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Xu M, Li F, Zhang X, Chen B, Geng Y, Ouyang P, Chen D, Li L, Huang X. Microbiome analysis reveals the intestinal microbiota characteristics and potential impact of Procambarus clarkii. Appl Microbiol Biotechnol 2024; 108:77. [PMID: 38204126 PMCID: PMC10781845 DOI: 10.1007/s00253-023-12914-5] [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: 07/19/2023] [Revised: 11/06/2023] [Accepted: 11/17/2023] [Indexed: 01/12/2024]
Abstract
The intestinal microbiota interacts with the host and plays an important role in the immune response, digestive physiology, and regulation of body functions. In addition, it is also well documented that the intestinal microbiota of aquatic animals are closely related to their growth rate. However, whether it resulted in different sizes of crayfish in the rice-crayfish coculture model remained vague. Here, we analyzed the intestinal microbiota characteristics of crayfish of three sizes in the same typical rice-crayfish coculture field by high-throughput sequencing technology combined with quantitative real-time polymerase chain reaction (qRT-PCR) and enzyme activity, investigating the relationship between intestinal microbiota in crayfish and water and sediments. The results showed that the dominant intestinal microbiota of crayfish was significantly different between the large size group (BS), normal size group (NS), and small size group (SS), where Bacteroides and Candidatus_Bacilloplasma contributed to the growth of crayfish by facilitating food digestion through cellulolysis, which might be one of the potential factors affecting the difference in sizes. Follow-up experiments confirmed that the activity of lipase (LPS) and protease was higher in BS, and the relative expression of development-related genes, including alpha-amylase (α-AMY), myocyte-specific enhancer factor 2a (MEF2a), glutathione reductase (GR), chitinase (CHI), and ecdysone receptor (EcR), in BS was significantly higher than that in SS. These findings revealed the intestinal microbiota characteristics of crayfish of different sizes and their potential impact on growth, which is valuable for managing and manipulating the intestinal microbiota in crayfish to achieve high productivity in practice. KEY POINTS: • Significant differences in the dominant microflora of BS, NS, and SS in crayfish. • Cellulolysis might be a potential factor affecting different sizes in crayfish. • Adding Bacteroides and Candidatus_Bacilloplasma helped the growth of crayfish.
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Affiliation(s)
- Ming Xu
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Fulong Li
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoli Zhang
- Fishery Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Wenjiang, Sichuan, China
| | - Baipeng Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Geng
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ping Ouyang
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Defang Chen
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Liangyu Li
- Fishery Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Wenjiang, Sichuan, China
| | - Xiaoli Huang
- Department of Aquaculture, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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2
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Guo Q, Liu W, Zhao L, Sui Y, Zhao H, Liu Y, Mu C, Wang X. Fermented bile acids improved growth performance and intestinal health by altering metabolic profiles and intestinal microbiome in Micropterus salmoides. Fish Shellfish Immunol 2024:109593. [PMID: 38697374 DOI: 10.1016/j.fsi.2024.109593] [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] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024]
Abstract
A type of fermented bile acids (FBAs) has been produced through a biological method, and its effects on growth performance, metabolism, and intestinal microbiota in largemouth bass were investigated. The results demonstrated that incorporating 0.03% to 0.05% FBAs diet could improve the final weight, weight gain and specific growth rate, and decrease the feed conversion ratio. Dietary FBAs did not significantly affect the levels of high-density lipoprotein, low-density lipoprotein, and triglycerides, but decreased the activities of α-amylase in most groups. Adding FBAs to the diet significantly increased the integrity of the microscopic structure of the intestine, thickened the muscular layer of the intestine, and notably enhanced its intestinal barrier function. The addition of FBAs to the diet increased the diversity of the gut microbiota in largemouth bass. At the phylum level, there was an increase in the abundance of Proteobacteria, Firmicutes, Tenericutes and Cyanobacteria and a significant decrease in Actinobacteria and Bacteroidetes. At the genus level, the relative abundance of beneficial bacteria Mycoplasma in the GN6 group and Coprococcus in the GN4 group significantly increased, while the pathogenic Enhydrobacter was inhibited. Meanwhile, the highest levels of AKP and ACP were observed in the groups treated with 0.03% FBAs, while the highest levels of TNF-α and IL-10 were detected in the group treated with 0.04% FBAs. Additionally, the highest levels of IL-1β, IL-8T, GF-β, IGF-1, and IFN-γ were noted in the group treated with 0.06% FBAs. These results suggested that dietary FBAs improved growth performance and intestinal wall health by altering lipid metabolic profiles and intestinal microbiota in largemouth bass.
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Affiliation(s)
- Qing Guo
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention & Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China; Anhui Chem-Bright Bioengineering Co., Ltd, Huaibei, 235025, PR China
| | - Wenwen Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention & Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China; Jining Leyuhui Ecological Agriculture Development Co., Ltd, Jining, 272000, PR China First author
| | - Lu Zhao
- Anhui Chem-Bright Bioengineering Co., Ltd, Huaibei, 235025, PR China.
| | - Yiming Sui
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention & Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China.
| | - Houfa Zhao
- Anhui Chem-Bright Bioengineering Co., Ltd, Huaibei, 235025, PR China.
| | - Yining Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention & Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China; Jining Leyuhui Ecological Agriculture Development Co., Ltd, Jining, 272000, PR China First author:.
| | - Cuimin Mu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention & Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China.
| | - Xuepeng Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention & Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Taian, 271018, PR China.
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Kotsou K, Chatzimitakos T, Athanasiadis V, Bozinou E, Lalas SI. Exploiting Agri-Food Waste as Feed for Tenebrio molitor Larvae Rearing: A Review. Foods 2024; 13:1027. [PMID: 38611333 PMCID: PMC11011778 DOI: 10.3390/foods13071027] [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: 02/23/2024] [Revised: 03/20/2024] [Accepted: 03/24/2024] [Indexed: 04/14/2024] Open
Abstract
The agri-food industry generates substantial amounts of waste, including by-products and residues. The increasing demand for sustainable and eco-friendly practices in the agri-food sector has sparked an interest in finding alternative uses for such waste materials. One promising approach is the utilization of waste from the agri-food industry as feed for the rearing of mealworms (Tenebrio molitor). Since agri-food waste is rich in proteins, carbohydrates, lipids, and vitamins, as well as other bioactive compounds, all of which are essential for insect growth and development, incorporating such waste into the diet of mealworms promotes sustainable insect production, reducing the economic and environmental problems associated with waste disposal. This practice can also be beneficial for the rearing of mealworms since their nutritional value can also be enhanced. To this end, various waste materials, such as fruit and vegetable peels, spent grains, and food processing residues, have been investigated as potential feed sources, leading to increased mass production, lower cost, and enhanced nutritional value. This review aims to highlight the potential of agri-food waste as a feed source for mealworms, as well as their potential to enhance their nutritional value. Furthermore, the potential applications of mealworms reared on agri-food waste are highlighted, including their potential as a sustainable protein source for human consumption and as feed ingredients in the livestock and aquaculture sectors.
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Affiliation(s)
- Konstantina Kotsou
- Department of Food Science and Nutrition, University of Thessaly, Terma N. Temponera Str., 43100 Karditsa, Greece; (T.C.); (V.A.); (E.B.); (S.I.L.)
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Zhang B, Hao B, Han M, Wang X. Impacts of pyraclostrobin on intestinal health and the intestinal microbiota in common carp (Cyprinus carpio L.). Pestic Biochem Physiol 2024; 199:105762. [PMID: 38458673 DOI: 10.1016/j.pestbp.2023.105762] [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] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/13/2023] [Accepted: 12/26/2023] [Indexed: 03/10/2024]
Abstract
Pyraclostrobin (PYR) is a strobilurin fungicide that is commonly used in agriculture, and its use in agriculture may lead to an increase in its residue in the aquatic environment and may have a deleterious influence on the intestinal health of aquatic creatures. Here, common carp were chronically exposed to PYR (0, 0.5, or 5.0 μg/L) for 30 d to determine its effect on the physical and immunological barrier and intestinal microbiota in the intestine. PYR exposure caused significant histological changes; altered the mRNA expression levels of occludin, claudin-2, and zonula occludens-1 (ZO-1); induced oxidative stress in the common carp intestine; and increased the serum D-lactate and diamine oxidase (DAO) levels. Moreover, PYR significantly increased the protein expression levels of tumour necrosis factor alpha (TNF-α), interleukin 1 beta (IL-1β), and IL-6 while decreasing the level of transforming growth factor beta (TGF-β). Further studies revealed that PYR significantly reduced lysozyme (LZM) and acid phosphatase (ACP) activities as well as complement 3 (C3) and immunoglobulin M (IgM) levels. Furthermore, PYR decreased gut microbial diversity while increasing the abundance of pathogenic bacteria such as Aeromonas and Shewanella, causing an intestinal microbial disturbances in common carp. These results imply that PYR has a negative impact on fish intestinal health and may pose serious health risks to fish by disrupting the intestinal microbiota, physical barrier, and immunological barrier in common carp.
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Affiliation(s)
- Bangjun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, Henan 453007, China; Henan International Joint Laboratory of Aquatic Ecotoxicology and Health Protection, Henan Normal University, Xinxiang, Henan 453007, China.
| | - Baozhen Hao
- School of Biological Engineering, Xinxiang University, Xinxiang, Henan 453003, China
| | - Maolin Han
- School of Biological Engineering, Xinxiang University, Xinxiang, Henan 453003, China
| | - Xiaojie Wang
- School of Biological Engineering, Xinxiang University, Xinxiang, Henan 453003, China
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Zhang S, Liu S, Liu H, Li H, Luo J, Zhang A, Ding Y, Ren T, Chen W. Stochastic Assembly Increases the Complexity and Stability of Shrimp Gut Microbiota During Aquaculture Progression. Mar Biotechnol (NY) 2024; 26:92-102. [PMID: 38165637 DOI: 10.1007/s10126-023-10279-4] [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] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
The gut microbiota of aquaculture species contributes to their food metabolism and regulates their health, which has been shown to vary during aquaculture progression of their hosts. However, limited research has examined the outcomes and mechanisms of these changes in the gut microbiota of hosts. Here, Kuruma shrimps from the beginning, middle, and late stages of aquaculture progression (about a time duration of 2 months between each stage) were collected and variations in the gut microbiota of Kuruma shrimp during the whole aquaculture process were examined. High-throughput sequencing demonstrated increases in the diversity and richness of the shrimp gut microbiota with aquaculture progression. In addition, the gut microbiota composition differed among cultural stages, with enrichment of Firmicutes, RF39, and Megamonas and a reduction in Proteobacteria in the mid-stage. Notably, only very few taxa were persistent in the shrimp gut microbiota during the whole aquaculture progression, while the number of taxa that specific to the end of aquaculture was high. Network analysis revealed increasing complexity of the shrimp gut microbiota during aquaculture progression. Moreover, the shrimp gut microbiota became significantly more stable towards the end of aquaculture. According to the results of neutral community model, contribution of stochastic processes for shaping the shrimp gut microbiota was elevated along the aquaculture progression. This study showed substantial variations in shrimp gut microbiota during aquaculture progression and explored the underlying mechanisms regulating these changes.
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Affiliation(s)
- Saisai Zhang
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Shuang Liu
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Hongwei Liu
- Dalian Ocean University, Dalian Liaoning, 116023, China
| | - Hui Li
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Jun Luo
- Dalian Sun Asia Tourism Holding Co. Ltd., Dalian, Liaoning, 116023, China
| | - Aili Zhang
- Dalian Ocean School, Dalian, Liaoning, 116023, China
| | - Yinpeng Ding
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China
| | - Tongjun Ren
- Dalian Ocean University, Dalian Liaoning, 116023, China
| | - Wenbo Chen
- Dalian Ocean Development Affairs Service, Dalian, Liaoning, 116023, China.
