The endometrium remains a difficult tissue for the analysis of microbiota, mainly due to the low bacterial presence and the sampling procedures. Among its pathologies, endometrial cancer has not yet been completely investigated for its relationship with microbiota composition. In this work, we report on possible correlations between endometrial microbiota dysbiosis and endometrial cancer. METHODS Women with endometrial cancer at various stages of tumor progression were enrolled together with women with a benign polymyomatous uterus as the control. Analyses were performed using biopsies collected at two specific endometrial sites during the surgery. This study adopted two approaches: the absolute quantification of the bacterial load, using droplet digital PCR (ddPCR), and the analysis of the bacterial composition, using a deep metabarcoding NGS procedure. RESULTS ddPCR provided the first-ever assessment of the absolute quantification of bacterial DNA in the endometrium, confirming a generally low microbial abundance. Metabarcoding analysis revealed a different microbiota distribution in the two endometrial sites, regardless of pathology, accompanied by an overall higher prevalence of pathogenic bacterial genera in cancerous tissues. CONCLUSIONS These results pave the way for future studies aimed at identifying potential biomarkers and gaining a deeper understanding of the role of bacteria associated with tumors.
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Affiliation(s)
- Claudia Leoni
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Amendola n. 122/O, 70126 Bari, Italy
| | - Lorenzo Vinci
- 2nd Unit of Obstetrics and Gynaecology, Department of Biomedical Science and Human Oncology, University of Bari "A. Moro", Piazza G. Cesare, 70124 Bari, Italy
| | - Marinella Marzano
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Amendola n. 122/O, 70126 Bari, Italy
| | - Anna Maria D'Erchia
- Department of Biosciences, Biotechnologies and Environment, University of Bari A. Moro, Via Orabona n. 4, 70126 Bari, Italy
| | - Miriam Dellino
- 2nd Unit of Obstetrics and Gynaecology, Department of Biomedical Science and Human Oncology, University of Bari "A. Moro", Piazza G. Cesare, 70124 Bari, Italy
| | - Sharon Natasha Cox
- Department of Biosciences, Biotechnologies and Environment, University of Bari A. Moro, Via Orabona n. 4, 70126 Bari, Italy
| | - Amerigo Vitagliano
- 2nd Unit of Obstetrics and Gynaecology, Department of Biomedical Science and Human Oncology, University of Bari "A. Moro", Piazza G. Cesare, 70124 Bari, Italy
| | - Grazia Visci
- Department of Biosciences, Biotechnologies and Environment, University of Bari A. Moro, Via Orabona n. 4, 70126 Bari, Italy
| | - Elisabetta Notario
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Amendola n. 122/O, 70126 Bari, Italy
| | - Ermes Filomena
- Department of Biosciences, Biotechnologies and Environment, University of Bari A. Moro, Via Orabona n. 4, 70126 Bari, Italy
| | - Ettore Cicinelli
- 2nd Unit of Obstetrics and Gynaecology, Department of Biomedical Science and Human Oncology, University of Bari "A. Moro", Piazza G. Cesare, 70124 Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnologies and Environment, University of Bari A. Moro, Via Orabona n. 4, 70126 Bari, Italy
| | - Luigi Ruggiero Ceci
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council (CNR), Via Amendola n. 122/O, 70126 Bari, Italy
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De La Cruz KF, Townsend EC, Alex Cheong JZ, Salamzade R, Liu A, Sandstrom S, Davila E, Huang L, Xu KH, Wu SY, Meudt JJ, Shanmuganayagam D, Gibson ALF, Kalan LR. The porcine skin microbiome exhibits broad fungal antagonism. Fungal Genet Biol 2024; 173:103898. [PMID: 38815692 DOI: 10.1016/j.fgb.2024.103898] [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: 01/12/2024] [Revised: 05/02/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
The skin and its microbiome function to protect the host from pathogen colonization and environmental stressors. In this study, using the Wisconsin Miniature Swine™ model, we characterize the porcine skin fungal and bacterial microbiomes, identify bacterial isolates displaying antifungal activity, and use whole-genome sequencing to identify biosynthetic gene clusters encoding for secondary metabolites that may be responsible for the antagonistic effects on fungi. Through this comprehensive approach of paired microbiome sequencing with culturomics, we report the discovery of novel species of Corynebacterium and Rothia. Further, this study represents the first comprehensive evaluation of the porcine skin mycobiome and the evaluation of bacterial-fungal interactions on this surface. Several diverse bacterial isolates exhibit potent antifungal properties against opportunistic fungal pathogens in vitro. Genomic analysis of inhibitory species revealed a diverse repertoire of uncharacterized biosynthetic gene clusters suggesting a reservoir of novel chemical and biological diversity. Collectively, the porcine skin microbiome represents a potential unique source of novel antifungals.
