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Defta CL, Albu CC, Albu ŞD, Bogdan-Andreescu CF. Oral Mycobiota: A Narrative Review. Dent J (Basel) 2024; 12:115. [PMID: 38668027 PMCID: PMC11049401 DOI: 10.3390/dj12040115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Numerous studies have proven the important role of the oral microbiota in health and disease. The dysfunctionality of the oral microbiota, known as dysbiosis, is incriminated in dental caries, periodontal disease, oral infectious diseases, oral cancer, and systemic disease. The lesser-known component of the oral microbiota, the mycobiota, is now assiduously investigated. Recent technological developments have helped foster the identification of new fungal species based on genomic research. Next-generation sequencing has expanded our knowledge about the diversity, architecture, and relationships of oral microorganisms within the oral cavity. The mycobiome structure and relationships with the bacteriome have been studied to identify a mycobiotic signature. This review aimed to emphasize the latest knowledge of the oral mycobiome.
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Affiliation(s)
- Carmen Liliana Defta
- Department of Microbiology, Faculty of Dentistry, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Cristina-Crenguţa Albu
- Department of Genetics, Faculty of Dentistry, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Ştefan-Dimitrie Albu
- Department of Periodontology, Faculty of Dentistry, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
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Makopa TP, Ncube T, Alwasel S, Boekhout T, Zhou N. Yeast-insect interactions in southern Africa: Tapping the diversity of yeasts for modern bioprocessing. Yeast 2024. [PMID: 38450792 DOI: 10.1002/yea.3935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Yeast-insect interactions are one of the most interesting long-standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect-derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern-day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.
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Affiliation(s)
- Tawanda P Makopa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Thembekile Ncube
- Department of Biology and Biochemistry, Faculty of Applied Science, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Saleh Alwasel
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Teun Boekhout
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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3
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Rizzello F, Viciani E, Gionchetti P, Filippone E, Imbesi V, Melotti L, Dussias NK, Salice M, Santacroce B, Padella A, Velichevskaya A, Marcante A, Castagnetti A. Signatures of disease outcome severity in the intestinal fungal and bacterial microbiome of COVID-19 patients. Front Cell Infect Microbiol 2024; 14:1352202. [PMID: 38510960 PMCID: PMC10952111 DOI: 10.3389/fcimb.2024.1352202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
Background COVID-19, whose causative pathogen is the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), was declared a pandemic in March 2020. The gastrointestinal tract is one of the targets of this virus, and mounting evidence suggests that gastrointestinal symptoms may contribute to disease severity. The gut-lung axis is involved in the immune response to SARS-CoV-2; therefore, we investigated whether COVID-19 patients' bacterial and fungal gut microbiome composition was linked to disease clinical outcome. Methods In May 2020, we collected stool samples and patient records from 24 hospitalized patients with laboratory-confirmed SARS-CoV-2 infection. Fungal and bacterial gut microbiome was characterized by amplicon sequencing on the MiSeq, Illumina's integrated next generation sequencing instrument. A cohort of 201 age- and sex-matched healthy volunteers from the project PRJNA661289 was used as a control group for the bacterial gut microbiota analysis. Results We observed that female COVID-19 patients had a lower gut bacterial microbiota richness than male patients, which was consistent with a different latency in hospital admittance time between the two groups. Both sexes in the COVID-19 patient study group displayed multiple positive associations with opportunistic bacterial pathogens such as Enterococcus, Streptococcus, and Actinomyces. Of note, the Candida genus dominated the gut mycobiota of COVID-19 patients, and adult patients showed a higher intestinal fungal diversity than elderly patients. We found that Saccharomycetales unassigned fungal genera were positively associated with bacterial short-chain fatty acid (SCFA) producers and negatively associated with the proinflammatory genus Bilophila in COVID-19 patients, and we observed that none of the patients who harbored it were admitted to the high-intensity unit. Conclusions COVID-19 was associated with opportunistic bacterial pathogens, and Candida was the dominant fungal taxon in the intestine. Together, we found an association between commensal SCFA-producers and a fungal genus that was present in the intestines of patients who did not experience the most severe outcome of the disease. We believe that this taxon could have played a role in the disease outcome, and that further studies should be conducted to understand the role of fungi in gastrointestinal and health protection.
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Affiliation(s)
- Fernando Rizzello
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | | | - Paolo Gionchetti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Eleonora Filippone
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Veronica Imbesi
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
| | - Laura Melotti
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Nikolas Konstantine Dussias
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
- Department of Medical and Surgical and Sciences, University of Bologna, Bologna, Italy
| | - Marco Salice
- IBD Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, University of Bologna, Bologna, Italy
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Sharma A, Ranout AS, Kaur R, Kumari P, Nadda G. Unearthing diverse culturable fungal communities associated with Ophiocordyceps indica sp. nov. from Indian Western Himalaya. J Basic Microbiol 2024; 64:e2300461. [PMID: 38115562 DOI: 10.1002/jobm.202300461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/04/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
Fungal communities colonizing Ophiocordyceps spp. plays a crucial ecological role in their natural habitat, contributing to infect the host larvae, and influencing their occurrence. Although associated fungi with the newly described Ophiocordyceps indica, from the Indian Western Himalaya remains unclear. Therefore, we untangled the culturable fungal communities associated with O. indica and soil adhered to it, collected from low-height areas of Himachal Pradesh, India. The study resulted in the identification of 111 fungal isolates representing 17 families, with maximum fungal isolates (36.03%) within Cordycipitaceae. Interestingly, a total of 24 genera were found associated with O. indica and adhered soil, of which 12 were common, 8 were exclusive to O. indica and 4 were only limited to soil. Additionally, the influence of soil physicochemical parameters on fungal diversity indices revealed a positive correlation with humidity and available nitrogen and a negative correlation with pH and available phosphorus. These findings provide insights into the culturable fungal diversity of O. indica and the soil adhering to it, thus can contribute to the understanding of host-microbial interactions. Furthermore, these associations can be explored as a source of bioactive metabolites to combat the unending industrial demands.
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Affiliation(s)
- Aakriti Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Entomology Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
| | - Aditya Singh Ranout
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Entomology Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
| | - Rupinder Kaur
- Entomology Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
| | - Pooja Kumari
- Entomology Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
| | - Gireesh Nadda
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Entomology Laboratory, Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (IHBT), Palampur, Himachal Pradesh, India
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5
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Rodriguez KA, Gurung M, Talatala R, Rearick JR, Ruebel ML, Stephens KE, Yeruva L. The Role of Early Life Gut Mycobiome on Child Health. Adv Nutr 2024; 15:100185. [PMID: 38311313 PMCID: PMC10907404 DOI: 10.1016/j.advnut.2024.100185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
The human gut microbiota is composed of bacteria (microbiota or microbiome), fungi (mycobiome), viruses, and archaea, but most of the research is primarily focused on the bacterial component of this ecosystem. Besides bacteria, fungi have been shown to play a role in host health and physiologic functions. However, studies on mycobiota composition during infancy, the factors that might shape infant gut mycobiota, and implications to child health and development are limited. In this review, we discuss the factors likely shaping gut mycobiota, interkingdom interactions, and associations with child health outcomes and highlight the gaps in our current knowledge of this ecosystem.
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Affiliation(s)
- Kayleigh Amber Rodriguez
- Arkansas Children's Research Institute, Little Rock, AR, United States; University of Arkansas for Medical Sciences, Department of Pediatrics, Division of Infectious Diseases, Little Rock, AR, United States
| | - Manoj Gurung
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Rachelanne Talatala
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States
| | - Jolene R Rearick
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Meghan L Ruebel
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States
| | - Kimberly E Stephens
- Arkansas Children's Research Institute, Little Rock, AR, United States; University of Arkansas for Medical Sciences, Department of Pediatrics, Division of Infectious Diseases, Little Rock, AR, United States.
| | - Laxmi Yeruva
- Microbiome and Metabolism Research Unit, United States Department of Agriculture, Agriculture Research Service, Little Rock, AR, United States; Arkansas Children's Nutrition Center, Little Rock, AR, United States.
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. Ascomycetes yeasts: The hidden part of human microbiome. WIREs Mech Dis 2024:e1641. [PMID: 38228159 DOI: 10.1002/wsbm.1641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/17/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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Baramidze V, Sella L, Japaridze T, Abashidze N, Lamazoshvili D, Dzotsenidze N, Tomashvili G. Long amplicon nanopore sequencing of Botrytis cinerea and other fungal species present in infected grapevine leaf samples. Biol Methods Protoc 2024; 9:bpad042. [PMID: 38229686 PMCID: PMC10789308 DOI: 10.1093/biomethods/bpad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/18/2023] [Indexed: 01/18/2024] Open
Abstract
Botrytis cinerea is a well-known plant pathogen responsible for grey mould disease infecting more than 500 plant species. It is listed as the second most important plant pathogen scientifically and economically. Its impact is particularly severe in grapes since it affects both the yield of grape berries and the quality of wines. While various methods for detecting B. cinerea have been investigated, the application of Oxford Nanopore Technology (ONT) for complete ribosomal operon sequencing, which has proven effective in human and animal fungal research and diagnostics, has not yet been explored in grapevine (Vitis vinifera) disease research. In this study, we sequenced complete ribosomal operons (∼5.5 kb amplicons), which encompass the 18S, ITS1, 5.8S, ITS2, and 28S regions, from both pure cultures of B. cinerea and infected grapevine leaf samples. Minimap2, a sequence alignment tool integrated into the EPI2ME software, served as a taxonomy classifier, utilizing the custom reference database FRODO. The results demonstrate that B. cinerea was detectable when this pathogen was not the dominant fungal species in leaf samples. Additionally, the method facilitates host DNA-free sequencing and might have a good potential to distinguish other pathogenic and non-pathogenic fungal species hosted within grapevine's infected leaves, such as Alternaria alternata, Saccharomyces cerevisiae, Saccharomyces boulardii, Mucor racemosus, and Ascochyta rabie. The sequences were uploaded to the NCBI database. Long amplicon sequencing method has the capacity to be broadened to other susceptible crops and pathogens, as a valuable tool for early grey rot detection and mycobiome research. Future large-scale studies are needed to overcome challenges, such as comprehensive reference databases for complete fungal ribosomal operons for grape mycobiome studies.
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Affiliation(s)
- Vladimer Baramidze
- Department of Plant Protection, , Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi 0159, Georgia
| | - Luca Sella
- Department of Land, Environment, Agriculture and Forestry, University of Padua, Padova, Italy
| | - Tamar Japaridze
- Department of Plant Protection, , Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi 0159, Georgia
| | - Nino Abashidze
- Department of Plant Protection, , Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi 0159, Georgia
| | - Daviti Lamazoshvili
- Department of Plant Protection, , Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi 0159, Georgia
| | - Nino Dzotsenidze
- Department of Plant Protection, , Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi 0159, Georgia
| | - Giorgi Tomashvili
- Department of Virology and Molecular Biology, National Center for Disease Control and Public Health (NCDC), Tbilisi 0198, Georgia
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Roy S, Ray D, Laha I, Choudhury L. Human Mycobiota and Its Role in Cancer Progression, Diagnostics and Therapeutics: A Link Lesser-Known. Cancer Invest 2024; 42:44-62. [PMID: 38186047 DOI: 10.1080/07357907.2024.2301733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/01/2024] [Indexed: 01/09/2024]
Abstract
Although not as well studied as the bacterial component of the human microbiota, the commensal fungi or mycobiota play important roles in maintaining our health by augmenting our immune system. This mycobiota is also associated with various fatal diseases like opportunistic mycoses, and even cancer, with different cancers having respective type-specific mycobiota. The different fungal species which comprise these different intratumoral mycobiota play important roles in cancer progression. The aim of this review paper is to decipher the association between mycobiota and cancer, and shed light on new avenues in cancer diagnosis, and the development of new anti-cancer therapeutics.
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Affiliation(s)
- Souvik Roy
- Post-Graduate & Research Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, India
| | - Dhrisaj Ray
- 5th Year Integrated M. Sc. (5 year integrated) students, Post-Graduate & Research Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, India
| | - Ishani Laha
- 5th Year Integrated M. Sc. (5 year integrated) students, Post-Graduate & Research Department of Biotechnology, St. Xavier's College (Autonomous), Kolkata, India
| | - Lopamudra Choudhury
- State-Aided College Teacher, Department of Microbiology, Sarsuna College (Affiliated to Calcutta University), Kolkata, India
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Sadek A, Taminiau B, Daube G, Sapountzis P, Chaucheyras-Durand F, Castex M, Coucheney F, Drider D. Impact of Dietary Regime and Seasonality on Hindgut's Mycobiota Diversity in Dairy Cows. Microorganisms 2023; 12:84. [PMID: 38257911 PMCID: PMC10820462 DOI: 10.3390/microorganisms12010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
We describe and discuss the intestinal mycobiota of dairy cows reared in France following variations in dietary regimes and two seasons. Two groups of 21 animals were followed over a summer and winter period, and another group of 28 animals was followed only during the same summer season. The summer diet was based on grazing supplemented with 3-5 kg/d of maize, grass silage and hay, while the winter diet consisted of 30% maize silage, 25% grass silage, 15% hay and 30% concentrate. A total of 69 DNA samples were extracted from the feces of these cows. Amplification and sequencing of the ITS2 region were used to assess mycobiota diversity. Analyses of alpha and beta diversity were performed and compared statistically. The mycobiota changed significantly from summer to winter conditions with a decrease in its diversity, richness and evenness parameters, while beta diversity analysis showed different mycobiota profiles. Of note, the Geotrichum operational taxonomic unit (OTU) was prevalent in the winter group, with a mean relative abundance (RA) of 65% of the total mycobiota. This Geotrichum OTU was also found in the summer group, but to a lesser extent (5%). In conclusion, a summer grazing diet allowed a higher fecal fungal diversity. These data show, for the first time, that a change in diet associated with seasonality plays a central role in shaping hindgut fungal diversity.