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Field CJ, Bowerman KL, Hugenholtz P. Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli. Microb Genom 2024; 10:001176. [PMID: 38189216 PMCID: PMC10868615 DOI: 10.1099/mgen.0.001176] [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: 10/24/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Many peptidoglycan-deficient bacteria such as the Mycoplasmatales are known host-associated lineages, lacking the environmental resistance mechanisms and metabolic capabilities necessary for a free-living lifestyle. Several peptidoglycan-deficient and non-sporulating orders of interest are thought to be descended from Gram-positive sporulating Bacilli through reductive evolution. Here we annotate 2650 genomes belonging to the class Bacilli, according to the Genome Taxonomy Database, to predict the peptidoglycan and sporulation phenotypes of three novel orders, RFN20, RF39 and ML615J-28, known only through environmental sequence surveys. These lineages are interspersed between peptidoglycan-deficient non-sporulating orders including the Mycoplasmatales and Acholeplasmatales, and more typical Gram-positive orders such as the Erysipelotrichales and Staphylococcales. We use the extant genotypes to perform ancestral state reconstructions. The novel orders are predicted to have small genomes with minimal metabolic capabilities and to comprise a mix of peptidoglycan-deficient and/or non-sporulating species. In contrast to expectations based on cultured representatives, the order Erysipelotrichales lacks many of the genes involved in peptidoglycan and endospore formation. The reconstructed evolutionary history of these traits suggests multiple independent whole-genome reductions and loss of phenotype via intermediate transition states that continue into the present. We suggest that the evolutionary history of the reduced-genome lineages within the class Bacilli is one driven by multiple independent transitions to host-associated lifestyles, with the degree of reduction in environmental resistance and metabolic capabilities correlated with degree of host association.
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Affiliation(s)
- Christian J. Field
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Kate L. Bowerman
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, The Australian Centre for Ecogenomics, The University of Queensland, St Lucia, QLD 4072, Australia
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Kakakhel MA, Narwal N, Kataria N, Johari SA, Zaheer Ud Din S, Jiang Z, Khoo KS, Xiaotao S. Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review. Environ Res 2023; 237:117002. [PMID: 37648194 DOI: 10.1016/j.envres.2023.117002] [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] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/01/2023]
Abstract
The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.
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Affiliation(s)
- Mian Adnan Kakakhel
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Nishita Narwal
- University School of Environment Management, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India
| | - Navish Kataria
- Department of Environmental Sciences, J.C. Bose University of Science and Technology, YMCA, Faridabad, Haryana, 121006, India
| | - Seyed Ali Johari
- Department of Fisheries, Faculty of Natural Resources, University of Kurdistan, Sanandaj, Kurdistan, Iran
| | - Syed Zaheer Ud Din
- International School for Optoelectronic Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Zewen Jiang
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China
| | - Kuan Shiong Khoo
- Department of Chemical Engineering and Materials Science, Yuan Ze University, Taoyuan, Taiwan
| | - Shi Xiaotao
- Hubei International Science and Technology Cooperation Base of Fish Passage, Three Gorges University, Yichang, 443002, Hubei, China; College of Hydraulic & Environmental Engineering, Three Gorges University, Yichang, 443002, Hubei, China.
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Séraphin MN, Bellot J, Klann E, Ukhanova M, Saulsberry FG, Peloquin CA, Mai V. Gut microbiota composition and diversity before, during, and two months after rifamycin-based tuberculosis preventive therapy. Sci Rep 2023; 13:18933. [PMID: 37919333 PMCID: PMC10622450 DOI: 10.1038/s41598-023-44854-5] [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: 11/25/2022] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Tuberculosis (TB) preventive therapy (TPT) is an effective strategy to eliminate TB in low-incidence settings. Shorter TPT regimens incorporating the antimicrobial class of rifamycins are designed to improve adherence and completion rates but carry the risk of modifications to the gut microbiota. We enrolled six subjects diagnosed with latent TB infection (LTBI) who accepted to initiate TPT. We also enrolled six healthy volunteers unexposed to the rifamycins. We profiled the gut microbiota using 16S rRNA amplicon sequencing (V1-V2 region) to document the immediate effect of rifamycin-based TPT on the gut microbiota composition and tracked recovery to baseline two months after TPT. Overall, TPT accounted for 17% of the variance in gut microbial community dissimilarity. This rifamycin-based TPT induced dysbiosis was characterized by a depletion of butyrate-producing taxa (Clostridium-XIVa and Roseburia) and expansion of potentially pathogenic taxa within the Firmicutes and Proteobacteria phyla. Recovery of the gut microbial composition was incomplete two months after TPT. Robust clinical studies are necessary to comprehensively catalogue TPT-induced gut microbiota dysbiosis to inform strategies to mitigate potential long-term sequelae of this important TB control intervention.
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Affiliation(s)
- Marie Nancy Séraphin
- Department of Medicine, Division of Infectious Diseases and Global Medicine, College of Medicine, University of Florida, Gainesville, FL, USA.
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Julia Bellot
- Department of Medicine, Division of Infectious Diseases and Global Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Emily Klann
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Maria Ukhanova
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
| | - Florence G Saulsberry
- Florida Department of Health in Alachua County, Disease Control Unit, Alachua County Health Department, Gainesville, FL, USA
| | - Charles A Peloquin
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Infectious Disease Pharmacokinetics Laboratory, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Volker Mai
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, University of Florida, Gainesville, FL, USA
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Szekeres E, Baricz A, Cristea A, Levei EA, Stupar Z, Brad T, Kenesz M, Moldovan OT, Banciu HL. Karst spring microbiome: Diversity, core taxa, and community response to pathogens and antibiotic resistance gene contamination. Sci Total Environ 2023; 895:165133. [PMID: 37364839 DOI: 10.1016/j.scitotenv.2023.165133] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/19/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Karst aquifers are important water resources for drinking water supplies worldwide. Although they are susceptible to anthropogenic contamination due to their high permeability, there is a lack of detailed knowledge on the stable core microbiome and how contamination may affect these communities. In this study, eight karst springs (distributed across three different regions in Romania) were sampled seasonally for one year. The core microbiota was analysed by 16S rRNA gene amplicon sequencing. To identify bacteria carrying antibiotic resistance genes and mobile genetic elements, an innovative method was applied, consisting of high-throughput antibiotic resistance gene quantification performed on potential pathogen colonies cultivated on Compact Dry™ plates. A taxonomically stable bacterial community consisting of Pseudomonadota, Bacteroidota, and Actinomycetota was revealed. Core analysis reaffirmed these results and revealed primarily freshwater-dwelling, psychrophilic/psychrotolerant species affiliated to Rhodoferax, Flavobacterium, and Pseudomonas genera. Both sequencing and cultivation methods indicated that more than half of the springs were contaminated with faecal bacteria and pathogens. These samples contained high levels of sulfonamide, macrolide, lincosamide and streptogramins B, and trimethoprim resistance genes spread primarily by transposase and insertion sequences. Differential abundance analysis found Synergistota, Mycoplasmatota, and Chlamydiota as suitable candidates for pollution monitoring in karst springs. This is the first study highlighting the applicability of a combined approach based on high-throughput SmartChip™ antibiotic resistance gene quantification and Compact Dry™ pathogen cultivation for estimating microbial contaminants in karst springs and other challenging low biomass environments.
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Affiliation(s)
- Edina Szekeres
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania; National Institute of Research and Development for Biological Sciences, Institute of Biological Research, Cluj-Napoca, Romania
| | - Andreea Baricz
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Adorján Cristea
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania; Department of Taxonomy and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Erika Andrea Levei
- INCDO-INOE 2000, Research Institute for Analytical Instrumentation, Cluj-Napoca, Romania
| | - Zamfira Stupar
- INCDO-INOE 2000, Research Institute for Analytical Instrumentation, Cluj-Napoca, Romania
| | - Traian Brad
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Marius Kenesz
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Oana Teodora Moldovan
- Department of Cluj-Napoca, Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
| | - Horia Leonard Banciu
- Department of Molecular Biology and Biotechnology, Faculty of Biology and Geology, Babeș-Bolyai University, Cluj-Napoca, Romania; Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, Cluj-Napoca, Romania.
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Akter S, Wos-Oxley ML, Catalano SR, Hassan MM, Li X, Qin JG, Oxley AP. Host Species and Environment Shape the Gut Microbiota of Cohabiting Marine Bivalves. Microb Ecol 2023; 86:1755-1772. [PMID: 36811710 PMCID: PMC10497454 DOI: 10.1007/s00248-023-02192-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Pacific oysters (Crassostrea gigas) and Mediterranean mussels (Mytilus galloprovincialis) are commercially important marine bivalves that frequently coexist and have overlapping feeding ecologies. Like other invertebrates, their gut microbiota is thought to play an important role in supporting their health and nutrition. Yet, little is known regarding the role of the host and environment in driving these communities. Here, bacterial assemblages were surveyed from seawater and gut aspirates of farmed C. gigas and co-occurring wild M. galloprovincialis in summer and winter using Illumina 16S rRNA gene sequencing. Unlike seawater, which was dominated by Pseudomonadata, bivalve samples largely consisted of Mycoplasmatota (Mollicutes) and accounted for >50% of the total OTU abundance. Despite large numbers of common (core) bacterial taxa, bivalve-specific species (OTUs) were also evident and predominantly associated with Mycoplasmataceae (notably Mycoplasma). An increase in diversity (though with varied taxonomic evenness) was observed in winter for both bivalves and was associated with changes in the abundance of core and bivalve-specific taxa, including several representing host-associated and environmental (free-living or particle-diet associated) organisms. Our findings highlight the contribution of the environment and the host in defining the composition of the gut microbiota in cohabiting, intergeneric bivalve populations.
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Affiliation(s)
- Shirin Akter
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | - Sarah R Catalano
- Aquatic Sciences Centre, South Australian Research and Development Institute, West Beach, SA, Australia
| | - Md Mahbubul Hassan
- Aquaculture Research and Development, Department of Primary Industries and Regional Development, Hillarys, WA, Australia
| | - Xiaoxu Li
- Aquatic Sciences Centre, South Australian Research and Development Institute, West Beach, SA, Australia
| | - Jian G Qin
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Andrew Pa Oxley
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia.
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11
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Yin H, Huang Y, Yan G, Huang Q, Wang Y, Liu H, Huang Z, Hong Y. Effects of chlorantraniliprole-based pesticide on transcriptional response and gut microbiota of the crucian carp, Carassius carassius. Ecotoxicol Environ Saf 2023; 263:115292. [PMID: 37494733 DOI: 10.1016/j.ecoenv.2023.115292] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 07/28/2023]
Abstract
Chlorantraniliprole (CAP) is a presentative diamide pesticide utilized in agricultural area and as well as rice-fish co-culture system for pest control. However, the understanding of toxic effects of CAP on fish species is still incomplete. In the present study, we performed an integrated study of the acute toxicity and bioaccumulation of CAP on the crucian carp, Carassius carassius, a fish species widely distributed in freshwater area in China and commonly farmed in the rice-fish co-culture systems. Besides, biochemical changes, transcriptional responses and gut microbiota of fish were investigated upon sub-chronic CAP exposure. The results showed that CAP is low toxic to crucian carp with a 96 h LC50 of 74.824 mg/L, but has considerable accumulation in the fish muscles when exposed to 3 mg/L of CAP for 14 d and still detectable after 18 d recovery in fresh water. For sub-chronic test, fish were exposed to CAP at 0, 0.3, 3 and 30 mg/L respectively for 14 d. CAP induced oxidative stress and detoxification inhibition in the liver of fish by decreasing antioxidative and detoxicated enzymes activities and downregulating relevant genes expression. In addition, disrupted gut flora composition was found in all experimental groups by the 16 S rRNA sequencing data, indicating the gut microbiota dysbiosis in crucian carp and potential adverse host effect. All the results suggest that CAP at sublethal concentrations has prominent toxic effect on crucian carp and more attentions should be paid especially using directly in an integrated aquaculture system.
