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Li P, Hong J, Yuan Z, Huang Y, Wu M, Ding T, Wu Z, Sun X, Lin D. Gut microbiota in parasite-transmitting gastropods. Infect Dis Poverty 2023; 12:105. [PMID: 38001502 PMCID: PMC10668521 DOI: 10.1186/s40249-023-01159-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Gastropoda, the largest class within the phylum Mollusca, houses diverse gut microbiota, and some gastropods serve as intermediate hosts for parasites. Studies have revealed that gut bacteria in gastropods are associated with various biological aspects, such as growth, immunity and host-parasite interactions. Here, we summarize our current knowledge of gastropod gut microbiomes and highlight future research priorities and perspectives. METHODS A literature search was undertaken using PubMed, Web of Science and CNKI for the articles on the gut microbiota of gastropods until December 31, 2022. We retrieved a total of 166 articles and identified 73 eligible articles for inclusion in this review based on the inclusion and exclusion criteria. RESULTS Our analysis encompassed freshwater, seawater and land snails, with a specific focus on parasite-transmitting gastropods. We found that most studies on gastropod gut microbiota have primarily utilized 16S rRNA gene sequencing to analyze microbial composition, rather than employing metagenomic, metatranscriptomic, or metabolomic approaches. This comprehensive review provided an overview of the parasites carried by snail species in the context of gut microbiota studies. We presented the gut microbial trends, a comprehensive summary of the diversity and composition, influencing factors, and potential functions of gastropod gut microbiota. Additionally, we discussed the potential applications, research gaps and future perspectives of gut microbiomes in parasite-transmitting gastropods. Furthermore, several strategies for enhancing our comprehension of gut microbiomes in snails were also discussed. CONCLUSIONS This review comprehensively summarizes the current knowledge on the composition, potential function, influencing factors, potential applications, limitations, and challenges of gut microbiomes in gastropods, with a specific emphasis on parasite-transmitting gastropods. These findings provide important insights for future studies aiming to understand the potential role of gastropod gut microbiota in controlling snail populations and snail-borne diseases.
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Affiliation(s)
- Peipei Li
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China
| | - Jinni Hong
- Department of Traditional Chinese Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhanhong Yuan
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Yun Huang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Mingrou Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Tao Ding
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China
| | - Zhongdao Wu
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China.
| | - Xi Sun
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
| | - Datao Lin
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-Sen University, Guangzhou, China.
- Chinese Atomic Energy Agency Center of Excellence on Nuclear Technology Applications for Insect Control, Provincial Engineering Technology Research Center for Diseases-Vectors Control, Sun Yat-Sen University, Guangzhou, China.
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2
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Madubuike H, Ferry N. Enhanced Activity and Stability of an Acetyl Xylan Esterase in Hydrophilic Alcohols through Site-Directed Mutagenesis. Molecules 2023; 28:7393. [PMID: 37959811 PMCID: PMC10647838 DOI: 10.3390/molecules28217393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/29/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
Current demands for the development of suitable biocatalysts showing high process performance is stimulated by the need to replace current chemical synthesis with cleaner alternatives. A drawback to the use of biocatalysts for unique applications is their low performance in industrial conditions. Hence, enzymes with improved performance are needed to achieve innovative and sustainable biocatalysis. In this study, we report the improved performance of an engineered acetyl xylan esterase (BaAXE) in a hydrophilic organic solvent. The structure of BaAXE was partitioned into a substrate-binding region and a solvent-affecting region. Using a rational design approach, charged residues were introduced at protein surfaces in the solvent-affecting region. Two sites present in the solvent-affecting region, A12D and Q143E, were selected for site-directed mutagenesis, which generated the mutants MUT12, MUT143 and MUT12-143. The mutants MUT12 and MUT143 reported lower Km (0.29 mM and 0.27 mM, respectively) compared to the wildtype (0.41 mM). The performance of the mutants in organic solvents was assessed after enzyme incubation in various strengths of alcohols. The mutants showed improved activity and stability compared to the wild type in low strengths of ethanol and methanol. However, the activity of MUT143 was lost in 40% methanol while MUT12 and MUT12-143 retained over 70% residual activity in this environment. Computational analysis links the improved performance of MUT12 and MUT12-143 to novel intermolecular interactions that are absent in MUT143. This work supports the rationale for protein engineering to augment the characteristics of wild-type proteins and provides more insight into the role of charged residues in conferring stability.
