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Demircan T, Gül S, Taşçı EA. Can Microbiome Modulate Regenerative Capacity? A Comparative Microbiome Study Reveals a Dominant Presence of Flavobacteriaceae in Blastema Tissue During Axolotl Limb Regeneration. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:291-302. [PMID: 38808529 DOI: 10.1089/omi.2024.0075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
The axolotl (Ambystoma mexicanum) is renowned for its remarkable regenerative capabilities, which are not diminished by the transition from a neotenic to a metamorphic state. This study explored the microbiome dynamics in axolotl limb regeneration by examining the microbial communities present in neotenic and metamorphic axolotls at two critical stages of limb regeneration: pre-amputation and during blastema formation. Utilizing 16S rRNA amplicon sequencing, we investigated the variations in microbiome profiles associated with different developmental and regenerative states. Our findings reveal a distinct separation in the microbiome profiles of neotenic and metamorphic samples, with a clear demarcation in microbial composition at both the phylum and genus levels. In neotenic 0DPA samples, Proteobacteria and Firmicutes were the most abundant, whereas in neotenic 7DPA samples, Proteobacteria and Bacteroidetes dominated. Conversely, metamorphic samples displayed a higher abundance of Firmicutes and Bacteroidetes at 0DPA and Proteobacteria and Firmicutes at 7DPA. Alpha and beta diversity analyses, along with dendrogram construction, demonstrated significant variations within and between the sample groups, suggesting a strong influence of both developmental stage and regenerative state on the microbiome. Notably, Flavobacterium and Undibacterium emerged as distinctive microbial entities in neotenic 7DPA samples, highlighting potential key players in the microbial ecology of regeneration. These findings suggest that the axolotl's microbiome is dynamically responsive to blastema formation, and they underscore the potential influence of microbial communities on the regeneration process. This study lays the groundwork for future research into the mechanisms by which the microbiome may modulate regenerative capacity.
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Affiliation(s)
- Turan Demircan
- School of Medicine, Department of Medical Biology, Muğla Sıtkı Koçman University, Muğla, Türkiye
| | - Sultan Gül
- Institute of Health Sciences, İstanbul Medipol University, İstanbul, Türkiye
- Graduate School of Science And Engineering, Yıldız Technical University, İstanbul, Türkiye
| | - Ebru Altuntaş Taşçı
- Institute of Natural Sciences, Muğla Sıtkı Koçman University, Muğla, Türkiye
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2
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Joubran P, Roux FA, Serino M, Deschamps JY. Gut and Urinary Microbiota in Cats with Kidney Stones. Microorganisms 2024; 12:1098. [PMID: 38930480 PMCID: PMC11205531 DOI: 10.3390/microorganisms12061098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/10/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
Upper urinary tract urolithiasis is an emerging disease in cats, with 98% of kidney stones composed of calcium oxalate. In humans, disturbances in the intestinal and urinary microbiota are suspected to contribute to the formation of calcium oxalate stones. We hypothesized that similar mechanisms may be at play in cats. This study examines the intestinal and urinary microbiota of nine cats with kidney stones compared to nine healthy cats before, during, and after treatment with the antibiotic cefovecin, a cephalosporin. Initially, cats with kidney stones displayed a less diverse intestinal microbiota. Antibiotic treatment reduced microbiota diversity in both groups. The absence of specific intestinal bacteria could lead to a loss of the functions these bacteria perform, such as oxalate degradation, which may contribute to the formation of calcium oxalate stones. This study confirms the presence of a distinct urobiome in cats with kidney stones, characterized by greater richness and diversity compared to healthy cats. These findings highlight the potential of microbiota modulation as a strategy to prevent renal lithiasis in cats.
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Affiliation(s)
- Patrick Joubran
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
| | - Françoise A. Roux
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
- Emergency and Critical Care Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France
| | - Matteo Serino
- IRSD, Institut de Recherche en Santé Digestive, Institut National de la Santé et de la Recherche Médicale (INSERM) U1220, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse III-Paul Sabatier (UPS), CS 60039, 31 024 Toulouse, France
| | - Jack-Yves Deschamps
- Nutrition, PathoPhysiology and Pharmacology (NP3) Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France; (P.J.); (F.A.R.)
- Emergency and Critical Care Unit, Oniris VetAgro Bio, Nantes-Atlantic College of Veterinary Medicine, Food Science and Engineering, La Chantrerie, CEDEX 03, 44 307 Nantes, France
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3
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Choy WH, Adler A, Morgan-Lang C, Gough EK, Hallam SJ, Manges AR, Chew BH, Penniston K, Miller A, Lange D. Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease. Urolithiasis 2024; 52:38. [PMID: 38413462 DOI: 10.1007/s00240-024-01534-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
Intestinal microbiome dysbiosis is a known risk factor for recurrent kidney stone disease (KSD) with prior data suggesting a role for dysfunctional metabolic pathways other than those directly utilizing oxalate. To identify alternative mechanisms, the current study analyzed differences in the metabolic potential of intestinal microbiomes of patients (n = 17) and live-in controls (n = 17) and determined their relevance to increased risk for KSD using shotgun metagenomic sequencing. We found no differences in the abundance of genes associated with known oxalate degradation pathways, supporting the notion that dysfunction in other metabolic pathways plays a role in KSD. Further analysis showed decreased abundance of key enzymes involved in butyrate biosynthesis in patient intestinal microbiomes. Furthermore, de novo construction of microbial genomes showed that the majority of genes significantly enriched in non-stone formers are affiliated with Faecalibacterium prausnitzii, a major butyrate producer. Specifically pertaining to butyrate metabolism, the majority of abundant genes mapped back to F. prausnitzii, Alistipes spp., and Akkermansia muciniphila. No differences were observed in ascorbate or glyoxylate metabolic pathways. Collectively, these data suggest that impaired bacterial-associated butyrate metabolism may be an oxalate-independent mechanism that contributes to an increased risk for recurrent KSD. This indicates that the role of the intestinal microbiome in recurrent KSD is multi-factorial, which is representative of the highly intertwined metabolic nature of this complex environment. Future bacteria-based treatments must not be restricted to targeting only oxalate metabolism.
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Affiliation(s)
- Wai Ho Choy
- Department of Urologic Sciences, The Stone Centre at VGH, University of British Columbia, Jack Bell Research Centre, Rm. 550-3, 2660 Oak Street, Vancouver, BC, V6J 1G7, Canada
| | - Ava Adler
- Departments of Urology and Immunology, Cleveland Clinic, Cleveland, OH, USA
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
| | - Ethan K Gough
- Johns Hopkins Bloomberg School of Public Health US, Baltimore, USA
| | - Steven J Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
- Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, BC, Canada
| | - Amee R Manges
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
- BC Centre for Disease Control, Vancouver, BC, Canada
| | - Ben H Chew
- Department of Urologic Sciences, The Stone Centre at VGH, University of British Columbia, Jack Bell Research Centre, Rm. 550-3, 2660 Oak Street, Vancouver, BC, V6J 1G7, Canada
| | - Kristina Penniston
- Department of Urology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - Aaron Miller
- Departments of Urology and Immunology, Cleveland Clinic, Cleveland, OH, USA
| | - Dirk Lange
- Department of Urologic Sciences, The Stone Centre at VGH, University of British Columbia, Jack Bell Research Centre, Rm. 550-3, 2660 Oak Street, Vancouver, BC, V6J 1G7, Canada.
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4
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Stepanova N, Tolstanova G, Aleksandrova I, Korol L, Dovbynchuk T, Driianska V, Savchenko S. Gut Microbiota's Oxalate-Degrading Activity and Its Implications on Cardiovascular Health in Patients with Kidney Failure: A Pilot Prospective Study. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:2189. [PMID: 38138292 PMCID: PMC10744410 DOI: 10.3390/medicina59122189] [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: 11/16/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]
Abstract
Background and Objectives: The present study aims to investigate the association between gut microbiota's oxalate-degrading activity (ODA) and the risk of developing cardiovascular disease (CVD) over a three-year follow-up period in a cohort of patients undergoing kidney replacement therapy (KRT). Additionally, various factors were examined to gain insight into the potential mechanisms underlying the ODA-CVD link. Materials and Methods: A cohort of 32 KRT patients and 18 healthy volunteers was enrolled in this prospective observational pilot study. Total fecal ODA, routine clinical data, plasma oxalic acid (POx), serum indoxyl sulfate, lipid profile, oxidative stress, and proinflammatory markers were measured, and the patients were followed up for three years to assess CVD events. Results: The results revealed that patients with kidney failure exhibited significantly lower total fecal ODA levels compared to the healthy control group (p = 0.017), with a higher proportion showing negative ODA status (≤-1% per 0.01 g) (p = 0.01). Negative total fecal ODA status was associated with a significantly higher risk of CVD events during the three-year follow-up period (HR = 4.1, 95% CI 1.4-16.3, p = 0.003), even after adjusting for potential confounders. Negative total fecal ODA status was significantly associated with elevated POx and indoxyl sulfate levels and linked to dyslipidemia, increased oxidative stress, and inflammation, which are critical contributors to CVD. Conclusions: The findings contribute novel insights into the relationship between gut microbiota's ODA and cardiovascular health in patients undergoing KRT, emphasizing the need for further research to elucidate underlying mechanisms and explore potential therapeutic implications of targeting gut microbiota's ODA in this vulnerable population.
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Affiliation(s)
- Natalia Stepanova
- State Institution “Institute of Nephrology of the National Academy of Medical Sciences of Ukraine”, 04050 Kyiv, Ukraine; (L.K.)
- Educational and Scientific Institute of High Technologies, Taras Shevchenko National University, 01601 Kyiv, Ukraine
| | - Ganna Tolstanova
- Educational and Scientific Institute of High Technologies, Taras Shevchenko National University, 01601 Kyiv, Ukraine
| | - Iryna Aleksandrova
- Educational and Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University, 01601 Kyiv, Ukraine (T.D.)
| | - Lesya Korol
- State Institution “Institute of Nephrology of the National Academy of Medical Sciences of Ukraine”, 04050 Kyiv, Ukraine; (L.K.)
| | - Taisa Dovbynchuk
- Educational and Scientific Centre “Institute of Biology and Medicine”, Taras Shevchenko National University, 01601 Kyiv, Ukraine (T.D.)
| | - Victoria Driianska
- State Institution “Institute of Nephrology of the National Academy of Medical Sciences of Ukraine”, 04050 Kyiv, Ukraine; (L.K.)
| | - Svitlana Savchenko
- State Institution “Institute of Nephrology of the National Academy of Medical Sciences of Ukraine”, 04050 Kyiv, Ukraine; (L.K.)
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5
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Al KF, Joris BR, Daisley BA, Chmiel JA, Bjazevic J, Reid G, Gloor GB, Denstedt JD, Razvi H, Burton JP. Multi-site microbiota alteration is a hallmark of kidney stone formation. MICROBIOME 2023; 11:263. [PMID: 38007438 PMCID: PMC10675928 DOI: 10.1186/s40168-023-01703-x] [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: 11/30/2022] [Accepted: 10/17/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified assessment of the bacterial contribution to KSD. RESULTS Amplicon and shotgun metagenomic sequencing approaches were consistent in identifying multi-site microbiota disturbances in SF relative to HC. Biomarker taxa, reduced taxonomic and functional diversity, functional replacement of core bioenergetic pathways with virulence-associated gene markers, and community network collapse defined SF, but differences between cohorts did not extend to oxalate metabolism. CONCLUSIONS We conclude that multi-site microbiota alteration is a hallmark of SF, and KSD treatment should consider microbial functional restoration and the avoidance of aberrant modulators such as poor diet and antibiotics where applicable to prevent stone recurrence. Video Abstract.