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Affiliation(s)
- Ali Sadek
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Bernard Taminiau
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Fundamental and Applied Research for Animal & Health (FARAH), Veterinary Medicine Faculty, Department of Food Sciences, University of Liège, 4000 Liège, Belgium
| | - Georges Daube
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
- Fundamental and Applied Research for Animal & Health (FARAH), Veterinary Medicine Faculty, Department of Food Sciences, University of Liège, 4000 Liège, Belgium
| | - Panagiotis Sapountzis
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France;
| | - Frédérique Chaucheyras-Durand
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
- Université Clermont Auvergne, INRAE, UMR 0454 MEDIS, 63000 Clermont-Ferrand, France;
| | - Mathieu Castex
- Lallemand SAS, 19 Rue des Briquetiers, 31702 Blagnac, France
| | - Françoise Coucheney
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
| | - Djamel Drider
- Unité Mixte de Recherche (UMR) Transfrontalière BioEcoAgro 1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte D’Opale, ICV—Institut Charles Viollette, 59000 Lille, France (B.T.); (G.D.)
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10
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Nenciarini S, Renzi S, di Paola M, Meriggi N, Cavalieri D. The yeast-human coevolution: Fungal transition from passengers, colonizers, and invaders. WIREs Mech Dis 2023:e1639. [PMID: 38146626 DOI: 10.1002/wsbm.1639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/27/2023]
Abstract
Fungi are the cause of more than a billion infections in humans every year, although their interactions with the host are still neglected compared to bacteria. Major systemic fungal infections are very unusual in the healthy population, due to the long history of coevolution with the human host. Humans are routinely exposed to environmental fungi and can host a commensal mycobiota, which is increasingly considered as a key player in health and disease. Here, we review the current knowledge on host-fungi coevolution and the factors that regulate their interaction. On one hand, fungi have learned to survive and inhabit the host organisms as a natural ecosystem, on the other hand, the host immune system finely tunes the response toward fungi. In turn, recognition of fungi as commensals or pathogens regulates the host immune balance in health and disease. In the human gut ecosystem, yeasts provide a fingerprint of the transient microbiota. Their status as passengers or colonizers is related to the integrity of the gut barrier and the risk of multiple disorders. Thus, the study of this less known component of the microbiota could unravel the rules of the transition from passengers to colonizers and invaders, as well as their dependence on the innate component of the host's immune response. This article is categorized under: Infectious Diseases > Environmental Factors Immune System Diseases > Environmental Factors Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
| | - Sonia Renzi
- Department of Biology, University of Florence, Florence, Italy
| | - Monica di Paola
- Department of Biology, University of Florence, Florence, Italy
| | - Niccolò Meriggi
- Department of Biology, University of Florence, Florence, Italy
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11
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Delavy M, Sertour N, Patin E, Le Chatelier E, Cole N, Dubois F, Xie Z, Saint-André V, Manichanh C, Walker AW, Quintana-Murci L, Duffy D, d’Enfert C, Bougnoux ME, Consortium MI. Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response. Gut Microbes 2023; 15:2287618. [PMID: 38017705 PMCID: PMC10732203 DOI: 10.1080/19490976.2023.2287618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
Candida albicans is a commensal yeast present in the gut of most healthy individuals but with highly variable concentrations. However, little is known about the host factors that influence colonization densities. We investigated how microbiota, host lifestyle factors, and genetics could shape C. albicans intestinal carriage in 695 healthy individuals from the Milieu Intérieur cohort. C. albicans intestinal carriage was detected in 82.9% of the subjects using quantitative PCR. Using linear mixed models and multiway-ANOVA, we explored C. albicans intestinal levels with regard to gut microbiota composition and lifestyle factors including diet. By analyzing shotgun metagenomics data and C. albicans qPCR data, we showed that Intestinimonas butyriciproducens was the only gut microbiota species whose relative abundance was negatively correlated with C. albicans concentration. Diet is also linked to C. albicans growth, with eating between meals and a low-sodium diet being associated with higher C. albicans levels. Furthermore, by Genome-Wide Association Study, we identified 26 single nucleotide polymorphisms suggestively associated with C. albicans colonization. In addition, we found that the intestinal levels of C. albicans might influence the host immune response, specifically in response to fungal challenge. We analyzed the transcriptional levels of 546 immune genes and the concentration of 13 cytokines after whole blood stimulation with C. albicans cells and showed positive associations between the extent of C. albicans intestinal levels and NLRP3 expression, as well as secreted IL-2 and CXCL5 concentrations. Taken together, these findings open the way for potential new interventional strategies to curb C. albicans intestinal overgrowth.
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Affiliation(s)
- Margot Delavy
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Natacha Sertour
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | | | - Nathaniel Cole
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Florian Dubois
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
| | - Zixuan Xie
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
| | - Violaine Saint-André
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Bioinformatics and Biostatistics HUB, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Chaysavanh Manichanh
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
| | - Alan W. Walker
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
| | - Darragh Duffy
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
| | - Christophe d’Enfert
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
| | - Marie-Elisabeth Bougnoux
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
- APHP, Hôpital Necker-Enfants-Malades, Service de Microbiologie Clinique, Unité de Parasitologie-Mycologie, Paris, France
| | - Milieu Intérieur Consortium
- Unité Biologie et Pathogénicité Fongiques, Institut Pasteur, Université Paris Cité INRAE, Paris, France
- Human Evolutionary Genetics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR2000, Paris, France
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy-en-Josas, France
- The Rowett Institute, University of Aberdeen, Aberdeen, UK
- Translational Immunology Unit, Institut Pasteur, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CBUTechS, Paris, France
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Vall d’Hebron Barcelona Hospital Campus, Gut Microbiome Group, Barcelona, Spain
- Bioinformatics and Biostatistics HUB, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Paris, France
- APHP, Hôpital Necker-Enfants-Malades, Service de Microbiologie Clinique, Unité de Parasitologie-Mycologie, Paris, France
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12
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Lederer AK, Rasel H, Kohnert E, Kreutz C, Huber R, Badr MT, Dellweg PKE, Bartsch F, Lang H. Gut Microbiota in Diagnosis, Therapy and Prognosis of Cholangiocarcinoma and Gallbladder Carcinoma-A Scoping Review. Microorganisms 2023; 11:2363. [PMID: 37764207 PMCID: PMC10538110 DOI: 10.3390/microorganisms11092363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/09/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Cancers of the biliary tract are more common in Asia than in Europe, but are highly lethal due to delayed diagnosis and aggressive tumor biology. Since the biliary tract is in direct contact with the gut via the enterohepatic circulation, this suggests a potential role of gut microbiota, but to date, the role of gut microbiota in biliary tract cancers has not been elucidated. This scoping review compiles recent data on the associations between the gut microbiota and diagnosis, progression and prognosis of biliary tract cancer patients. Systematic review of the literature yielded 154 results, of which 12 studies and one systematic review were eligible for evaluation. The analyses of microbiota diversity indices were inconsistent across the included studies. In-depth analyses revealed differences between gut microbiota of biliary tract cancer patients and healthy controls, but without a clear tendency towards particular species in the studies. Additionally, most of the studies showed methodological flaws, for example non-controlling of factors that affect gut microbiota. At the current stage, there is a lack of evidence to support a general utility of gut microbiota diagnostics in biliary tract cancers. Therefore, no recommendation can be made at this time to include gut microbiota analyses in the management of biliary tract cancer patients.
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Affiliation(s)
- Ann-Kathrin Lederer
- Department of General, Visceral and Transplant Surgery, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Hannah Rasel
- Department of General, Visceral and Transplant Surgery, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Eva Kohnert
- Institute of Medical Biometry and Statistics (IMBI), Faculty of Medicine and Medical Center, University of Freiburg, 79104 Freiburg, Germany
| | - Clemens Kreutz
- Institute of Medical Biometry and Statistics (IMBI), Faculty of Medicine and Medical Center, University of Freiburg, 79104 Freiburg, Germany
| | - Roman Huber
- Center for Complementary Medicine, Department of Medicine II, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Mohamed Tarek Badr
- Institute of Medical Microbiology and Hygiene, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany;
| | - Patricia K. E. Dellweg
- Department of General, Visceral and Transplant Surgery, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Fabian Bartsch
- Department of General, Visceral and Transplant Surgery, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
| | - Hauke Lang
- Department of General, Visceral and Transplant Surgery, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany
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Orieux A, Enaud R, Imbert S, Boyer P, Begot E, Camino A, Boyer A, Berger P, Gruson D, Delhaes L, Prevel R. The gut microbiota composition is linked to subsequent occurrence of ventilator-associated pneumonia in critically ill patients. Microbiol Spectr 2023; 11:e0064123. [PMID: 37713505 PMCID: PMC10581192 DOI: 10.1128/spectrum.00641-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 07/26/2023] [Indexed: 09/17/2023] Open
Abstract
Ventilator-associated pneumonia (VAP) is the most frequent nosocomial infection in critically ill-ventilated patients. Oropharyngeal and lung microbiota have been demonstrated to be associated with VAP occurrence, but the involvement of gut microbiota has not been investigated so far. Therefore, the aim of this study is to compare the composition of the gut microbiota between patients who subsequently develop VAP and those who do not. A rectal swab was performed at admission of every consecutive patient into the intensive care unit (ICU) from October 2019 to March 2020. After DNA extraction, V3-V4 and internal transcribed spacer 2 regions deep-sequencing was performed on MiSeq sequencer (Illumina) and data were analyzed using Divisive Amplicon Denoising Algorithm 2 (DADA2) pipeline. Among 255 patients screened, 42 (16%) patients with invasive mechanical ventilation for more than 48 h were included, 18 (43%) with definite VAP and 24 without (57%). Patients who later developed VAP had similar gut bacteriobiota and mycobiota α-diversities compared to those who did not develop VAP. However, gut mycobiota was dissimilar (β-diversity) between these two groups. The presence of Megasphaera massiliensis was associated with the absence of VAP occurrence, whereas the presence of the fungal genus Alternaria sp. was associated with the occurrence of VAP. The composition of the gut microbiota, but not α-diversity, differs between critically ill patients who subsequently develop VAP and those who do not. This study encourages large multicenter cohort studies investigating the role of gut-lung axis and oropharyngeal colonization in the development of VAP in ICU patients. Trial registration number: NCT04131569, date of registration: 18 October 2019. IMPORTANCE The composition of the gut microbiota, but not α-diversity, differs between critically ill patients who subsequently develop ventilator-associated pneumonia (VAP) and those who do not. Investigating gut microbiota composition could help to tailor probiotics to provide protection against VAP.
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Affiliation(s)
- Arthur Orieux
- CHU Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Raphaël Enaud
- Univ Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Bordeaux, France
- CHU Bordeaux, CRCM Pédiatrique, Bordeaux, France
| | - Sébastien Imbert
- Univ Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Bordeaux, France
- Mycology-Parasitology Department, CHU Bordeaux, Bordeaux, France
| | - Philippe Boyer
- CHU Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Erwan Begot
- CHU Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Adrian Camino
- Univ Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Bordeaux, France
| | - Alexandre Boyer
- CHU Bordeaux, Medical Intensive Care Unit, Bordeaux, France
- Univ Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Bordeaux, France
| | - Patrick Berger
- Univ Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Bordeaux, France
| | - Didier Gruson
- CHU Bordeaux, Medical Intensive Care Unit, Bordeaux, France
- Univ Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Bordeaux, France
| | - Laurence Delhaes
- Univ Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Bordeaux, France
- Mycology-Parasitology Department, CHU Bordeaux, Bordeaux, France
| | - Renaud Prevel
- CHU Bordeaux, Medical Intensive Care Unit, Bordeaux, France
- Univ Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, Inserm UMR 1045, Bordeaux, France
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14
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Lussac-Sorton F, Charpentier É, Imbert S, Lefranc M, Bui S, Fayon M, Berger P, Enaud R, Delhaes L. The gut-lung axis in the CFTR modulator era. Front Cell Infect Microbiol 2023; 13:1271117. [PMID: 37780857 PMCID: PMC10540301 DOI: 10.3389/fcimb.2023.1271117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
The advent of CFTR modulators represents a turning point in the history of cystic fibrosis (CF) management, changing profoundly the disease's clinical course by improving mucosal hydration. Assessing changes in airway and digestive tract microbiomes is of great interest to better understand the mechanisms and to predict disease evolution. Bacterial and fungal dysbiosis have been well documented in patients with CF; yet the impact of CFTR modulators on microbial communities has only been partially deciphered to date. In this review, we aim to summarize the current state of knowledge regarding the impact of CFTR modulators on both pulmonary and digestive microbiomes. Our analysis also covers the inter-organ connections between lung and gut communities, in order to highlight the gut-lung axis involvement in CF pathophysiology and its evolution in the era of novel modulators therapies.