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Affiliation(s)
- Hongmei Yin
- Key Laboratory of Animal Disease Detection and Prevention in Panxi District, Xichang University, Xichang 415000, China
| | - Yi Huang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, China
| | - Guangwen Yan
- Key Laboratory of Animal Disease Detection and Prevention in Panxi District, Xichang University, Xichang 415000, China
| | - Qiang Huang
- Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, China
| | - Yan Wang
- Guangyuan Agricultural and Rural Bureau, Guangyuan 628017, China
| | - Hongming Liu
- Guangyuan Agricultural and Rural Bureau, Guangyuan 628017, China
| | - Zhiqiu Huang
- Key Laboratory of Animal Disease Detection and Prevention in Panxi District, Xichang University, Xichang 415000, China; Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, China
| | - Yuhang Hong
- Key Laboratory of Animal Disease Detection and Prevention in Panxi District, Xichang University, Xichang 415000, China; Key Laboratory of Application of Ecology and Environmental Protection in Plateau Wetland of Sichuan, Xichang University, Xichang 415000, China.
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12
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Zheng R, Wang C, Cai R, Shan Y, Sun C. Mechanisms of nucleic acid degradation and high hydrostatic pressure tolerance of a novel deep-sea wall-less bacterium. mBio 2023; 14:e0095823. [PMID: 37551978 PMCID: PMC10470597 DOI: 10.1128/mbio.00958-23] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 06/26/2023] [Indexed: 08/09/2023] Open
Abstract
Wall-less bacteria are broadly distributed in diverse habitats. They evolved from a common ancestor within the Firmicutes phylum through reductive evolution. Here, we report the cultivation, characterization, and polyphasic taxonomic analysis of the novel free-living wall-less bacterium, Hujiaoplasma nucleasis zrk29. We demonstrated that strain zrk29 had a strong ability to degrade DNA and RNA both under laboratory conditions and in the deep sea. We found that nucleic acids induced strain zrk29 to release chronic bacteriophages which supported strain zrk29 and other marine bacteria to metabolize nucleic acids without lysing host cells. We also showed that strain zrk29 tolerated high hydrostatic pressure via two pathways: (i) by transporting cations into its cells to increase intracellular osmotic pressure and (ii) by adjusting the unsaturated fatty acid chain content in its cell membrane phospholipids to increase cell membrane fluidity. This study extends our understanding of free-living wall-less bacteria and provides a useful model to explore the unique adaptation mechanisms of deep-sea microbes. IMPORTANCE The unique physiology and survival strategies of the Tenericutes bacterium-a typical wall-less bacterium-have fascinated scientists and the public, especially in extreme deep-sea environments where there is high hydrostatic pressure (HHP) and limited availability of nutrients. Here, we have isolated a novel free-living Tenericutes strain from deep-sea sediment and have found that it metabolizes nucleic acids with the support of chronic bacteriophages. This Tenericutes strain tolerates HHP stress by increasing intracellular osmotic pressure and the unsaturated fatty acid chain content of phospholipids in its cell membrane. Our results provide insights into the unique physiology of deep-sea free-living Tenericutes bacteria and highlight the significant role that chronic bacteriophages play in assisting wall-less bacteria to adapt to harsh conditions.
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Affiliation(s)
- Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Chong Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yeqi Shan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing, China
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13
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He P, Wang H, Shi J, Xin M, Wang W, Xie L, Wei Q, Huang M, Shi X, Fan Y, Chen H. Prokaryote Distribution Patterns along a Dissolved Oxygen Gradient Section in the Tropical Pacific Ocean. Microorganisms 2023; 11:2172. [PMID: 37764016 PMCID: PMC10534896 DOI: 10.3390/microorganisms11092172] [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: 07/07/2023] [Revised: 08/09/2023] [Accepted: 08/13/2023] [Indexed: 09/29/2023] Open
Abstract
Oceanic oxygen levels are decreasing significantly in response to global climate change; however, the microbial diversity and ecological functional responses to dissolved oxygen (DO) in the open ocean are largely unknown. Here, we present prokaryotic distribution coupled with physical and biogeochemical variables and DO gradients from the surface to near the bottom of a water column along an approximately 12,000-km transect from 13° N to 18° S in the Tropical Pacific Ocean. Nitrate (11.42%), temperature (10.90%), pH (10.91%), silicate (9.34%), phosphate (4.25%), chlorophyll a (3.66%), DO (3.50%), and salinity (3.48%) significantly explained the microbial community variations in the studied area. A distinct microbial community composition broadly corresponding to the water masses formed vertically. Additionally, distinct ecotypes of Thaumarchaeota and Nitrospinae belonging to diverse phylogenetic clades that coincided with specific vertical niches were observed. Moreover, the correlation analysis revealed large-scale natural feedback in which chlorophyll a (organic matter) promoted Thaumarchaeotal biomass at depths that subsequently coupled with Nitrospina, produced and replenished nitrate for phytoplankton productivity at the surface. Low DO also favored Thaumarchaeota growth and fueled nitrate production.
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Affiliation(s)
- Peiqing He
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Huan Wang
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Jie Shi
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
| | - Ming Xin
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Weimin Wang
- Center for Ocean and Climate Research, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China;
| | - Linping Xie
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Qinsheng Wei
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Mu Huang
- Key Laboratory of State Oceanic Administration for Marine Sedimentology & Environmental Geology, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (M.H.); (X.S.)
| | - Xuefa Shi
- Key Laboratory of State Oceanic Administration for Marine Sedimentology & Environmental Geology, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (M.H.); (X.S.)
| | - Yaqin Fan
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
| | - Hao Chen
- Key Laboratory of Science and Technology for Marine Ecology and Environment, First Institute of Oceanography, Ministry of Natural Resources, 6 Xianxialing Road, Qingdao 266061, China; (P.H.); (H.W.); (J.S.); (M.X.); (L.X.); (Q.W.); (Y.F.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, 168 Wenhai Middle Road, Aoshanwei, Jimo District, Qingdao 266071, China
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14
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Li H, Christman LM, Yagiz Y, Washington TL, Wang GP, Gu L. Dealcoholized muscadine wine was partially effective in preventing and treating dextran sulfate sodium-induced colitis and restoring gut dysbiosis in mice. Food Funct 2023; 14:5994-6011. [PMID: 37310366 DOI: 10.1039/d3fo00047h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Muscadine wine has a unique polyphenol profile consisting of anthocyanins, ellagic acids, and flavonols. This study aims to compare the prevention, treatment, and combined activity (P + T) of dealcoholized muscadine wine (DMW) on DSS-induced colitis in mice and its impact on the gut microbiome. Male C57BL/6 mice in the healthy and colitis group received an AIN-93M diet for 28 days. In the prevention, treatment, and P + T (prevention + treatment) groups, mice received an AIN-93M diet containing 2.79% (v/w) DMW on days 1-14, 15-28, and 1-28, respectively. Except for mice in the healthy group, all mice were given water with 2.5% (w/v) DSS on days 8-14 to induce colitis. DMW in all three receiving groups reduced myeloperoxidase activity, histology scores, and phosphorylation of Iκb-α in the colon. Colon shortening, serum IL-6, and colonic mRNA of TNF-α were blunted only in the P + T group. Gut permeability was reduced in the treatment and P + T groups. DMW in P + T group showed higher activity to increase microbiome evenness, modulate β-diversity, elevate the cecal content of SCFAs, and enrich SCFA-producing bacteria, including Lactobacillaceae, Lachnospiraceae, Ruminococcaceae, and Peptococcaceae. This was accompanied by a decrease in pathogenic Burkholderiaceae in mice. This study suggests that muscadine wine has partial preventive and therapeutic effects against inflammatory bowel disease. The combination of prevention and treatment using DMW showed better activities than either prevention or treatment.
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Affiliation(s)
- Hao Li
- Food Science and Human Nutrition Department, College of Agricultural and Life Sciences, USA.
| | - Lindsey M Christman
- Food Science and Human Nutrition Department, College of Agricultural and Life Sciences, USA.
| | - Yavuz Yagiz
- Food Science and Human Nutrition Department, College of Agricultural and Life Sciences, USA.
| | - Taylor L Washington
- Food Science and Human Nutrition Department, College of Agricultural and Life Sciences, USA.
| | - Gary P Wang
- Division of Infectious Diseases and Global Medicine, College of Medicine, University of Florida, Gainesville, Florida 32611, USA
| | - Liwei Gu
- Food Science and Human Nutrition Department, College of Agricultural and Life Sciences, USA.
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15
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Alvanou MV, Feidantsis K, Staikou A, Apostolidis AP, Michaelidis B, Giantsis IA. Probiotics, Prebiotics, and Synbiotics Utilization in Crayfish Aquaculture and Factors Affecting Gut Microbiota. Microorganisms 2023; 11:1232. [PMID: 37317206 DOI: 10.3390/microorganisms11051232] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 04/28/2023] [Accepted: 05/05/2023] [Indexed: 06/16/2023] Open
Abstract
Aquaculture is affected by numerous factors that may cause various health threats that have to be controlled by the most environmentally friendly approaches. In this context, prebiotics, probiotics, and synbiotics are frequently incorporated into organisms' feeding rations to ameliorate the health status of the host's intestine, enhancing its functionality and physiological performance, and to confront increasing antimicrobial resistance. The first step in this direction is the understanding of the complex microbiome system of the organism in order to administer the optimal supplement, in the best concentration, and in the correct way. In the present review, pre-, pro-, and synbiotics as aquaculture additives, together with the factors affecting gut microbiome in crayfish, are discussed, combined with their future prospective outcomes. Probiotics constitute non-pathogenic bacteria, mainly focused on organisms' energy production and efficient immune response; prebiotics constitute fiber indigestible by the host organism, which promote the preferred gastrointestinal tract microorganisms' growth and activity towards the optimum balance between the gastrointestinal and immune system's microbiota; whereas synbiotics constitute their combination as a blend. Among pro-, pre-, and synbiotics' multiple benefits are boosted immunity, increased resistance towards pathogens, and overall welfare promotion. Furthermore, we reviewed the intestinal microbiota abundance and composition, which are found to be influenced by a plethora of factors, including the organism's developmental stage, infection by pathogens, diet, environmental conditions, culture methods, and exposure to toxins. Intestinal microbial communities in crayfish exhibit high plasticity, with infections leading to reduced diversity and abundance. The addition of synbiotic supplementation seems to provide better results than probiotics and prebiotics separately; however, there are still conflicting results regarding the optimal concentration.