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Affiliation(s)
- Henry Madubuike
- School of Science Engineering and Environment, University of Salford, Manchester M5 4WT, UK
| | - Natalie Ferry
- School of Science Engineering and Environment, University of Salford, Manchester M5 4WT, UK
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3
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Sheehy L, MacDonald‐Howard K, Williams CD, Weedall GD, Jones H, Rae R. A parasitic nematode induces dysbiosis in susceptible but not resistant gastropod hosts. Microbiologyopen 2023; 12:e1346. [PMID: 37186232 PMCID: PMC9999464 DOI: 10.1002/mbo3.1346] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 03/12/2023] Open
Abstract
Animals’ gut microbiomes affect a wide array of biological processes including immunity and protection from pathogens. However, how the microbiome changes due to infection by parasites is still largely unknown, as is how the microbiome changes in hosts that differ in their susceptibility to parasites. To investigate this, we exposed two slug species of differing susceptibility to the parasitic nematode Phasmarhabditis hermaphrodita (Deroceras reticulatum is highly susceptible and Ambigolimax valentianus resistant to the nematode) and profiled the gut microbiota after 7 and 14 days. Before infection, both slug species’ microbiota was dominated by similar bacterial genera: Pseudomonas (by far the most abundant), Sphingobacterium, Pedobacter, Chryseobacterium, and Flavobacterium. In the resistant host A. valentianus, there was no significant change in the bacterial genera after infection, but in D. reticulatum, the bacterial profile changed, with a decrease in the abundance of Pseudomonadaceae and an increase in the abundance of Flavobacteriaceae and Sphingobacteriaceae after 7 days postinfection. This suggests nematode infection causes dysbiosis in hosts that are susceptible to infection, but the microbiome of resistant species remains unaltered. In summary, the regulation of the immune system is tightly linked with host survival, and nematode infection can alter the microbiome structure.
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Affiliation(s)
- Laura Sheehy
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Kerry MacDonald‐Howard
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Chris D. Williams
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Gareth D. Weedall
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
| | - Hayley Jones
- Royal Horticultural Society GardenWisley, WokingSurreyUK
| | - Robbie Rae
- School of Biological and Environmental SciencesLiverpool John Moores UniversityLiverpoolUK
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4
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Kukkar D, Sharma PK, Kim KH. Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass. ENVIRONMENTAL RESEARCH 2022; 215:114369. [PMID: 36165858 DOI: 10.1016/j.envres.2022.114369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.
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Affiliation(s)
- Deepak Kukkar
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India; University Centre for Research and Development, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India.
| | | | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Wangsimni-ro, Seoul - 04763, South Korea.
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Xu T, Sun H, Yi L, Yang M, Zhu J, Huang Y, Pan H, Li H, Li W, Zhao H, Wei H, Zhao S. Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing. Front Genet 2022; 13:999535. [PMID: 36313418 PMCID: PMC9614230 DOI: 10.3389/fgene.2022.999535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/28/2022] [Indexed: 11/24/2022] Open
Abstract
To investigate the difference of microbial communities among Diannan small-ear (DNSE), Dahe black (DHB) and Yorkshire (YS) pigs, we compared the microbial taxonomic and functional composition using a metagenomic approach. A total of 1,002,362 non-redundant microbial genes were identified, DHB and YS pigs had more similar genetic makeup compared with DNSE pigs. Bacteroidetes, Firmicutes and Spirochetes were the three most abundant phyla for all pig breeds, and DNSE pigs had a higher abundance of Prevotella genus than DHB and YS pigs. The functional profiles varied among the three pig breeds, DNSE pigs had more active carbohydrate metabolism and more abundant antibiotic resistance genes than the other two pig breeds. Moreover, we found that peptide and macrolide resistances genes in DNSE pigs were more abundant than that in DHB pigs (p < 0.05). This study will help to provide a theoretical basis for the development of native pig breeds in Yunnan Province, China.
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Affiliation(s)
- Taojie Xu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Haichao Sun
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Lanlan Yi
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Minghua Yang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Junhong Zhu
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Ying Huang
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Hongbin Pan
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
| | - Honghui Li
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
| | - Weizhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Hongye Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Hongjiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
- *Correspondence: Hongjiang Wei, ; Sumei Zhao,
| | - Sumei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- *Correspondence: Hongjiang Wei, ; Sumei Zhao,
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Schurkman J, Liu R, Alavi S, Tandingan De Ley I, Hsiao A, Dillman AR. The Native Microbial Community of Gastropod-Associated Phasmarhabditis Species Across Central and Southern California. Front Microbiol 2022; 13:903136. [PMID: 35910595 PMCID: PMC9329066 DOI: 10.3389/fmicb.2022.903136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
Nematodes in the genus Phasmarhabditis can infect and kill slugs and snails, which are important agricultural pests. This useful trait has been commercialized by the corporation BASF after they mass produced a product labeled Nemaslug®. The product contains Phasmarhabditis hermaphrodita, which has been cultured with Moraxella osloensis, a bacterial strain that was originally thought to be responsible for causing mortality in slugs and snails. The exact mechanism leading to death in a Phasmarhabditis infected host is unknown but may involve contributions from nematode-associated bacteria. The naturally occurring microbial community of Phasmarhabditis is unexplored; the previous Phasmarhabditis microbial community studies have focused on laboratory grown or commercially reared nematodes, and in order to obtain a deeper understanding of the parasite and its host interactions, it is crucial to characterize the natural microbial communities associated with this organism in the wild. We sampled Phasmarhabditis californica, Phasmarhabditis hermaphrodita, and Phasmarhabditis papillosa directly from their habitats in Central and Southern California nurseries and garden centers and identified their native microbial community via 16S amplicon sequencing. We found that the Phasmarhabditis microbial community was influenced by species, location, and possibly gastropod host from which the nematode was collected. The predominant bacteria of the Phasmarhabditis isolates collected included Shewanella, Clostridium perfringens, Aeromonadaceae, Pseudomonadaceae, and Acinetobacter. Phasmarhabditis papillosa isolates exhibited an enrichment with species belonging to Acinetobacter or Pseudomonadaceae. However, further research must be performed to determine if this is due to the location of isolate collection or a species specific microbial community pattern. More work on the natural microbial community of Phasmarhabditis is needed to determine the role of bacteria in nematode virulence.