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Affiliation(s)
- Karinda F De La Cruz
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Elizabeth C Townsend
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States; Medical Scientist Training Program, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - J Z Alex Cheong
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Rauf Salamzade
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Aiping Liu
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Evelin Davila
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; National Summer Undergraduate Research Project, University of Arizona, Tucson, AZ, United States
| | - Lynda Huang
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Kayla H Xu
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Sherrie Y Wu
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Jennifer J Meudt
- Department of Animal & Dairy Sciences, University of Wisconsin, Madison, WI, United States; Center for Biomedical Swine Research & Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Dhanansayan Shanmuganayagam
- Department of Animal & Dairy Sciences, University of Wisconsin, Madison, WI, United States; Center for Biomedical Swine Research & Innovation, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Angela L F Gibson
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin School of Medicine and Public Health, Madison, WI, United States; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada; David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Ontario, Canada.
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Chen M, Acharya SM, Yee MO, Cabugao KGM, Chakraborty R. Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture. Front Microbiol 2024; 15:1401794. [PMID: 38846575 PMCID: PMC11153752 DOI: 10.3389/fmicb.2024.1401794] [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: 03/15/2024] [Accepted: 05/07/2024] [Indexed: 06/09/2024] Open
Abstract
The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.
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Affiliation(s)
| | | | | | | | - Romy Chakraborty
- Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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47
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Bouchali R, Mandon C, Danty-Berger E, Géloën A, Marjolet L, Youenou B, Pozzi ACM, Vareilles S, Galia W, Kouyi GL, Toussaint JY, Cournoyer B. Runoff microbiome quality assessment of a city center rainwater harvesting zone shows a differentiation of pathogen loads according to human mobility patterns. Int J Hyg Environ Health 2024; 260:114391. [PMID: 38781750 DOI: 10.1016/j.ijheh.2024.114391] [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: 09/04/2023] [Revised: 03/15/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024]
Abstract
The hygienic quality of urban surfaces can be impaired by multiple sources of microbiological contaminants. These surfaces can trigger the development of multiple bacterial taxa and favor their spread during rain events through the circulation of runoff waters. These runoff waters are commonly directed toward sewer networks, stormwater infiltration systems or detention tanks prior a release into natural water ways. With water scarcity becoming a major worldwide issue, these runoffs are representing an alternative supply for some usage like street cleaning and plant watering. Microbiological hazards associated with these urban runoffs, and surveillance guidelines must be defined to favor these uses. Runoff microbiological quality from a recently implemented city center rainwater harvesting zone was evaluated through classical fecal indicator bacteria (FIB) assays, quantitative PCR and DNA meta-barcoding analyses. The incidence of socio-urbanistic patterns on the organization of these urban microbiomes were investigated. FIB and DNA from Human-specific Bacteroidales and pathogens such as Staphylococcus aureus were detected from most runoffs and showed broad distribution patterns. 16S rRNA DNA meta-barcoding profilings further identified core recurrent taxa of health concerns like Acinetobacter, Mycobacterium, Aeromonas and Pseudomonas, and divided these communities according to two main groups of socio-urbanistic patterns. One of these was highly impacted by heavy traffic, and showed recurrent correlation networks involving bacterial hydrocarbon degraders harboring significant virulence properties. The tpm-based meta-barcoding approach identified some of these taxa at the species level for more than 30 genera. Among these, recurrent pathogens were recorded such as P. aeruginosa, P. paraeruginosa, and Aeromonas caviae. P. aeruginosa and A. caviae tpm reads were found evenly distributed over the study site but those of P. paraeruginosa were higher among sub-catchments impacted by heavy traffic. Health risks associated with these runoff P. paraeruginosa emerging pathogens were high and associated with strong cytotoxicity on A549 lung cells. Recurrent detections of pathogens in runoff waters highlight the need of a microbiological surveillance prior allowing their use. Good microbiological quality can be obtained for certain typologies of sub-catchments with good hygienic practices but not all. A reorganization of Human mobility and behaviors would likely trigger changes in these bacterial diversity patterns and reduce the occurrences of the most hazardous groups.