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Affiliation(s)
- Maria V Alvanou
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
| | - Konstantinos Feidantsis
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Alexandra Staikou
- Laboratory of Marine and Terrestrial Animal Diversity, Department of Zoology, Facultyof Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki,Greece
| | - Apostolos P Apostolidis
- Laboratory of Ichthyology & Fisheries, Department of Animal Production, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Basile Michaelidis
- Laboratory of Animal Physiology, Department of Zoology, Faculty of Science, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Ioannis A Giantsis
- Department of Animal Science, Faculty of Agricultural Sciences, University of Western Macedonia, 53100 Florina, Greece
- Laboratory of Ichthyology & Fisheries, Department of Animal Production, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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16
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Muhammad S, Xu X, Zhou W, Wu L. Alternative splicing: An efficient regulatory approach towards plant developmental plasticity. Wiley Interdiscip Rev RNA 2023; 14:e1758. [PMID: 35983878 DOI: 10.1002/wrna.1758] [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] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/28/2022] [Accepted: 07/19/2022] [Indexed: 05/13/2023]
Abstract
Alternative splicing (AS) is a gene regulatory mechanism that plants adapt to modulate gene expression (GE) in multiple ways. AS generates alternative isoforms of the same gene following various development and environmental stimuli, increasing transcriptome plasticity and proteome complexity. AS controls the expression levels of certain genes and regulates GE networks that shape plant adaptations through nonsense-mediated decay (NMD). This review intends to discuss AS modulation, from interaction with noncoding RNAs to the established roles of splicing factors (SFs) in response to endogenous and exogenous cues. We aim to gather such studies that highlight the magnitude and impact of AS, which are not always clear from individual articles, when AS is increasing in individual genes and at a global level. This work also anticipates making plant researchers know that AS is likely to occur in their investigations and that dynamic changes in AS and their effects must be frequently considered. We also review our understanding of AS-mediated posttranscriptional modulation of plant stress tolerance and discuss its potential application in crop improvement in the future. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
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Affiliation(s)
- Sajid Muhammad
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoli Xu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Weijun Zhou
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liang Wu
- Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan, China
- State Key Laboratory of Rice Biology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, China
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17
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Prem EM, Schwarzenberger A, Markt R, Wagner AO. Effects of phenyl acids on different degradation phases during thermophilic anaerobic digestion. Front Microbiol 2023; 14:1087043. [PMID: 37089573 PMCID: PMC10113666 DOI: 10.3389/fmicb.2023.1087043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/06/2023] [Indexed: 04/08/2023] Open
Abstract
Aromatic compounds like phenyl acids (PA) can accumulate during anaerobic digestion (AD) of organic wastes due to an increased entry of lignocellulose, secondary plant metabolites or proteins, and thermodynamic challenges in degrading the benzene ring. The effects of aromatic compounds can be various – from being highly toxic to be stimulating for methanogenesis – depending on many parameters like inoculum or molecular characteristics of the aromatic compound. To contribute to a better understanding of the consequences of PA exposure during AD, the aim was to evaluate the effects of 10 mM PA on microbial communities degrading different, degradation phase–specific substrates in thermophilic batch reactors within 28 days: Microcrystalline cellulose (MCC, promoting hydrolytic to methanogenic microorganisms), butyrate or propionate (promoting syntrophic volatile fatty acid (VFA) oxidisers to methanogens), or acetate (promoting syntrophic acetate oxidisers to methanogens). Methane production, VFA concentrations and pH were evaluated, and microbial communities and extracellular polymeric substances (EPS) were assessed. The toxicity of PA depended on the type of substrate which in turn determined the (i) microbial diversity and composition and (ii) EPS quantity and quality. Compared with the respective controls, methane production in MCC reactors was less impaired by PA than in butyrate, propionate and acetate reactors which showed reductions in methane production of up to 93%. In contrast to the controls, acetate concentrations were high in all PA reactors at the end of incubation thus acetate was a bottle-neck intermediate in those reactors. Considerable differences in EPS quantity and quality could be found among substrates but not among PA variants of each substrate. Methanosarcina spp. was the dominant methanogen in VFA reactors without PA exposure and was inhibited when PA were present. VFA oxidisers and Methanothermobacter spp. were abundant in VFA assays with PA exposure as well as in all MCC reactors. As MCC assays showed higher methane yields, a higher microbial diversity and a higher EPS quantity and quality than VFA reactors when exposed to PA, we conclude that EPS in MCC reactors might have been beneficial for absorbing/neutralising phenyl acids and keeping (more susceptible) microorganisms shielded in granules or biofilms.
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Affiliation(s)
- Eva Maria Prem
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
| | | | - Rudolf Markt
- Department of Microbiology, Universität Innsbruck, Innsbruck, Austria
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Hernández-Pérez A, Söderhäll I. Intestinal microbiome in crayfish: Its role upon growth and disease presentation. Dev Comp Immunol 2023; 145:104703. [PMID: 37004928 DOI: 10.1016/j.dci.2023.104703] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/31/2023] [Accepted: 03/29/2023] [Indexed: 05/20/2023]
Abstract
The intestine-associated microbiota in crustaceans are considered a key element for maintaining homeostasis and health within the organisms. Recently, efforts have been made to characterize bacterial communities of freshwater crustaceans, including crayfish, and their interplay with the host's physiology and the aquatic environments. As a result, it has become evident that crayfish intestinal microbial communities display high plasticity, which is strongly influenced by both the diet, especially in aquaculture, and the environment. Moreover, studies regarding the characterization and distribution of the microbiota along the gut portions led to the discovery of bacteria with probiotic potential. The addition of these microorganisms to their food has shown a limited positive correlation with the growth and development of crayfish freshwater species. Finally, there is evidence that infections, particularly those from viral etiology, lead to low diversity and abundance of the intestinal microbial communities. In the present article, we have reviewed data on the crayfish' intestinal microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of phylum within this community. In addition, we have also searched for evidence of microbiome manipulation and its potential impact on productive parameters, and discussed the role of the microbiome in the regulation of diseases presentation, and environmental perturbations.
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Affiliation(s)
- Ariadne Hernández-Pérez
- Departamento de Medicina y Zootecnia de Abejas, Conejos y Organismos Acuáticos. Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Circuito de la Investigación Científica s/n, 04510, Ciudad Universitaria, México.
| | - Irene Söderhäll
- Department of Organismal Biology, Uppsala University, Norbyvägen 18A, 752 36, Uppsala, Sweden
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Xiang X, Peng B, Liu K, Wang T, Ding P, Li H, Zhu Y, Ming Y. Association between salivary microbiota and renal function in renal transplant patients during the perioperative period. Front Microbiol 2023; 14:1122101. [PMID: 37065138 PMCID: PMC10090686 DOI: 10.3389/fmicb.2023.1122101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
IntroductionRenal transplantation is an effective treatment for the end stage renal disease (ESRD). However, how salivary microbiota changes during perioperative period of renal transplant recipients (RTRs) has not been elucidated.MethodsFive healthy controls and 11 RTRs who had good recovery were enrolled. Saliva samples were collected before surgery and at 1, 3, 7, and 14 days after surgery. 16S rRNA gene sequencing was performed.ResultsThere was no significant difference in the composition of salivary microbiota between ESRD patients and healthy controls. The salivary microbiota of RTRs showed higher operational taxonomic units (OTUs) amount and greater alpha and beta diversity than those of ESRD patients and healthy controls, but gradually stabilized over time. At the phylum level, the relative abundance of Actinobacteria, Tenericutes and Spirochaetes was about ten times different from ESRD patients or healthy controls for RTRs overall in time. The relative abundance of Bacteroidetes, Fusobacteria, Patescibacteria, Leptotrichiaceae and Streptococcaceae was correlated with serum creatinine (Scr) after renal transplantation.DiscussionIn short, salivary microbiota community altered in the perioperative period of renal transplantation and certain species of salivary microbiota had the potential to be a biomarker of postoperative recovery.
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Affiliation(s)
- Xuyu Xiang
- The Transplantation Center of the Third Xiangya Hospital, Central South University, Changsha, China
- Engineering and Technology Research Center for Transplantation Medicine of National Health Commission, Changsha, China
| | - Bo Peng
- The Transplantation Center of the Third Xiangya Hospital, Central South University, Changsha, China
- Engineering and Technology Research Center for Transplantation Medicine of National Health Commission, Changsha, China
| | - Kai Liu
- The Transplantation Center of the Third Xiangya Hospital, Central South University, Changsha, China
- Engineering and Technology Research Center for Transplantation Medicine of National Health Commission, Changsha, China
| | - Tianyin Wang
- The Transplantation Center of the Third Xiangya Hospital, Central South University, Changsha, China
- Engineering and Technology Research Center for Transplantation Medicine of National Health Commission, Changsha, China
| | - Peng Ding
- The Transplantation Center of the Third Xiangya Hospital, Central South University, Changsha, China
- Engineering and Technology Research Center for Transplantation Medicine of National Health Commission, Changsha, China
| | - Hao Li
- The Transplantation Center of the Third Xiangya Hospital, Central South University, Changsha, China
- Engineering and Technology Research Center for Transplantation Medicine of National Health Commission, Changsha, China
| | - Yi Zhu
- The Transplantation Center of the Third Xiangya Hospital, Central South University, Changsha, China
- Engineering and Technology Research Center for Transplantation Medicine of National Health Commission, Changsha, China
| | - Yingzi Ming
- The Transplantation Center of the Third Xiangya Hospital, Central South University, Changsha, China
- Engineering and Technology Research Center for Transplantation Medicine of National Health Commission, Changsha, China
- *Correspondence: Yingzi Ming
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Cheatham CN, Gustafson KL, McAdams ZL, Turner GM, Dorfmeyer RA, Ericsson AC. Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice. Microorganisms 2023; 11:484. [PMID: 36838449 PMCID: PMC9961083 DOI: 10.3390/microorganisms11020484] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Obesity places a tremendous burden on individual health and the healthcare system. The gut microbiome (GM) influences host metabolism and behaviors affecting body weight (BW) such as feeding. The GM of mice varies between suppliers and significantly influences BW. We sought to determine whether GM-associated differences in BW are associated with differences in intake, fecal energy loss, or fetal growth. Pair-housed mice colonized with a low or high microbial richness GM were weighed, and the total and BW-adjusted intake were measured at weaning and adulthood. Pups were weighed at birth to determine the effects of the maternal microbiome on fetal growth. Fecal samples were collected to assess the fecal energy loss and to characterize differences in the microbiome. The results showed that supplier-origin microbiomes were associated with profound differences in fetal growth and excessive BW-adjusted differences in intake during adulthood, with no detected difference in fecal energy loss. Agreement between the features of the maternal microbiome associated with increased birth weight here and in recent human studies supports the value of this model to investigate the mechanisms by which the maternal microbiome regulates offspring growth and food intake.
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Affiliation(s)
- Christa N. Cheatham
- Comparative Medicine Program, Department of Veterinary Pathobiology, University of Missouri (MU), Columbia, MO 65201, USA
| | - Kevin L. Gustafson
- Comparative Medicine Program, Department of Veterinary Pathobiology, University of Missouri (MU), Columbia, MO 65201, USA
| | - Zachary L. McAdams
- Molecular Pathogenesis and Therapeutics Program, University of Missouri (MU), Columbia, MO 65201, USA
| | - Giedre M. Turner
- Mutant Mouse Resource and Research Center, University of Missouri (MU), Columbia, MO 65201, USA
- University of Missouri Metagenomics Center, University of Missouri (MU), Columbia, MO 65201, USA
| | - Rebecca A. Dorfmeyer
- Mutant Mouse Resource and Research Center, University of Missouri (MU), Columbia, MO 65201, USA
- University of Missouri Metagenomics Center, University of Missouri (MU), Columbia, MO 65201, USA
| | - Aaron C. Ericsson
- Comparative Medicine Program, Department of Veterinary Pathobiology, University of Missouri (MU), Columbia, MO 65201, USA
- Molecular Pathogenesis and Therapeutics Program, University of Missouri (MU), Columbia, MO 65201, USA
- Mutant Mouse Resource and Research Center, University of Missouri (MU), Columbia, MO 65201, USA
- University of Missouri Metagenomics Center, University of Missouri (MU), Columbia, MO 65201, USA
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Wang X, Li L, Bian C, Bai M, Yu H, Gao H, Zhao J, Zhang C, Zhao R. Alterations and correlations of gut microbiota, fecal, and serum metabolome characteristics in a rat model of alcohol use disorder. Front Microbiol 2023; 13:1068825. [PMID: 36687619 PMCID: PMC9846065 DOI: 10.3389/fmicb.2022.1068825] [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: 10/13/2022] [Accepted: 11/22/2022] [Indexed: 01/05/2023] Open
Abstract
Background Growing evidence suggests the gut microbiota and metabolites in serum or fecal may play a key role in the process of alcohol use disorder (AUD). However, the correlations of gut microbiota and metabolites in both feces and serum in AUD subjects are not well understood. Methods We established a rat model of AUD by a chronic intermittent ethanol voluntary drinking procedure, then the AUD syndromes, the gut microbiota, metabolomic profiling in feces and serum of the rats were examined, and correlations between gut microbiota and metabolites were analyzed. Results Ethanol intake preference increased and maintained at a high level in experimental rats. Anxiety-like behaviors was observed by open field test and elevated plus maze test after ethanol withdraw, indicating that the AUD rat model was successfully developed. The full length 16S rRNA gene sequencing showed AUD significantly changed the β-diversity of gut microbial communities, and significantly decreased the microbial diversity but did not distinctly impact the microbial richness. Microbiota composition significantly changed in AUD rats, such as the abundance of Romboutsia and Turicibacter were significantly increased, whereas uncultured_bacterium_o_Mollicutes_RF39 was decreased. In addition, the untargeted metabolome analysis revealed that many metabolites in both feces and serum were altered in the AUD rats, especially involved in sphingolipid metabolism and glycerophospholipid metabolism pathways. Finally, multiple correlations among AUD behavior, gut microbiota and co-changed metabolites were identified, and the metabolites were directly correlated with the gut microbiota and alcohol preference. Conclusion The altered metabolites in feces and serum are important links between the gut microbiota dysbiosis and alcohol preference in AUD rats, and the altered gut microbiota and metabolites can be potentially new targets for treating AUD.