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Affiliation(s)
- Florian Lussac-Sorton
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
| | - Éléna Charpentier
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
| | - Sébastien Imbert
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Maxime Lefranc
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Stéphanie Bui
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Michael Fayon
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Patrick Berger
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Raphaël Enaud
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
| | - Laurence Delhaes
- Univ. Bordeaux, Centre de Recherche Cardio-Thoracique de Bordeaux, INSERM U1045, Pessac, France
- INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, Pessac, France
- CHU Bordeaux, Service de Parasitologie et Mycologie, Centre de Ressources et de Compétences de la Mucoviscidose (CRCM), Service de Pédiatrie, Service d’Exploration Fonctionnelle Respiratoire, CIC, Bordeaux, France
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15
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Reinoso S, Gutiérrez MS, Reyes-Jara A, Toro M, García K, Reyes G, Argüello-Guevara W, Bohórquez-Cruz M, Sonnenholzner S, Navarrete P. Feed Regime Slightly Modifies the Bacterial but Not the Fungal Communities in the Intestinal Mucosal Microbiota of Cobia Fish ( Rachycentron canadum). Microorganisms 2023; 11:2315. [PMID: 37764158 PMCID: PMC10535204 DOI: 10.3390/microorganisms11092315] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
The bacterial community of the intestinal microbiota influences many host functions, and similar effects have been recently reported for the fungal community (mycobiota). Cobia is a tropical fish that has been studied for its potential in marine aquaculture. However, the study of its bacterial community has been underreported and the mycobiota has not been investigated. We analyzed the gut bacterial and fungal profile present in the intestinal mucosa of reared adult cobias fed two diets (frozen fish pieces (FFPs) and formulated feed (FF)) for 4 months by sequencing the 16S rRNA (V3-V4) and internal transcribed spacer-2 (ITS2) regions using Illumina NovaSeq 6000. No significant differences in the alpha diversity of the bacterial community were observed, which was dominated by the phyla Proteobacteria (~96%) and Firmicutes (~1%). Cobia fed FF showed higher abundance of 10 genera, mainly UCG-002 (Family Oscillospiraceae) and Faecalibacterium, compared to cobia fed FFPs, which showed higher abundance of 7 genera, mainly Methylobacterium-Methylorubrum and Cutibacterium. The inferred bacterial functions were related to metabolism, environmental information processing and cellular processes; and no differences were found between diets. In mycobiota, no differences were observed in the diversity and composition of cobia fed the two diets. The mycobiota was dominated by the phyla Ascomycota (~88%) and Basidiomycota (~11%). This is the first study to describe the gut bacterial and fungal communities in cobia reared under captive conditions and fed on different diets and to identify the genus Ascobulus as a new member of the core fish mycobiota.
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Affiliation(s)
- Samira Reinoso
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology (INTA), University of Chile, Avenida El Libano 5524, Macul, Santiago 7830490, Chile; (M.S.G.); (A.R.-J.); (M.T.)
- Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Escuela Superior Politécnica del Litoral, ESPOL Polytechnic University, Guayaquil 090211, Ecuador; (G.R.); (W.A.-G.); (M.B.-C.); (S.S.)
| | - María Soledad Gutiérrez
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology (INTA), University of Chile, Avenida El Libano 5524, Macul, Santiago 7830490, Chile; (M.S.G.); (A.R.-J.); (M.T.)
| | - Angélica Reyes-Jara
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology (INTA), University of Chile, Avenida El Libano 5524, Macul, Santiago 7830490, Chile; (M.S.G.); (A.R.-J.); (M.T.)
- Millenium Institute Center for Genome Regulation (CRG), Santiago 8331150, Chile
| | - Magaly Toro
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology (INTA), University of Chile, Avenida El Libano 5524, Macul, Santiago 7830490, Chile; (M.S.G.); (A.R.-J.); (M.T.)
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland, College Park, MD 20910, USA
| | - Katherine García
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8900000, Chile;
| | - Guillermo Reyes
- Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Escuela Superior Politécnica del Litoral, ESPOL Polytechnic University, Guayaquil 090211, Ecuador; (G.R.); (W.A.-G.); (M.B.-C.); (S.S.)
| | - Wilfrido Argüello-Guevara
- Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Escuela Superior Politécnica del Litoral, ESPOL Polytechnic University, Guayaquil 090211, Ecuador; (G.R.); (W.A.-G.); (M.B.-C.); (S.S.)
- Facultad de Ingeniería Marítima y Ciencias del Mar, FIMCM, Escuela Superior Politécnica del Litoral, ESPOL Polytechnic University, Guayaquil 090211, Ecuador
| | - Milton Bohórquez-Cruz
- Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Escuela Superior Politécnica del Litoral, ESPOL Polytechnic University, Guayaquil 090211, Ecuador; (G.R.); (W.A.-G.); (M.B.-C.); (S.S.)
| | - Stanislaus Sonnenholzner
- Centro Nacional de Acuicultura e Investigaciones Marinas, CENAIM, Escuela Superior Politécnica del Litoral, ESPOL Polytechnic University, Guayaquil 090211, Ecuador; (G.R.); (W.A.-G.); (M.B.-C.); (S.S.)
- Facultad de Ingeniería Marítima y Ciencias del Mar, FIMCM, Escuela Superior Politécnica del Litoral, ESPOL Polytechnic University, Guayaquil 090211, Ecuador
| | - Paola Navarrete
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology (INTA), University of Chile, Avenida El Libano 5524, Macul, Santiago 7830490, Chile; (M.S.G.); (A.R.-J.); (M.T.)
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Ansari L, Asgari B, Zare R, Zamanizadeh HR. Penicillium rhizophilum, a novel species in the section Exilicaulis isolated from the rhizosphere of sugarcane in Southwest Iran. Int J Syst Evol Microbiol 2023; 73. [PMID: 37676702 DOI: 10.1099/ijsem.0.006028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
During a survey of species diversity of Penicillium and Talaromyces in sugarcane (Saccharum officinarum) rhizosphere in the Khuzestan province of Iran [1], 195 strains were examined, from which 187 belonged to Penicillium (11 species) and eight to Talaromyces (one species). In the present study, three strains of Penicillium belonging to section Exilicaulis series Restricta, identified as P. restrictum by Ansari et al. [1], were subjected to a phylogenetic study. The multilocus phylogeny of partial β-tubulin, calmodulin and RNA polymerase II second largest subunit genes enabled the recognition of one new phylogenetic species that is here formally described as Penicillium rhizophilum sp. nov. This species is phylogenetically distinct in series Restricta, but it does not show significant morphological differences from other species previously classified in the series. Therefore, we here placed bias on the phylogenetic species concept. The holotype of Penicillium rhizophilum sp. nov. is IRAN 18169F and the ex-type culture is LA30T (=IRAN 4042CT=CBS 149737T).
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Affiliation(s)
- Laleh Ansari
- Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Bita Asgari
- Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Rasoul Zare
- Department of Botany, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
| | - Hamid Reza Zamanizadeh
- Department of Plant Protection, Science and Research Branch, Islamic Azad University, Tehran, Iran
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17
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Luo J, Walsh E, Groben G, Justiniano B, Zhang N. Larger presence of ectomycorrhizae detected from pygmy pine ecotype in the fire-frequent pine barrens ecosystem. Mycologia 2023; 115:602-613. [PMID: 37561445 DOI: 10.1080/00275514.2023.2234269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 07/05/2023] [Indexed: 08/11/2023]
Abstract
Pine barrens ecosystem has acidic, sandy, and nutrient-poor soil and is prone to drought and fire. In the New Jersey Pine Barrens, the predominant pitch pine (Pinus rigida) consists of two ecotypes: the regular pitch pines with heights of 4.6-12 m, and the pygmy pines of low stature (1.2-1.8 m) in the New Jersey Pine Plains. Previous ecological studies suggested that the dwarf pines in the Pine Plains that are embedded within the Pine Barrens were an evolutionary adaptation to frequent fire. Pines are obligate ectomycorrhizal (EcM) mutualists, and their root mycobiota may contribute to stress protection and plant health. However, information on the mycobiota associated with plants in the pine barrens ecosystem is lacking. To have a holistic understanding of the evolution and adaptation in this stressed environment, we used both culture-independent metabarcoding and culture-based method to characterize the mycobiota from soil and root of the two ecotypes and to identify core mycobiota. We found that Agaricomycetes, Leotiomycetes, and Mucoromycotina are predominant fungi in the New Jersey Pine Barrens ecosystem, which is rich in root mutualistic fungi. We observed that the pygmy pine roots had significantly higher density of EcM tips than the regular pine roots. This was corroborated by our metabarcoding analysis, which showed that the pygmy pine trees had higher ratio of ectomycorrhiza-forming fungi than the regular-statured pines. We hypothesize that symbiotrophic EcM fungi associated with pygmy pines are capable of mitigating high fire stress in the Pine Plains.
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Affiliation(s)
- Jing Luo
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
| | - Emily Walsh
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
| | - Glen Groben
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
| | - Brandon Justiniano
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, 59 Dudley Road, New Brunswick, New Jersey, 08901
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, New Jersey, 08901
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18
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Finne CK. Mycobiota of Potato-Cereal Soft Wraps and the Production Facility. Foods 2023; 12:3238. [PMID: 37685171 PMCID: PMC10486551 DOI: 10.3390/foods12173238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The aim of this study was to investigate the mycobiota of potato-cereal soft wraps and in the processing area. Potato-cereal soft wraps are cooked, cold-stored and mashed potatoes that are kneaded together, usually with wheat flour, to form dough. In order to identify the main spoilage mould of this product, 150 visible mould colonies from mouldy wraps were identified. Five different mould species were isolated; Aspergillus niger, Penicillium brevicompactum, Penicillium commune, Penicllium corylophilum and Pencillium discolor. The dominating spoilage mould was Penicillium commune with 83.9% of the colonies. In order to study the mycobiota of the production area, 271 samples of air and surfaces were collected. In total, 647 mould colonies were isolated from air and surface samples. The mycobiota of air consisted of 27 different species within 9 different genera, and the mycobiota of surfaces consisted of 14 species within 4 different genera. Penicllium species were the dominating genera both in air and on surfaces, and Penicillium commune was the dominating species in the processing environment as well. Penicillium commune was found in the bakery and also in other production rooms. Spores from the flour and from soil on potatoes can disperse in the air as aerosols and may contaminate the wraps after baking when the product is cooled before packaging.
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Affiliation(s)
- Cathrine Kure Finne
- Nofima-Norwegian Institute of Food, Fisheries and Aquaculture Research, P.O. Box 210, N-1431 Ås, Norway
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19
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Spatz M, Wang Y, Lapiere A, Da Costa G, Michaudel C, Danne C, Michel ML, Langella P, Sokol H, Richard ML. Saccharomyces boulardii CNCM I-745 supplementation during and after antibiotic treatment positively influences the bacterial gut microbiota. Front Med (Lausanne) 2023; 10:1087715. [PMID: 37601783 PMCID: PMC10436532 DOI: 10.3389/fmed.2023.1087715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/04/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Antibiotic effects on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the mycobiota, the fungal part of the microbiota and how the length of administration influences both microbiota. Here, we examined the effect of antibiotics (ATB) on the composition of bacterial and fungal microbiota and how the administration of Saccharomyces boulardii CNCM I-745 influences both microbiota. Methods In order to get closer to the human microbiota, the mice used in this study were subjected to fecal microbiota transfer (FMT) using human feces and subsequently called human microbiotaassociated (HMA) mice. These mice were then treated with amoxicillinclavulanate antibiotics and supplemented with S. boulardii during and after ATB treatment to understand the effect of the yeast probiotic on both bacterial and fungal microbiota. Bacterial and fungal microbiota analyses were done using 16S and ITS2 rRNA amplicon-based sequencing. Results We showed that the administration of S. boulardii during ATB treatment had very limited effect on the fungal populations on the long term, once the yeast probiotic has been cleared from the gut. Concerning bacterial microbiota, S. boulardii administration allowed a better recovery of bacterial populations after the end of the ATB treatment period. Additionally, 16S and ITS2 rRNA sequence analysis revealed that 7 additional days of S. boulardii administration (17 days in total) enhanced the return of the initial bacterial equilibrium. Discussion In this study, we provide a comprehensive analysis of how probiotic yeast administration can influence the fungal and bacterial microbiota in a model of broad-spectrum antibiotherapy.
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Affiliation(s)
- Madeleine Spatz
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Yazhou Wang
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Alexia Lapiere
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Gregory Da Costa
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Chloé Michaudel
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Camille Danne
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- INSERM UMRS-938, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Sorbonne Université, Paris, France
| | - Marie-Laure Michel
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Philippe Langella
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
| | - Harry Sokol
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- INSERM UMRS-938, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Sorbonne Université, Paris, France
| | - Mathias L. Richard
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, Jouy-en-Josas, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
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20
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Perlin CM, Longo L, Keingeski MB, Picon RV, Álvares-da-Silva MR. Gut mycobiota changes in liver diseases: A systematic review. Med Mycol 2023; 61:myad071. [PMID: 37463798 DOI: 10.1093/mmy/myad071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 07/20/2023] Open
Abstract
Intestinal fungi play an important role in the health-disease process. We observed that in liver diseases, fungal infections lead to high mortality. In this review, we were able to gather and evaluate the available scientific evidence on intestinal mycobiota and liver diseases. We searched PubMed and Embase, using a combination of several entry terms. Only studies in adults ≥ 18 years old with liver disease and published after 2010 were included. We observed that individuals with liver disease have an altered intestinal mycobioma, which accompanies the progression of these diseases. In cirrhotic patients, there are a high number of Candida sp. strains, especially Candida albicans. In early chronic liver disease, there is an increase in alpha diversity at the expense of Candida sp. and conversely, in advanced liver disease, there is a negative correlation between alpha diversity and model for end-stage liver disease score. On the other hand, patients with non-alcoholic fatty liver disease demonstrate greater diversity compared to controls. Our study concluded that the evidence on the subject is sparse, with few studies and a lack of standardization of outcome measures and reporting, and it was not possible to perform a meta-analysis capable of synthesizing relevant parameters of the human mycobiotic profile. However, certain fungal genera such as Candida play an important role in the context of liver disease and that adults with liver disease have a distinct gut mycobiotic profile from healthy controls.