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Affiliation(s)
- Kait F Al
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Benjamin R Joris
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - Brendan A Daisley
- Molecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada
| | - John A Chmiel
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
| | - Jennifer Bjazevic
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Gregor Reid
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Gregory B Gloor
- Department of Biochemistry, The University of Western Ontario, London, ON, Canada
| | - John D Denstedt
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Hassan Razvi
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada
| | - Jeremy P Burton
- Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.
- Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.
- Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada.
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6
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Stepanova N. Oxalate Homeostasis in Non-Stone-Forming Chronic Kidney Disease: A Review of Key Findings and Perspectives. Biomedicines 2023; 11:1654. [PMID: 37371749 DOI: 10.3390/biomedicines11061654] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Chronic kidney disease (CKD) is a significant global public health concern associated with high morbidity and mortality rates. The maintenance of oxalate homeostasis plays a critical role in preserving kidney health, particularly in the context of CKD. Although the relationship between oxalate and kidney stone formation has been extensively investigated, our understanding of oxalate homeostasis in non-stone-forming CKD remains limited. This review aims to present an updated analysis of the existing literature, focusing on the intricate mechanisms involved in oxalate homeostasis in patients with CKD. Furthermore, it explores the key factors that influence oxalate accumulation and discusses the potential role of oxalate in CKD progression and prognosis. The review also emphasizes the significance of the gut-kidney axis in CKD oxalate homeostasis and provides an overview of current therapeutic strategies, as well as potential future approaches. By consolidating important findings and perspectives, this review offers a comprehensive understanding of the present knowledge in this field and identifies promising avenues for further research.
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Affiliation(s)
- Natalia Stepanova
- State Institution «Institute of Nephrology of the National Academy of Medical Sciences of Ukraine», 04050 Kyiv, Ukraine
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7
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Jaunet-Lahary T, Shimamura T, Hayashi M, Nomura N, Hirasawa K, Shimizu T, Yamashita M, Tsutsumi N, Suehiro Y, Kojima K, Sudo Y, Tamura T, Iwanari H, Hamakubo T, Iwata S, Okazaki KI, Hirai T, Yamashita A. Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota. Nat Commun 2023; 14:1730. [PMID: 37012268 PMCID: PMC10070484 DOI: 10.1038/s41467-023-36883-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/20/2023] [Indexed: 04/05/2023] Open
Abstract
An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.
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Affiliation(s)
- Titouan Jaunet-Lahary
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Tatsuro Shimamura
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
| | - Masahiro Hayashi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Norimichi Nomura
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Kouta Hirasawa
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | | | | | - Naotaka Tsutsumi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
- School of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yuta Suehiro
- School of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Tamura
- Graduate School of Environmental and Life Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Hiroko Iwanari
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Takao Hamakubo
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - So Iwata
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Kei-Ichi Okazaki
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan.
| | | | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- RIKEN SPring-8 Center, Sayo, 679-5148, Japan.
- School of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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8
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Biomarkers in Urolithiasis. Urol Clin North Am 2023; 50:19-29. [DOI: 10.1016/j.ucl.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Ermer T, Nazzal L, Tio MC, Waikar S, Aronson PS, Knauf F. Oxalate homeostasis. Nat Rev Nephrol 2023; 19:123-138. [PMID: 36329260 DOI: 10.1038/s41581-022-00643-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Oxalate homeostasis is maintained through a delicate balance between endogenous sources, exogenous supply and excretion from the body. Novel studies have shed light on the essential roles of metabolic pathways, the microbiome, epithelial oxalate transporters, and adequate oxalate excretion to maintain oxalate homeostasis. In patients with primary or secondary hyperoxaluria, nephrolithiasis, acute or chronic oxalate nephropathy, or chronic kidney disease irrespective of aetiology, one or more of these elements are disrupted. The consequent impairment in oxalate homeostasis can trigger localized and systemic inflammation, progressive kidney disease and cardiovascular complications, including sudden cardiac death. Although kidney replacement therapy is the standard method for controlling elevated plasma oxalate concentrations in patients with kidney failure requiring dialysis, more research is needed to define effective elimination strategies at earlier stages of kidney disease. Beyond well-known interventions (such as dietary modifications), novel therapeutics (such as small interfering RNA gene silencers, recombinant oxalate-degrading enzymes and oxalate-degrading bacterial strains) hold promise to improve the outlook of patients with oxalate-related diseases. In addition, experimental evidence suggests that anti-inflammatory medications might represent another approach to mitigating or resolving oxalate-induced conditions.
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Affiliation(s)
- Theresa Ermer
- Department of Surgery, Division of Thoracic Surgery, Yale School of Medicine, New Haven, CT, USA
| | - Lama Nazzal
- Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Maria Clarissa Tio
- Division of Nephrology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Sushrut Waikar
- Department of Medicine, Section of Nephrology, Boston University, Boston, MA, USA
| | - Peter S Aronson
- Department of Internal Medicine, Section of Nephrology, Yale School of Medicine, New Haven, CT, USA
| | - Felix Knauf
- Department of Internal Medicine, Section of Nephrology, Yale School of Medicine, New Haven, CT, USA. .,Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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10
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Miller AW, Penniston KL, Fitzpatrick K, Agudelo J, Tasian G, Lange D. Mechanisms of the intestinal and urinary microbiome in kidney stone disease. Nat Rev Urol 2022; 19:695-707. [PMID: 36127409 PMCID: PMC11234243 DOI: 10.1038/s41585-022-00647-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2022] [Indexed: 02/08/2023]
Abstract
Kidney stone disease affects ~10% of the global population and the incidence continues to rise owing to the associated global increase in the incidence of medical conditions associated with kidney stone disease including, for example, those comprising the metabolic syndrome. Considering that the intestinal microbiome has a substantial influence on host metabolism, that evidence has suggested that the intestinal microbiome might have a role in maintaining oxalate homeostasis and kidney stone disease is unsurprising. In addition, the discovery that urine is not sterile but, like other sites of the human body, harbours commensal bacterial species that collectively form a urinary microbiome, is an additional factor that might influence the induction of crystal formation and stone growth directly in the kidney. Collectively, the microbiomes of the host could influence kidney stone disease at multiple levels, including intestinal oxalate absorption and direct crystal formation in the kidneys.
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Affiliation(s)
- Aaron W Miller
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH, USA
| | - Kristina L Penniston
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kate Fitzpatrick
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - José Agudelo
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gregory Tasian
- Division of Urology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Dirk Lange
- The Stone Centre at Vancouver General Hospital, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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11
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Probiotic Oxalate-Degrading Bacteria: New Insight of Environmental Variables and Expression of the oxc and frc Genes on Oxalate Degradation Activity. Foods 2022; 11:foods11182876. [PMID: 36141002 PMCID: PMC9498451 DOI: 10.3390/foods11182876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/30/2022] Open
Abstract
Oxalate, a compound produced by many edible plants and as a terminal metabolite in the liver of mammals, is a toxin that has a detrimental role to human health. Humans and other mammals do possess enzymatic systems to degrade oxalate. Moreover, numerous oxalate-degrading bacteria reside in the mammalian gut and, thus, provide an important function for hosts. The current review focuses on the environmental factors that influence the efficacy of probiotic oxalate-degrading bacteria, relative to oxalate metabolism. We describe the mechanism of oxalate catabolism and its consumption by obligate and facultative anaerobic oxalate-degrading bacteria, in both in vitro and in vivo environments. We also explore the environmental variables that impact oxalate degradation. Studies on single species degrade oxalate have not shown a strong impact on oxalate metabolism, especially in high oxalate conditions such as consumption of foods high in oxalate (such as coffee and chocolate for humans or halogeton in animal feed). Considering effective variables which enhance oxalate degradation could be used in application of effective probiotic as a therapeutic tool in individuals with hyperoxaluria. This study indicates probiotics can be considered a good source of naturally occurring oxalate degrading agent in human colon.
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12
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Dearing MD, Kaltenpoth M, Gershenzon J. Demonstrating the role of symbionts in mediating detoxification in herbivores. Symbiosis 2022; 87:59-66. [PMID: 36164313 PMCID: PMC9499882 DOI: 10.1007/s13199-022-00863-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/23/2022] [Indexed: 11/30/2022]
Abstract
AbstractPlant toxins constitute an effective defense against herbivorous animals. However, many herbivores have evolved adaptations to cope with dietary toxins through detoxification, excretion, sequestration, target site insensitivity and/or via behavioral avoidance. While these adaptations are often directly encoded in herbivore genomes, evidence is accumulating that microbial symbionts can reduce the dose of plant toxins by metabolizing or sequestering them prior to absorption by the herbivore. Here, we describe a few well-studied examples to assess such symbiont-mediated detoxification and showcase different approaches that have been used for their analyses. These include: (i) a host phenotypic route in which the symbiotic association is manipulated to reveal host fitness costs upon toxin exposure in the presence/absence of detoxifying symbionts, including function restoration after symbiont re-infection, (ii) a molecular microbiological approach that focuses on the identification and characterization of microbial genes involved in plant toxin metabolism, and (iii) an analytical chemical route that aims to characterize the conversion of the toxin to less harmful metabolites in vivo and link conversion to the activities of a detoxifying symbiont. The advantages and challenges of each approach are discussed, and it is argued that a multi-pronged strategy combining phenotypic, molecular, and chemical evidence is needed to unambiguously demonstrate microbial contributions to plant toxin reduction and the importance of these processes for host fitness. Given the interdisciplinary nature of the topic, we aim to provide a guideline to researchers interested in symbiont-mediated detoxification and hope to encourage future studies that contribute to a more comprehensive and mechanistic understanding of detoxification in herbivores and their symbionts.
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Affiliation(s)
- M. Denise Dearing
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112 USA
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Martin Kaltenpoth
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str.8, 07745 Jena, Germany
| | - Jonathan Gershenzon
- Department of Biochemistry, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745 Jena, Germany
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13
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Popkov VA, Zharikova AA, Demchenko EA, Andrianova NV, Zorov DB, Plotnikov EY. Gut Microbiota as a Source of Uremic Toxins. Int J Mol Sci 2022; 23:ijms23010483. [PMID: 35008909 PMCID: PMC8745165 DOI: 10.3390/ijms23010483] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/26/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
Uremic retention solutes are the compounds that accumulate in the blood when kidney excretory function is impaired. Some of these compounds are toxic at high concentrations and are usually known as “uremic toxins”. The cumulative detrimental effect of uremic toxins results in numerous health problems and eventually mortality during acute or chronic uremia, especially in end-stage renal disease. More than 100 different solutes increase during uremia; however, the exact origin for most of them is still debatable. There are three main sources for such compounds: exogenous ones are consumed with food, whereas endogenous ones are produced by the host metabolism or by symbiotic microbiota metabolism. In this article, we identify uremic retention solutes presumably of gut microbiota origin. We used database analysis to obtain data on the enzymatic reactions in bacteria and human organisms that potentially yield uremic retention solutes and hence to determine what toxins could be synthesized in bacteria residing in the human gut. We selected biochemical pathways resulting in uremic retention solutes synthesis related to specific bacterial strains and revealed links between toxin concentration in uremia and the proportion of different bacteria species which can synthesize the toxin. The detected bacterial species essential for the synthesis of uremic retention solutes were then verified using the Human Microbiome Project database. Moreover, we defined the relative abundance of human toxin-generating enzymes as well as the possibility of the synthesis of a particular toxin by the human metabolism. Our study presents a novel bioinformatics approach for the elucidation of the origin of both uremic retention solutes and uremic toxins and for searching for the most likely human microbiome producers of toxins that can be targeted and used for the therapy of adverse consequences of uremia.