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Affiliation(s)
- Xiaolong Wang
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Lin Li
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Cong Bian
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Mingjian Bai
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Haitao Yu
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Han Gao
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China
| | - Jiaxin Zhao
- National and Local United Engineering Laboratory for Chinese Herbal Medicine Breeding and Cultivation, School of Life Sciences, Jilin University, Changchun, China
| | - Chunjing Zhang
- Department of Medical Technology, Qiqihar Medical University, Qiqihar, Heilongjiang, China,*Correspondence: Chunjing Zhang,
| | - Rongjie Zhao
- Department of Psychiatry, Qiqihar Medical University, Qiqihar, Heilongjiang, China,Rongjie Zhao,
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Magagnoli S, Alberoni D, Baffoni L, Martini A, Marini F, Di Gioia D, Mazzon M, Marzadori C, Campanelli G, Burgio G. The ground beetle Pseudoophonus rufipes gut microbiome is influenced by the farm management system. Sci Rep 2022; 12:22638. [PMID: 36587034 PMCID: PMC9805440 DOI: 10.1038/s41598-022-25408-7] [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: 09/07/2022] [Accepted: 11/29/2022] [Indexed: 01/01/2023] Open
Abstract
Intensive conventional farm management, characterized by high agrochemicals input, could alter the composition of microbial communities with potential negative effects on both functional traits and the ecosystem services provided. In this study, we investigated the gut microbial composition of a high ecological relevance carabid Pseudoophonus rufipes, sampled in two fields subjected to conventional and organic management practices. Carabids' gut microbiota was analyzed via qPCR and NGS. Profound differences between the microbial composition of organic and conventional samples were detected: the abundance of Tenericutes and Proteobacteria was significant higher in organic and conventional samples, respectively. Spiroplasmataceae and Bifidobacteriaceae families were significantly more abundant in samples from organic management, while Enterococcaceae, Morganellaceae and Yersiniaceae were more abundant in samples from conventional management. The diverse gut microbial composition of insects between the two management systems is related to the pressure of environmental stressors and it may representing an important bioindication of ecological functions and services provided by a carabid species.
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Affiliation(s)
- Serena Magagnoli
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Daniele Alberoni
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Loredana Baffoni
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Antonio Martini
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Francesca Marini
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Diana Di Gioia
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Martina Mazzon
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Claudio Marzadori
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
| | - Gabriele Campanelli
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia – Centro di ricerca Orticoltura e Florovivaismo (CREA -OF) - Sede di Monsampolo del Tronto, via Salaria 1, 63077 Monsampolo del Tronto, Italy
| | - Giovanni Burgio
- grid.6292.f0000 0004 1757 1758Dipartimento di Scienze e Tecnologie Agro-Alimentari (DISTAL), Università di Bologna, Viale Fanin 50, 40127 Bologna, Italy
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Gao Y, Wei W, Tian F, Li J, Wang Y, Qi J, Xue S. Corn Straw Total Mix Dietary Supplementation of Bacillus Subtilis-Enhanced Growth Performance of Lambs by Favorably Modulating Rumen Bacterial Microbiome. Fermentation 2022; 9:32. [DOI: 10.3390/fermentation9010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
In this experiment, B. subtilis was added to pelletized straw-based total mixed ration, and the rumen microbial diversity of house-fed Duhan hybrid sheep was compared. Ten 3-month-old weaned Duhan hybrid lambs were separated into two groups and fattened for 80 days using a single-factor trial design. During the fattening period, the control and the experiment groups were fed with the same ration, except that the experiment group was supplemented with B. subtilis. The results showed that the addition of B. subtilis could significantly increase the daily weight gain, total weight gain, rumen microbial abundance, and rumen microbial diversity of the Duhan lamb. Among them, the proportion of microbial flora such as Bacteroidetes was significantly increased, producing more acetate, iso-butyrate, and butyrate, obtaining higher energy efficiency.
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Ruaud A, Pfister N, Ley RE, Youngblut ND. Interpreting tree ensemble machine learning models with endoR. PLoS Comput Biol 2022; 18:e1010714. [PMID: 36516158 DOI: 10.1371/journal.pcbi.1010714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 12/28/2022] [Accepted: 11/07/2022] [Indexed: 12/15/2022] Open
Abstract
Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.
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Liu W, Yang J, Meng Y, Wu D, Cui L, Li T, Sun B, Liu P. The divergent effects of moderate climate warming on the gut microbiota and energetic state of cold-climate lizards from open and semi-closed microhabitats. Front Microbiol 2022; 13:1050750. [PMID: 36483215 PMCID: PMC9722725 DOI: 10.3389/fmicb.2022.1050750] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 10/29/2023] Open
Abstract
INTRODUCTION Understanding the physiological responses to warming temperatures is critical for evaluating the vulnerabilities of animals to climate warming. The physiological responses are increasingly affected by gut microbiota. However, the interactions between physiological responses and the gut microbiota of sympatric animals from various microhabitats in the face of climate change remain largely unknown. METHODS To evaluate the effects of warming temperatures on animals from different microhabitats, we compared locomotor performance, metabolic rate, growth, survival, and gut microbiota of two sympatric ectothermic species (Eremias argus and Takydromus amurensis) from open and semi-closed microhabitats under present and moderate warming climate conditions, respectively. RESULTS AND DISCUSSION We found that locomotor performance and growth rates of snout-vent length (SVL) were enhanced in both lizard species by warming climate. Interestingly, warming temperatures enhanced resting metabolic rates (RMR) in the open-habitat lizard, E. argus, but depressed them in the semi-closed habitat lizard, T. amurensis. Reversely, the metabolism-related gut microbiota was not affected by warming in E. argus, whereas it was significantly enhanced by warming in T. amurensis, indicating a plausible compensatory effect of the gut microbiota on the metabolic regulation of T. amurensis. Furthermore, warming likely improved immunity in both lizard species by significantly reducing pathogenic bacteria while increasing probiotics. This study found that high-latitude sympatric lizards from both open and semi-closed habitats were beneficial to warming temperatures by physiological modification and regulation of the gut microbiota and highlighted the importance of integrating the physiology and gut microbiota in evaluating the vulnerability of animals to climate warming.
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Affiliation(s)
- Wanli Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China
| | - Jing Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yu Meng
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China
| | - Danyang Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Luoxin Cui
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China
| | - Teng Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baojun Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Peng Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China
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Stragier P. To Feed or to Stick? Genomic Analysis Offers Clues for the Role of a Molecular Machine in Endospore Formers. J Bacteriol 2022; 204:e0018722. [PMID: 35913150 DOI: 10.1128/jb.00187-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Sporulation in Firmicutes starts with the formation of two adjacent cells and proceeds with the engulfment of the smaller one, the forespore, by the larger one, the mother cell. This critical step involves a core set of conserved genes, some transcribed in the forespore, such as spoIIQ, and others transcribed in the mother cell, such as the eight-gene spoIIIA operon. A model has been proposed in which the SpoIIIA and the SpoIIQ proteins form a channel connecting the mother cell and the forespore, playing the role of a secretion apparatus allowing the mother cell to nurture the fully engulfed forespore. Exploration of the genomes of Caryophanaceae and Erysipelotrichales has provided informations that are not fully congruent with data from Bacillaceae or Clostridia. The differences observed are correlated with specific physiological features, and alternate, not mutually exclusive views of the function of the SpoIIIA-SpoIIQ complex are presented.
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Li H, Miller T, Lu J, Goel R. Nitrogen fixation contribution to nitrogen cycling during cyanobacterial blooms in Utah Lake. Chemosphere 2022; 302:134784. [PMID: 35504465 PMCID: PMC10149033 DOI: 10.1016/j.chemosphere.2022.134784] [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] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/23/2022] [Accepted: 04/27/2022] [Indexed: 05/03/2023]
Abstract
Nitrogen (N) cycling is an essential process in lake systems and N-fixation is an important component of it. Recent studies have also found that nitrate reduction through heterotrophic denitrification in lake systems did not prevent harmful cyanobacterial blooms, but instead, may have favored the dominance of N2-fixing cyanobacteria. The overall objective of this study was to estimate nitrogen fixation rates and the expressions of associated nitrogenase (nif gene) functional gene at several sites at different occasions in freshwater Utah Lake. For comparison purposes, one time sampling was also conducted in the brackish Farmington Bay of Great Salt Lake (GSL). The microbial ecology of the top 20-cm of surface water was investigated to assess the dominant cyanobacterial communities and N-related metabolisms. Our study revealed that Dolichospermum and Nodularia were potential N2-fixers for Utah Lake and brackish Farmington Bay, respectively. The in situ N2-fixation rates were 0-0.73 nmol N hr-1L-1 for Utah Lake and 0-0.85 nmol N hr-1L-1 for Farmington Bay, and these rates positively correlated with the abundance and expressions of the nif gene. In addition, nitrate reduction was measured in sediment (0.002-0.094 mg N VSS-1 hr-1). Significantly positive correlations were found among amoA, nirS and nirK abundance (R = 0.56-0.87, p < 0.05, Spearman) in both lakes. An exception was the lower nirK gene abundance detected at one site in Farmington Bay where high ammonium retentions were also detected. Based on a mass balance approach, we concluded that the amount of inorganic N loss through denitrification still exceeded the N input by N2-fixation, much like in most lakes, rivers, and marine ecosystems. This indicates that N cycling processes such as denitrification mediated by heterotrophic bacteria contributes to N-export from the lakes resulting in N limitations.
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Affiliation(s)
- Hanyan Li
- Department of Civil and Environmental Engineering, The University of Utah, 110 S Central Campus Drive, Salt Lake City, UT, 84112, USA
| | - Theron Miller
- Wasatch Front Water Quality Council, Salt Lake City, UT, USA
| | - Jingrang Lu
- United States Environmental Protection Agency, Office of Research and Development, Cincinnati, OH, USA.
| | - Ramesh Goel
- Department of Civil and Environmental Engineering, The University of Utah, 110 S Central Campus Drive, Salt Lake City, UT, 84112, USA.