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Affiliation(s)
- Rayan Bouchali
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Claire Mandon
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Emmanuelle Danty-Berger
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Alain Géloën
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Laurence Marjolet
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Benjamin Youenou
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Adrien C M Pozzi
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | - Sophie Vareilles
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Wessam Galia
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France
| | | | - Jean-Yves Toussaint
- Université de Lyon, INSA Lyon, UMR Environnement, Ville, Société, CNRS 5600, 18 rue Chevreul, 69362, Lyon, France
| | - Benoit Cournoyer
- Université de Lyon, Université Claude Bernard Lyon 1, VetAgro Sup, UMR Ecologie Microbienne / Microbial Ecology (LEM), CNRS 5557, INRAE 1418, 69280, Marcy L'Etoile, France.
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Starr K, Montesanto F, Perisho E, Aluthge N, Pegg M, Fernando SC. Gut Microbial Composition of Cyprinella lutrensis (Red Shiner) and Notropis stramineus (Sand Shiner): Insights from Wild Fish Populations. MICROBIAL ECOLOGY 2024; 87:75. [PMID: 38775958 PMCID: PMC11111511 DOI: 10.1007/s00248-024-02386-z] [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: 01/13/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024]
Abstract
The gut microbiome is a highly intricate ecosystem that exerts a pivotal influence on the host's physiology. Characterizing fish microbiomes is critical to understanding fish physiology and health, but little is known about the ecology and colonization dynamics of microorganisms inhabiting fish species. In this study, we investigated the bacterial communities of two small-bodied fish species, Cyprinella lutrensis (red shiner) and Notropis stramineus (sand shiner), two fish species where gut microbiomes have not been investigated previously and surrounding waters, collected from rivers in Nebraska, USA. Our study focused on evaluating microbial diversity in small-bodied fish and identifying autochthonous microbes present within these species irrespective of location to better understand bacterial community composition and possible roles of such bacterial species. Our results revealed that both red shiner and sand shiner exhibited gut bacterial communities dominated by typical bacterial phyla found in freshwater fish. The phylum Bacteroidota was minimally abundant in both species and significantly lower in relative abundance compared to the surrounding water microbial community. Furthermore, we found that the gut microbiomes of red shiner and sand shiner differed from the microbial community in the surrounding water, suggesting that these fish species contain host-associated bacterial species that may provide benefits to the host such as nutrient digestion and colonization resistance of environmental pathogens. The fish gut bacterial communities were sensitive to environmental conditions such as turbidity, dissolved oxygen, temperature, and total nitrogen. Our findings also show bacterial community differences between fish species; although they shared notable similarities in bacterial taxa at phyla level composition, ASV level analysis of bacterial taxa displayed compositional differences. These findings contribute to a better understanding of the gut bacterial composition of wild, freshwater, small-bodied fish and highlight the influence of intrinsic (host) and environmental factors on shaping the bacterial composition.
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Affiliation(s)
- Krista Starr
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | | | - Esther Perisho
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Nirosh Aluthge
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA
| | - Mark Pegg
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA.
| | - Samodha C Fernando
- University of NE-Lincoln, 3310 Holdrege Street, Lincoln, NE, 68583, USA.