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Affiliation(s)
- Vasily A. Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (V.A.P.); (A.A.Z.); (E.A.D.); (N.V.A.); (D.B.Z.)
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Anastasia A. Zharikova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (V.A.P.); (A.A.Z.); (E.A.D.); (N.V.A.); (D.B.Z.)
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Evgenia A. Demchenko
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (V.A.P.); (A.A.Z.); (E.A.D.); (N.V.A.); (D.B.Z.)
| | - Nadezda V. Andrianova
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (V.A.P.); (A.A.Z.); (E.A.D.); (N.V.A.); (D.B.Z.)
| | - Dmitry B. Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (V.A.P.); (A.A.Z.); (E.A.D.); (N.V.A.); (D.B.Z.)
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
| | - Egor Y. Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia; (V.A.P.); (A.A.Z.); (E.A.D.); (N.V.A.); (D.B.Z.)
- V.I. Kulakov National Medical Research Center of Obstetrics, Gynecology and Perinatology, 117997 Moscow, Russia
- Correspondence: ; Tel.: +7-(495)939-59-44
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14
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Wei Z, Cui Y, Tian L, Liu Y, Yu Y, Jin X, Li H, Wang K, Sun Q. Probiotic Lactiplantibacillus plantarum N-1 could prevent ethylene glycol-induced kidney stones by regulating gut microbiota and enhancing intestinal barrier function. FASEB J 2021; 35:e21937. [PMID: 34606628 DOI: 10.1096/fj.202100887rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 02/05/2023]
Abstract
Defective permeability barrier is considered to be an incentive of hyperuricemia, however, the link between them has not been proven. Here, we evaluated the potential preventive effects of Lactiplantibacillus plantarum N-1 (LPN1) on gut microbiota and intestinal barrier function in rats with hyperoxaluria-induced kidney stones. Male rats were supplied with 1% ethylene glycol (EG) dissolved in drinking water for 4 weeks to develop hyperoxaluria, and some of them were administered with LPN1 for 4 weeks before EG treatment as a preventive intervention. We found that EG not only resulted hyperoxaluria and kidney stone formation, but also promoted the intestinal inflammation, elevated intestinal permeability, and gut microbiota disorders. Supplementation of LPN1 inhibited the renal crystalline deposits through reducing urinary oxalic acid and renal osteopontin and CD44 expression and improved EG-induced intestinal inflammation and barrier function by decreasing the serum LPS and TLR4/NF-κB signaling and up-regulating tight junction Claudin-2 in the colon, as well as increasing the production of short-chain fatty acid (SCFAs) and the abundance of beneficial SCFAs-producing bacteria, mainly from the families of Lachnospiraceae and Ruminococcaceae. Probiotic LPN1 could prevent EG-induced hyperoxaluria by regulating gut microbiota and enhancing intestinal barrier function.
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Affiliation(s)
- Zhitao Wei
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Yaqian Cui
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Lei Tian
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yu Liu
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Yang Yu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Xi Jin
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Hong Li
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Kunjie Wang
- Department of Urology, Institute of Urology (Laboratory of Reconstructive Urology), West China Hospital, Sichuan University, Chengdu, China
| | - Qun Sun
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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15
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Malaviya R, Pandey A, Yadav N. Ameliorating color value, antinutrients, phenolic content of sesame seed cake with better oil recovery by response surface methodology. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ritika Malaviya
- Centre of Food Technology Science Faculty Campus University of Allahabad Allahabad India
| | - Anil Pandey
- Centre of Food Technology Science Faculty Campus University of Allahabad Allahabad India
| | - Neelam Yadav
- Centre of Food Technology Science Faculty Campus University of Allahabad Allahabad India
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16
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Activity of probiotics from food origin for oxalate degradation. Arch Microbiol 2021; 203:5017-5028. [PMID: 34282467 DOI: 10.1007/s00203-021-02484-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Kidney stones composed of oxalate are a significant health problem. It has been suggested that modification of the intestinal microbiota to reduce the amount of oxalate in the digestive system could be an effective treatment. There have been several studies into the use of lactic acid bacteria for the degradation of intestinal oxalates. We isolated 88 lactic acid bacteria strains from a range of dairy products, and screened for their ability to degrade oxalate. Using the oxalate-degrading Enzymatic Activity Index and the viable cell counts, five strains of Lactobacillus fermentum and two strains of Lactobacillus gastricus were identified as having strong oxalate degradation abilities, and were further investigated. All seven strains were able to tolerate acid (pH 4 and 3), bile salts (0.3%), phenol (0.3%), and to produce exopolysaccharides. They were resistant to a wide range of antibiotics. Among these strains, Lactobacillus fermentum NRAMJ5 and Lactobacillus gastricus NRAMJ2 were, therefore, good candidates as probiotics for managing hyperoxaluria.
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17
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Wang Z, Zhang Y, Zhang J, Deng Q, Liang H. Recent advances on the mechanisms of kidney stone formation (Review). Int J Mol Med 2021; 48:149. [PMID: 34132361 PMCID: PMC8208620 DOI: 10.3892/ijmm.2021.4982] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/31/2021] [Indexed: 12/14/2022] Open
Abstract
Kidney stone disease is one of the oldest diseases known to medicine; however, the mechanisms of stone formation and development remain largely unclear. Over the past decades, a variety of theories and strategies have been developed and utilized in the surgical management of kidney stones, as a result of recent technological advances. Observations from the authors and other research groups suggest that there are five entirely different main mechanisms for kidney stone formation. Urinary supersaturation and crystallization are the driving force for intrarenal crystal precipitation. Randall's plaques are recognized as the origin of calcium oxalate stone formation. Sex hormones may be key players in the development of nephrolithiasis and may thus be potential targets for new drugs to suppress kidney stone formation. The microbiome, including urease-producing bacteria, nanobacteria and intestinal microbiota, is likely to have a profound effect on urological health, both positive and negative, owing to its metabolic output and other contributions. Lastly, the immune response, and particularly macrophage differentiation, play crucial roles in renal calcium oxalate crystal formation. In the present study, the current knowledge for each of these five aspects of kidney stone formation is reviewed. This knowledge may be used to explore novel research opportunities and improve the understanding of the initiation and development of kidney stones for urologists, nephrologists and primary care.
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Affiliation(s)
- Zhu Wang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Ying Zhang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Jianwen Zhang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Qiong Deng
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Hui Liang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
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18
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Akter S, Netzel M, Tinggi U, Fletcher M, Osborne S, Sultanbawa Y. Interactions Between Phytochemicals and Minerals in Terminalia ferdinandiana and Implications for Mineral Bioavailability. Front Nutr 2021; 7:598219. [PMID: 33425972 PMCID: PMC7793935 DOI: 10.3389/fnut.2020.598219] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/09/2020] [Indexed: 11/13/2022] Open
Abstract
Oxalic and phytic acid are phytochemicals considered to be anti-nutritional factors as they are predominantly found as oxalates and phytates bound to minerals like calcium and potassium. Studies have associated excessive oxalate consumption with increased urinary excretion of oxalate (hyperoxaluria) and calcium oxalate kidney stone formation, and excessive phytate consumption with decreased bioaccessibility and bioavailability of certain minerals and reduced utilization of dietary protein. However, other studies suggest that dietary consumption of phytate may be beneficial and inhibit formation of calcium oxalate kidney stones. In light of these conflicting reports, dietary intake of oxalate and phytate enriched plants should be considered in relation to potential health outcomes following consumption. Terminalia ferdinandiana is one such plant and is investigated here with respect to oxalate, phytate, and mineral contents. Assessment of oxalate and phytate contents in T. ferdinandiana fruit, leaf, and seedcoat tissues through hydrolysis into acid forms revealed oxalic acid contents ranging from 327 to 1,420 mg/100 g on a dry weight (DW) basis whilst phytic acid contents ranged from 8.44 to 121.72 mg/100 g DW. Calcium content in the different tissues ranged from 131 to 1,343 mg/100 g. There was no correlation between oxalic acid and calcium, however a significant, positive correlation was observed between phytic acid and calcium (r = 0.9917; p < 0.001), indicating that tissues rich in phytic acid also contain higher levels of calcium. The high content of phytic acid in comparison to oxalic acid in T. ferdinandiana fruit found in this study and the dietary significance of this in terms of calcium bioavailability, needs to be investigated further.
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Affiliation(s)
- Saleha Akter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Health and Food Sciences Precinct, Coopers Plains, QLD, Australia
| | - Michael Netzel
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Health and Food Sciences Precinct, Coopers Plains, QLD, Australia
| | - Ujang Tinggi
- Queensland Health Forensic and Scientific Services, Coopers Plains, QLD, Australia
| | - Mary Fletcher
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Health and Food Sciences Precinct, Coopers Plains, QLD, Australia
| | - Simone Osborne
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, St Lucia, QLD, Australia
| | - Yasmina Sultanbawa
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Health and Food Sciences Precinct, Coopers Plains, QLD, Australia
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19
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Metabolomic Alteration in the Mouse Distal Colonic Mucosa after Oral Gavage with Oxalobacter formigenes. Metabolites 2020; 10:metabo10100405. [PMID: 33065971 PMCID: PMC7650779 DOI: 10.3390/metabo10100405] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 12/03/2022] Open
Abstract
Oxalobacter formigenes has been investigated for years due to its proposed ability to produce a secretagogue compound that initiates net intestinal oxalate secretion, thereby theoretically reducing circulating oxalate and risk of kidney stone formation. Strains which have been shown to exhibit this function in vivo across native tissue include the human strain, HC1, and the wild rat strain, OxWR. While previous work on these secretagogue-relevant strains has focused on profiling their metabolome and lipidome in vitro, efforts to characterize their influence on host intestinal mucosal biochemistry in vivo are yet to be reported. Much work has been done over the years with O. formigenes in relation to the secretagogue hypothesis, but it has never been clearly demonstrated that this microorganism is capable of inducing metabolic changes in native host tissue, which would be expected with the production of a transport-inducing compound. In this work, we show how the distal colonic mucosal metabolomic profile in a mouse model exhibited significant changes in the levels of a variety of metabolites as a result of oral gavage with O. formigenes HC1. Among these significant metabolites was nicotinic acid, an essential nutrient shown in past work to be produced in the gut by the native microbiome. Our finding that the in vivo biochemical state of the distal colon was altered with O. formigenes lends support to the secretagogue hypothesis and serves as a pioneering step in characterizing the biochemical interplay between O. formigenes and the mammalian host.