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Nabavi-Rad A, Sadeghi A, Asadzadeh Aghdaei H, Yadegar A, Smith SM, Zali MR. The double-edged sword of probiotic supplementation on gut microbiota structure in Helicobacter pylori management. Gut Microbes 2022; 14:2108655. [PMID: 35951774 PMCID: PMC9373750 DOI: 10.1080/19490976.2022.2108655] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
As Helicobacter pylori management has become more challenging and less efficient over the last decade, the interest in innovative interventions is growing by the day. Probiotic co-supplementation to antibiotic therapies is reported in several studies, presenting a moderate reduction in drug-related side effects and a promotion in positive treatment outcomes. However, the significance of gut microbiota involvement in the competence of probiotic co-supplementation is emphasized by a few researchers, indicating the alteration in the host gastrointestinal microbiota following probiotic and drug uptake. Due to the lack of long-term follow-up studies to determine the efficiency of probiotic intervention in H. pylori eradication, and the delicate interaction of the gut microbiota with the host wellness, this review aims to discuss the gut microbiota alteration by probiotic co-supplementation in H. pylori management to predict the comprehensive effectiveness of probiotic oral administration.Abbreviations: acyl-CoA- acyl-coenzyme A; AMP- antimicrobial peptide; AMPK- AMP-activated protein kinase; AP-1- activator protein 1; BA- bile acid; BAR- bile acid receptor; BCAA- branched-chain amino acid; C2- acetate; C3- propionate; C4- butyrate; C5- valeric acid; CagA- Cytotoxin-associated gene A; cAMP- cyclic adenosine monophosphate; CD- Crohn's disease; CDI- C. difficile infection; COX-2- cyclooxygenase-2; DC- dendritic cell; EMT- epithelial-mesenchymal transition; FMO- flavin monooxygenases; FXR- farnesoid X receptor; GPBAR1- G-protein-coupled bile acid receptor 1; GPR4- G protein-coupled receptor 4; H2O2- hydrogen peroxide; HCC- hepatocellular carcinoma; HSC- hepatic stellate cell; IBD- inflammatory bowel disease; IBS- irritable bowel syndrome; IFN-γ- interferon-gamma; IgA immunoglobulin A; IL- interleukin; iNOS- induced nitric oxide synthase; JAK1- janus kinase 1; JAM-A- junctional adhesion molecule A; LAB- lactic acid bacteria; LPS- lipopolysaccharide; MALT- mucosa-associated lymphoid tissue; MAMP- microbe-associated molecular pattern; MCP-1- monocyte chemoattractant protein-1; MDR- multiple drug resistance; mTOR- mammalian target of rapamycin; MUC- mucin; NAFLD- nonalcoholic fatty liver disease; NF-κB- nuclear factor kappa B; NK- natural killer; NLRP3- NLR family pyrin domain containing 3; NOC- N-nitroso compounds; NOD- nucleotide-binding oligomerization domain; PICRUSt- phylogenetic investigation of communities by reconstruction of unobserved states; PRR- pattern recognition receptor; RA- retinoic acid; RNS- reactive nitrogen species; ROS- reactive oxygen species; rRNA- ribosomal RNA; SCFA- short-chain fatty acids; SDR- single drug resistance; SIgA- secretory immunoglobulin A; STAT3- signal transducer and activator of transcription 3; T1D- type 1 diabetes; T2D- type 2 diabetes; Th17- T helper 17; TLR- toll-like receptor; TMAO- trimethylamine N-oxide; TML- trimethyllysine; TNF-α- tumor necrosis factor-alpha; Tr1- type 1 regulatory T cell; Treg- regulatory T cell; UC- ulcerative colitis; VacA- Vacuolating toxin A.
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Affiliation(s)
- Ali Nabavi-Rad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran,CONTACT Abbas Yadegar ; Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Shahid Arabi Ave., Yemen St., Velenjak, Tehran, Iran
| | - Sinéad Marian Smith
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin, Ireland,Sinéad Marian Smith Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Mansilla FI, Ficoseco CA, Miranda MH, Puglisi E, Nader-Macías MEF, Vignolo GM, Fontana CA. Administration of probiotic lactic acid bacteria to modulate fecal microbiome in feedlot cattle. Sci Rep 2022; 12:12957. [PMID: 35902668 PMCID: PMC9334624 DOI: 10.1038/s41598-022-16786-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 07/15/2022] [Indexed: 11/20/2022] Open
Abstract
Modulation of animal gut microbiota is a prominent function of probiotics to improve the health and performance of livestock. In this study, a large-scale survey to evaluate the effect of lactic acid bacteria probiotics on shaping the fecal bacterial community structure of feedlot cattle during three experimental periods of the fattening cycle (163 days) was performed. A commercial feedlot located in northwestern Argentina was enrolled with cattle fed mixed rations (forage and increasing grain diet) and a convenience-experimental design was conducted. A pen (n = 21 animals) was assigned to each experimental group that received probiotics during three different periods. Groups of n = 7 animals were sampled at 40, 104 and 163 days and these samples were then pooled to one, thus giving a total of 34 samples that were subjected to high-throughput sequencing. The microbial diversity of fecal samples was significantly affected (p < 0.05) by the administration period compared with probiotic group supplementation. Even though, the three experimental periods of probiotic administration induced changes in the relative abundance of the most representative bacterial communities, the fecal microbiome of samples was dominated by the Firmicutes (72–98%) and Actinobacteria (0.8–27%) phyla, while a lower abundance of Bacteroidetes (0.08–4.2%) was present. Probiotics were able to modulate the fecal microbiota with a convergence of Clostridiaceae, Lachnospiraceae, Ruminococcaceae and Bifidobacteriaceae associated with health and growth benefits as core microbiome members. Metabolic functional prediction comparing three experimental administration periods (40, 104 and 163 days) showed an enrichment of metabolic pathways related to complex plant-derived polysaccharide digestion as well as amino acids and derivatives during the first 40 days of probiotic supplementation. Genomic-based knowledge on the benefits of autochthonous probiotics on cattle gastrointestinal tract (GIT) microbiota composition and functions will contribute to their selection as antibiotic alternatives for commercial feedlot.
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Affiliation(s)
| | | | | | - Edoardo Puglisi
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy
| | | | | | - Cecilia Alejandra Fontana
- Instituto Nacional de Tecnología Agropecuaria INTA EEA-Famaillá, Tucumán, Argentina. .,Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Cremona-Piacenza, Italy.
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Malik H, Ratovonamana YR, Rakotondranary SJ, Ganzhorn JU, Sommer S. Anthropogenic Disturbance Impacts Gut Microbiome Homeostasis in a Malagasy Primate. Front Microbiol 2022; 13:911275. [PMID: 35801106 PMCID: PMC9253676 DOI: 10.3389/fmicb.2022.911275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/19/2022] [Indexed: 12/05/2022] Open
Abstract
Increasing anthropogenic disturbances in Madagascar are exerting constrains on endemic Malagasy lemurs and their habitats, with possible effects on their health and survival. An important component of health is the gut microbiome, which might be disrupted by various stressors associated with environmental change. We have studied the gut microbiome of gray-brown mouse lemurs (Microcebus griseorufus), one of the smallest Malagasy primates and an important model of the convergent evolution of diseases. We sampled two sites: one situated in a national park and the other consisting of a more disturbed site around human settlement. We found that more intense anthropogenic disturbances indeed disrupted the gut microbiome of this lemur species marked by a reduction in bacterial diversity and a shift in microbial community composition. Interestingly, we noted a decrease in beneficial bacteria (i.e., members of the Bacteroidaceae family) together with a slight increase in disease-associated bacteria (i.e., members of the Veillonellaceae family), and alterations in microbial metabolic functions. Because of the crucial services provided by the microbiome to pathogen resistance and host health, such negative alterations in the gut microbiome of mouse lemurs inhabiting anthropogenically disturbed habitats might render them susceptible to diseases and ultimately affecting their survival in the shrinking biodiversity seen in Madagascar. Gut microbiome analyses might thus serve as an early warning signal for pending threats to lemur populations.
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Affiliation(s)
- Hina Malik
- Centre for One Health, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India
| | - Yedidya R Ratovonamana
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
- Département Biologie Animale, Faculté des Sciences, Université d' Antananarivo, Antananarivo, Madagascar
| | - Solofomalala Jacques Rakotondranary
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
- Département Biologie Animale, Faculté des Sciences, Université d' Antananarivo, Antananarivo, Madagascar
| | - Jörg U Ganzhorn
- Institute of Zoology, Animal Ecology and Conservation, Universität Hamburg, Hamburg, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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Cotta SR, Pellegrinetti TA, Andreote APD, Costa JS, Sarmento H, Fiore MF. Disentangling the lifestyle of bacterial communities in tropical soda lakes. Sci Rep 2022; 12:7939. [PMID: 35562544 PMCID: PMC9106740 DOI: 10.1038/s41598-022-12046-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Microbial lifestyles may reveal niche-specific signatures and can contribute to detecting the effects of abiotic fluctuations on biogeochemical cycles. Microorganisms make a tradeoff between optimizing nutrient uptake, improving biomass yield, and overcoming environmental changes according to environmental hostility. Soda lakes are natural environments rich in carbonate and bicarbonate water, resulting in elevated pH and salinities that frequently approach saturation. We hypothesized that during the dry period (elevated pH and salinity), microorganisms try to overcome this harshness by allocating energy to the cellular maintenance process. As these environmental conditions improve during the wet period, microorganisms will begin to invest in nutrient uptake. To test this hypothesis, we evaluated four soda lakes in two different seasons by applying metagenomics combined with flow cytometry (estimate heterotrophic bacterial biomass). The natural occurrence of cyanobacterial blooms in some lakes is the main driver of carbon. These primary producers provide organic carbon that supports heterotrophic bacterial growth and, consequently, a high biomass yield. Under harsh conditions (dry season), cyanobacteria invest in nutrient uptake mechanisms, whereas heterotrophic bacteria allocate energy to survive at the expense of biomass yield. Lakes without cyanobacteria blooms invest in nutrient uptake independent of environmental hostility. This study clarifies the microbial tradeoffs in hostile environments and the impact of this choice on carbon and energy flux in tropical alkaline lakes.
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Affiliation(s)
- Simone R Cotta
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Thierry A Pellegrinetti
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Ana Paula D Andreote
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Juliana S Costa
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil
| | - Hugo Sarmento
- Department of Hydrobiology, Federal University of São Carlos, São Carlos, SP, Brazil
| | - Marli F Fiore
- Center of Nuclear Energy in Agriculture (CENA/USP), University of São Paulo, Piracicaba, SP, CEP: 13416-903, Brazil.
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Brealey JC, Lecaudey LA, Kodama M, Rasmussen JA, Sveier H, Dheilly NM, Martin MD, Limborg MT. Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host. mBio 2022;:e0067922. [PMID: 35502903 DOI: 10.1128/mbio.00679-22] [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] [Indexed: 11/20/2022] Open
Abstract
The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections.
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Reid CH, Patrick PH, Rytwinski T, Taylor JJ, Willmore WG, Reesor B, Cooke SJ. An updated review of cold shock and cold stress in fish. J Fish Biol 2022; 100:1102-1137. [PMID: 35285021 DOI: 10.1111/jfb.15037] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/23/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Temperature is critical in regulating virtually all biological functions in fish. Low temperature stress (cold shock/stress) is an often-overlooked challenge that many fish face as a result of both natural events and anthropogenic activities. In this study, we present an updated review of the cold shock literature based on a comprehensive literature search, following an initial review on the subject by M.R. Donaldson and colleagues, published in a 2008 volume of this journal. We focus on how knowledge on cold shock and fish has evolved over the past decade, describing advances in the understanding of the generalized stress response in fish under cold stress, what metrics may be used to quantify cold stress and what knowledge gaps remain to be addressed in future research. We also describe the relevance of cold shock as it pertains to environmental managers, policymakers and industry professionals, including practical applications of cold shock. Although substantial progress has been made in addressing some of the knowledge gaps identified a decade ago, other topics (e.g., population-level effects and interactions between primary, secondary and tertiary stress responses) have received little or no attention despite their significance to fish biology and thermal stress. Approaches using combinations of primary, secondary and tertiary stress responses are crucial as a research priority to better understand the mechanisms underlying cold shock responses, from short-term physiological changes to individual- and population-level effects, thereby providing researchers with better means of quantifying cold shock in laboratory and field settings.
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Affiliation(s)
- Connor H Reid
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | | | - Trina Rytwinski
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
- Canadian Centre for Evidence-Based Conservation, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | - Jessica J Taylor
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
- Canadian Centre for Evidence-Based Conservation, Department of Biology and Institute of Environmental and Interdisciplinary Science, Carleton University, Ottawa, Ontario, Canada
| | | | | | - Steven J Cooke
- Fish Ecology and Conservation Physiology Laboratory, Department of Biology, Carleton University, Ottawa, Ontario, Canada
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Lutsiv T, Mcginley JN, Neil-mcdonald ES, Weir TL, Foster MT, Thompson HJ. Relandscaping the Gut Microbiota with a Whole Food: Dose–Response Effects to Common Bean. Foods 2022; 11:1153. [PMID: 35454741 PMCID: PMC9025344 DOI: 10.3390/foods11081153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/06/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
Underconsumption of dietary fiber and the milieu of chemicals with which it is associated is a health concern linked to the increasing global burden of chronic diseases. The benefits of fiber are partially attributed to modulation of the gut microbiota, whose composition and function depend on the amount and quality of microbiota-accessible substrates in the diet. However, not all types of fiber are equally accessible to the gut microbiota. Phaseolus vulgaris L., or common bean, is a food type rich in fiber as well as other prebiotics posing a great potential to positively impact diet-microbiota-host interactions. To elucidate the magnitude of bean’s effects on the gut microbiota, increasing doses of common bean were administered in macronutrient-matched diet formulations. The microbial communities in the ceca of female and male mice were evaluated via 16S rRNA gene sequencing. As the bean dose increased, the Bacillota:Bacteroidota ratio (formerly referred to as the Firmicutes:Bacteroidetes ratio) was reduced and α-diversity decreased, whereas the community composition was distinctly different between the diet groups according to β-diversity. These effects were more pronounced in female mice compared to male mice. Compositional analyses identified a dose-responsive bean-induced shift in microbial composition. With an increasing bean dose, Rikenellaceae, Bacteroides, and RF39, which are associated with health benefits, were enhanced. More taxa, however, were suppressed, among which were Allobaculum, Oscillospira, Dorea, and Ruminococcus, which are predominantly associated with chronic disease risk. Investigation of the origins of the dose dependent and biological sex differences in response to common bean consumption may provide insights into bean-gut microbiota-host interactions important to developing food-based precision approaches to chronic disease prevention and control.