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Affiliation(s)
- Jacob Schurkman
- Department of Nematology, University of California Riverside, Riverside, CA, United States
| | - Rui Liu
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, United States
| | - Salma Alavi
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, United States
| | - Irma Tandingan De Ley
- Department of Nematology, University of California Riverside, Riverside, CA, United States
| | - Ansel Hsiao
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, United States
- *Correspondence: Adler R. Dillman,
| | - Adler R. Dillman
- Department of Nematology, University of California Riverside, Riverside, CA, United States
- *Correspondence: Adler R. Dillman,
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7
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Sheehy L, Cutler J, Weedall GD, Rae R. Microbiome Analysis of Malacopathogenic Nematodes Suggests No Evidence of a Single Bacterial Symbiont Responsible for Gastropod Mortality. Front Immunol 2022; 13:878783. [PMID: 35515005 PMCID: PMC9065361 DOI: 10.3389/fimmu.2022.878783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/22/2022] [Indexed: 11/13/2022] Open
Abstract
Nematodes and bacteria are prevalent in soil ecosystems, and some have evolved symbiotic relationships. In some cases, symbionts carry out highly specialized functions: a prime example being entomopathogenic nematodes (EPNs), which vector bacteria (Xenorhabdus or Photorhabdus) into insect hosts, killing them to provide a food source for the nematodes. It is thought that the commercially available malacopathogenic (kills slugs and snails) biocontrol nematode Phasmarhabditis hermaphrodita vectors a bacterium (Moraxella osloensis) into slugs to kill them. To investigate this further we used a metagenomic approach to profile the bacteria present in the commercial strain of P. hermaphrodita, a wild strain of P. hermaphrodita and two other Phasmarhabditis species (P. californica and P. neopapillosa), after they had killed their slug host (Deroceras invadens). We show that these nematodes do not exclusively associate with one bacterium but a range of species, with members of the phyla Pseudomonadota, Bacillota, Actinobacteriota and Bacteroidota the most prevalent. The commercial strain of P. hermaphrodita had the least diverse bacterial community. Furthermore, we found that the bacterium P. hermaphrodita has been cultured on for 25 years is not the expected species M. osloensis but is Psychrobacter spp. and the only strain of the Phasmarhabditis species to associate with Psychrobacter spp. was the commercial strain of P. hermaphrodita. In summary, we found no evidence to show that P. hermaphrodita rely exclusively on one bacterium to cause host mortality but found variable and diverse bacterial communities associated with these nematodes in their slug hosts.
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Affiliation(s)
- Laura Sheehy
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - James Cutler
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Gareth D Weedall
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Robbie Rae
- School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
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8
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Madubuike H, Ferry N. Characterisation of a Novel Acetyl Xylan Esterase (BaAXE) Screened from the Gut Microbiota of the Common Black Slug ( Arion ater). Molecules 2022; 27:2999. [PMID: 35566348 PMCID: PMC9104356 DOI: 10.3390/molecules27092999] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/24/2022] Open
Abstract
Acetyl xylan esterases (AXEs) are enzymes capable of hydrolysing the acetyl bonds in acetylated xylan, allowing for enhanced activity of backbone-depolymerizing enzymes. Bioprospecting novel AXE is essential in designing enzyme cocktails with desired characteristics targeting the complete breakdown of lignocellulose. In this article, we report the characterisation of a novel AXE identified as Gene_id_40363 in the metagenomic library analysed from the gut microbiota of the common black slug. The conserved domain description was identified with an NCBI BLASTp search using the translated nucleotide sequence as a query. The activity of the recombinant enzyme was tested on various synthetic substrates and acetylated substrates. The protein sequence matched the conserved domain described as putative hydrolase and aligned closely to an uncharacterized esterase from Buttiauxella agrestis, hence the designation as BaAXE. BaAXE showed low sequence similarity among characterized CE family proteins with an available 3D structure. BaAXE was active on 4-nitrophenyl acetate, reporting a specific activity of 78.12 U/mg and a Km value of 0.43 mM. The enzyme showed optimal activity at 40 °C and pH 8 and showed high thermal stability, retaining over 40% activity after 2 h of incubation from 40 °C to 100 °C. BaAXE hydrolysed acetyl bonds, releasing acetic acid from acetylated xylan and β-D-glucose pentaacetate. BaAXE has great potential for biotechnological applications harnessing its unique characteristics. In addition, this proves the possibility of bioprospecting novel enzymes from understudied environments.