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Abstract
Kidney stone disease is a morbid condition that is increasing in prevalence, with few nonsurgical treatment options. The majority of stones are composed of calcium oxalate. Unlike humans, some microbes can break down oxalate, suggesting that microbial therapeutics may provide a novel treatment for kidney stone patients. This study demonstrated that Bacillus subtilis 168 (BS168) decreased stone burden, improved health, and complemented the microbiota in a Drosophila melanogaster urolithiasis model, while not exacerbating calcium oxalate aggregation or adhesion to renal cells in vitro. These results identify this bacterium as a candidate for ameliorating stone formation; given that other strains of B. subtilis are components of fermented foods and are used as probiotics for digestive health, strain 168 warrants testing in humans. With the severe burden that recurrent kidney stone disease imposes on patients and the health care system, this microbial therapeutic approach could provide an inexpensive therapeutic adjunct. Kidney stones affect nearly 10% of the population in North America and are associated with high morbidity and recurrence, yet novel prevention strategies are lacking. Recent evidence suggests that the human gut microbiota can influence the development of nephrolithiasis, although clinical trials have been limited and inconclusive in determining the potential for microbially based interventions. Here, we used an established Drosophila melanogaster model of urolithiasis as a high-throughput screening platform for evaluation of the therapeutic potential of oxalate-degrading bacteria in calcium oxalate (CaOx) nephrolithiasis. The results demonstrated that Bacillus subtilis 168 (BS168) is a promising candidate based on its preferential growth in high oxalate concentrations, its ability to stably colonize the D. melanogaster intestinal tract for as long as 5 days, and its prevention of oxalate-induced microbiota dysbiosis. Single-dose BS168 supplementation exerted beneficial effects on D. melanogaster for as long as 14 days, decreasing stone burden in dissected Malpighian tubules and fecal excreta while increasing survival and behavioral markers of health over those of nonsupplemented lithogenic controls. These findings were complemented by in vitro experiments using the established MDCK renal cell line, which demonstrated that BS168 pretreatment prevented increased CaOx crystal adhesion and aggregation. Taking our results together, this study supports the notion that BS168 can functionally reduce CaOx stone burden in vivo through its capacity for oxalate degradation. Given the favorable safety profile of many B. subtilis strains already used as digestive aids and in fermented foods, these findings suggest that BS168 could represent a novel therapeutic adjunct to reduce the incidence of recurrent CaOx nephrolithiasis in high-risk patients. IMPORTANCE Kidney stone disease is a morbid condition that is increasing in prevalence, with few nonsurgical treatment options. The majority of stones are composed of calcium oxalate. Unlike humans, some microbes can break down oxalate, suggesting that microbial therapeutics may provide a novel treatment for kidney stone patients. This study demonstrated that Bacillus subtilis 168 (BS168) decreased stone burden, improved health, and complemented the microbiota in a Drosophila melanogaster urolithiasis model, while not exacerbating calcium oxalate aggregation or adhesion to renal cells in vitro. These results identify this bacterium as a candidate for ameliorating stone formation; given that other strains of B. subtilis are components of fermented foods and are used as probiotics for digestive health, strain 168 warrants testing in humans. With the severe burden that recurrent kidney stone disease imposes on patients and the health care system, this microbial therapeutic approach could provide an inexpensive therapeutic adjunct.
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21
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Stanford J, Charlton K, Stefoska-Needham A, Ibrahim R, Lambert K. The gut microbiota profile of adults with kidney disease and kidney stones: a systematic review of the literature. BMC Nephrol 2020; 21:215. [PMID: 32503496 PMCID: PMC7275316 DOI: 10.1186/s12882-020-01805-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 04/14/2020] [Indexed: 12/24/2022] Open
Abstract
Background There is mounting evidence that individuals with kidney disease and kidney stones have an abnormal gut microbiota composition. No studies to date have summarised the evidence to categorise how the gut microbiota profile of these individuals may differ from controls. Synthesis of this evidence is essential to inform future clinical trials. This systematic review aims to characterise differences of the gut microbial community in adults with kidney disease and kidney stones, as well as to describe the functional capacity of the gut microbiota and reporting of diet as a confounder in these studies. Methods Included studies were those that investigated the gut microbial community in adults with kidney disease or kidney stones and compared this to the profile of controls. Six scientific databases (CINHAL, Medline, PubMed, Scopus, Web of Science and Cochrane Library), as well as selected grey literature sources, were searched. Quality assessment was undertaken independently by three authors. The system of evidence level criteria was employed to quantitatively evaluate the alteration of microbiota by strictly considering the number, methodological quality and consistency of the findings. Additional findings relating to altered functions of the gut microbiota, dietary intakes and dietary methodologies used were qualitatively summarised. Results Twenty-five articles met the eligibility criteria and included data from a total of 892 adults with kidney disease or kidney stones and 1400 controls. Compared to controls, adults with kidney disease had increased abundances of several microbes including Enterobacteriaceae, Streptococcaceae, Streptococcus and decreased abundances of Prevotellaceae, Prevotella, Prevotella 9 and Roseburia among other taxa. Adults with kidney stones also had an altered microbial composition with variations to Bacteroides, Lachnospiraceae NK4A136 group, Ruminiclostridium 5 group, Dorea, Enterobacter, Christensenellaceae and its genus Christensenellaceae R7 group. Differences in the functional potential of the microbial community between controls and adults with kidney disease or kidney stones were also identified. Only three of the 25 articles presented dietary data, and of these studies, only two used a valid dietary assessment method. Conclusions The gut microbiota profile of adults with kidney disease and kidney stones differs from controls. Future study designs should include adequate reporting of important confounders such as dietary intake to assist with interpretation of findings.
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Affiliation(s)
- Jordan Stanford
- University of Wollongong, School of Medicine, Faculty of Science, Medicine and Health, Wollongong, New South Wales, 2522, Australia. .,Illawarra Health and Medical Research Institute, Wollongong, New South Wales, 2522, Australia.
| | - Karen Charlton
- University of Wollongong, School of Medicine, Faculty of Science, Medicine and Health, Wollongong, New South Wales, 2522, Australia.,University of Wollongong, Health Impacts Research Cluster, Wollongong, New South Wales, 2522, Australia
| | - Anita Stefoska-Needham
- University of Wollongong, School of Medicine, Faculty of Science, Medicine and Health, Wollongong, New South Wales, 2522, Australia.,University of Wollongong, Health Impacts Research Cluster, Wollongong, New South Wales, 2522, Australia
| | - Rukayat Ibrahim
- University of Surrey, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, Guildford, GU2 7XH, UK
| | - Kelly Lambert
- University of Wollongong, School of Medicine, Faculty of Science, Medicine and Health, Wollongong, New South Wales, 2522, Australia.,University of Wollongong, Health Impacts Research Cluster, Wollongong, New South Wales, 2522, Australia
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22
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Denburg MR, Koepsell K, Lee JJ, Gerber J, Bittinger K, Tasian GE. Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease. J Am Soc Nephrol 2020; 31:1358-1369. [PMID: 32381601 DOI: 10.1681/asn.2019101131] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/22/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The relationship between the composition and function of gut microbial communities and early-onset calcium oxalate kidney stone disease is unknown. METHODS We conducted a case-control study of 88 individuals aged 4-18 years, which included 44 individuals with kidney stones containing ≥50% calcium oxalate and 44 controls matched for age, sex, and race. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool samples. RESULTS Participants who were kidney stone formers had a significantly less diverse gut microbiome compared with controls. Among bacterial taxa with a prevalence >0.1%, 31 taxa were less abundant among individuals with nephrolithiasis. These included seven taxa that produce butyrate and three taxa that degrade oxalate. The lower abundance of these bacteria was reflected in decreased abundance of the gene encoding butyryl-coA dehydrogenase (P=0.02). The relative abundance of these bacteria was correlated with the levels of 18 fecal metabolites, and levels of these metabolites differed in individuals with kidney stones compared with controls. The oxalate-degrading bacterial taxa identified as decreased in those who were kidney stone formers were components of a larger abundance correlation network that included Eggerthella lenta and several Lactobacillus species. The microbial (α) diversity was associated with age of stone onset, first decreasing and then increasing with age. For the individuals who were stone formers, we found the lowest α diversity among individuals who first formed stones at age 9-14 years, whereas controls displayed no age-related differences in diversity. CONCLUSIONS Loss of gut bacteria, particularly loss of those that produce butyrate and degrade oxalate, associates with perturbations of the metabolome that may be upstream determinants of early-onset calcium oxalate kidney stone disease.
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Affiliation(s)
- Michelle R Denburg
- Division of Nephrology, Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Pediatric Clinical Effectiveness, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kristen Koepsell
- Division of Pediatric Urology, Department of Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jung-Jin Lee
- Division of Gastroenterology, Department of Pediatrics, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jeffrey Gerber
- Center for Pediatric Clinical Effectiveness, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Infectious Diseases, Department of Pediatrics, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kyle Bittinger
- Division of Gastroenterology, Department of Pediatrics, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Gregory E Tasian
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania .,Center for Pediatric Clinical Effectiveness, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Division of Pediatric Urology, Department of Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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Wang X, Bhutani G, Vaughan LE, Enders FT, Haskic Z, Milliner D, Lieske JC. Urinary monocyte chemoattractant protein 1 associated with calcium oxalate crystallization in patients with primary hyperoxaluria. BMC Nephrol 2020; 21:133. [PMID: 32293313 PMCID: PMC7161151 DOI: 10.1186/s12882-020-01783-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/23/2020] [Indexed: 01/18/2023] Open
Abstract
Background Patients with primary hyperoxaluria (PH) often develop kidney stones and chronic kidney disease. Noninvasive urine markers reflective of active kidney injury could be useful to gauge the effectiveness of ongoing treatments. Methods A panel of biomarkers that reflect different nephron sites and potential mechanisms of injury (clusterin, neutrophil gelatinase-associated lipocalin (NGAL), 8-isoprostane (8IP), monocyte-chemoattractant protein 1(MCP-1), liver-type fatty acid binding protein (L-FABP), heart-type fatty acid binding protein (H-FABP), and osteopontin (OPN)) were measured in 114 urine specimens from 30 PH patients over multiple visits. Generalized estimating equations were used to assess associations between biomarkers and 24 h urine excretions, calculated proximal tubular oxalate concentration (PTOx), and eGFR. Results Mean (±SD) age at first visit was 19.5 ± 16.6 years with an estimated glomerular filtration rate (eGFR) of 68.4 ± 21.0 ml/min/1.73m2. After adjustment for age, sex, and eGFR, a higher urine MCP-1 concentration and MCP-1/creatinine ratio was positively associated with CaOx supersaturation (SS). Higher urine NGAL and NGAL/creatinine as well as OPN and OPN/creatinine were associated with higher eGFR. 8IP was negatively associated with PTOx and urinary Ox, but positively associated with CaOx SS. Conclusion In PH patients greater urine MCP-1 and 8IP excretion might reflect ongoing collecting tubule crystallization, while greater NGAL and OPN excretion may reflect preservation of kidney mass and function. CaOx crystals, rather than oxalate ion may mediate oxidative stress in hyperoxaluric conditions. Further studies are warranted to determine whether urine MCP-1 excretion predicts long term outcome or is altered in response to treatment.