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Affiliation(s)
- Cássio Marques Perlin
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- Experimental Laboratory of Hepatology and Gastroenterology, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Larisse Longo
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- Experimental Laboratory of Hepatology and Gastroenterology, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Melina Belén Keingeski
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- Experimental Laboratory of Hepatology and Gastroenterology, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Rafael V Picon
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- School of Medicine, Department of Internal Medicine, Universidade Federal do Rio Grande do Sul; Division of Gastroenterology, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
| | - Mário Reis Álvares-da-Silva
- Graduate Program in Gastroenterology and Hepatology, Universidade Federal do Rio Grande do Sul, Porto Alegre, 90035-002, Brazil
- Experimental Laboratory of Hepatology and Gastroenterology, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
- School of Medicine, Department of Internal Medicine, Universidade Federal do Rio Grande do Sul; Division of Gastroenterology, Hospital de Clínicas de Porto Alegre, Porto Alegre, 90035-903, Brazil
- CNPq researcher
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21
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Pulcini L, Bona E, Vaudano ET, Tsolakis C, Garcia-Moruno E, Costantini A, Gamalero E. The Impact of a Commercial Biostimulant on the Grape Mycobiota of Vitis vinifera cv. Barbera. Microorganisms 2023; 11:1873. [PMID: 37630432 PMCID: PMC10457965 DOI: 10.3390/microorganisms11081873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/22/2023] [Accepted: 07/23/2023] [Indexed: 08/27/2023] Open
Abstract
Reducing the use of fungicides, insecticides, and herbicides in order to limit environmental pollution and health risks for agricultural operators and consumers is one of the goals of European regulations. In fact, the European Commission developed a package of measures (the European Green Deal) to promote the sustainable use of natural resources and strengthen the resilience of European agri-food systems. As a consequence, new plant protection products, such as biostimulants, have been proposed as alternatives to agrochemicals. Their application in agroecosystems could potentially open new scenarios regarding the microbiota. In particular, the vineyard microbiota and the microbiota on the grape surface can be affected by biostimulants and lead to different wine features. The aim of this work was to assess the occurrence of a possible variation in the mycobiota due to the biostimulant application. Therefore, our attention has been focused on the yeast community of grape bunches from vines subjected to the phytostimulant BION®50WG treatment. This work was carried out in the CREA-VE experimental vineyard of Vitis vinifera cv. Barbera in Asti (Piedmont, Italy). The composition of fungal communities on grapes from three experimental conditions such as IPM (integrated pest management), IPM+BION®50WG, and IPM+water foliar nebulization was compared by a metabarcoding approach. Our results revealed the magnitude of alpha and beta diversity, and the microbial biodiversity index and specific fungal signatures were highlighted by comparing the abundance of yeast and filamentous fungi in IPM and BION®50WG treatments. No significant differences in the mycobiota of grapevines subjected to the three treatments were detected.
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Affiliation(s)
- Laura Pulcini
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
| | - Elisa Bona
- Dipartimento per lo Sviluppo Sostenibile e la Transizione Ecologica (DISSTE), Università del Piemonte Orientale, Piazza San Eusebio 5, 13100 Vercelli, Italy;
| | - Enrico Tommaso Vaudano
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Christos Tsolakis
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Emilia Garcia-Moruno
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Antonella Costantini
- Consiglio per la Ricerca e l’analisi dell’Economia Agraria—Centro di Ricerca Viticoltura ed Enologia (CREA-VE), Via P. Micca 35, 14100 Asti, Italy; (E.T.V.); (C.T.); (E.G.-M.)
| | - Elisa Gamalero
- Dipartimento di Scienze e Innovazione Tecnologica (DISIT), Università del Piemonte Orientale, Viale T. Michel 11, 15121 Alessandria, Italy;
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22
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Dos Reis JBA, Pappas Junior GJ, Lorenzi AS, Pinho DB, Costa AM, Bustamante MMDC, Vale HMMD. How Deep Can the Endophytic Mycobiome Go? A Case Study on Six Woody Species from the Brazilian Cerrado. J Fungi (Basel) 2023; 9:jof9050508. [PMID: 37233219 DOI: 10.3390/jof9050508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/27/2023] Open
Abstract
Elucidating the complex relationship between plants and endophytic fungi is very important in order to understand the maintenance of biodiversity, equity, stability, and ecosystem functioning. However, knowledge about the diversity of endophytic fungi from species of the native Brazilian Cerrado biome is poorly documented and remains largely unknown. These gaps led us to characterize the diversity of Cerrado endophytic foliar fungi associated with six woody species (Caryocar brasiliense, Dalbergia miscolobium, Leptolobium dasycarpum, Qualea parviflora, Ouratea hexasperma, and Styrax ferrugineus). Additionally, we investigated the influence of host plant identities on the structure of fungal communities. Culture-dependent methods coupled with DNA metabarcoding were employed. Irrespective of the approach, the phylum Ascomycota and the classes Dothideomycetes and Sordariomycetes were dominant. Using the cultivation-dependent method, 114 isolates were recovered from all the host species and classified into more than 20 genera and 50 species. Over 50 of the isolates belonged to the genus Diaporthe, and were distributed into more than 20 species. Metabarcoding revealed the phyla Chytridiomycota, Glomeromycota, Monoblepharomycota, Mortierellomycota, Olpidiomycota, Rozellomycota, and Zoopagomycota. These groups are reported for the first time as components of the endophytic mycobiome of Cerrado plant species. In total, 400 genera were found in all host species. A unique leaf endophytic mycobiome was identified in each host species, which differed not only by the distribution of fungal species, but also by the abundance of shared species. These findings highlight the importance of the Brazilian Cerrado as a reservoir of microbial species, and emphasize how endophytic fungal communities are diversified and adapted.
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Affiliation(s)
| | - Georgios Joannis Pappas Junior
- University of Brasília (UnB), Institute of Biological Sciences, Department of Cellular Biology, Brasília 70910-900, DF, Brazil
| | - Adriana Sturion Lorenzi
- University of Brasília (UnB), Institute of Biological Sciences, Department of Cellular Biology, Brasília 70910-900, DF, Brazil
| | - Danilo Batista Pinho
- University of Brasília (UnB), Institute of Biological Sciences, Department of Phytopathology, Brasília 70910-900, DF, Brazil
| | - Alexandra Martins Costa
- University of Brasília (UnB), Institute of Biological Sciences, Department of Ecology, Brasília 70910-900, DF, Brazil
| | | | - Helson Mario Martins do Vale
- University of Brasília (UnB), Institute of Biological Sciences, Department of Phytopathology, Brasília 70910-900, DF, Brazil
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23
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Enaud R, Sioniac P, Imbert S, Janvier PL, Camino A, Bui HN, Pillet O, Orieux A, Boyer A, Berger P, Gruson D, Delhaes L, Prevel R. Lung Mycobiota α-Diversity Is Linked to Severity in Critically Ill Patients with Acute Exacerbation of Chronic Obstructive Pulmonary Disease. Microbiol Spectr 2023:e0506222. [PMID: 36976010 PMCID: PMC10100765 DOI: 10.1128/spectrum.05062-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) affects more than 200 million people worldwide. The chronic course of COPD is frequently worsened by acute exacerbations (AECOPD). Mortality in patients hospitalized for severe AECOPD remains dramatically high, and the underlying mechanisms are poorly understood. Lung microbiota is associated with COPD outcomes in nonsevere AECOPD, but no study specifically investigated severe AECOPD patients. The aim of this study is thus to compare lung microbiota composition between severe AECOPD survivors and nonsurvivors. Induced sputum or endotracheal aspirate was collected at admission from every consecutive severe AECOPD patient. After DNA extraction, the V3-V4 and ITS2 regions were amplified by PCR. Deep-sequencing was performed on a MiSeq sequencer (Illumina); the data were analyzed using DADA2 pipeline. Among 47 patients admitted for severe AECOPD, 25 (53%) with samples of sufficient quality were included: 21 of 25 (84%) survivors and 4 of 25 (16%) nonsurvivors. AECOPD nonsurvivors had lower α-diversities indices than survivors for lung mycobiota but not for lung bacteriobiota. Similar results were demonstrated comparing patients receiving invasive mechanical ventilation (n = 13 [52%]) with those receiving only noninvasive ventilation (n = 12 [48%]). Previous systemic antimicrobial therapy and long-term inhaled corticosteroid therapy could alter the lung microbiota composition in severe AECOPD patients. In acidemic AECOPD, lower lung mycobiota α-diversity is linked to the severity of the exacerbation, assessed by mortality and the requirement for invasive mechanical ventilation, whereas lung bacteriobiota α-diversity is not. This study encourages a multicenter cohort study investigating the role of lung microbiota, especially fungal kingdom, in severe AECOPD. IMPORTANCE In AECOPD with acidemia, more severe patients-i.e., nonsurvivors and patients requiring invasive mechanical ventilation-have lower lung mycobiota α-diversity than survivors and patients receiving only noninvasive ventilation, respectively. This study encourages a large multicenter cohort study investigating the role of lung microbiota in severe AECOPD and urges investigation of the role of the fungal kingdom in severe AECOPD.
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Affiliation(s)
- Raphaël Enaud
- Université Bordeaux, Center de Recherche Cardio-Thoracique de Bordeaux, INSERM UMR 1045, Bordeaux, France
- Centre Hospitalier Universitaire Bordeaux, Le Centre de Ressources et de Compétences de la Mucoviscidose Pédiatrique, CIC 1401, Bordeaux, France
| | - Pierre Sioniac
- Centre Hospitalier Universitaire Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Sebastien Imbert
- Université Bordeaux, Center de Recherche Cardio-Thoracique de Bordeaux, INSERM UMR 1045, Bordeaux, France
- Centre Hospitalier Universitaire Bordeaux, Mycology-Parasitology Department, CIC 1401, Bordeaux, France
| | - Pierre-Laurent Janvier
- Centre Hospitalier Universitaire Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Adrian Camino
- Université Bordeaux, Center de Recherche Cardio-Thoracique de Bordeaux, INSERM UMR 1045, Bordeaux, France
| | - Hoang-Nam Bui
- Centre Hospitalier Universitaire Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Odile Pillet
- Centre Hospitalier Universitaire Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Arthur Orieux
- Centre Hospitalier Universitaire Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Alexandre Boyer
- Université Bordeaux, Center de Recherche Cardio-Thoracique de Bordeaux, INSERM UMR 1045, Bordeaux, France
- Centre Hospitalier Universitaire Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Patrick Berger
- Université Bordeaux, Center de Recherche Cardio-Thoracique de Bordeaux, INSERM UMR 1045, Bordeaux, France
| | - Didier Gruson
- Université Bordeaux, Center de Recherche Cardio-Thoracique de Bordeaux, INSERM UMR 1045, Bordeaux, France
- Centre Hospitalier Universitaire Bordeaux, Medical Intensive Care Unit, Bordeaux, France
| | - Laurence Delhaes
- Université Bordeaux, Center de Recherche Cardio-Thoracique de Bordeaux, INSERM UMR 1045, Bordeaux, France
- Centre Hospitalier Universitaire Bordeaux, Mycology-Parasitology Department, CIC 1401, Bordeaux, France
| | - Renaud Prevel
- Université Bordeaux, Center de Recherche Cardio-Thoracique de Bordeaux, INSERM UMR 1045, Bordeaux, France
- Centre Hospitalier Universitaire Bordeaux, Medical Intensive Care Unit, Bordeaux, France
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24
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Matos M, Baptista CJ, Oliveira PA, Matos AC, Soares AS, Santos M, Figueira L, Coelho AC. Talaromyces marneffei isolated from nasal swabs in Portugal. Med Mycol 2023; 61:7084023. [PMID: 36948603 DOI: 10.1093/mmy/myad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 03/24/2023] Open
Abstract
Mycobiota are essential to the health of any living being, creating a balanced and complex interaction between bacteria, the immune system and the tissue cells of the host. Talaromyces marneffei (also known as Penicillium marneffei) is a dimorphic fungus, endemic in South Asia, that often causes a life-threatening systemic fungal infection (called penicilliosis), particularly in immunocompromised hosts. Nasal swabs from 73 healthy volunteers were analysed to characterise their mycobiota, through its cultural characteristics, morphology and molecular methods (PCR). All volunteers were also asked to answer to an anonymous questionnaire. Three women were positive (and asymptomatic) for T. marneffei. One of them was reported to have lupus. This study contributes to improving our knowledge about human normal mycobiota, identifying mycotic agents that may cause complicated systemic infections (as T. marneffei), especially in immunosuppressed patients, as well as other possible risk factors of exposure or prognosis.