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Affiliation(s)
- Henry Madubuike
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK
| | - Natalie Ferry
- School of Science, Engineering and Environment, University of Salford, Manchester M5 4WT, UK
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9
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Du S, Sun X, Zhang J, Lin D, Chen R, Cui Y, Xiang S, Wu Z, Ding T. Metagenome-Assembled Genomes Reveal Mechanisms of Carbohydrate and Nitrogen Metabolism of Schistosomiasis-Transmitting Vector Biomphalaria Glabrata. Microbiol Spectr 2022; 10:e0184321. [PMID: 35254167 PMCID: PMC9045156 DOI: 10.1128/spectrum.01843-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/04/2022] [Indexed: 12/11/2022] Open
Abstract
Biomphalaria glabrata transmits schistosomiasis mansoni which poses considerable risks to hundreds of thousands of people worldwide, and is widely used as a model organism for studies on the snail-schistosome relationship. Gut microbiota plays important roles in multiple aspects of host including development, metabolism, immunity, and even behavior; however, detailed information on the complete diversity and functional profiles of B. glabrata gut microbiota is still limited. This study is the first to reveal the gut microbiome of B. glabrata based on metagenome-assembled genome (MAG). A total of 28 gut samples spanning diet and age were sequenced and 84 individual microbial genomes with ≥ 70% completeness and ≤ 5% contamination were constructed. Bacteroidota and Proteobacteria were the dominant bacteria in the freshwater snail, unlike terrestrial organisms harboring many species of Firmicutes and Bacteroidota. The microbial consortia in B. glabrata helped in the digestion of complex polysaccharide such as starch, hemicellulose, and chitin for energy supply, and protected the snail from food poisoning and nitrate toxicity. Both microbial community and metabolism of B. glabrata were significantly altered by diet. The polysaccharide-degrading bacterium Chryseobacterium was enriched in the gut of snails fed with high-digestibility protein and high polysaccharide diet (HPHP). Notably, B. glabrata as a mobile repository can escalate biosafety issues regarding transmission of various pathogens such as Acinetobacter nosocomialis and Vibrio parahaemolyticus as well as multiple antibiotic resistance genes in the environment and to other organisms. IMPORTANCE The spread of aquatic gastropod Biomphalaria glabrata, an intermediate host of Schistosoma mansoni, exacerbates the burden of schistosomiasis disease worldwide. This study provides insights into the importance of microbiome for basic biological activities of freshwater snails, and offers a valuable microbial genome resource to fill the gap in the analysis of the snail-microbiota-parasite relationship. The results of this study clarified the reasons for the high adaptability of B. glabrata to diverse environments, and further illustrated the role of B. glabrata in accumulation of antibiotic resistance in the environment and spread of various pathogens. These findings have important implications for further exploration of the control of snail dissemination and schistosomiasis from a microbial perspective.
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Affiliation(s)
- Shuling Du
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
| | - Xi Sun
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Jingxiang Zhang
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Datao Lin
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Runzhi Chen
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Ying Cui
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Suoyu Xiang
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhongdao Wu
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
| | - Tao Ding
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, China
- Provincial Engineering Technology Research Center for Biological Vector Control, Guangzhou, China
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10
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Show BK, Banerjee S, Banerjee A, GhoshThakur R, Hazra AK, Mandal NC, Ross AB, Balachandran S, Chaudhury S. Insect gut bacteria: a promising tool for enhanced biogas production. REVIEWS IN ENVIRONMENTAL SCIENCE AND BIO/TECHNOLOGY 2022; 21:1-25. [DOI: 10.1007/s11157-021-09607-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/29/2021] [Indexed: 07/19/2023]
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11
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Wu X, Wang X, Shang Y, Sun G, Wei Q, Zhang H. Complete mitochondrial genome sequence and phylogenetic analysis of Arion ater (Stylommatophora: Arionidae). Mitochondrial DNA B Resour 2021; 6:2928-2930. [PMID: 34532588 PMCID: PMC8439229 DOI: 10.1080/23802359.2021.1972862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Xiaoyang Wu
- College of Life Science, Qufu Normal University, Qufu, Shandong, PR China
| | - Xibao Wang
- College of Life Science, Qufu Normal University, Qufu, Shandong, PR China
| | - Yongquan Shang
- College of Life Science, Qufu Normal University, Qufu, Shandong, PR China
| | - Guolei Sun
- College of Life Science, Qufu Normal University, Qufu, Shandong, PR China
| | - Qinguo Wei
- College of Life Science, Qufu Normal University, Qufu, Shandong, PR China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu, Shandong, PR China
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Pees B, Johnke J, Möhl M, Hamerich IK, Leippe M, Petersen C. Microbes to-go: slugs as source for Caenorhabditis elegans microbiota acquisition. Environ Microbiol 2021; 23:6721-6733. [PMID: 34414649 DOI: 10.1111/1462-2920.15730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022]
Abstract
Research on the Caenorhabditis elegans microbiota only recently started, with little known about how C. elegans acquires its microbiota. Slugs live in the same habitat as C. elegans and are known vectors for the worm. Hence, we wondered how the passage through a slug affects the C. elegans gut microbiota and whether worms can acquire bacteria from the slug. Using fluorescently labelled microbiota and 16S rRNA gene amplicon sequencing, we evaluated microbiota persistence and acquisition in C. elegans after slug passage. We compared C. elegans gut microbiomes isolated from wild-caught slugs to the microbiomes of worms after experimental slug passage to compare similarities and differences in microbiome composition. We found that microbiota persists in C. elegans while passing the slug gut and that worms simultaneously acquire additional bacteria species from the slug. Although the amplicon sequencing variant (ASV) richness of worms from the experiment did not exceed the richness of worms that naturally occur in slugs, we found a high number of shared ASVs indicating the importance of commonly associated microbiota. We demonstrate that C. elegans can take advantage of its passage through the slug by acquiring new potential microbiota without losing its native microbiota.