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Affiliation(s)
- Xiangling Wang
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Gauri Bhutani
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Lisa E Vaughan
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Felicity T Enders
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Zejfa Haskic
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Dawn Milliner
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - John C Lieske
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA. .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA.
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Millán Rodríguez F, Sabiote Rubio L, Girón Nanne I, Sánchez Martín F, Emiliani E, Angerri Feu O. The relationship between calcium oxalate lithiasis and chronic proinflammatory intestinal dysbiosis pattern: a prospective study. Urolithiasis 2020; 48:321-328. [DOI: 10.1007/s00240-020-01181-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/13/2020] [Indexed: 12/18/2022]
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25
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Calcium Oxalate Nephrolithiasis and Gut Microbiota: Not just a Gut-Kidney Axis. A Nutritional Perspective. Nutrients 2020; 12:nu12020548. [PMID: 32093202 PMCID: PMC7071363 DOI: 10.3390/nu12020548] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
Recent studies have shown that patients with kidney stone disease, and particularly calcium oxalate nephrolithiasis, exhibit dysbiosis in their fecal and urinary microbiota compared with controls. The alterations of microbiota go far beyond the simple presence and representation of Oxalobacter formigenes, a well-known symbiont exhibiting a marked capacity of degrading dietary oxalate and stimulating oxalate secretion by the gut mucosa. Thus, alterations of the intestinal microbiota may be involved in the pathophysiology of calcium kidney stones. However, the role of nutrition in this gut-kidney axis is still unknown, even if nutritional imbalances, such as poor hydration, high salt, and animal protein intake and reduced fruit and vegetable intake, are well-known risk factors for kidney stones. In this narrative review, we provide an overview of the gut-kidney axis in nephrolithiasis from a nutritional perspective, summarizing the evidence supporting the role of nutrition in the modulation of microbiota composition, and their relevance for the modulation of lithogenic risk.
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26
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Abstract
OBJECTIVES Patients requiring oral and/or enteral nutrition support, delivered via nasogastric, gastric, or intestinal routes, have a relatively high incidence of calcium oxalate (CaOx) kidney stones. Nutrition formulas are frequently made from corn and/or or soy, both of which contain ample oxalate. Excessive oxalate intake contributes to hyperoxaluria (>45 mg urine oxalate/day) and CaOx stones especially when unopposed by concomitant calcium intake, gastrointestinal malabsorption is present, and/or oxalate degrading gut bacteria are limiting or absent. Our objective was to assess the oxalate content of commonly used commercial enteral nutrition formulas. METHODS Enteral nutrition formulas were selected from the formulary at our clinical inpatient institution. Multiple samples of each were assessed for oxalate concentration with ion chromatography. RESULTS Results from 26 formulas revealed highly variable oxalate concentration ranging from 4 to 140 mg oxalate/L of formula. No definitive patterns for different types of formulas (eg, flavored vs unflavored, high protein vs not) were evident. Coefficients of variation for all formulas ranged from 0.68% to 43% (mean ± SD 19% ± 12%; median 18%). CONCLUSIONS Depending on the formula and amount delivered, patients requiring nutrition support could obtain anywhere from 12 to 150 mg oxalate/day or more and are thus at risk for hyperoxaluria and CaOx stones.
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27
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Panyushkina AE, Babenko VV, Nikitina AS, Selezneva OV, Tsaplina IA, Letarova MA, Kostryukova ES, Letarov AV. Sulfobacillus thermotolerans: new insights into resistance and metabolic capacities of acidophilic chemolithotrophs. Sci Rep 2019; 9:15069. [PMID: 31636299 PMCID: PMC6803676 DOI: 10.1038/s41598-019-51486-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 09/23/2019] [Indexed: 11/09/2022] Open
Abstract
The first complete genome of the biotechnologically important species Sulfobacillus thermotolerans has been sequenced. Its 3 317 203-bp chromosome contains an 83 269-bp plasmid-like region, which carries heavy metal resistance determinants and the rusticyanin gene. Plasmid-mediated metal resistance is unusual for acidophilic chemolithotrophs. Moreover, most of their plasmids are cryptic and do not contribute to the phenotype of the host cells. A polyphosphate-based mechanism of metal resistance, which has been previously unknown in the genus Sulfobacillus or other Gram-positive chemolithotrophs, potentially operates in two Sulfobacillus species. The methylcitrate cycle typical for pathogens and identified in the genus Sulfobacillus for the first time can fulfill the energy and/or protective function in S. thermotolerans Kr1 and two other Sulfobacillus species, which have incomplete glyoxylate cycles. It is notable that the TCA cycle, disrupted in all Sulfobacillus isolates under optimal growth conditions, proved to be complete in the cells enduring temperature stress. An efficient antioxidant defense system gives S. thermotolerans another competitive advantage in the microbial communities inhabiting acidic metal-rich environments. The genomic comparisons revealed 80 unique genes in the strain Kr1, including those involved in lactose/galactose catabolism. The results provide new insights into metabolism and resistance mechanisms in the Sulfobacillus genus and other acidophiles.
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Affiliation(s)
- Anna E Panyushkina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia.
| | - Vladislav V Babenko
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Anastasia S Nikitina
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Oksana V Selezneva
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Iraida A Tsaplina
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Maria A Letarova
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
| | - Elena S Kostryukova
- Federal Medical Biological Agency, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Andrey V Letarov
- Research Center of Biotechnology of the Russian Academy of Sciences, Winogradsky Institute of Microbiology, Moscow, 119071, Russia
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28
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Metabolomic profiling of oxalate-degrading probiotic Lactobacillus acidophilus and Lactobacillus gasseri. PLoS One 2019; 14:e0222393. [PMID: 31545840 PMCID: PMC6756784 DOI: 10.1371/journal.pone.0222393] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/28/2019] [Indexed: 12/12/2022] Open
Abstract
Oxalate, a ubiquitous compound in many plant-based foods, is absorbed through the intestine and precipitates with calcium in the kidneys to form stones. Over 80% of diagnosed kidney stones are found to be calcium oxalate. People who form these stones often experience a high rate of recurrence and treatment options remain limited despite decades of dedicated research. Recently, the intestinal microbiome has become a new focus for novel therapies. Studies have shown that select species of Lactobacillus, the most commonly included genus in modern probiotic supplements, can degrade oxalate in vitro and even decrease urinary oxalate in animal models of Primary Hyperoxaluria. Although the purported health benefits of Lactobacillus probiotics vary significantly between species, there is supporting evidence for their potential use as probiotics for oxalate diseases. Defining the unique metabolic properties of Lactobacillus is essential to define how these bacteria interact with the host intestine and influence overall health. We addressed this need by characterizing and comparing the metabolome and lipidome of the oxalate-degrading Lactobacillus acidophilus and Lactobacillus gasseri using ultra-high-performance liquid chromatography-high resolution mass spectrometry. We report many species-specific differences in the metabolic profiles of these Lactobacillus species and discuss potential probiotic relevance and function resulting from their differential expression. Also described is our validation of the oxalate-degrading ability of Lactobacillus acidophilus and Lactobacillus gasseri, even in the presence of other preferred carbon sources, measuring in vitro 14C-oxalate consumption via liquid scintillation counting.
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29
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Kohl KD, Oakeson KF, Orr TJ, Miller AW, Forbey JS, Phillips CD, Dale C, Weiss RB, Dearing MD. Metagenomic sequencing provides insights into microbial detoxification in the guts of small mammalian herbivores (Neotoma spp.). FEMS Microbiol Ecol 2019; 94:5092587. [PMID: 30202961 DOI: 10.1093/femsec/fiy184] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/06/2018] [Indexed: 12/22/2022] Open
Abstract
Microbial detoxification of plant toxins influences the use of plants as food sources by herbivores. Stephen's woodrats (Neotoma stephensi) specialize on juniper, which is defended by oxalate, phenolics and monoterpenes, while closely related N. albigula specialize on cactus, which only contains oxalate. Woodrats maintain two gut chambers harboring dense microbial communities: a foregut chamber proximal to the major site of toxin absorption, and a cecal chamber in their hindgut. We performed several experiments to investigate the location and nature of microbial detoxification in the woodrat gut. First, we measured toxin concentrations across gut chambers of N. stephensi. Compared to food material, oxalate concentrations were immediately lower in the foregut, while concentrations of terpenes remained high in the foregut, and were lowest in the cecal chamber. We conducted metagenomic sequencing of the foregut chambers of both woodrat species and cecal chambers of N. stephensi to compare microbial functions. We found that most genes associated with detoxification were more abundant in the cecal chambers of N. stephensi. However, some genes associated with degradation of oxalate and phenolic compounds were more abundant in the foregut chambers. Thus, microbial detoxification may take place in various chambers depending on the class of chemical compound.
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Affiliation(s)
- Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Ave., Pittsburgh, PA, 15260, USA.,Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Kelly F Oakeson
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Teri J Orr
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Aaron W Miller
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA.,Departments of Urology and Immunology, Cleveland Clinic Foundation, 9500 Euclid Ave, Cleveland, OH, 44195, USA
| | - Jennifer Sorensen Forbey
- Department of Biological Sciences, Boise State University, 1910 University Drive, Boise, ID, 83725 USA
| | - Caleb D Phillips
- Department of Biological Sciences, Texas Tech University, 2901 Main Street, Lubbock, TX, 79409, USA
| | - Colin Dale
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Robert B Weiss
- Department of Human Genetics, University of Utah, 15 North 2030 East, Salt Lake City, UT, 84112, USA
| | - M Denise Dearing
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, 84112, USA
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30
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Shi S, Tian L, Xu S, Ji L, Nasir F, Li X, Song Z, Tian C. The rhizomicrobiomes of wild and cultivated crops react differently to fungicides. Arch Microbiol 2019; 201:477-486. [PMID: 30361816 DOI: 10.1007/s00203-018-1586-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/13/2018] [Accepted: 10/17/2018] [Indexed: 12/18/2022]
Abstract
The fungicides used to control diseases in cereal production can have adverse effects on non-target microbial communities, with possible consequences for plant health and productivity. Although we know that fungicides affect microbial community structure and soil activities, it is unclear how crop cultivars have altered the impact of fungicides on rhizomicrobiomes. In this study, the rhizosphere bacterial and fungal communities and structures of cultivated crops and their wild relatives were studied by Illumina MiSeq sequencing analysis. The results indicated that the rhizomicrobiome communities of wild crops reacted more strongly to fungicides than that of their cultivated relatives. Furthermore, fungal community composition was more affected by fungicides than bacterial community composition. Remarkably, the same trend was observed in both soybean and rice with regard to the influence of crop cultivar on the response of the rhizomicrobiome to fungicide application, although the level of the response was not similar. We report for the first time that the rhizomicrobiomes of wild crops reacted more strongly to fungicides than the rhizomicrobiomes of cultivated crops.
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Affiliation(s)
- Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shangqi Xu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Li Ji
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Zhiping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, 200433, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.