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Liu L, Du C, Liu Y, Gao L. Comparative Analysis of the Fecal Microbiota of Relict Gull ( Larus relictus) in Mu Us Desert (Hao Tongcha Nur) and Bojiang Haizi in Inner Mongolia, China. Front Vet Sci 2022; 9:860540. [PMID: 35464369 PMCID: PMC9018992 DOI: 10.3389/fvets.2022.860540] [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: 01/23/2022] [Accepted: 03/04/2022] [Indexed: 01/06/2023] Open
Abstract
The gut microbiota contributes to host health by improving digestive efficiency and maintaining homeostasis. The relict gull (Larus relictus), a national first-class protected bird in China, is listed as vulnerable in the International Union for Conservation of Nature Red List. Here, 16S rRNA gene sequencing was performed to characterize and compare the community composition and diversity of the gut microbiota sampled from relict gulls in two breeding sites. In total, 418 operational taxonomic units (OUTs) were obtained and classified into 15 phyla and 228 genera. Alpha diversity analysis revealed no significant differences in community diversity among the two breeding sites. Beta diversity analyses showed that the microbial communities at the two sites were different. Six dominant phyla and fourteen dominant genera were identified. The most abundant bacterial genera had a significant relationship with the diet and living environment, and some bacterial genera were found to adapt to the plateau environment in which relict gulls live, which enables the relict gulls to use local resources effectively to accumulate energy. Simultaneously, a variety of highly abundant pathogenic bacteria were found, suggesting that these gulls may spread diseases among the local gull population. Certain measures should be taken to protect this species and to prevent the spread of diseases.
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Affiliation(s)
| | | | | | - Li Gao
- Faculty of Biological Science and Technology, Baotou Teacher's College, Baotou, China
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Zhou Z, Wu H, Li D, Zeng W, Huang J, Wu Z. Comparison of gut microbiome in the Chinese mud snail ( Cipangopaludina chinensis) and the invasive golden apple snail ( Pomacea canaliculata). PeerJ 2022; 10:e13245. [PMID: 35402093 PMCID: PMC8992660 DOI: 10.7717/peerj.13245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/10/2021] [Accepted: 03/18/2022] [Indexed: 01/13/2023] Open
Abstract
Background Gut microbiota play a critical role in nutrition absorption and environmental adaptation and can affect the biological characteristics of host animals. The invasive golden apple snail (Pomacea canaliculata) and native Chinese mud snail (Cipangopaludina chinensis) are two sympatric freshwater snails with similar ecological niche in southern China. However, gut microbiota comparison of interspecies remains unclear. Comparing the difference of gut microbiota between the invasive snail P. canaliculata and native snail C. chinensis could provide new insight into the invasion mechanism of P.canaliculata at the microbial level. Methods Gut samples from 20 golden apple snails and 20 Chinese mud snails from wild freshwater habitats were collected and isolated. The 16S rRNA gene V3-V4 region of the gut microbiota was analyzed using high throughput Illumina sequencing. Results The gut microbiota dominantly composed of Proteobacteria, Bacteroidetes, Firmicutes and Epsilonbacteraeota at phylum level in golden apple snail. Only Proteobacteria was the dominant phylum in Chinese mud snail. Alpha diversity analysis (Shannon and Simpson indices) showed there were no significant differences in gut microbial diversity, but relative abundances of the two groups differed significantly (P < 0.05). Beta diversity analysis (Bray Curtis and weighted UniFrac distance) showed marked differences in the gut microbiota structure (P < 0.05). Unique or high abundance microbial taxa were more abundant in the invasive snail compared to the native form. Functional prediction analysis indicated that the relative abundances of functions differed significantly regarding cofactor prosthetic group electron carrier and vitamin biosynthesis, amino acid biosynthesis, and nucleoside and nucleotide biosynthesis (P < 0.05). These results suggest an enhanced potential to adapt to new habitats in the invasive snail.
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Affiliation(s)
- Zihao Zhou
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Hongying Wu
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Dinghong Li
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Wenlong Zeng
- Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
| | - Jinlong Huang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China,College of Life Sciences, Guangxi Normal University, Guilin, Guangxi, China
| | - Zhengjun Wu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University), Ministry of Education, Guilin, Guangxi, China,Guangxi Key Laboratory of Rare and Endangered Animal Ecology, Guangxi Normal University, Guilin, Guangxi, China,Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin Institute for Sustainable Development and Innovation, Guangxi Normal University, Guilin, Guangxi, China
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Nuppunen-Puputti M, Kietäväinen R, Raulio M, Soro A, Purkamo L, Kukkonen I, Bomberg M. Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock. Front Microbiol 2022; 13:826048. [PMID: 35300483 PMCID: PMC8921683 DOI: 10.3389/fmicb.2022.826048] [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: 11/30/2021] [Accepted: 01/12/2022] [Indexed: 01/03/2023] Open
Abstract
The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8–40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.
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Affiliation(s)
| | | | - Mari Raulio
- European Chemicals Agency (ECHA), Helsinki, Finland
| | - Aino Soro
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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Watanabe M, Kojima H, Okano K, Fukui M. Mariniplasma anaerobium gen. nov., sp. nov., a novel anaerobic marine mollicute, and proposal of three novel genera to reclassify members of Acholeplasma clusters II-IV. Int J Syst Evol Microbiol 2021; 71. [PMID: 34874244 DOI: 10.1099/ijsem.0.005138] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel strictly anaerobic chemoorganotrophic bacterium, designated Mahy22T, was isolated from sulfidic bottom water of a shallow brackish meromictic lake in Japan. Cells of the strain were Gram-stain-negative, non-motile and coccoid in shape with diameters of about 600-800 nm. The temperature range for growth was 15-37 °C, with optimum growth at 30-32 °C. The pH range for growth was pH 6.2-8.9, with optimum growth at pH 7.2-7.4. The strain grew with NaCl concentrations of 5% or below (optimum, 2-3%). Growth of the strain was enhanced by the addition of thiosulfate. The major cellular fatty acids were C16:0 and anteiso-C15:0. Respiratory quinones were not detected. The complete genome sequence of strain Mahy22T possessed a 1 885 846 bp circular chromosome and a 12 782 bp circular genetic element. The G+C content of the genome sequence was 30.1 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Acholeplasmataceae, class Mollicutes. The closest relative of strain Mahy22T with a validly published name was Acholeplasma palmae J233T with a 16S rRNA gene sequence similarity of 90.5%. Based on the results of polyphasic analysis, the name Mariniplasma anaerobium gen. nov., sp. nov. is proposed to accommodate strain Mahy22T, along with reclassification of some Acholeplasma species into Alteracholeplasma gen. nov., Haploplasma gen. nov. and Paracholeplasma gen. nov.
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Affiliation(s)
- Miho Watanabe
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan.,Department of Biological Environment, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
| | - Kunihiro Okano
- Department of Biological Environment, Akita Prefectural University, Shimoshinjyo-Nakano, Akita 010-0195, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Japan
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Nourrisson C, Scanzi J, Brunet J, Delbac F, Dapoigny M, Poirier P. Prokaryotic and Eukaryotic Fecal Microbiota in Irritable Bowel Syndrome Patients and Healthy Individuals Colonized With Blastocystis. Front Microbiol 2021; 12:713347. [PMID: 34603241 PMCID: PMC8486285 DOI: 10.3389/fmicb.2021.713347] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/26/2021] [Indexed: 12/30/2022] Open
Abstract
Blastocystis is the most frequently isolated protozoan from human stool. Its role in human health is still debated, and a high prevalence was reported in irritable bowel syndrome (IBS) subjects, suggesting a potential link with microbiota. In the present study, we aimed to investigate prokaryotic and eukaryotic microbiota in both IBS-C (constipated) and healthy individuals. We recruited 35 IBS-C patients and 23 healthy subjects, from which 12 and 11 carried Blastocystis, respectively. We performed 16S and 18S rRNA high-throughput sequencing on feces. Whereas we did not observe differences between infected and non-infected controls, several phyla were significantly modified in IBS-C patients according to the presence of Blastocystis. Tenericutes phylum and Ruminococcaceae family were especially increased in Blastocystis carriers. Furthermore, colonization with Blastocystis was associated with discrete changes in the microbial eukaryome, particularly among the Fungi taxa. Depending on the group of patients considered, the mycobiota changes do not go in the same direction and seem more deleterious in the IBS-C group. These results encourage further in vivo and in vitro investigations concerning the role of Blastocystis in the gut environment.
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Affiliation(s)
- Céline Nourrisson
- Service de Parasitologie-Mycologie, CHU de Clermont-Ferrand, 3IHP, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julien Scanzi
- Service de Médecine Digestive et Hépatobiliaire, CHU de Clermont-Ferrand, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Julie Brunet
- Service de Parasitologie-Mycologie, CHU de Clermont-Ferrand, 3IHP, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Michel Dapoigny
- Service de Médecine Digestive et Hépatobiliaire, CHU de Clermont-Ferrand, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Philippe Poirier
- Service de Parasitologie-Mycologie, CHU de Clermont-Ferrand, 3IHP, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
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Wang Y, Wang C, Chen Y, Zhang D, Zhao M, Li H, Guo P. Microbiome Analysis Reveals Microecological Balance in the Emerging Rice-Crayfish Integrated Breeding Mode. Front Microbiol 2021; 12:669570. [PMID: 34168630 PMCID: PMC8219076 DOI: 10.3389/fmicb.2021.669570] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 02/19/2021] [Accepted: 05/11/2021] [Indexed: 01/15/2023] Open
Abstract
The interaction between the microbial communities in aquatic animals and those in the ambient environment is important for both healthy aquatic animals and the ecological balance of aquatic environment. Crayfish (Procambarus clarkii), with their high commercial value, have become the highest-yield freshwater shrimp in China. The traditional cultivation in ponds (i.e., monoculture, MC) and emerging cultivation in rice co-culture fields (i.e., rice–crayfish co-culture, RC) are the two main breeding modes for crayfish, and the integrated RC is considered to be a successful rice-livestock integration practice in eco-agricultural systems. This study explored the ecological interactions between the microbial communities in crayfish intestine and the ambient environment, which have not been fully described to date. The bacterial communities in crayfish intestine, the surrounding water, and sediment in the two main crayfish breeding modes were analyzed with MiSeq sequencing and genetic networks. In total, 53 phyla and 1,206 genera were identified, among which Proteobacteria, Actinobacteria, Tenericutes, Firmicutes, Cyanobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, RsaHF231, and Nitrospirae were the dominant phyla. The microbiota composition significantly differed between the water, sediment, and crayfish intestine, while it did not between the two breeding modes. We also generated a co-occurrence correlation network based on the high-confidence interactions with Spearman correlation ρ ≥ 0.75. In the genera co-correlation network, 95 nodes and 1,158 edges were identified, indicating significant genera interactions between crayfish intestine and the environment. Furthermore, the genera clustered into three modules, based on the different environments. Additionally, Candidatus_Bacilloplasma, g_norank_f_Steroidobacteraceae, Dinghuibacter, Hydrogenophaga, Methyloparacoccus, and Defluviicoccus had the highest betweenness centrality and might be important in the interaction between crayfish and the ambient environment. Overall, this study enhances our understanding of the characteristics of the microbiota in crayfish and their surrounding environment. Moreover, our findings provide insights into the microecological balance in crayfish eco-agricultural systems and theoretical reference for the development of such systems.