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Affiliation(s)
- Barbara Pees
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Julia Johnke
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Michelle Möhl
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Inga K Hamerich
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Matthias Leippe
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Carola Petersen
- Department of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
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13
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Current Status of Mining, Modification, and Application of Cellulases in Bioactive Substance Extraction. Curr Issues Mol Biol 2021; 43:687-703. [PMID: 34287263 PMCID: PMC8929041 DOI: 10.3390/cimb43020050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
Cellulases have been used to extract bioactive ingredients from medical plants; however, the poor enzymatic properties of current cellulases significantly limit their application. Two strategies are expected to address this concern: (1) new cellulase gene mining strategies have been promoted, optimized, and integrated, thanks to the improvement of gene sequencing, genomic data, and algorithm optimization, and (2) known cellulases are being modified, thanks to the development of protein engineering, crystal structure data, and computing power. Here, we focus on mining strategies and provide a systemic overview of two approaches based on sequencing and function. Strategies based on protein structure modification, such as introducing disulfide bonds, proline, salt bridges, N-glycosylation modification, and truncation of loop structures, have already been summarized. This review discusses four aspects of cellulase-assisted extraction. Initially, cellulase alone was used to extract bioactive substances, and later, mixed enzyme systems were developed. Physical methods such as ultrasound, microwave, and high hydrostatic pressure have assisted in improving extraction efficiency. Cellulase changes the structure of biomolecules during the extraction process to convert them into effective ingredients with better activity and bioavailability. The combination of cellulase with other enzymes and physical technologies is a promising strategy for future extraction applications.
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Jackson D, Maltz MR, Freund HL, Borneman J, Aronson E. Environment and Diet Influence the Bacterial Microbiome of Ambigolimax valentianus, an Invasive Slug in California. INSECTS 2021; 12:575. [PMID: 34201881 PMCID: PMC8307491 DOI: 10.3390/insects12070575] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022]
Abstract
Ambigolimax valentianus is an invasive European terrestrial gastropod distributed throughout California. It is a serious pest of gardens, plant nurseries, and greenhouses. We evaluated the bacterial microbiome of whole slugs to capture a more detailed picture of bacterial diversity and composition in this host. We concentrated on the influences of diet and environment on the Ambigolimax valentianus core bacterial microbiome as a starting point for obtaining valuable information to aid in future slug microbiome studies. Ambigolimax valentianus were collected from two environments (gardens or reared from eggs in a laboratory). DNA from whole slugs were extracted and next-generation 16S rRNA gene sequencing was performed. Slug microbiomes differed between environmental sources (garden- vs. lab-reared) and were influenced by a sterile diet. Lab-reared slugs fed an unsterile diet harbored greater bacterial species than garden-reared slugs. A small core microbiome was present that was shared across all slug treatments. This is consistent with our hypothesis that a core microbiome is present and will not change due to these treatments. Findings from this study will help elucidate the impacts of slug-assisted bacterial dispersal on soils and plants, while providing valuable information about the slug microbiome for potential integrated pest research applications.
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Affiliation(s)
- Denise Jackson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Natural Science Division, Porterville College, Porterville, CA 93257, USA
| | - Mia R. Maltz
- Center for Conservation Biology, University of California, Riverside, CA 92521, USA;
- Division of Biomedical Sciences, University of California, Riverside, CA 92521, USA
| | - Hannah L. Freund
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Genetics, Genomics, and Bioinformatics Program, University of California, Riverside, CA 92521, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
| | - Emma Aronson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (D.J.); (H.L.F.); (J.B.)