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Miller AW, Orr T, Dearing D, Monga M. Loss of function dysbiosis associated with antibiotics and high fat, high sugar diet. ISME JOURNAL 2019; 13:1379-1390. [PMID: 30700790 DOI: 10.1038/s41396-019-0357-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 02/08/2023]
Abstract
The incidence of urinary stone disease (USD) has increased four-fold in 50 years. Oxalate, which is degraded exclusively by gut bacteria, is an important constituent in 80% of urinary stones. We quantified the effects of antibiotics and a high fat/high sugar (HFHS) diet on the microbial metabolism of oxalate in the gut. High and low oxalate-degrading mouse models were developed by administering fecal transplants from either the wild mammalian rodent Neotoma albigula or Swiss-Webster mice to Swiss-Webster mice, which produces a microbiota with or without the bacteria necessary for persistent oxalate metabolism, respectively. Antibiotics led to an acute loss of both transplant bacteria and associated oxalate metabolism. Transplant bacteria exhibited some recovery over time but oxalate metabolism did not. In contrast, a HFHS diet led to an acute loss of function coupled with a gradual loss of transplant bacteria, indicative of a shift in overall microbial metabolism. Thus, the effects of oral antibiotics on the microbiome form and function were greater than the effects of diet. Results indicate that both antibiotics and diet strongly influence microbial oxalate metabolism.
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Affiliation(s)
- Aaron W Miller
- Department of Urology, Cleveland Clinic, 9500 Euclid Ave., Cleveland, OH, USA. .,Department of Inflammation & Immunity, Cleveland Clinic, 9500 Euclid Ave., Cleveland, OH, USA.
| | - Teri Orr
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, USA
| | - Denise Dearing
- Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT, USA
| | - Manoj Monga
- Department of Urology, Cleveland Clinic, 9500 Euclid Ave., Cleveland, OH, USA
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32
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Ticinesi A, Milani C, Guerra A, Allegri F, Lauretani F, Nouvenne A, Mancabelli L, Lugli GA, Turroni F, Duranti S, Mangifesta M, Viappiani A, Ferrario C, Dodi R, Dall'Asta M, Del Rio D, Ventura M, Meschi T. Understanding the gut-kidney axis in nephrolithiasis: an analysis of the gut microbiota composition and functionality of stone formers. Gut 2018; 67:2097-2106. [PMID: 29705728 DOI: 10.1136/gutjnl-2017-315734] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/12/2018] [Accepted: 04/13/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVES The involvement of the gut microbiota in the pathogenesis of calcium nephrolithiasis has been hypothesised since the discovery of the oxalate-degrading activity of Oxalobacter formigenes, but never comprehensively studied with metagenomics. The aim of this case-control study was to compare the faecal microbiota composition and functionality between recurrent idiopathic calcium stone formers (SFs) and controls. DESIGN Faecal samples were collected from 52 SFs and 48 controls (mean age 48±11). The microbiota composition was analysed through 16S rRNA microbial profiling approach. Ten samples (five SFs, five controls) were also analysed with deep shotgun metagenomics sequencing, with focus on oxalate-degrading microbial metabolic pathways. Dietary habits, assessed through a food-frequency questionnaire, and 24-hour urinary excretion of prolithogenic and antilithogenic factors, including calcium and oxalate, were compared between SFs and controls, and considered as covariates in the comparison of microbiota profiles. RESULTS SFs exhibited lower faecal microbial diversity than controls (Chao1 index 1460±363vs 1658±297, fully adjusted p=0.02 with stepwise backward regression analysis). At multivariate analyses, three taxa (Faecalibacterium, Enterobacter, Dorea) were significantly less represented in faecal samples of SFs. The Oxalobacter abundance was not different between groups. Faecal samples from SFs exhibited a significantly lower bacterial representation of genes involved in oxalate degradation, with inverse correlation with 24-hour oxalate excretion (r=-0.87, p=0.002). The oxalate-degrading genes were represented in several bacterial species, whose cumulative abundance was inversely correlated with oxaluria (r=-0.85, p=0.02). CONCLUSIONS Idiopathic calcium SFs exhibited altered gut microbiota composition and functionality that could contribute to nephrolithiasis physiopathology.
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Affiliation(s)
- Andrea Ticinesi
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Angela Guerra
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Franca Allegri
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Fulvio Lauretani
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Antonio Nouvenne
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Microbiome Research Hub, University of Parma, Parma, Italy.,Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.,GenProbio S.r.l., Parma, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rossella Dodi
- Department of Food and Drugs, University of Parma, Parma, Italy
| | | | - Daniele Del Rio
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Veterinary Science, University of Parma, Parma, Italy
| | - Marco Ventura
- Microbiome Research Hub, University of Parma, Parma, Italy.,Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Tiziana Meschi
- Microbiome Research Hub, University of Parma, Parma, Italy.,Department of Medicine and Surgery, University of Parma, Parma, Italy.,Dipartimento Medico-Geriatrico-Riabilitativo, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
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Batagello CA, Monga M, Miller AW. Calcium Oxalate Urolithiasis: A Case of Missing Microbes? J Endourol 2018; 32:995-1005. [PMID: 29808727 DOI: 10.1089/end.2018.0294] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Urinary stone disease (USD) has known associations with the gut microbiota. Approximately 80% of kidney stones contain oxalate as a primary constituent and diverse oxalate-degrading bacteria exist within the human gut, which may protect against USD. Although bacteriotherapy represents a promising strategy to eliminate oxalate and reduce the risk of USD, oxalate-degrading probiotics have had limited success. To identify limitations of oxalate-degrading probiotics and refine development of bacteriotherapies to prevent USD, we review the literature associated with the gut microbiota and USD. MATERIALS AND METHODS A literature search was performed to identify publications that examine the role of oxalate-degrading bacteria or the whole gut microbiota in oxalate metabolism and the pathophysiology of USD. We conducted a meta-analysis of studies that examined the association of the whole gut microbiota with USD. In addition, we evaluated the gut microbiota of healthy individuals and those with comorbidities related to USD using publically available data from the American Gut Project (AGP). RESULTS Studies on Oxalobacter formigenes reveal that colonization by this species is not a good predictor of USD risk or urinary oxalate excretion. The species of oxalate-degrading bacteria used in probiotics and duration of administration do not impact efficacy or persistence. Studies focused on the whole gut microbiota reveal broad shifts in the gut microbiota associated with USD and a diverse microbial network is associated with oxalate metabolism. AGP data analysis demonstrated a strong overlap in microbial genera depleted in diseased individuals among USD and comorbidities. CONCLUSIONS The associations between the gut microbiota and USD extend beyond individual functional microbial species. Common shifts in the gut microbiota may facilitate the onset of USD and/or comorbidities. The successful development of bacteriotherapies to inhibit USD will need to incorporate strategies that target a broad diversity of bacteria rather than focus on a few specialist species.
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Affiliation(s)
| | - Manoj Monga
- 2 Department of Immunology, Cleveland Clinic , Cleveland, Ohio
| | - Aaron W Miller
- 1 Department of Urology, Cleveland Clinic , Cleveland, Ohio.,2 Department of Immunology, Cleveland Clinic , Cleveland, Ohio
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34
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Schlemper TR, van Veen JA, Kuramae EE. Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent. MICROBIAL ECOLOGY 2018; 76:205-214. [PMID: 29147973 PMCID: PMC6061463 DOI: 10.1007/s00248-017-1108-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/03/2017] [Indexed: 05/29/2023]
Abstract
Rhizosphere microbial community composition can be influenced by different biotic and abiotic factors. We investigated the composition and co-variation of rhizosphere bacterial and fungal communities from two sorghum genotypes (BRS330 and SRN-39) in three different plant growth stages (emergence of the second leaf, (day10), vegetative to reproductive differentiation point (day 35), and at the last visible emerged leaf (day 50)) in two different soil types, Clue field (CF) and Vredepeel (VD). We observed that either bacterial or fungal community had its composition stronger influenced by soil followed by plant growth stage and cultivar. However, the influence of plant growth stage was higher on fungal community composition than on the bacterial community composition. Furthermore, we showed that sorghum rhizosphere bacterial and fungal communities can affect each other's composition and structure. The decrease in relative abundance of the fungus genus Gibberella over plant growth stages was followed by decrease of the bacterial families Oxalobacteracea and Sphingobacteriacea. Although cultivar effect was not the major responsible for bacterial and fungal community composition, cultivar SRN-39 showed to promote a stronger co-variance between bacterial and fungal communities.
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Affiliation(s)
- Thiago R Schlemper
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
- Department of Biology, Leiden University, Leiden, The Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.
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Weerasinghe Mohottige TN, Ginige MP, Kaksonen AH, Sarukkalige R, Cheng KY. Rapid start-up of a bioelectrochemical system under alkaline and saline conditions for efficient oxalate removal. BIORESOURCE TECHNOLOGY 2018; 250:317-327. [PMID: 29179053 DOI: 10.1016/j.biortech.2017.11.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 06/07/2023]
Abstract
This study examined a new approach for starting up a bioelectrochemical system (BES) for oxalate removal from an alkaline (pH > 12) and saline (NaCl 25 g/L) liquor. An oxalotrophic biofilm pre-grown aerobically onto granular graphite carriers was used directly as both the microbial inoculum and the BES anode. At anode potential of +200 mV (Ag/AgCl) the biofilm readily switched from using oxygen to graphite as sole electron acceptor for oxalate oxidation. BES performance was characterised at various hydraulic retention times (HRTs, 3-24 h), anode potentials (-600 to +200 mV vs. Ag/AgCl) and influent oxalate (25 mM) to acetate (0-30 mM) ratios. Maximum current density recorded was 363 A/m3 at 3 h HRT with a high coulombic efficiency (CE) of 70%. The biofilm could concurrently degrade acetate and oxalate (CE 80%) without apparent preference towards acetate. Pyro-sequencing analysis revealed that known oxalate degraders Oxalobacteraceae became abundant signifying their role in this novel bioprocess.
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Affiliation(s)
- Tharanga N Weerasinghe Mohottige
- CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia; Department of Civil Engineering, Curtin University, Bentley, Western Australia 6102, Australia
| | - Maneesha P Ginige
- CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia
| | - Anna H Kaksonen
- CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia; School of Pathology and Laboratory Medicine, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia 6009, Australia
| | - Ranjan Sarukkalige
- Department of Civil Engineering, Curtin University, Bentley, Western Australia 6102, Australia
| | - Ka Yu Cheng
- CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia; School of Engineering and Information Technology, Murdoch University, Western Australia 6150, Australia.