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49
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Ketagoda DHK, Varga P, Fitzsimmons TR, Moore NE, Weyrich LS, Zilm PS. Development of an in vitro biofilm model of the human supra-gingival microbiome for Oral microbiome transplantation. J Microbiol Methods 2024; 223:106961. [PMID: 38788981 DOI: 10.1016/j.mimet.2024.106961] [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: 04/05/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 05/26/2024]
Abstract
The high prevalence of dental caries and periodontal disease place a significant burden on society, both socially and economically. Recent advances in genomic technologies have linked both diseases to shifts in the oral microbiota - a community of >700 bacterial species that live within the mouth. The development of oral microbiome transplantation draws on the success of fecal microbiome transplantation for the treatment of gut pathologies associated with disease. Many current in vitro oral biofilm models have been developed but do not fully capture the complexity of the oral microbiome which is required for successful OMT. To address this, we developed an in vitro biofilm system that maintained an oral microbiome with 252 species on average over 14 days. Six human plaque samples were grown in 3D printed flow cells on hydroxyapatite discs using artificial saliva medium (ASM). Biofilm composition and growth were monitored by high throughput sequencing and confocal microscopy/SEM, respectively. While a significant drop in bacterial diversity occurred, up to 291 species were maintained in some flow cells over 14 days with 70% viability grown with ASM. This novel in vitro biofilm model represents a marked improvement on existing oral biofilm systems and provides new opportunities to develop oral microbiome transplant therapies.
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Affiliation(s)
| | - Peter Varga
- Adelaide Dental School, University of Adelaide, SA, Australia
| | | | - Nicole E Moore
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, SA, Australia; Department of Anthropology, The Pennsylvania State University, University Park, PA, United States of America
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, SA, Australia; Department of Anthropology, The Pennsylvania State University, University Park, PA, United States of America; Huck Institutes of the Life Sciences, The Pennsylvania State University, PA, United States of America
| | - Peter S Zilm
- Adelaide Dental School, University of Adelaide, SA, Australia.
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50
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Vasco KA, Hansen ZA, Schilmiller AL, Bowcutt B, Carbonell SL, Ruegg PL, Quinn RA, Zhang L, Manning SD. Untargeted metabolomics and metagenomics reveal signatures for intramammary ceftiofur treatment and lactation stage in the cattle hindgut. Front Mol Biosci 2024; 11:1364637. [PMID: 38836107 PMCID: PMC11148447 DOI: 10.3389/fmolb.2024.1364637] [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: 01/02/2024] [Accepted: 04/29/2024] [Indexed: 06/06/2024] Open
Abstract
The gut microbiota in cattle is essential for protein, energy, and vitamin production and hence, microbiota perturbations can affect cattle performance. This study evaluated the effect of intramammary (IMM) ceftiofur treatment and lactation stage on the functional gut microbiome and metabolome. Forty dairy cows were enrolled at dry-off. Half received IMM ceftiofur and a non-antibiotic teat sealant containing bismuth subnitrate (cases), while the other half received the teat sealant (controls). Fecal samples were collected before treatment at dry off, during the dry period (weeks 1 and 5) and the first week after calving (week 9). Shotgun metagenomic sequencing was applied to predict microbial metabolic pathways whereas untargeted metabolomics was used identify polar and nonpolar metabolites. Compared to controls, long-term changes were observed in the cows given ceftiofur, including a lower abundance of microbial pathways linked to energy production, amino acid biosynthesis, and other vital molecules. The metabolome of treated cows had elevated levels of stachyose, phosphatidylethanolamine diacylglycerol (PE-DAG), and inosine a week after the IMM ceftiofur application, indicating alterations in microbial fermentation, lipid metabolism, energy, and cellular signaling. Differences were also observed by sampling, with cows in late lactation having more diverse metabolic pathways and a unique metabolome containing higher levels of histamine and histamine-producing bacteria. These data illustrate how IMM ceftiofur treatment can alter the functionality of the hindgut metabolome and microbiome. Understanding how antibiotics and lactation stages, which are each characterized by unique diets and physiology, impact the function of resident microbes is critical to define normal gut function in dairy cattle.
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Affiliation(s)
- Karla A Vasco
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
| | - Zoe A Hansen
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
| | - Anthony L Schilmiller
- Research Technology Support Facility, Mass Spectrometry and Metabolomics Core, Michigan State University, East Lansing, MI, United States
| | - Bailey Bowcutt
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
| | - Samantha L Carbonell
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
| | - Pamela L Ruegg
- Department of Large Animal and Clinical Sciences, Michigan State University, East Lansing, MI, United States
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Lixin Zhang
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States
| | - Shannon D Manning
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
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