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Affiliation(s)
- Yi Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Chen Wang
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China.,College of Biology and Pharmacy, Three Gorges University, Yichang, China
| | - Yonglun Chen
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China.,College of Biology and Pharmacy, Three Gorges University, Yichang, China
| | - Dongdong Zhang
- Institute of Marine Biology, Ocean College, Zhejiang University, Zhoushan, China
| | - Mingming Zhao
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Hailan Li
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Peng Guo
- Institute of Agricultural Products Processing and Nuclear Agriculture Technology Research, Hubei Academy of Agricultural Sciences, Wuhan, China.,College of Biology and Pharmacy, Three Gorges University, Yichang, China
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Rasmussen JA, Villumsen KR, Duchêne DA, Puetz LC, Delmont TO, Sveier H, Jørgensen LVG, Præbel K, Martin MD, Bojesen AM, Gilbert MTP, Kristiansen K, Limborg MT. Genome-resolved metagenomics suggests a mutualistic relationship between Mycoplasma and salmonid hosts. Commun Biol 2021; 4:579. [PMID: 33990699 PMCID: PMC8121932 DOI: 10.1038/s42003-021-02105-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/14/2021] [Indexed: 11/08/2022] Open
Abstract
Salmonids are important sources of protein for a large proportion of the human population. Mycoplasma species are a major constituent of the gut microbiota of salmonids, often representing the majority of microbiota. Despite the frequent reported dominance of salmonid-related Mycoplasma species, little is known about the phylogenomic placement, functions and potential evolutionary relationships with their salmonid hosts. In this study, we utilise 2.9 billion metagenomic reads generated from 12 samples from three different salmonid host species to I) characterise and curate the first metagenome-assembled genomes (MAGs) of Mycoplasma dominating the intestines of three different salmonid species, II) establish the phylogeny of these salmonid candidate Mycoplasma species, III) perform a comprehensive pangenomic analysis of Mycoplasma, IV) decipher the putative functionalities of the salmonid MAGs and reveal specific functions expected to benefit the host. Our data provide a basis for future studies examining the composition and function of the salmonid microbiota.
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Affiliation(s)
- Jacob A Rasmussen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Kasper R Villumsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - David A Duchêne
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lara C Puetz
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tom O Delmont
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | | | - Louise von Gersdorff Jørgensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Parasitology and Aquatic Pathobiology, Copenhagen, Denmark
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT the Arctic University of Norway, Tromsø, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anders M Bojesen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Veterinary Clinical Microbiology, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Institute of Metagenomics, BGI-Shenzhen, Shenzhen, China
| | - Morten T Limborg
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Center for Evolutionary Hologenomics, GLOBE institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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42
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Vander Wyst KB, Ortega-Santos CP, Toffoli SN, Lahti CE, Whisner CM. Diet, adiposity, and the gut microbiota from infancy to adolescence: A systematic review. Obes Rev 2021; 22:e13175. [PMID: 33590719 PMCID: PMC10762698 DOI: 10.1111/obr.13175] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 12/14/2022]
Abstract
Early life gut microbiota are affected by several factors that make identification of microbial-adiposity relationships challenging. This review evaluates studies that have investigated the gut microbiota composition associated with adiposity in infants, children, and adolescents and provides evidence-based nutrition recommendations that address microbiota-adiposity links. Electronic databases were systematically searched through January 2020. Eligible studies were published in English and analyzed gut microbiota and adiposity among individuals aged birth to 18 years. Abstracts and full-text articles were reviewed by three independent reviewers. Of 45 full-text articles reviewed, 33 were included. No difference in abundance was found for Bacteroidetes (n = 7/15 articles), Firmicutes (n = 10/17), Actinobacteria (n = 8/12), Proteobacteria (n = 8/12), Tenericutes (n = 4/5), and Verrucomicrobia (n = 4/6) with adiposity. Lower abundance of Christensenellaceae (n = 3/5) and Rikenellaceae (n = 6/8) but higher abundance of F. prausnitzii (n = 3/5) and Prevotella (n = 5/7) were associated with adiposity. A lack of consensus exists for gut microbial composition associations with adiposity. A healthy gut microbiota is associated with a diet rich in fruits and vegetables with moderate consumption of animal fat and protein. Future research should use more robust sequencing technologies to identify all bacterial taxa associated with adiposity and evaluate how diet effects these adiposity-associated microbes.
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Affiliation(s)
- Kiley B Vander Wyst
- College of Health Solutions, Arizona State University, Phoenix, Arizona, USA
- Center for Health Promotion and Disease Prevention, Arizona State University, Phoenix, Arizona, USA
| | | | - Samantha N Toffoli
- College of Health Solutions, Arizona State University, Phoenix, Arizona, USA
| | - Caroline E Lahti
- College of Liberal Arts and Sciences, Arizona State University, Phoenix, Arizona, USA
| | - Corrie M Whisner
- College of Health Solutions, Arizona State University, Phoenix, Arizona, USA
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43
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Li QM, Zhou YL, Wei ZF, Wang Y. Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters. Microorganisms 2021; 9:757. [PMID: 33916768 PMCID: PMC8067016 DOI: 10.3390/microorganisms9040757] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 02/22/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 11/23/2022] Open
Abstract
Bdellovibrionota is composed of obligate predators that can consume some Gram-negative bacteria inhabiting various environments. However, whether genomic traits influence their distribution and marine adaptation remains to be answered. In this study, we performed phylogenomics and comparative genomics studies using 132 Bdellovibrionota genomes along with five metagenome-assembled genomes (MAGs) from deep sea zones. Four phylogenetic groups, Oligoflexia, Bdello-group1, Bdello-group2 and Bacteriovoracia, were revealed by constructing a phylogenetic tree, of which 53.84% of Bdello-group2 and 48.94% of Bacteriovoracia were derived from the ocean. Bacteriovoracia was more prevalent in deep sea zones, whereas Bdello-group2 was largely distributed in the epipelagic zone. Metabolic reconstruction indicated that genes involved in chemotaxis, flagellar (mobility), type II secretion system, ATP-binding cassette (ABC) transporters and penicillin-binding protein were necessary for the predatory lifestyle of Bdellovibrionota. Genes involved in glycerol metabolism, hydrogen peroxide (H2O2) degradation, cell wall recycling and peptide utilization were ubiquitously present in Bdellovibrionota genomes. Comparative genomics between marine and non-marine Bdellovibrionota demonstrated that betaine as an osmoprotectant is probably widely used by marine Bdellovibrionota, and all the marine genomes have a number of genes for adaptation to marine environments. The genes encoding chitinase and chitin-binding protein were identified for the first time in Oligoflexia, which implied that Oligoflexia may prey on a wider spectrum of microbes. This study expands our knowledge on adaption strategies of Bdellovibrionota inhabiting deep seas and the potential usage of Oligoflexia for biological control.
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Affiliation(s)
- Qing-Mei Li
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying-Li Zhou
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhan-Fei Wei
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong Wang
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (Q.-M.L.); (Y.-L.Z.); (Z.-F.W.)
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44
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Gharechahi J, Vahidi MF, Bahram M, Han JL, Ding XZ, Salekdeh GH. Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen. ISME J 2021; 15:1108-1120. [PMID: 33262428 PMCID: PMC8114923 DOI: 10.1038/s41396-020-00837-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 02/08/2023]
Abstract
Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.
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Affiliation(s)
- Javad Gharechahi
- grid.411521.20000 0000 9975 294XHuman Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- grid.473705.20000 0001 0681 7351Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Mohammad Bahram
- grid.6341.00000 0000 8578 2742Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden ,grid.10939.320000 0001 0943 7661Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
| | - Jian-Lin Han
- grid.419369.00000 0000 9378 4481Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100 Nairobi, Kenya ,grid.410727.70000 0001 0526 1937CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193 Beijing, China
| | - Xue-Zhi Ding
- grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), 730050 Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- grid.473705.20000 0001 0681 7351Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran ,grid.1004.50000 0001 2158 5405Department of Molecular Sciences, Macquarie University, North Ryde, NSW Australia
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45
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Zheng R, Liu R, Shan Y, Cai R, Liu G, Sun C. Characterization of the first cultured free-living representative of Candidatus Izemoplasma uncovers its unique biology. ISME J 2021; 15:2676-2691. [PMID: 33746205 PMCID: PMC8397711 DOI: 10.1038/s41396-021-00961-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/02/2021] [Accepted: 03/09/2021] [Indexed: 02/07/2023]
Abstract
Candidatus Izemoplasma, an intermediate in the reductive evolution from Firmicutes to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria within the phylum Tenericutes. Unfortunately, the paucity of pure cultures has limited further insights into their physiological and metabolic features as well as ecological roles. Here, we report the first successful isolation of an Izemoplasma representative from the deep-sea methane seep, strain zrk13, using a DNA degradation-driven method given Izemoplasma’s prominent DNA-degradation potentials. We further present a detailed description of the physiological, genomic and metabolic traits of the novel strain, which allows for the first time the reconstruction of the metabolic potential and lifestyle of a member of the tentatively defined Candidatus Izemoplasma. On the basis of the description of strain zrk13, the novel species and genus Xianfuyuplasma coldseepsis is proposed. Using a combined biochemical and transcriptomic method, we further show the supplement of organic matter, thiosulfate or bacterial genomic DNA could evidently promote the growth of strain zrk13. In particular, strain zrk13 could degrade and utilize the extracellular DNA for growth in both laboraterial and deep-sea conditions. Moreover, the predicted genes determining DNA-degradation broadly distribute in the genomes of other Izemoplasma members. Given that extracellular DNA is a particularly crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor, Izemoplasma bacteria are thought to be important contributors to the biogeochemical cycling in the deep ocean.
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Affiliation(s)
- Rikuan Zheng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Rui Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Yeqi Shan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ruining Cai
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,College of Earth Science, University of Chinese Academy of Sciences, Beijing, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Ge Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Chaomin Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China. .,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China. .,Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China.
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46
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Zhu FC, Lian CA, He LS. Genomic Characterization of a Novel Tenericutes Bacterium from Deep-Sea Holothurian Intestine. Microorganisms 2020; 8:microorganisms8121874. [PMID: 33260795 PMCID: PMC7761423 DOI: 10.3390/microorganisms8121874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and immunity of animals, but little is known about the composition and function of intestinal microbiota in deep-sea invertebrates. In this study, the intestinal microbiota of six holothurian Molpadia musculus were investigated, showing that their midguts were predominantly occupied by Izemoplasmatales bacteria. Using metagenomic sequencing, a draft genome of 1,822,181 bp was successfully recovered. After comparison with phylogenetically related bacteria, genes involved in saccharide usage and de novo nucleotide biosynthesis were reduced. However, a set of genes responsible for extracellular nucleoside utilization and 14 of 20 amino acid synthesis pathways were completely retained. Under oligotrophic condition, the gut-associated bacterium may make use of extracellular DNA for carbon and energy supplement, and may provide essential amino acids to the host. The clustered regularly interspaced short palindromic repeat (CRISPR) and restriction–modification (RM) systems presented in the genome may provide protection against invading viruses. A linear azol(in)e-containing peptide gene cluster for bacteriocin synthesize was also identified, which may inhibit the colonization and growth of harmful bacteria. Known virulence factors were not found by database searching. On the basis of its phylogenetic position and metabolic characteristics, we proposed that the bacterium represented a novel genus and a novel family within the Izemoplasmatales order and suggested it be named “Candidatus Bathyoplasma sp. NZ”. This was the first time describing host-associated Izemoplasmatales.
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Affiliation(s)
- Fang-Chao Zhu
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (F.-C.Z.); (C.-A.L.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Chun-Ang Lian
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (F.-C.Z.); (C.-A.L.)
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China; (F.-C.Z.); (C.-A.L.)
- Correspondence: ; Tel.: +86-898-88380060
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