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Amin R, Asplin J, Jung D, Bashir M, Alshaikh A, Ratakonda S, Sharma S, Jeon S, Granja I, Matern D, Hassan H. Reduced active transcellular intestinal oxalate secretion contributes to the pathogenesis of obesity-associated hyperoxaluria. Kidney Int 2018; 93:1098-1107. [PMID: 29395336 DOI: 10.1016/j.kint.2017.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 10/26/2017] [Accepted: 11/09/2017] [Indexed: 02/07/2023]
Abstract
Most kidney stones are composed of calcium oxalate, and minor changes in urine oxalate affect the stone risk. Obesity is a risk factor for kidney stones and a positive correlation of unknown etiology between increased body size, and elevated urinary oxalate excretion has been reported. Here, we used obese ob/ob (ob) mice to elucidate the pathogenesis of obesity-associated hyperoxaluria. These ob mice have significant hyperoxaluria (3.3-fold) compared with control mice, which is not due to overeating as shown by pair-feeding studies. Dietary oxalate removal greatly ameliorated this hyperoxaluria, confirming that it is largely enteric in origin. Transporter SLC26A6 (A6) plays an essential role in active transcellular intestinal oxalate secretion, and ob mice have significantly reduced jejunal A6 mRNA (- 80%) and total protein (- 62%) expression. While net oxalate secretion was observed in control jejunal tissues mounted in Ussing chambers, net absorption was seen in ob tissues, due to significantly reduced secretion. We hypothesized that the obesity-associated increase in intestinal and systemic inflammation, as reflected by elevated proinflammatory cytokines, suppresses A6-mediated intestinal oxalate secretion and contributes to obesity-associated hyperoxaluria. Indeed, proinflammatory cytokines (elevated in ob mice) significantly decreased intestinal oxalate transport in vitro by reducing A6 mRNA and total protein expression. Proinflammatory cytokines also significantly reduced active mouse jejunal oxalate secretion, converting oxalate transport from net secretion in vehicle-treated tissues to net absorption in proinflammatory cytokines-treated tissues. Thus, reduced active intestinal oxalate secretion, likely secondary to local and systemic inflammation, contributes to the pathogenesis of obesity-associated hyperoxaluria. Hence, proinflammatory cytokines represent potential therapeutic targets.
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Affiliation(s)
- Ruhul Amin
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - John Asplin
- Litholink Corporation, Laboratory Corporation of America Holdings, Chicago, Illinois, USA
| | - Daniel Jung
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Mohamed Bashir
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Altayeb Alshaikh
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Sireesha Ratakonda
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Sapna Sharma
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Sohee Jeon
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Ignacio Granja
- Litholink Corporation, Laboratory Corporation of America Holdings, Chicago, Illinois, USA
| | - Dietrich Matern
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Hatim Hassan
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA.
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Liu M, Koh H, Kurtz ZD, Battaglia T, PeBenito A, Li H, Nazzal L, Blaser MJ. Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project. MICROBIOME 2017; 5:108. [PMID: 28841836 PMCID: PMC5571629 DOI: 10.1186/s40168-017-0316-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/25/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND Increasing evidence shows the importance of the commensal microbe Oxalobacter formigenes in regulating host oxalate homeostasis, with effects against calcium oxalate kidney stone formation, and other oxalate-associated pathological conditions. However, limited understanding of O. formigenes in humans poses difficulties for designing targeted experiments to assess its definitive effects and sustainable interventions in clinical settings. We exploited the large-scale dataset from the American Gut Project (AGP) to study O. formigenes colonization in the human gastrointestinal (GI) tract and to explore O. formigenes-associated ecology and the underlying host-microbe relationships. RESULTS In >8000 AGP samples, we detected two dominant, co-colonizing O. formigenes operational taxonomic units (OTUs) in fecal specimens. Multivariate analysis suggested that O. formigenes abundance was associated with particular host demographic and clinical features, including age, sex, race, geographical location, BMI, and antibiotic history. Furthermore, we found that O. formigenes presence was an indicator of altered host gut microbiota structure, including higher community diversity, global network connectivity, and stronger resilience to simulated disturbances. CONCLUSIONS Through this study, we identified O. formigenes colonizing patterns in the human GI tract, potential underlying host-microbe relationships, and associated microbial community structures. These insights suggest hypotheses to be tested in future experiments. Additionally, we proposed a systematic framework to study any bacterial taxa of interest to computational biologists, using large-scale public data to yield novel biological insights.
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Affiliation(s)
- Menghan Liu
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine, New York, NY 10016 USA
- Department of Microbiology, New York University School of Medicine, New York, NY 10016 USA
- Department of Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Hyunwook Koh
- Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
| | - Zachary D. Kurtz
- Department of Microbiology, New York University School of Medicine, New York, NY 10016 USA
- Department of Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Thomas Battaglia
- Department of Microbiology, New York University School of Medicine, New York, NY 10016 USA
- Department of Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Amanda PeBenito
- Department of Microbiology, New York University School of Medicine, New York, NY 10016 USA
- Department of Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Huilin Li
- Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
| | - Lama Nazzal
- Department of Microbiology, New York University School of Medicine, New York, NY 10016 USA
- Department of Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Martin J. Blaser
- Department of Microbiology, New York University School of Medicine, New York, NY 10016 USA
- Department of Medicine, New York University School of Medicine, New York, NY 10016 USA
- Medical Service, New York Harbor Department of Veterans Affairs Medical Center, New York, NY 10010 USA
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Bayer SB, Gearry RB, Drummond LN. Putative mechanisms of kiwifruit on maintenance of normal gastrointestinal function. Crit Rev Food Sci Nutr 2017; 58:2432-2452. [PMID: 28557573 DOI: 10.1080/10408398.2017.1327841] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Kiwifruits are recognized as providing relief from constipation and symptoms of constipation-predominant irritable bowel syndrome (IBS-C). However, the underlying mechanisms, specifically in regards to gastrointestinal transit time and motility, are still not completely understood. This review provides an overview on the physiological and pathophysiological processes underlying constipation and IBS-C, the composition of kiwifruit, and recent advances in the research of kiwifruit and abdominal comfort. In addition, gaps in the research are highlighted and scientific studies of other foods with known effects on the gastrointestinal tract are consulted to find likely mechanisms of action. While the effects of kiwifruit fiber are well documented, observed increases in gastrointestinal motility caused by kiwifruit are not fully characterized. There are a number of identified mechanisms that may be activated by kiwifruit compounds, such as the induction of motility via protease-activated signaling, modulation of microflora, changes in colonic methane status, bile flux, or mediation of inflammatory processes.
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Affiliation(s)
- Simone Birgit Bayer
- a Department of Pathology , Center for Free Radical Research, University of Otago , 2 Riccarton Avenue, PO Box 4345, Christchurch , New Zealand
| | - Richard Blair Gearry
- b Department of Medicine , University of Otago , 2 Riccarton Avenue, PO Box 4345, Christchurch , New Zealand
| | - Lynley Ngaio Drummond
- c Drummond Food Science Advisory Ltd. , 1137 Drain Road, Killinchy RD 2, Leeston , New Zealand
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Welch KD, Stonecipher CA, Gardner DR, Cook D, Pfister JA. Changes in the rumen bacterial microbiome of cattle exposed to ponderosa pine needles. J Anim Sci 2017; 95:2314-2322. [PMID: 28727013 DOI: 10.2527/jas.2016.1228] [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: 11/13/2022] Open
Abstract
Consumption of ponderosa pine needles, as well as needles and bark from a number of other trees, can cause abortions in cattle. The abortifacient compounds in these trees are labdane resin acids, including isocupressic acid and agathic acid. Previous research has demonstrated that cattle conditioned to pine needles metabolize the labdane resin acids more quickly than naïve cattle. The results from that study indicated that changes had occurred in the rumen of conditioned cattle. Therefore, in this study, the changes that occurred in the rumen bacterial microflora of cattle during exposure to ponderosa pine needles were evaluated. Cattle were dosed with ground pine needles twice daily for 7 d. Rumen samples were collected on d 0, 3, 7, and 14 (7 d after treatment stopped) and ruminal bacterial microbiome analyses were performed. There were 372 different genera of bacteria identified in the rumen samples. Principal coordinate analysis indicated that there was a significant difference in the rumen bacterial composition between the time points. There were 18 genera that increased in abundance from d 0 to d 7. Twenty three genera decreased in abundance from d 0 to d 7. The results from this study demonstrated that exposure of cattle to pine needles caused a clear shift in the rumen microbiome composition. In general, this shift lasted less than 1 wk post exposure, which indicates that any prophylactic treatment to manipulate the ruminal metabolism of the abortifacient compounds in pine needles would need to be continuously administered to maintain the necessary microbial composition in the rumen.
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Abstract
Nephrolithiasis is a condition marked by the presence or formation of stones in kidneys. Several factors contribute to kidney stones development such as environmental conditions, type of dietary intake, gender and gastrointestinal flora. Most of the kidney stones are composed of calcium phosphate and calcium oxalate, which enter in to the body through diet. Both sources of oxalates become dangerous when normal flora of gastrointestinal tract is disturbed. Oxalobacter and Lactobacillus species exist symbiotically in the human gut and prevent stone formation by altering some biochemical pathways through production of specific enzymes which help in the degradation of oxalate salts. Both Oxalobacter and Lactobacillus have potential probiotic characteristics for the prevention of kidney stone formation and this avenue should be further explored.
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Affiliation(s)
- Humaira Sadaf
- Department of Biosciences, University of Wah, Wah City, Pakistan
| | - Syed Irfan Raza
- Department of Biosciences, University of Wah, Wah City, Pakistan
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Abstract
BACKGROUND Urinary supersaturation is one key determinant of calcium oxalate (CaOx) urinary stone formation, and urinary excretions of oxalate and citrate are two key determinants. Each is influenced by gastrointestinal processes. METHODS Open label and randomized placebo studies have examined the effect of oral probiotic preparations on urinary supersaturation and oxalate excretion. Cross sectional studies in humans have studied the association of Oxalobacter formigenes colonization status and urinary oxalate excretion and prevalence of urinary stones. The intestinal microbiome of representative animals adapted to a high oxalate diet has been defined. RESULTS The fecal content of O. formigenes, the best studied oxalate-degrader, varies depending on stone status. However, trials with probiotics designed to degrade oxalate including those containing O. formigenes, Lactobacillus, and/or Bifidobacterium spp., have been disappointing. Multiple intestinal segments of animals on a high oxalate diet contains diverse communities of microorganisms that can function together to degrade and detoxify a large oxalate load. CONCLUSIONS Although the intestinal microbiome seems likely to play a role to modify gastrointestinal absorption of lithogenic substances and hence urinary stone risk, whether we can develop tools to manipulate it and decrease this kidney stone risk remains to be determined.
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Affiliation(s)
- John C Lieske
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905, USA
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Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis: Relevance to Human Inflammatory Bowel Disease. Inflamm Bowel Dis 2016; 22:2767-2787. [PMID: 27824648 DOI: 10.1097/mib.0000000000000970] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Dysbiosis of the gut microbiota may be involved in the pathogenesis of inflammatory bowel disease (IBD). However, the mechanisms underlying the role of the intestinal microbiome and metabolome in IBD onset and its alteration during active treatment and recovery remain unknown. Animal models of chronic intestinal inflammation with similar microbial and metabolomic profiles would enable investigation of these mechanisms and development of more effective treatments. Recently, the Winnie mouse model of colitis closely representing the clinical symptoms and characteristics of human IBD has been developed. In this study, we have analyzed fecal microbial and metabolomic profiles in Winnie mice and discussed their relevance to human IBD. METHODS The 16S rRNA gene was sequenced from fecal DNA of Winnie and C57BL/6 mice to define operational taxonomic units at ≥97% similarity threshold. Metabolomic profiling of the same fecal samples was performed by gas chromatography-mass spectrometry. RESULTS Composition of the dominant microbiota was disturbed, and prominent differences were evident at all levels of the intestinal microbiome in fecal samples from Winnie mice, similar to observations in patients with IBD. Metabolomic profiling revealed that chronic colitis in Winnie mice upregulated production of metabolites and altered several metabolic pathways, mostly affecting amino acid synthesis and breakdown of monosaccharides to short chain fatty acids. CONCLUSIONS Significant dysbiosis in the Winnie mouse gut replicates many changes observed in patients with IBD. These results provide justification for the suitability of this model to investigate mechanisms underlying the role of intestinal microbiota and metabolome in the pathophysiology of IBD.