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Affiliation(s)
- Manuela Matos
- Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro (UTAD), Quinta dos Prados, 5000-801, Vila Real, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB); Inov4Agro - Institute for Innovation, Capacity Building and Sustainability of Agri-food Production, UTAD, Vila Real, Portugal
- Department of Veterinary Sciences, UTAD, Quinta dos Prados, 5000-801, Vila Real, Portugal
| | - Catarina Jota Baptista
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB); Inov4Agro - Institute for Innovation, Capacity Building and Sustainability of Agri-food Production, UTAD, Vila Real, Portugal
- Department of Veterinary Sciences, UTAD, Quinta dos Prados, 5000-801, Vila Real, Portugal
- Instituto de Biomedicina (IBIOMED), Universidad de León, Spain
| | - Paula A Oliveira
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB); Inov4Agro - Institute for Innovation, Capacity Building and Sustainability of Agri-food Production, UTAD, Vila Real, Portugal
- Department of Veterinary Sciences, UTAD, Quinta dos Prados, 5000-801, Vila Real, Portugal
| | - Ana Cristina Matos
- CERNAS - Research Center for Natural Resources, Environment and Society - Polytechnic Institute of Castelo Branco, 6000-084 Castelo Branco, Portugal
- QRural- Quality of Life in the Rural World- Research Unit. Polytechnic Institute of Castelo Branco, 6000-084 Castelo Branco, Portugal
| | - Ana Sofia Soares
- Animal and Veterinary Research Centre (CECAV), Quinta dos Prados, 5000-801, Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Portugal
| | - Marlene Santos
- Department of Genetics and Biotechnology, University of Trás-os-Montes e Alto Douro (UTAD), Quinta dos Prados, 5000-801, Vila Real, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB); Inov4Agro - Institute for Innovation, Capacity Building and Sustainability of Agri-food Production, UTAD, Vila Real, Portugal
| | - Luís Figueira
- QRural- Quality of Life in the Rural World- Research Unit. Polytechnic Institute of Castelo Branco, 6000-084 Castelo Branco, Portugal
| | - Ana Cláudia Coelho
- Department of Veterinary Sciences, UTAD, Quinta dos Prados, 5000-801, Vila Real, Portugal
- Animal and Veterinary Research Centre (CECAV), Quinta dos Prados, 5000-801, Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Portugal
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25
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Chen Q, Fan Y, Zhang B, Yan C, Chen Z, Wang L, Hu Y, Huang Q, Su J, Ren J, Xu H. Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis. Front Cell Infect Microbiol 2023; 12:1086885. [PMID: 36683707 PMCID: PMC9849685 DOI: 10.3389/fcimb.2022.1086885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023] Open
Abstract
Objective Fecal microbiota transplantation (FMT) is a novel microbial treatment for patients with ulcerative colitis (UC). In this study, we performed a clinical trial of capsulized FMT in UC patients to determine the association between the gut fungal community and capsulized FMT outcomes. Design This study recruited patients with active UC (N = 22) and healthy individuals (donor, N = 9) according to the criteria. The patients received capsulized FMT three times a week. Patient stool samples were collected before (week 0) and after FMT follow-up visits at weeks 1, 4, and 12. Fungal communities were analysed using shotgun metagenomic sequencing. Results According to metagenomic analysis, fungal community evenness index was greater in samples collected from patients, and the overall fungal community was clustered among the samples collected from donors. The dominant fungi in fecal samples collected from donors and patients were Ascomycota and Basidiomycota. However, capsulized FMT ameliorated microbial fungal diversity and altered fungal composition, based on metagenomic analysis of fecal samples collected before and during follow-up visits after capsulized FMT. Fungal diversity decreased in samples collected from patients who achieved remission after capsulized FMT, similar to samples collected from donors. Patients achieving remission after capsulized FMT had specific enrichment of Kazachstania naganishii, Pyricularia grisea, Lachancea thermotolerans, and Schizosaccharomyces pombe compared with patients who did not achieve remission. In addition, the relative abundance of P. grisea was higher in remission fecal samples during the follow-up visit. Meanwhile, decreased levels of pathobionts, such as Candida and Debaryomyces hansenii, were associated with remission in patients receiving capsulized FMT. Conclusion In the metagenomic analysis of fecal samples from donors and patients with UC receiving capsulized FMT, shifts in gut fungal diversity and composition were associated with capsulized FMT and validated in patients with active UC. We also identified the specific fungi associated with the induction of remission. ClinicalTrails.gov (NCT03426683).
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Affiliation(s)
- Qiongyun Chen
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Yanyun Fan
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Bangzhou Zhang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Changsheng Yan
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Zhangran Chen
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China
| | - Lin Wang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Yiqun Hu
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Qingwen Huang
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jingling Su
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
| | - Jianlin Ren
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China,Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Zhongshan Hospital of Xiamen University, Xiamen, China,Department of Digestive Disease, School of Medicine, Xiamen University, Xiamen, China,*Correspondence: Jianlin Ren, ; Hongzhi Xu,
| | - Hongzhi Xu
- Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China,Institute for Microbial Ecology, School of Medicine, Xiamen University, Xiamen, China,Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Zhongshan Hospital of Xiamen University, Xiamen, China,Department of Digestive Disease, School of Medicine, Xiamen University, Xiamen, China,*Correspondence: Jianlin Ren, ; Hongzhi Xu,
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van Thiel I, de Jonge W, van den Wijngaard R. Fungal feelings in the irritable bowel syndrome: the intestinal mycobiome and abdominal pain. Gut Microbes 2023; 15:2168992. [PMID: 36723172 PMCID: PMC9897793 DOI: 10.1080/19490976.2023.2168992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Although the gut microbiota consists of bacteria, viruses, and fungi, most publications addressing the microbiota-gut-brain axis in irritable bowel syndrome (IBS) have a sole focus on bacteria. This may relate to the relatively low presence of fungi and viruses as compared to bacteria. Yet, in the field of inflammatory bowel disease research, the publication of several papers addressing the role of the intestinal mycobiome now suggested that these low numbers do not necessarily translate to irrelevance. In this review, we discuss the available clinical and preclinical IBS mycobiome data, and speculate how these recent findings may relate to earlier observations in IBS. By surveying literature from the broader mycobiome research field, we identified questions open to future IBS-oriented investigations.
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Affiliation(s)
- Iam van Thiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Amsterdam UMC, University of Amsterdam, Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands
| | - Wj de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Amsterdam UMC, University of Amsterdam, Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Department of General, Visceral-, Thoracic and Vascular Surgery, University Hospital Bonn, Bonn, Germany
| | - Rm van den Wijngaard
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands,Amsterdam UMC, University of Amsterdam, Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, The Netherlands,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, The Netherlands,CONTACT RM van den Wijngaard Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Meibergdreef 69-71, Amsterdam1105 BK, The Netherlands
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Ljaljević Grbić M, Dimkić I, Savković Ž, Stupar M, Knežević A, Jelikić A, Unković N. Mycobiome Diversity of the Cave Church of Sts. Peter and Paul in Serbia-Risk Assessment Implication for the Conservation of Rare Cavern Habitat Housing a Peculiar Fresco Painting. J Fungi (Basel) 2022; 8. [PMID: 36547596 DOI: 10.3390/jof8121263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
The mycobiome of the cave Church of Sts. Peter and Paul, housing the peculiar fresco painting of “The Bald-headed Jesus”, was analyzed via culture-dependent and -independent methods. Salt efflorescence, colored patinas, and biofilm, as well as biopitting, discolorations, and fruiting bodies of wood-decay fungi were observed on surfaces within the church. Microscopic analyses showed an abundance of fungal structures, i.e., conidiophores, conidia, chlamydospores, and ascospores. The estimated values of the contamination classified all surfaces as the “Danger zone”. A total of 24 fungi from 17 genera were determined as part of the culturable mycobiome, with a dominance of Ascomycota of genera Penicillium. Biodegradative profiles analyzed via plate assays demonstrated positive reactions for 16 isolates: most commonly acid production (8), followed by pigment production and ligninolytic activity (6), protein degradation (5), cellulolytic activity (3) and carbonate dissolution (2). Metabarcoding analysis showed a dominance of Ascomycota in all samples (79.9−99.7%), with high relative abundance documented for Hypoxylon fuscopurpureum on the iconostasis and unclassified Mycosphaerellaceae family within order Capnodiales on fresco and stone, as well as moderate relative abundance for unclassified Dothideomycetes, Botryolepraria lesdainii, Verrucaria sp. and Cladosporium sp. on stone walls. The used set of integrative methods pointed out species of genus Neodevriesia and H. fuscopurpureum as the main deteriogenic agents of fresco and iconostasis surfaces, respectively.
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Response of the wheat mycobiota to flooding revealed substantial shifts towards plant pathogens. Front Plant Sci 2022; 13:1028153. [PMID: 36518495 PMCID: PMC9742542 DOI: 10.3389/fpls.2022.1028153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Rainfall extremes are intensifying as a result of climate change, leading to increased flood risk. Flooding affects above- and belowground ecosystem processes, representing a substantial threat to crop productivity under climate change. Plant-associated fungi play important roles in plant performance, but their response to abnormal rain events is unresolved. Here, we established a glasshouse experiment to determine the effects of flooding stress on the spring wheat-mycobiota complex. Since plant phenology could be an important factor in the response to hydrological stress, flooding was induced only once and at different plant growth stages, such as tillering, booting and flowering. We assessed the wheat mycobiota response to flooding in three soil-plant compartments (phyllosphere, roots and rhizosphere) using metabarcoding. Key soil and plant traits were measured to correlate physiological plant and edaphic changes with shifts in mycobiota structure and functional guilds. Flooding reduced plant fitness, and caused dramatic shifts in mycobiota assembly across the entire plant. Notably, we observed a functional transition consisting of a decline in mutualist abundance and richness with a concomitant increase in plant pathogens. Indeed, fungal pathogens associated with important cereal diseases, such as Gibberella intricans, Mycosphaerella graminicola, Typhula incarnata and Olpidium brassicae significantly increased their abundance under flooding. Overall, our study demonstrate the detrimental effect of flooding on the wheat mycobiota complex, highlighting the urgent need to understand how climate change-associated abiotic stressors alter plant-microbe interactions in cereal crops.
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Affiliation(s)
- Davide Francioli
- Institute of Crop Science, Faculty of Agricultural Sciences, University of Hohenheim, Stuttgart, Germany
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research e.V. (ZALF), Müncheberg, Germany
- Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Regecová I, Semjon B, Jevinová P, Očenáš P, Výrostková J, Šuľáková L, Nosková E, Marcinčák S, Bartkovský M. Detection of Microbiota during the Fermentation Process of Wine in Relation to the Biogenic Amine Content. Foods 2022; 11:3061. [PMID: 36230137 DOI: 10.3390/foods11193061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022] Open
Abstract
Viticulture is one of the traditional industries in Slovakia, where there are six wine-growing regions: Malokarpatska, Southern Slovakia, Central Slovakia, Nitra, Eastern Slovakia, and Tokaj. This study focuses on the detection of microbiota in soil samples, grape leaves and berries, and samples taken from fermenting must and young wine (the variety Tramín červený) in relation to the detected concentrations of biogenic amines during the fermentation process. In the examined samples, the number of yeasts and molds (from 3.8 to 6.8 log cfu/g or mL) and TVC (from 3.7 to 6.5 log cfu/g or mL) were determined via culture examination. At the same time, the number of LAB (from ˂3.0 to 4.4 log cfu/g or mL) was determined, which was the highest on day 4 of the must fermentation process and was related to the detected of the highest concentration of biogenic amines (histamine and tyramine) on day 6 in the investigated must samples using the UHPLC system. Mycobiota species were identified by MALDI-TOF MS, PCR, ITS-PCR-RFLP, and PCR sequencing of the amplified products. The study confirmed the presence of the yeasts Saccharomyces cerevisiae, Metschnikowia pulcherrima, Hanseniospora uvarum, Pichia kudriavzevii, Pichia kluyveri, Pichia fermentas, Torulaspora delbrueckii, and Candida tenuis. At the same time, the presence of molds (Cladosporium herbarum, Cladosporium cladosporioides, Penicillium granulatum, Penicillium mononematosum, Botritis cinerea, and Penicillium glabrum) was also confirmed in soil samples, leaves, grape berries, and fresh grape must. The study confirmed the reduction in the species diversity of the microbiota during the must fermentation process, which resulted in decreases in the concentrations of the monitored biogenic amines in the early stages of the must fermentation process and young wine of the variety Tramín červený.
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Flores GAM, Lopez RP, Cerrudo CS, Consolo VF, Berón CM. Culex quinquefasciatus Holobiont: A Fungal Metagenomic Approach. Front Fungal Biol 2022; 3:918052. [PMID: 37746232 PMCID: PMC10512223 DOI: 10.3389/ffunb.2022.918052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/24/2022] [Indexed: 09/26/2023]
Abstract
Microorganisms associated with mosquitoes have fundamental roles, not only in their nutrition, but also in physiological and immunological processes, and in their adaptation to the environment as well. Studies on mosquito hologenomes have increased significantly during the last years, achieving important advances in the characterization of the "core bacteriome" of some species of health importance. However, the fungal mycobiome has not been exhaustively researched, especially throughout the life cycle of some hematophagous mosquito species. In this work, the diversity and composition of fungal communities in different developmental stages, sexes, and adult nutrition of Culex quinquefasciatus reared on laboratory conditions were characterized, using internal transcribed spacer high throughput amplicon sequencing. Larvae presented a higher fungal richness, while sucrose-fed males and females showed a similar diversity between them. Blood-fed females presented few operational taxonomic units with an even distribution. Results are consistent with the reduction of larval microbiota after molting, observed for the bacterial microbiome in other mosquito species. The filamentous Ascomycota Penicillium polonicum and Cladosporium sp. were present in all stages of the mosquitoes; in addition, the presence of yeasts in the insects or their subsequent colonization associated with their diet is also discussed. These results suggest that some species of fungi could be essential for the nutrition and development of mosquitoes throughout their life cycle.