- Center for Conservation Biology, University of California, Riverside, CA 92521, USA;
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15
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Rajeswari G, Jacob S, Chandel AK, Kumar V. Unlocking the potential of insect and ruminant host symbionts for recycling of lignocellulosic carbon with a biorefinery approach: a review. Microb Cell Fact 2021; 20:107. [PMID: 34044834 PMCID: PMC8161579 DOI: 10.1186/s12934-021-01597-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/17/2021] [Indexed: 12/02/2022] Open
Abstract
Uprising fossil fuel depletion and deterioration of ecological reserves supply have led to the search for alternative renewable and sustainable energy sources and chemicals. Although first generation biorefinery is quite successful commercially in generating bulk of biofuels globally, the food versus fuel debate has necessitated the use of non-edible feedstocks, majorly waste biomass, for second generation production of biofuels and chemicals. A diverse class of microbes and enzymes are being exploited for biofuels production for a series of treatment process, however, the conversion efficiency of wide range of lignocellulosic biomass (LCB) and consolidated way of processing remains challenging. There were lot of research efforts in the past decade to scour for potential microbial candidate. In this context, evolution has developed the gut microbiota of several insects and ruminants that are potential LCB degraders host eco-system to overcome its host nutritional constraints, where LCB processed by microbiomes pretends to be a promising candidate. Synergistic microbial symbionts could make a significant contribution towards recycling the renewable carbon from distinctly abundant recalcitrant LCB. Several studies have assessed the bioprospection of innumerable gut symbionts and their lignocellulolytic enzymes for LCB degradation. Though, some reviews exist on molecular characterization of gut microbes, but none of them has enlightened the microbial community design coupled with various LCB valorization which intensifies the microbial diversity in biofuels application. This review provides a deep insight into the significant breakthroughs attained in enrichment strategy of gut microbial community and its molecular characterization techniques which aids in understanding the holistic microbial community dynamics. Special emphasis is placed on gut microbial role in LCB depolymerization strategies to lignocellulolytic enzymes production and its functional metagenomic data mining eventually generating the sugar platform for biofuels and renewable chemicals production.
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Affiliation(s)
- Gunasekaran Rajeswari
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist. , Kattankulathur, 603203, Tamil Nadu, India
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist. , Kattankulathur, 603203, Tamil Nadu, India.
| | - Anuj Kumar Chandel
- Department of Biotechnology, Engineering School of Lorena (EEL), University of São Paulo, Lorena, 12.602.810, Brazil
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
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16
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Silva JP, Ticona ARP, Hamann PRV, Quirino BF, Noronha EF. Deconstruction of Lignin: From Enzymes to Microorganisms. Molecules 2021; 26:2299. [PMID: 33921125 PMCID: PMC8071518 DOI: 10.3390/molecules26082299] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 11/20/2022] Open
Abstract
Lignocellulosic residues are low-cost abundant feedstocks that can be used for industrial applications. However, their recalcitrance currently makes lignocellulose use limited. In natural environments, microbial communities can completely deconstruct lignocellulose by synergistic action of a set of enzymes and proteins. Microbial degradation of lignin by fungi, important lignin degraders in nature, has been intensively studied. More recently, bacteria have also been described as able to break down lignin, and to have a central role in recycling this plant polymer. Nevertheless, bacterial deconstruction of lignin has not been fully elucidated yet. Direct analysis of environmental samples using metagenomics, metatranscriptomics, and metaproteomics approaches is a powerful strategy to describe/discover enzymes, metabolic pathways, and microorganisms involved in lignin breakdown. Indeed, the use of these complementary techniques leads to a better understanding of the composition, function, and dynamics of microbial communities involved in lignin deconstruction. We focus on omics approaches and their contribution to the discovery of new enzymes and reactions that impact the development of lignin-based bioprocesses.
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Affiliation(s)
- Jéssica P. Silva
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Alonso R. P. Ticona
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Pedro R. V. Hamann
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
| | - Betania F. Quirino
- Genetics and Biotechnology Laboratory, Embrapa-Agroenergy, 70770-901 Brasília, Brazil;
| | - Eliane F. Noronha
- Enzymology Laboratory, Cell Biology Department, University of Brasilia, 70910-900 Brasília, Brazil; (J.P.S.); (A.R.P.T.); (P.R.V.H.)