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Kohl KD, Dearing MD. The Woodrat Gut Microbiota as an Experimental System for Understanding Microbial Metabolism of Dietary Toxins. Front Microbiol 2016; 7:1165. [PMID: 27516760 PMCID: PMC4963388 DOI: 10.3389/fmicb.2016.01165] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/13/2016] [Indexed: 01/22/2023] Open
Abstract
The microbial communities inhabiting the alimentary tracts of mammals, particularly those of herbivores, are estimated to be one of the densest microbial reservoirs on Earth. The significance of these gut microbes in influencing the physiology, ecology and evolution of their hosts is only beginning to be realized. To understand the microbiome of herbivores with a focus on nutritional ecology, while evaluating the roles of host evolution and environment in sculpting microbial diversity, we have developed an experimental system consisting of the microbial communities of several species of herbivorous woodrats (genus Neotoma) that naturally feed on a variety of dietary toxins. We designed this system to investigate the long-standing, but experimentally neglected hypothesis that ingestion of toxic diets by herbivores is facilitated by the gut microbiota. Like several other rodent species, the woodrat stomach has a sacculated, non-gastric foregut portion. We have documented a dense and diverse community of microbes in the woodrat foregut, with several genera potentially capable of degrading dietary toxins and/or playing a role in stimulating hepatic detoxification enzymes of the host. The biodiversity of these gut microbes appears to be a function of host evolution, ecological experience and diet, such that dietary toxins increase microbial diversity in hosts with experience with these toxins while novel toxins depress microbial diversity. These microbial communities are critical to the ingestion of a toxic diet as reducing the microbial community with antibiotics impairs the host's ability to feed on dietary toxins. Furthermore, the detoxification capacity of gut microbes can be transferred from Neotoma both intra and interspecifically to naïve animals that lack ecological and evolutionary history with these toxins. In addition to advancing our knowledge of complex host-microbes interactions, this system holds promise for identifying microbes that could be useful in the treatment of diseases in humans and domestic animals.
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Affiliation(s)
- Kevin D. Kohl
- Department of Biological Sciences, Vanderbilt University, NashvilleTN, USA
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Hervé V, Junier T, Bindschedler S, Verrecchia E, Junier P. Diversity and ecology of oxalotrophic bacteria. World J Microbiol Biotechnol 2016; 32:28. [PMID: 26748805 DOI: 10.1007/s11274-015-1982-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 11/16/2015] [Indexed: 11/27/2022]
Abstract
Oxalate is present in environments as diverse as soils or gastrointestinal tracts. This organic acid can be found as free acid or forming metal salts (e.g. calcium, magnesium). Oxalotrophy, the ability to use oxalate as carbon and energy sources, is mainly the result of bacterial catabolism, which can be either aerobic or anaerobic. Although some oxalotrophic bacterial strains are commonly used as probiotics, little is known about the diversity and ecology of this functional group. This review aims at exploring the taxonomic distribution and the phylogenetic diversity of oxalotrophic bacteria across biomes. In silico analyses were conducted using the two key enzymes involved in oxalotrophy: formyl-coenzyme A (CoA) transferase (EC 2.8.3.16) and oxalyl-CoA decarboxylase (EC 4.1.1.8), encoded by the frc and oxc genes, respectively. Our analyses revealed that oxalate-degrading bacteria are restricted to three phyla, namely Actinobacteria, Firmicutes and Proteobacteria and originated from terrestrial, aquatic and clinical environments. Diversity analyses at the protein level suggest that total Oxc diversity is more constrained than Frc diversity and that bacterial oxalotrophic diversity is not yet fully described. Finally, the contribution of oxalotrophic bacteria to ecosystem functioning as well as to the carbon cycle is discussed.
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Affiliation(s)
- Vincent Hervé
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Laboratory of Biogeosciences, Institute of Earth Sciences, University of Lausanne, Geopolis, 1015, Lausanne, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
- Vital-IT Group, Swiss Institute of Bioinformatics, Genopode, 1015, Lausanne, Switzerland
| | - Saskia Bindschedler
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Eric Verrecchia
- Laboratory of Biogeosciences, Institute of Earth Sciences, University of Lausanne, Geopolis, 1015, Lausanne, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland.
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Affiliation(s)
- Sungmi Choi
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Korea
| | - Sang-Heon Cho
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hana Yi
- Department of Public Health Sciences, Graduate School, Korea University, Seoul, Korea
- School of Biosystem and Biomedical Science, Korea University, Seoul, Korea
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46
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Peck AB, Canales BK, Nguyen CQ. Oxalate-degrading microorganisms or oxalate-degrading enzymes: which is the future therapy for enzymatic dissolution of calcium-oxalate uroliths in recurrent stone disease? Urolithiasis 2015; 44:45-50. [PMID: 26645869 DOI: 10.1007/s00240-015-0845-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/05/2015] [Indexed: 12/25/2022]
Abstract
Renal urolithiasis is a pathological condition common to a multitude of genetic, physiological and nutritional disorders, ranging from general hyperoxaluria to obesity. The concept of quickly dissolving renal uroliths via chemolysis, especially calcium-oxalate kidney stones, has long been a clinical goal, but yet to be achieved. Over the past 25 years, there has been a serious effort to examine the prospects of using plant and microbial oxalate-degrading enzymes known to catabolize oxalic acid and oxalate salts. While evidence is emerging that bacterial probiotics can reduce recurrent calcium-oxalate kidney stone disease by lowering systemic hyperoxaluria, the possible use of free oxalate-degrading enzyme therapy remains a challenge with several hurdles to overcome before reaching clinical practice.
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Affiliation(s)
- Ammon B Peck
- Department of Infectious Diseases and Pathology, University of Florida College of Veterinary Medicine, P.O Box 100125, VAB, Bldg 1017, Gainesville, FL, 32610, USA.
| | - Benjamin K Canales
- Department of Urology, University of Florida College of Medicine, P.O. Box 100247, 1600 SW Archer Rd, Gainesville, FL, 32610, USA
| | - Cuong Q Nguyen
- Department of Infectious Diseases and Pathology, University of Florida College of Veterinary Medicine, P.O Box 100125, VAB, Bldg 1017, Gainesville, FL, 32610, USA
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47
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Raditic DM. Complementary and Integrative Therapies for Lower Urinary Tract Diseases. Vet Clin North Am Small Anim Pract 2015; 45:857-78. [DOI: 10.1016/j.cvsm.2015.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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48
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Oxalic acid and diacylglycerol 36:3 are cross-species markers of sleep debt. Proc Natl Acad Sci U S A 2015; 112:2569-74. [PMID: 25675494 DOI: 10.1073/pnas.1417432112] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Sleep is an essential biological process that is thought to have a critical role in metabolic regulation. In humans, reduced sleep duration has been associated with risk for metabolic disorders, including weight gain, diabetes, obesity, and cardiovascular disease. However, our understanding of the molecular mechanisms underlying effects of sleep loss is only in its nascent stages. In this study we used rat and human models to simulate modern-day conditions of restricted sleep and addressed cross-species consequences via comprehensive metabolite profiling. Serum from sleep-restricted rats was analyzed using polar and nonpolar methods in two independent datasets (n = 10 per study, 3,380 measured features, 407 identified). A total of 38 features were changed across independent experiments, with the majority classified as lipids (18 from 28 identified). In a parallel human study, 92 metabolites were identified as potentially significant, with the majority also classified as lipids (32 of 37 identified). Intriguingly, two metabolites, oxalic acid and diacylglycerol 36:3, were robustly and quantitatively reduced in both species following sleep restriction, and recovered to near baseline levels after sleep restriction (P < 0.05, false-discovery rate < 0.2). Elevated phospholipids were also noted after sleep restriction in both species, as well as metabolites associated with an oxidizing environment. In addition, polar metabolites reflective of neurotransmitters, vitamin B3, and gut metabolism were elevated in sleep-restricted humans. These results are consistent with induction of peroxisome proliferator-activated receptors and disruptions of the circadian clock. The findings provide a potential link between known pathologies of reduced sleep duration and metabolic dysfunction, and potential biomarkers for sleep loss.
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Klimesova K, Whittamore JM, Hatch M. Bifidobacterium animalis subsp. lactis decreases urinary oxalate excretion in a mouse model of primary hyperoxaluria. Urolithiasis 2014; 43:107-17. [PMID: 25269440 DOI: 10.1007/s00240-014-0728-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/18/2014] [Indexed: 01/16/2023]
Abstract
Hyperoxaluria significantly increases the risk of calcium oxalate kidney stone formation. Since several bacteria have been shown to metabolize oxalate in vitro, including probiotic bifidobacteria, we focused on the efficiency and possible mechanisms by which bifidobacteria can influence oxalate handling in vivo, especially in the intestines, and compared these results with the reported effects of Oxalobacter formigenes. Bifidobacterium animalis subsp. lactis DSM 10140 and B. adolescentis ATCC 15703 were administered to wild-type (WT) mice and to mice deficient in the hepatic enzyme alanine-glyoxylate aminotransferase (Agxt(-/-), a mouse model of Primary Hyperoxaluria) that were fed an oxalate-supplemented diet. The administration of B. animalis subsp. lactis led to a significant decrease in urinary oxalate excretion in WT and Agxt(-/-) mice when compared to treatment with B. adolescentis. Detection of B. animalis subsp. lactis in feces revealed that 3 weeks after oral gavage with the bacteria 64% of WT mice, but only 37% of Agxt(-/-) mice were colonized. Examining intestinal oxalate fluxes showed there were no significant changes to net oxalate secretion in colonized animals and were therefore not associated with the changes in urinary oxalate excretion. These results indicate that colonization with B. animalis subsp. lactis decreased urinary oxalate excretion by degrading dietary oxalate thus limiting its absorption across the intestine but it did not promote enteric oxalate excretion as reported for O. formigenes. Preventive or therapeutic administration of B. animalis subsp. lactis appears to have some potential to beneficially influence dietary hyperoxaluria in mice.
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Affiliation(s)
- Klara Klimesova
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, 1600 SW Archer Road, Gainesville, FL, USA,
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50
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Carmody RN, Turnbaugh PJ. Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics. J Clin Invest 2014; 124:4173-81. [PMID: 25105361 DOI: 10.1172/jci72335] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Our associated microbial communities play a critical role in human health and predisposition to disease, but the degree to which they also shape therapeutic interventions is not well understood. Here, we integrate results from classic and current studies of the direct and indirect impacts of the gut microbiome on the metabolism of therapeutic drugs and diet-derived bioactive compounds. We pay particular attention to microbial influences on host responses to xenobiotics, adding to the growing consensus that treatment outcomes reflect our intimate partnership with the microbial world, and providing an initial framework from which to consider a more comprehensive view of pharmacology and nutrition.
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