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Affiliation(s)
- Guillermo A. M. Flores
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Buenos Aires, Argentina
| | - Rocio P. Lopez
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Buenos Aires, Argentina
| | - Carolina S. Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular (LIGBCM), Area Virosis de Insectos (AVI), Departamento Ciencia y Tecnología, Universidad Nacional de Quilmes and CONICET, Bernal, Argentina
| | - V. Fabiana Consolo
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Buenos Aires, Argentina
| | - Corina M. Berón
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Mar del Plata, Buenos Aires, Argentina
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31
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Watts PC, Mappes T, Tukalenko E, Mousseau TA, Boratyński Z, Møller AP, Lavrinienko A. Interpretation of gut microbiota data in the 'eye of the beholder': A commentary and re-evaluation of data from 'Impacts of radiation exposure on the bacterial and fungal microbiome of small mammals in the Chernobyl Exclusion Zone'. J Anim Ecol 2022; 91:1535-1545. [PMID: 35694772 PMCID: PMC9541917 DOI: 10.1111/1365-2656.13667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Evidence that exposure to environmental pollutants can alter the gut microbiota composition of wildlife includes studies of rodents exposed to radionuclides. Antwis et al. (2021) used amplicon sequencing to characterise the gut microbiota of four species of rodent (Myodes glareolus, Apodemus agrarius, A. flavicollis and A. sylvaticus) inhabiting the Chernobyl Exclusion Zone (CEZ) to examine possible changes in gut bacteria (microbiota) and gut fungi (mycobiota) associated with exposure to radionuclides and whether the sample type (from caecum or faeces) affected the analysis. The conclusions derived from the analyses of gut mycobiota are based on data that represent a mixture of ingested fungi (e.g. edible macrofungi, polypores, lichens and ectomycorrhizae) and gut mycobiota (e.g. microfungi and yeasts), which mask the patterns of inter‐ and intraspecific variation in the authentic gut mycobiota. Implying that ‘faecal samples are not an accurate indicator of gut composition’ creates an unnecessary controversy about faecal sampling because the comparison of samples from the caecum and faeces confounds many other possible drivers (including different animals from different locations, sampled in different years) of variation in gut microbiota. It is relevant also that Antwis et al.'s (2021) data lack statistical power to detect an effect of exposure to radionuclides on the gut microbiota because (1) all of their samples of Apodemus mice had experienced a medium or high total absorbed dose rate and (2) they did not collect samples of bank voles (M. glareolus) from replicate contaminated and uncontaminated locations. Discussion of Antwis et al.'s (2021) analysis, especially the claims presented in the Abstract, is important to prevent controversy about the outcome of research on the biological impacts of wildlife inhabiting the CEZ.
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Affiliation(s)
- Phillip C Watts
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Eugene Tukalenko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,National Research Center for Radiation Medicine of the National Academy of Medical Science, Kyiv, Ukraine
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
| | - Zbyszek Boratyński
- CIBIO/InBio, Research Centre in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Anders P Møller
- Laboratoire d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud 11, Orsay Cedex, France
| | - Anton Lavrinienko
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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Ventin-Holmberg R, Saqib S, Korpela K, Nikkonen A, Peltola V, Salonen A, de Vos WM, Kolho KL. The Effect of Antibiotics on the Infant Gut Fungal Microbiota. J Fungi (Basel) 2022; 8. [PMID: 35448562 DOI: 10.3390/jof8040328] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotics are commonly used drugs in infants, causing disruptions in the developing gut microbiota with possible detrimental long-term effects such as chronic inflammatory diseases. The focus has been on bacteria, but research shows that fungi might have an important role as well. There are only a few studies on the infant gut fungal microbiota, the mycobiota, in relation to antibiotic treatment. Here, the aim was to investigate the impact of antibiotics on the infant gut mycobiota, and the interkingdom associations between bacteria and fungi. We had 37 antibiotic-naïve patients suffering from respiratory syncytial virus, of which 21 received one to four courses of antibiotics due to complications, and 16 remained antibiotic-naïve throughout the study. Fecal samples were collected before, during and after antibiotic treatment with a follow-up period of up to 9.5 months. The gut mycobiota was studied by Illumina MiSeq sequencing of the ITS1 region. We found that antibiotic use affected the gut mycobiota, most prominently seen as a higher relative abundance of Candida (p < 0.001), and a higher fungal diversity (p = 0.005−0.04) and richness (p = 0.03) in the antibiotic-treated infants compared to the antibiotic-naïve ones at multiple timepoints. This indicates that the gut mycobiota could contribute to the long-term consequences of antibiotic treatments.
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Leonardi I, Gao IH, Lin WY, Allen M, Li XV, Fiers WD, De Celie MB, Putzel GG, Yantiss RK, Johncilla M, Colak D, Iliev ID. Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity. Cell 2022; 185:831-846.e14. [PMID: 35176228 PMCID: PMC8897247 DOI: 10.1016/j.cell.2022.01.017] [Citation(s) in RCA: 117] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 11/30/2021] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
Fungal communities (the mycobiota) are an integral part of the gut microbiota, and the disruption of their integrity contributes to local and gut-distal pathologies. Yet, the mechanisms by which intestinal fungi promote homeostasis remain unclear. We characterized the mycobiota biogeography along the gastrointestinal tract and identified a subset of fungi associated with the intestinal mucosa of mice and humans. Mucosa-associated fungi (MAF) reinforced intestinal epithelial function and protected mice against intestinal injury and bacterial infection. Notably, intestinal colonization with a defined consortium of MAF promoted social behavior in mice. The gut-local effects on barrier function were dependent on IL-22 production by CD4+ T helper cells, whereas the effects on social behavior were mediated through IL-17R-dependent signaling in neurons. Thus, the spatial organization of the gut mycobiota is associated with host-protective immunity and epithelial barrier function and might be a driver of the neuroimmune modulation of mouse behavior through complementary Type 17 immune mechanisms.
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Affiliation(s)
- Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Iris H. Gao
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Woan-Yu Lin
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Megan Allen
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York City, NY, USA
| | - Xin V. Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - William D. Fiers
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Meghan Bialt De Celie
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Gregory G. Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Rhonda K. Yantiss
- MJ Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Melanie Johncilla
- MJ Department of Pathology & Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
| | - Dilek Colak
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medical College, Cornell University, New York City, NY, USA.,Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medical College, Cornell University, New York City, NY, USA
| | - Iliyan D. Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA.,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY 10065, USA
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Zouache K, Martin E, Rahola N, Gangue MF, Minard G, Dubost A, Van VT, Dickson L, Ayala D, Lambrechts L, Moro CV. Larval habitat determines the bacterial and fungal microbiota of the mosquito vector Aedes aegypti. FEMS Microbiol Ecol 2022; 98:6526867. [PMID: 35147188 DOI: 10.1093/femsec/fiac016] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 11/12/2022] Open
Abstract
Mosquito larvae are naturally exposed to microbial communities present in a variety of larval development sites. Several earlier studies have highlighted that the larval habitat influences the composition of the larval bacterial microbiota. However, little information is available on their fungal microbiota, i.e. the mycobiota. In this study, we provide the first simultaneous characterization of the bacterial and fungal microbiota in field-collected Aedes aegypti larvae and their respective aquatic habitats. We evaluated whether the microbial communities associated with the breeding site may affect the composition of both the bacterial and fungal communities in Ae. aegypti larvae. Our results show a higher similarity in microbial community structure for both bacteria and fungi between larvae and the water in which larvae develop than between larvae from different breeding sites. This supports the hypothesis that larval habitat is a major factor driving microbial composition in mosquito larvae. Since the microbiota plays an important role in mosquito biology, unravelling the network of interactions that operate between bacteria and fungi is essential to better understand the functioning of the mosquito holobiont.
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Affiliation(s)
- Karima Zouache
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Edwige Martin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Nil Rahola
- CIRMF, Franceville, Gabon.,UMR MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
| | | | - Guillaume Minard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Van Tran Van
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Laura Dickson
- Institut Pasteur, Université de Paris, CNRS UMR2000, Insect-Virus Interactions Unit, Paris, France.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Diego Ayala
- CIRMF, Franceville, Gabon.,UMR MIVEGEC, Univ. Montpellier, CNRS, IRD, Montpellier, France
| | - Louis Lambrechts
- Institut Pasteur, Université de Paris, CNRS UMR2000, Insect-Virus Interactions Unit, Paris, France
| | - Claire Valiente Moro
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
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Abstract
The fungus Candida albicans is a ubiquitous member of the human gut microbiota. Hundreds or thousands of bacterial taxa reside together with this fungus in the intestine, creating a milieu with myriad opportunities for inter-kingdom interactions. Indeed, recent studies examining the broader composition - that is, monitoring not only bacteria but also the often neglected fungal component - of the gut microbiota hint that there are significant interdependencies between fungi and bacteria. Gut bacteria closely associate with C. albicans cells in the colon, break down and feed on complex sugars decorating the fungal cell wall, and shape the intestinal microhabitats occupied by the fungus. Peptidoglycan subunits released by bacteria upon antibiotic treatment can promote C. albicans dissemination from the intestine, seeding bloodstream infections that often become life-threatening. Elucidating the principles that govern the fungus-bacteria interplay may open the door to novel approaches to prevent C. albicans infections originating in the gut.
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Affiliation(s)
- J. Christian Pérez
- Department of Microbiology and Molecular Genetics, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, USA,CONTACT J.Christian Pérez Department of Microbiology and Molecular Genetics, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, USA
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Yalcin SS, Aksu T, Kuskonmaz B, Ozbek NY, Pérez-Brocal V, Celik M, Uckan Cetinkaya D, Moya A, Dinleyici EC. Intestinal mycobiota composition and changes in children with thalassemia who underwent allogeneic hematopoietic stem cell transplantation. Pediatr Blood Cancer 2022; 69:e29411. [PMID: 34699120 DOI: 10.1002/pbc.29411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/27/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Allogeneic hematopoietic stem cell transplantation (HSCT) alters the diversity of the intestinal bacterial microbiota. This study aimed to evaluate human mycobiota composition pre-HSCT and post-HSCT in children with thalassemia. METHOD Ten children with thalassemia undergoing allogeneic HSCT were enrolled. The stool samples were collected before the transplantation regimen, before the transplant day, and +15, +30 days, and three months after transplantation. Stool samples were also collected from the donor and the patient's caregivers. Gut mycobiota composition was evaluated with metagenomic analysis. RESULTS Pretransplant mycobiota of children with thalassemia (the predominant genus was Saccharomyces, 64.1%) has been shown to approximate the diverse mycobiota compositions of healthy adult donors but becomes altered (lower diversity) following transplant procedures. Three months after HSCT, phyla Ascomycota and Basidiomycota were 83.4% and 15.6%, respectively. The predominant species were Saccaharomyces_uc and Saccharomyces cerevisiae (phylum Ascomycota); we also observed Malassezia restricta and Malassezia globosa (phylum Basidiomycota) (∼13%). On day 90 after HSCT, we observed 65.3% M. restricta and 18.4% M. globosa predominance at the species level in a four-year-old boy with acute graft-versus-host disease (GVHD) (skin and gut involvement) 19 days after transplantation included. CONCLUSION The mycobiota composition of children with thalassemia altered after HSCT. We observed Malassezia predominance in a child with GVHD. Further studies in children with GVHD will identify this situation.
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Affiliation(s)
- Siddika Songul Yalcin
- Department of Social Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Tekin Aksu
- Department of Pediatric Hematology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Baris Kuskonmaz
- Department of Pediatric Hematology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Namık Yasar Ozbek
- Ankara City Hospital, Department of Pediatric Hematology, Health Science University Faculty of Medicine, Ankara, Turkey
| | - Vicente Pérez-Brocal
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain.,CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain
| | - Melda Celik
- Department of Social Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Duygu Uckan Cetinkaya
- Department of Pediatric Hematology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Andrés Moya
- Area of Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research of Valencia Region (FISABIO-Public Health), Valencia, Spain.,CIBER in Epidemiology and Public Health (CIBEResp), Madrid, Spain.,Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish National Research Council (CSIC), Valencia, Spain
| | - Ener Cagri Dinleyici
- Department of Pediatrics, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
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Abstract
Fungi form a major and diverse component of most ecosystems on Earth. They are both micro and macroorganisms with high and varying functional diversity as well as great variation in dispersal modes. With our growing knowledge of microbial biogeography, it has become increasingly clear that fungal assembly patterns and processes differ from other microorganisms such as bacteria, but also from macroorganisms such as plants. The success of fungi as organisms and their influence on the environment lies in their ability to span multiple dimensions of time, space, and biological interactions, that is not rivalled by other organism groups. There is also growing evidence that fungi mediate links between different organisms and ecosystems, with the potential to affect the macroecology and evolution of those organisms. This suggests that fungal interactions are an ecological driving force, interconnecting different levels of biological and ecological organisation of their hosts, competitors, and antagonists with the environment and ecosystem functioning. Here we review these emerging lines of evidence by focusing on the dynamics of fungal interactions with other organism groups across various ecosystems. We conclude that the mediating role of fungi through their complex and dynamic ecological interactions underlie their importance and ubiquity across Earth's ecosystems.
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Affiliation(s)
- Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden.,Institute of Ecology and Earth Sciences, University of Tartu, Tartu, 40 Lai St. Estonia
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Ulls väg 16, 756 51 Sweden
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Enaud R, Cambos S, Viaud E, Guichoux E, Chancerel E, Marighetto A, Etchamendy N, Clark S, Mohammedi K, Cota D, Delhaes L, Gatta-Cherifi B. Gut Microbiota and Mycobiota Evolution Is Linked to Memory Improvement after Bariatric Surgery in Obese Patients: A Pilot Study. Nutrients 2021; 13:nu13114061. [PMID: 34836316 PMCID: PMC8620125 DOI: 10.3390/nu13114061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 12/23/2022] Open
Abstract
Patients with obesity are known to exhibit gut microbiota dysbiosis and memory deficits. Bariatric surgery (BS) is currently the most efficient anti-obesity treatment and may improve both gut dysbiosis and cognition. However, no study has investigated association between changes of gut microbiota and cognitive function after BS. We prospectively evaluated 13 obese patients on anthropometric data, memory functions, and gut microbiota-mycobiota before and six months after BS. The Rey Auditory Verbal Learning Test (AVLT) and the symbol span (SS) of the Weschler Memory Scale were used to assess verbal and working memory, respectively. Fecal microbiota and mycobiota were longitudinally analyzed by 16S and ITS2 rRNA sequencing respectively. AVLT and SS scores were significantly improved after BS (AVLT scores: 9.7 ± 1.7 vs. 11.2 ± 1.9, p = 0.02, and SS scores: 9.7 ± 23.0 vs. 11.6 ± 2.9, p = 0.05). An increase in bacterial alpha-diversity, and Ruminococcaceae, Prevotella, Agaricus, Rhodotorula, Dipodascus, Malassezia, and Mucor were significantly associated with AVLT score improvement after BS, while an increase in Prevotella and a decrease in Clostridium, Akkermansia, Dipodascus and Candida were linked to SS scores improvement. We identified several changes in the microbial communities that differ according to the improvement of either the verbal or working memories, suggesting a complex gut-brain-axis that evolves after BS.