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17
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Hu Z, Tong Q, Chang J, Yu J, Li S, Niu H, Ma D. Gut bacterial communities in the freshwater snail Planorbella trivolvis and their modification by a non-herbivorous diet. PeerJ 2021; 9:e10716. [PMID: 33614273 PMCID: PMC7883694 DOI: 10.7717/peerj.10716] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022] Open
Abstract
The freshwater pulmonate snail Planorbella trivolvis is a common species in various bodies of water but is not native to China. Planorbella trivolvis usually live on diets with high fiber content, such as water grasses, algae and fallen leaves. These snails can attach to the wall of a water tank or to water grass and can be transported overseas to China through the ornamental fish trade. There are few studies investigating the intestinal microbiota of freshwater snails. In this study, using culture-independent molecular analysis, we assessed for the first time the complexity of bacterial communities in the intestines of reared snails. The intestinal microbiota in the snails fed different diets, that is, herbivorous feed (HV) with high cellulose and non-herbivorous feed (NHV) with low cellulose, were analyzed by Illumina sequencing. The results showed that the NHV-based diet significantly increased the body mass, shell diameter and specific growth rate of the snails after 60 days of rearing (P < 0.05). Histological experiments showed that the fat droplets in the epithelium columnar cells of the intestines of the NHV snails increased, and the cilia on these cells fell off. The sequencing results identified 486 and 195 OTUs in HV and NHV, respectively. Lots of bacteria were not reported previously in snails. The intestinal microbiota diversity index (Shannon, Simpson, Ace and Chao) in the NHV snails was significantly lower than that in the HV snails. The gut microbiota in the HV snails were predominantly Proteobacteria (52.97%) and Bacteroidetes (28.75%), while the gut microbiota in NHV snails were predominantly Proteobacteria (95.23%). At the genus level, Cloacibacterium (24.60%), Pseudomonas (4.47%), OM6ON (6.12%), and Rhodobacter (5.79%) were observed to be abundant in HV snails. However, Aeromonas (85.4%) was determined to be predominant in NHV snails. Functional prediction of the gut microbiome in snails by PICRUSt demonstrated a significant difference between the two groups, and the HV snails exhibited higher lignocellulose enzyme activity than did the NHV snails. This study represents a first step in characterizing the gut microbiota of the freshwater snail. Most of these microbes can process plant biomass and digest cellulose and lignocellulose, and the enzymes of these bacteria may have potential biotechnological applications in a variety of industrial processes.
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Affiliation(s)
- Zongfu Hu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Qing Tong
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jie Chang
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Jianhua Yu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Shuguo Li
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Huaxin Niu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Deying Ma
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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18
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Bredon M, Depuydt E, Brisson L, Moulin L, Charles C, Haenn S, Moumen B, Bouchon D. Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod. Microorganisms 2021; 9:microorganisms9010148. [PMID: 33440837 PMCID: PMC7826753 DOI: 10.3390/microorganisms9010148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/27/2020] [Accepted: 01/08/2021] [Indexed: 02/07/2023] Open
Abstract
The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host’s diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the “eco-holobiont” conceptualization of macroorganisms.
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Affiliation(s)
- Marius Bredon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
| | - Elisabeth Depuydt
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
| | - Lucas Brisson
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
| | - Laurent Moulin
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l’Eau, R&D Biologie, F-94200 Ivry sur Seine, France; (L.M.); (C.C.); (S.H.)
| | - Ciriac Charles
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l’Eau, R&D Biologie, F-94200 Ivry sur Seine, France; (L.M.); (C.C.); (S.H.)
- Agence Nationale de Sécurité Sanitaire de l’Alimentation, de l’Environnement et du Travail, F-94700 Maisons-Alfort, France
| | - Sophie Haenn
- Eau de Paris, Direction de la Recherche et du Développement pour la Qualité de l’Eau, R&D Biologie, F-94200 Ivry sur Seine, France; (L.M.); (C.C.); (S.H.)
| | - Bouziane Moumen
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
| | - Didier Bouchon
- UMR CNRS 7267, Ecologie et Biologie des Interactions, Université de Poitiers, F-86073 Poitiers, France; (M.B.); (E.D.); (L.B.); (B.M.)
- Correspondence: ; Tel.: +33-(0)5-49-45-38-95; Fax: +33-(0)5-49-45-40-15
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19
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Insects' potential: Understanding the functional role of their gut microbiome. J Pharm Biomed Anal 2020; 194:113787. [PMID: 33272789 DOI: 10.1016/j.jpba.2020.113787] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022]
Abstract
The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.
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20
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Guerrero EB, de Villegas RMD, Soria MA, Santangelo MP, Campos E, Talia PM. Characterization of two GH5 endoglucanases from termite microbiome using synthetic metagenomics. Appl Microbiol Biotechnol 2020; 104:8351-8366. [DOI: 10.1007/s00253-020-10831-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
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21
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Klein AH, Ballard KR, Storey KB, Motti CA, Zhao M, Cummins SF. Multi-omics investigations within the Phylum Mollusca, Class Gastropoda: from ecological application to breakthrough phylogenomic studies. Brief Funct Genomics 2020; 18:377-394. [PMID: 31609407 DOI: 10.1093/bfgp/elz017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/06/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022] Open
Abstract
Gastropods are the largest and most diverse class of mollusc and include species that are well studied within the areas of taxonomy, aquaculture, biomineralization, ecology, microbiome and health. Gastropod research has been expanding since the mid-2000s, largely due to large-scale data integration from next-generation sequencing and mass spectrometry in which transcripts, proteins and metabolites can be readily explored systematically. Correspondingly, the huge data added a great deal of complexity for data organization, visualization and interpretation. Here, we reviewed the recent advances involving gastropod omics ('gastropodomics') research from hundreds of publications and online genomics databases. By summarizing the current publicly available data, we present an insight for the design of useful data integrating tools and strategies for comparative omics studies in the future. Additionally, we discuss the future of omics applications in aquaculture, natural pharmaceutical biodiscovery and pest management, as well as to monitor the impact of environmental stressors.