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Affiliation(s)
- Raphaël Enaud
- Centre Hospitalier de Bordeaux, CRCM Pédiatrique, CIC 1401, 33000 Bordeaux, France;
- Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, Hôpital Xavier Arnozan, University of Bordeaux, Avenue du Haut Lévêque, 33604 Pessac, France;
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU ACRONIM, 33000 Bordeaux, France;
| | - Sophie Cambos
- Centre Hospitalier de Bordeaux, Department of Endocrinology, Diabetes and Nutrition, University Hospital of Bordeaux, 33604 Pessac, France;
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Esther Viaud
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Erwan Guichoux
- BIOGECO, INRAE, University of Bordeaux, 69 route d’Arcachon, 33610 Cestas, France; (E.G.); (E.C.)
| | - Emilie Chancerel
- BIOGECO, INRAE, University of Bordeaux, 69 route d’Arcachon, 33610 Cestas, France; (E.G.); (E.C.)
| | - Aline Marighetto
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Nicole Etchamendy
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Samantha Clark
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
| | - Kamel Mohammedi
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU ACRONIM, 33000 Bordeaux, France;
- Centre Hospitalier de Bordeaux, Department of Endocrinology, Diabetes and Nutrition, University Hospital of Bordeaux, 33604 Pessac, France;
| | - Daniela Cota
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU TALISMENT, 33000 Bordeaux, France
| | - Laurence Delhaes
- Centre de Recherche Cardio-Thoracique de Bordeaux, U1045, Hôpital Xavier Arnozan, University of Bordeaux, Avenue du Haut Lévêque, 33604 Pessac, France;
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU ACRONIM, 33000 Bordeaux, France;
| | - Blandine Gatta-Cherifi
- Centre Hospitalier de Bordeaux, Department of Endocrinology, Diabetes and Nutrition, University Hospital of Bordeaux, 33604 Pessac, France;
- Neurocentre Magendie, Physiopathologie de la Plasticité Neuronale, U862, INSERM, 146 rue Léo Saignat, 33076 Bordeaux, France; (E.V.); (A.M.); (N.E.); (S.C.); (D.C.)
- Centre Hospitalier de Bordeaux, University of Bordeaux, FHU TALISMENT, 33000 Bordeaux, France
- Correspondence:
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Abstract
Mosquito larvae encounter diverse assemblages of bacteria (i.e., "microbiota") and fungi in the aquatic environments that they develop in. However, while a number of studies have addressed the diversity and function of microbiota in mosquito life history, relatively little is known about mosquito-fungus interactions outside several key fungal entomopathogens. In this study, we used high-throughput sequencing of internal transcribed spacer 2 (ITS2) metabarcode markers to provide the first simultaneous characterization of the fungal communities in field-collected Aedes albopictus larvae and their associated aquatic environments. Our results reveal unprecedented variation in fungal communities among adjacent but discrete larval breeding habitats. Our results also reveal a distinct fungal community assembly in the mosquito gut versus other tissues, with gut-associated fungal communities being most similar to those present in the environment where larvae feed. Altogether, our results identify the environment as the dominant factor shaping the fungal community associated with mosquito larvae, with no evidence of environmental filtering by the gut. These results also identify mosquito feeding behavior and fungal mode of nutrition as potential drivers of tissue-specific fungal community assembly after environmental acquisition. IMPORTANCE The Asian tiger mosquito, Aedes albopictus, is the dominant mosquito species in the United States and an important vector of arboviruses of major public health concern. One aspect of mosquito control to curb mosquito-borne diseases has been the use of biological control agents such as fungal entomopathogens. Recent studies also demonstrate the impact of mosquito-associated microbial communities on various mosquito traits, including vector competence. However, while much research attention has been dedicated to understanding the diversity and function of mosquito-associated bacterial communities, relatively little is known about mosquito-associated fungal communities. A better understanding of the factors that drive fungal community diversity and assembly in mosquitoes will be essential for future efforts to target mosquito-associated bacteria and fungi for mosquito and mosquito-borne disease control.
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Affiliation(s)
- Patil Tawidian
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Kerri L. Coon
- Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
| | - Lee W. Cohnstaedt
- Arthropod-Borne Animal Diseases Research Unit, Center for Grain and Animal Health Research, Manhattan, Kansas, USA
| | - Kristin Michel
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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Heitmann N, Glemnitz M, Lentzsch P, Platen R, Müller MEH. Quantifying the Role of Ground Beetles for the Dispersal of Fusarium and Alternaria Fungi in Agricultural Landscapes. J Fungi (Basel) 2021; 7:863. [PMID: 34682284 DOI: 10.3390/jof7100863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/13/2022] Open
Abstract
The spread by arthropods (zoochory) is an essential dispersal mechanism for many microorganisms, like plant pathogens. Carabid beetles are very abundant and mobile ground-dwelling insects. However, their role in the dispersal of economically relevant phytopathogens, like Fusarium and Alternaria fungi is basically unknown. We quantified the total fungal, Fusarium, and Alternaria load of carabid species collected in the transition zones between small water bodies and wheat fields by screening (i) their body surface for fungal propagules with a culture-dependent method and (ii) their entire bodies for fungal DNA with a qPCR approach. The analysis of entire bodies detects fungal DNA in all carabid beetles but Alternaria DNA in 98% of them. We found that 74% of the carabids carried fungal propagules on the body surface, of which only half (49%) carried Fusarium propagules. We identified eight Fusarium and four Alternaria species on the body surface; F. culmorum was dominant. The fungal, Fusarium and Alternaria, load differed significantly between the carabid species and was positively affected by the body size and weight of the carabids. Carabid beetles reveal a remarkable potential to disseminate different fungi. Dispersal by ground-dwelling arthropods could affect the spatial-temporal patterns of plant disease and microorganisms in general.
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Alonso-Monge R, Prieto D, Coman I, Rochas S, Arana DM, Hidalgo-Vico S, Román E, Pla J. Identification of Clinical Isolates of Candida albicans with Increased Fitness in Colonization of the Murine Gut. J Fungi (Basel) 2021; 7:695. [PMID: 34575733 DOI: 10.3390/jof7090695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 12/22/2022] Open
Abstract
The commensal and opportunistic pathogen Candida albicans is an important cause of fungal diseases in humans, with the gastrointestinal tract being an important reservoir for its infections. The study of the mechanisms promoting the C. albicans commensal state has attracted considerable attention over the last few years, and several studies have focused on the identification of the intestinal human mycobiota and the characterization of Candida genes involved in its establishment as a commensal. In this work, we have barcoded 114 clinical C. albicans isolates to identify strains with an enhanced fitness in a murine gastrointestinal commensalism model. The 114 barcoded clinical isolates were pooled in four groups of 28 to 30 strains that were inoculated by gavage in mice previously treated with antibacterial therapy. Eight strains that either exhibited higher colonization load and/or remained in the gut after antibiotic removal were selected. The phenotypic analysis of these strains compared to an RFP-tagged SC5314 wild type strain did not reveal any specific trait associated with its increased colonization; all strains were able to filament and six of the eight strains displayed invasive growth on Spider medium. Analysis of one of these strains, CaORAL3, revealed that although mice required previous bacterial microbiota reduction with antibiotics to be able to be colonized, removal of this procedure could take place the same day (or even before) Candida inoculation. This strain was able to colonize the intestine of mice already colonized with Candida without antibiotic treatment in co-housing experiments. CaORAL3 was also able to be established as a commensal in mice previously colonized by another (CaHG43) or the same (CaORAL3) C. albicans strain. Therefore, we have identified C. albicans isolates that display higher colonization load than the standard strain SC5314 which will surely facilitate the analysis of the factors that regulate fungal colonization.
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Francis F, Enaud R, Soret P, Lussac-Sorton F, Avalos-Fernandez M, Bui S, Fayon M, Thiébaut R, Delhaes L. New Insights in Microbial Species Predicting Lung Function Decline in CF: Lessons from the MucoFong Project. J Clin Med 2021; 10:jcm10163725. [PMID: 34442021 PMCID: PMC8396880 DOI: 10.3390/jcm10163725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
Several predictive models have been proposed to understand the microbial risk factors associated with cystic fibrosis (CF) progression. Very few have integrated fungal airways colonisation, which is increasingly recognized as a key player regarding CF progression. To assess the association between the percent predicted forced expiratory volume in 1 s (ppFEV1) change and the fungi or bacteria identified in the sputum, 299 CF patients from the “MucoFong” project were included and followed-up with over two years. The relationship between the microorganisms identified in the sputum and ppFEV1 course of patients was longitudinally analysed. An adjusted linear mixed model analysis was performed to evaluate the effect of a transient or chronic bacterial and/or fungal colonisation at inclusion on the ppFEV1 change over a two-year period. Pseudomonas aeruginosa, Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and Candida albicans were associated with a significant ppFEV1 decrease. No significant association was found with other fungal colonisations. In addition, the ppFEV1 outcome in our model was 11.26% lower in patients presenting with a transient colonisation with non-pneumoniae Streptococcus species compared to other patients. These results confirm recently published data and provide new insights into bacterial and fungal colonisation as key factors for the assessment of lung function decline in CF patients.
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Affiliation(s)
- Florence Francis
- CHU de Bordeaux, Department of Public Health, F-33000 Bordeaux, France; (F.F.); (R.T.)
- Bordeaux Population Health Research Center, Univ. Bordeaux, Inserm, UMR 1219, F-33000 Bordeaux, France; (P.S.); (M.A.-F.)
| | - Raphael Enaud
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC 1401, F-33000 Bordeaux, France
| | - Perrine Soret
- Bordeaux Population Health Research Center, Univ. Bordeaux, Inserm, UMR 1219, F-33000 Bordeaux, France; (P.S.); (M.A.-F.)
- INRIA SISTM Team, F-33405 Talence, France
- Laboratoire Servier, 50 Rue Carnot, 92284 Suresnes, France
| | - Florian Lussac-Sorton
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, Service de Parasitologie-Mycologie, F-33000 Bordeaux, France
| | - Marta Avalos-Fernandez
- Bordeaux Population Health Research Center, Univ. Bordeaux, Inserm, UMR 1219, F-33000 Bordeaux, France; (P.S.); (M.A.-F.)
- INRIA SISTM Team, F-33405 Talence, France
| | | | - Stéphanie Bui
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC 1401, F-33000 Bordeaux, France
| | - Michael Fayon
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, CRCM Pédiatrique, CIC 1401, F-33000 Bordeaux, France
| | - Rodolphe Thiébaut
- CHU de Bordeaux, Department of Public Health, F-33000 Bordeaux, France; (F.F.); (R.T.)
- Bordeaux Population Health Research Center, Univ. Bordeaux, Inserm, UMR 1219, F-33000 Bordeaux, France; (P.S.); (M.A.-F.)
- INRIA SISTM Team, F-33405 Talence, France
| | - Laurence Delhaes
- Centre de Recherche Cardio-Thoracique de Bordeaux, Univ. Bordeaux, U1045, F-33000 Bordeaux, France; (R.E.); (F.L.-S.); (S.B.); (M.F.)
- CHU de Bordeaux, Univ. Bordeaux, FHU ACRONIM, F-33000 Bordeaux, France
- CHU de Bordeaux, Service de Parasitologie-Mycologie, F-33000 Bordeaux, France
- Correspondence: ; Tel.: +33-05-47-30-27-50
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Biolcati F, Ferrocino I, Bottero MT, Dalmasso A. Mycobiota Composition of Robiola di Roccaverano Cheese along the Production Chain. Foods 2021; 10:1859. [PMID: 34441636 DOI: 10.3390/foods10081859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 01/04/2023] Open
Abstract
Robiola di Roccaverano is a Protected Designation of Origin (PDO) cheese from the Piedmont region of Italy. In this study, the mycobiota occurring during Robiola di Roccaverano production was elucidated. Samples of milk, Natural Milk Cultures (NMC), curd, 5- and 15-days ripened cheese were collected from one dairy plant and the mycobiota was analyzed by the metataxonomic approach. Milk samples showed a high diversity and Cladosporium, Kluyveromyces marxianus, Geotrichum candidum and Debaryomyces hansenii were found with higher relative abundance. This mycobiota remains quite stable in NMC and curd matrices although the relative abundance of K. marxianus and G. candidum yeasts increased significantly and shaped the fungal composition of 5- and 15-day ripened cheese.
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Malassigné S, Minard G, Vallon L, Martin E, Valiente Moro C, Luis P. Diversity and Functions of Yeast Communities Associated with Insects. Microorganisms 2021; 9:microorganisms9081552. [PMID: 34442634 PMCID: PMC8399037 DOI: 10.3390/microorganisms9081552] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/14/2021] [Accepted: 07/19/2021] [Indexed: 12/28/2022] Open
Abstract
Following the concept of the holobiont, insect-microbiota interactions play an important role in insect biology. Many examples of host-associated microorganisms have been reported to drastically influence insect biological processes such as development, physiology, nutrition, survival, immunity, or even vector competence. While a huge number of studies on insect-associated microbiota have focused on bacteria, other microbial partners including fungi have been comparatively neglected. Yeasts, which establish mostly commensal or symbiotic relationships with their host, can dominate the mycobiota of certain insects. This review presents key advances and progress in the research field highlighting the diversity of yeast communities associated with insects, as well as their impact on insect life-history traits, immunity, and behavior.
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Zuo Y, Li X, Yang J, Liu J, Zhao L, He X. Fungal Endophytic Community and Diversity Associated with Desert Shrubs Driven by Plant Identity and Organ Differentiation in Extremely Arid Desert Ecosystem. J Fungi (Basel) 2021; 7:jof7070578. [PMID: 34356957 PMCID: PMC8306007 DOI: 10.3390/jof7070578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/23/2022] Open
Abstract
Despite desert ecosystem being crucial to our understanding of natural geography, species evolution and global climate change, there is limited information on the dynamics of their composition and the diversity of endophytic fungi communities driven by plant identity and organ differentiation. Here, an extensive investigation of endophytic fungal microbiome in root, stem, and leaf organs associated with five xerophyte shrubs in an extremely arid desert, Northwest China, were examined. The fungal community dominated by Dothideomycetes and Pleosporales. Shrub species strongly drive the niche-based processes of endophytic fungi across the root, stem and leaf compartments. The diversity and composition of endophytic fungi in stem showed higher variability among plant species than leaf and root. The fungal communities in root libraries were more diverse and exhibited a remarkable differentiation of community composition. We further demonstrated the significant host preferences and tissue specificity of desert endophytic fungi, and unique specific taxa were also observed. The co-occurrence network revealed the coexistence of fungal endophytes in arid desert, and the root fungal network harbored the highest interspecies connectivity. Members of Pleosporales were the most common keystone species in the root fungal network. This is the first report of mycobiota in both plant species and organ differentiation in an extremely arid desert ecosystem.
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Affiliation(s)
| | | | | | | | | | - Xueli He
- Correspondence: ; Tel.: +86-31-2507-9364
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Krumbeck JA, Reiter AM, Pohl JC, Tang S, Kim YJ, Linde A, Prem A, Melgarejo T. Characterization of Oral Microbiota in Cats: Novel Insights on the Potential Role of Fungi in Feline Chronic Gingivostomatitis. Pathogens 2021; 10:904. [PMID: 34358054 DOI: 10.3390/pathogens10070904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 01/04/2023] Open
Abstract
Previous studies have suggested the involvement of viral and bacterial components in the initiation and progression of feline chronic gingivostomatitis (FCGS), but the role of fungi remains entirely unknown. This pilot study aimed to investigate the bacteriome and mycobiome in feline oral health and disease. Physical exams, including oral health assessment, of privately owned, clinically healthy (CH) cats (n = 14) and cats affected by FCGS (n = 14) were performed. Using a sterile swab, oral tissue surfaces of CH and FCGS cats were sampled and submitted for 16S rRNA and ITS-2 next-generation DNA sequencing. A high number of fungal species (n = 186) was detected, with Malassezia restricta, Malassezia arunalokei, Cladosporium penidielloides/salinae, and Aspergillaceae sp. being significantly enriched in FCGS samples, and Saccharomyces cerevisiae in CH samples. The bacteriome was significantly distinct between groups, and significant inter-kingdom interactions were documented. Bergeyella zoohelcum was identified as a potential biomarker of a healthy feline oral microbiome. These data suggest that fungi might play a role in the etiology and pathogenesis of FCGS, and that oral health should not simply be regarded as the absence of microbial infections. Instead, it may be viewed as the biological interactions between bacterial and fungal populations that coexist to preserve a complex equilibrium in the microenvironment of the mouth. Additional investigations are needed to improve our understanding of the feline oral ecosystem and the potential interactions between viruses, bacteria, and fungi in FCGS.
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Dellière S, Dannaoui E, Fieux M, Bonfils P, Gricourt G, Demontant V, Podglajen I, Woerther PL, Angebault C, Botterel F. Analysis of Microbiota and Mycobiota in Fungal Ball Rhinosinusitis: Specific Interaction between Aspergillus fumigatus and Haemophilus influenza? J Fungi (Basel) 2021; 7:550. [PMID: 34356929 DOI: 10.3390/jof7070550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Fungal ball (FB) rhinosinusitis (RS) is the main type of non-invasive fungal RS. Despite positive direct examination (DE) of biopsies, culture remains negative in more than 60% of cases. The aim of the study was to evaluate the performance/efficacy of targeted metagenomics (TM) to analyze microbiota and mycobiota in FB and find microbial associations. Forty-five sinus biopsies from patients who underwent surgery for chronic RS were included. After DE and culture, DNA was extracted, then fungal ITS1–ITS2 and bacterial V3–V4 16S rDNA loci were sequenced (MiSeqTM Illumina). Operational taxonomic units (OTUs) were defined via QIIME and assigned to SILVA (16S) and UNITE (ITS) databases. Statistical analyses were performed using SHAMAN. Thirty-eight patients had FB and seven had non-fungal rhinosinusitis (NFRS). DE and culture of FB were positive for fungi in 97.3 and 31.6% of patients, respectively. TM analysis of the 38 FB yielded more than one fungal genus in 100% of cases, with Aspergillus in 89.5% (34/38). Haemophilus was over-represented in FB with >1000 reads/sample in 47.3% (18/38) compared to NFRS (p < 0.001). TM allowed fungal identification in biopsies with negative culture. Haemophilus was associated with FB. Pathogenesis could result from fungi–bacteria interactions in a mixed biofilm-like structure.
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Schei K, Simpson MR, Øien T, Salamati S, Rudi K, Ødegård RA. Allergy-related diseases and early gut fungal and bacterial microbiota abundances in children. Clin Transl Allergy 2021; 11:e12041. [PMID: 34194728 PMCID: PMC8238386 DOI: 10.1002/clt2.12041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/07/2021] [Accepted: 06/16/2021] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The early gut microbiota has been proposed as an important link between environmental exposures and development of allergy-related diseases. Beyond the widely investigated associations between the gut bacterial microbiota, we investigated the involvement of early gut mycobiota and gut permeability in the pathogenesis of asthma, allergic rhinoconjunctivitis (AR) and eczema. METHODS In the Probiotics in the Prevention of Allergy among Children in Trondheim trial with maternal probiotic supplementation, we collected faecal samples at four timepoints between 0 and 2 years from a cohort of 278 children. Clinical information on allergy-related diseases was collected in a paediatric examination at 2 years and questionnaires at 6 weeks and 1, 2 and 6 years. By quantitative PCR and 16S/ITS1 MiSeq rRNA gene sequencing, we analysed the gut bacterial and fungal microbiota abundance and bacterial diversity and explored associations with allergy-related diseases. We also measured gut permeability markers (lipopolysaccharide-binding protein [LBP] and fatty acid-binding protein 2 [FABP2]). RESULTS Children with higher fungal abundance at 2 years were more likely to develop asthma and AR by 6 years, odds ratios 1.70 (95% CI: 1.06-2.75) and 1.41 (1.03-1.93), respectively. We explored causal connections, and children with eczema at 1-2 years appeared to have more mature bacterial microbiota, as well as being depleted of Enterococcus genus. Although LBP and FABP2 did not correlate with eczema, increased bacterial abundance was associated with increased serum FABP2. CONCLUSIONS We observed positive associations between gut fungal abundance and allergy-related disease, but increased gut permeability does not appear to be involved in the underlying mechanisms for this association. Our findings should be confirmed in future microbiota studies.
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Affiliation(s)
- Kasper Schei
- Department of Clinical and Molecular MedicineFaculty of Medicine and Health SciencesNTNU–Norwegian University of Science and TechnologyTrondheimNorway
| | - Melanie Rae Simpson
- Department of Public Health and NursingFaculty of Medicine and Health SciencesNTNU–Norwegian University of Science and TechnologyTrondheimNorway
- Clinic of Laboratory MedicineSt. Olav's HospitalTrondheimNorway
| | - Torbjørn Øien
- Department of Public Health and NursingFaculty of Medicine and Health SciencesNTNU–Norwegian University of Science and TechnologyTrondheimNorway
| | - Saideh Salamati
- Regional Centre of Obesity Research and Innovation (ObeCe)St. Olav's HospitalTrondheimNorway
| | - Knut Rudi
- Faculty of Chemistry, Biotechnology and Food ScienceNorwegian University of Life SciencesÅsNorway
| | - Rønnaug Astri Ødegård
- Department of Clinical and Molecular MedicineFaculty of Medicine and Health SciencesNTNU–Norwegian University of Science and TechnologyTrondheimNorway
- Regional Centre of Obesity Research and Innovation (ObeCe)St. Olav's HospitalTrondheimNorway
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Santona A, Mhmoud NA, Siddig EE, Deligios M, Fiamma M, Bakhiet SM, Barac A, Paglietti B, Rubino S, Fahal AH. Metagenomics of black grains: new highlights in the understanding of eumycetoma. Trans R Soc Trop Med Hyg 2021; 115:307-314. [PMID: 33449116 DOI: 10.1093/trstmh/traa177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/19/2020] [Accepted: 12/16/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Eumycetoma is a chronic subcutaneous granulomatous disease that is endemic in Sudan and other countries. It can be caused by eight different fungal orders. The gold standard diagnostic test is culture, however, culture-independent methods such as imaging, histopathological and molecular techniques can support diagnosis, especially in cases of negative cultures. METHODS The amplicon-based internal transcribed spacer 2 metagenomic technique was used to study black grains isolated from 14 tissue biopsies from patients with mycetoma. Furthermore, mycological culture and surgical biopsy histopathological examinations of grains were performed. RESULTS Madurella mycetomatis (n=5) and Falciformispora spp. (n=4) organisms were identified by culture and confirmed by metagenomics. Metagenomics recognised, at the species level, Falciformispora as Falciformispora tompkinsii (n=3) and Falciformispora senegalensis (n=1), while in culture-negative cases (n=5), Madurella mycetomatis (n=3), Falciformispora senegalensis (n=1) and Fusarium spp. (n=1) were identified. Interestingly, the metagenomics results showed a 'consortium' of different fungi in each sample, mainly Ascomycota phylum, including various species associated with eumycetoma. The microbial co-occurrence in eumycetoma showed the co-presence of Madurella with Trichoderma, Chaetomium, Malasseziales and Sordariales spp., while Falciformispora co-presented with Inocybe and Alternaria and was in mutual exclusion with Subramaniula, Aspergillus and Trichothecium. CONCLUSION Metagenomics provides new insights into the aetiology of eumycetoma in samples with negative culture and into the diversity and complexity of grains mycobiota, calling into question the accuracy of traditional culture for the identification of causative agents.
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Affiliation(s)
- Antonella Santona
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Najwa A Mhmoud
- Mycetoma Research Centre, University of Khartoum, PO Box 102, Khartoum, Sudan.,Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Emmanuel Edwar Siddig
- Mycetoma Research Centre, University of Khartoum, PO Box 102, Khartoum, Sudan.,Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Maura Fiamma
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Sahar Mubarak Bakhiet
- Mycetoma Research Centre, University of Khartoum, PO Box 102, Khartoum, Sudan.,Institute for Endemic Diseases, University of Khartoum, PO Box 102, Khartoum, Sudan
| | - Aleksandra Barac
- Clinic for Infectious and Tropical Diseases, Clinical Centre of Serbia, Bu. Oslobodjenja 16, 11000 Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Dr Subotica 1, 11000 Belgrade, Serbia
| | - Bianca Paglietti
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Ahmed Hassan Fahal
- Mycetoma Research Centre, University of Khartoum, PO Box 102, Khartoum, Sudan
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50
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Raveau R, Lounès-Hadj Sahraoui A, Hijri M, Fontaine J. Clary Sage Cultivation and Mycorrhizal Inoculation Influence the Rhizosphere Fungal Community of an Aged Trace-Element Polluted Soil. Microorganisms 2021; 9:1333. [PMID: 34205382 DOI: 10.3390/microorganisms9061333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 11/17/2022] Open
Abstract
Soil fungal communities play a central role in natural systems and agroecosystems. As such, they have attracted significant research interest. However, the fungal microbiota of aromatic plants, such as clary sage (Salvia sclarea L.), remain unexplored. This is especially the case in trace element (TE)-polluted conditions and within the framework of phytomanagement approaches. The presence of high concentrations of TEs in soils can negatively affect not only microbial diversity and community composition but also plant establishment and growth. Hence, the objective of this study is to investigate the soil fungal and arbuscular mycorrhizal fungi (AMF) community composition and their changes over time in TE-polluted soils in the vicinity of a former lead smelter and under the cultivation of clary sage. We used Illumina MiSeq amplicon sequencing to evaluate the effects of in situ clary sage cultivation over two successive years, combined or not with exogenous AMF inoculation, on the rhizospheric soil and root fungal communities. We obtained 1239 and 569 fungal amplicon sequence variants (ASV), respectively, in the rhizospheric soil and roots of S. sclarea under TE-polluted conditions. Remarkably, 69 AMF species were detected at our experimental site, belonging to 12 AMF genera. Furthermore, the inoculation treatment significantly shaped the fungal communities in soil and increased the number of AMF ASVs in clary sage roots. In addition, clary sage cultivation over successive years could be one of the explanatory parameters for the inter-annual variation in both fungal and AMF communities in the soil and root biotopes. Our data provide new insights on fungal and AMF communities in the rhizospheric soil and roots of an aromatic plant, clary sage, grown in TE-polluted agricultural soil.
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