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Affiliation(s)
- Anne H Klein
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kaylene R Ballard
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, Ottawa, ON, Canada K1S 5B6
| | - Cherie A Motti
- Australian Institute of Marine Science (AIMS), Cape Ferguson, Townsville Queensland 4810, Australia
| | - Min Zhao
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Scott F Cummins
- Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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22
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Microorganisms for Cellulase Production: Availability, Diversity, and Efficiency. Fungal Biol 2019. [DOI: 10.1007/978-3-030-14726-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Hu Z, Chen X, Chang J, Yu J, Tong Q, Li S, Niu H. Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing. PeerJ 2018; 6:e5537. [PMID: 30186698 PMCID: PMC6118204 DOI: 10.7717/peerj.5537] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/08/2018] [Indexed: 12/14/2022] Open
Abstract
Due to its wide distribution across the world, the snail Radix auricularia plays a central role in the transferal of energy and biomass by consuming plant biomass in freshwater systems. The gut microbiota are involved in the nutrition, digestion, immunity, and development of snails, particularly for cellulolytic bacteria, which greatly contribute to the digestion of plant fiber. For the first time, this study characterized the gut bacterial communities of R. auricularia, as well as predicted functions, using the Illumina Miseq platform to sequence 16S rRNA amplicons. Both juvenile snails (JS) and adult snails (AS) were sampled. The obtained 251,072 sequences were rarefied to 214,584 sequences and clustered into 1,196 operational taxonomic units (OTUs) with 97% sequence identity. The predominant phyla were Proteobacteria (JS: 36.0%, AS: 31.6%) and Cyanobacteria (JS: 16.3%, AS: 19.5%), followed by Chloroflexi (JS: 9.7%, AS: 13.1%), Firmicutes (JS: 14.4%, AS: 6.7%), Actinobacteria (JS: 8.2%, AS: 12.6%), and Tenericutes (JS: 7.3%, AS: 6.2%). The phylum Cyanobacteria may have originated from the plant diet instead of the gut microbiome. A total of 52 bacterial families and 55 genera were found with >1% abundance in at least one sample. A large number of species could not be successfully identified, which could indicate the detection of novel ribotypes or result from insufficient availability of snail microbiome data. The core microbiome consisted of 469 OTUs, representing 88.4% of all sequences. Furthermore, the predicted function of bacterial community of R. auricularia performed by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States suggests that functions related to metabolism and environmental information processing were enriched. The abundance of carbohydrate suggests a strong capability of the gut microbiome to digest lignin. Our results indicate an abundance of bacteria in both JS and AS, and thus the bacteria in R. auricularia gut form a promising source for novel enzymes, such as cellulolytic enzymes, that may be useful for biofuel production. Furthermore, searching for xenobiotic biodegradation bacteria may be a further important application of these snails.
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Affiliation(s)
- Zongfu Hu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China.,College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China.,Inner Mongolia Key Laboratory of Toxicant Monitoring and Toxicology, Tongliao, People's Republic of China
| | - Xi Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Jie Chang
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Jianhua Yu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Qing Tong
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, People's Republic of China
| | - Shuguo Li
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
| | - Huaxin Niu
- College of Animal Science and Technology, Inner Mongolia University for Nationalities, Tongliao, People's Republic of China
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Reich I, Ijaz UZ, Gormally M, Smith CJ. 16S rRNA sequencing reveals likely beneficial core microbes within faecal samples of the EU protected slug Geomalacus maculosus. Sci Rep 2018; 8:10402. [PMID: 29991804 PMCID: PMC6039444 DOI: 10.1038/s41598-018-28720-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/25/2018] [Indexed: 01/20/2023] Open
Abstract
The EU-protected slug Geomalacus maculosus Allman occurs only in the West of Ireland and in northern Spain and Portugal. We explored the microbial community found within the faeces of Irish specimens with a view to determining whether a core microbiome existed among geographically isolated slugs which could give insight into the adaptations of G. maculosus to the available food resources within its habitat. Faecal samples of 30 wild specimens were collected throughout its Irish range and the V3 region of the bacterial 16S rRNA gene was sequenced using Illumina MiSeq. To investigate the influence of diet on the microbial composition, faecal samples were taken and sequenced from six laboratory reared slugs which were raised on two different foods. We found a widely diverse microbiome dominated by Enterobacteriales with three core OTUs shared between all specimens. While the reared specimens appeared clearly separated by diet in NMDS plots, no significant difference between the slugs fed on the two different diets was found. Our results indicate that while the majority of the faecal microbiome of G. maculosus is probably dependent on the microhabitat of the individual slugs, parts of it are likely selected for by the host.
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Affiliation(s)
- Inga Reich
- Applied Ecology Unit, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland.
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA.
| | - Umer Zeeshan Ijaz
- School of Engineering, University of Glasgow, Glasgow, Scotland, UK.
| | - Mike Gormally
- Applied Ecology Unit, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Cindy J Smith
- School of Engineering, University of Glasgow, Glasgow, Scotland, UK.
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