1
|
Wu Z, Wu W, Yang S, Cheng F, Lv J, Shao Y, Tang X, Li E, Zhao Q. Safety evaluation and effects of dietary phlorotannins on the growth, health, and intestinal microbiota of Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2024; 150:109569. [PMID: 38641216 DOI: 10.1016/j.fsi.2024.109569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/03/2024] [Accepted: 04/15/2024] [Indexed: 04/21/2024]
Abstract
Phlorotannins are phenolic compounds with diverse biological activities, yet their efficacy in aquatic animals currently remains unclear. This investigation scrutinized the influence of phlorotannins on the growth, immunity, antioxidant capacity, and intestinal microbiota in Litopenaeus vannamei, concurrently evaluating the potential adverse effects of phlorotannins on L. vannamei. A base diet without phlorotannins supplementation was used as a control, and 4 groups of diets with different concentrations (0, 0.5, 1.0, 2.0 g kg-1) of phlorotannins were formulated and fed to juvenile shrimp (0.25 ± 0.01 g) for 60 days followed by a 24-h challenge with Vibrio parahaemolyticus with triplicate in each group. Compared with the control, dietary 2.0 g kg-1 phlorotannins significantly improved the growth of the shrimp. The activities of enzymes related to cellular immunity, humoral immunity, and antioxidants, along with a notable upregulation in the expression of related genes, significantly increased. After V. parahaemolyticus challenge, the cumulative survival rates of the shrimp demonstrated a positive correlation with elevated concentrations of phlorotannins. In addition, the abundance of Bacteroidetes and functional genes associated with metabolism increased in phlorotannins supplementation groups. Phlorotannins did not elicit any detrimental effects on the biological macromolecules or histological integrity of the hepatopancreas or intestines. Simultaneously, it led to a significant reduction in malondialdehyde content. All results indicated that phlorotannins at concentrations of 2.0 g kg-1 can be used as safe feed additives to promote the growth, stimulate the immune response, improve the antioxidant capacity and intestinal health of L. vannamei, and an protect shrimp from damage caused by oxidative stress.
Collapse
Affiliation(s)
- Zijie Wu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China
| | - Wenbo Wu
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China
| | - Shouguo Yang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan, 571126, China
| | - Fen Cheng
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan, 571126, China
| | - Jingyi Lv
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China
| | - Yingjin Shao
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China
| | - Xianming Tang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou, Hainan, 571126, China
| | - Erchao Li
- School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
| | - Qun Zhao
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province, Hainan Aquaculture Breeding Engineering Research Center, College of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, 570228, China.
| |
Collapse
|
2
|
Sutanti S, Sukenda S, Widanarni W, Alimuddin A, Siti Aliah R. Novel indigenous probiotic isolated from the healthy Pacific white shrimp Litopenaeus vannamei intestine in differing stages based on metagenomic and screening approaches. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109678. [PMID: 38849107 DOI: 10.1016/j.fsi.2024.109678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
The healthy intestinal microbiota of shrimp can be used as an indicator sustainable shrimp production. In this study, the integrated of metagenomic and screening probiotic approach from healthy Litopenaeus vannamei intestines in differing stages was studied to find novel indigenous probiotics. The microbiota from intestine of naupli, post larva (PL-10), juvenile (40 days), and adult (80 days) of Pacific white shrimp were characterized using a high-quality sequence of V3-V4 of 16S rRNA gene as the hypervariable region. The classifiable sequence number was detected in 54 phyla. Several core intestine bacteria, 35 of these 557 genera, have a prevalence >10 sequences across all samples. We found microbiota were different taxa in the difference stages, such as Proteobacteria, Firmicutes, and Bacteriodetes. The top 10 most abundant genera were Vibrio, Pseudoalteromonas, Spingomonas, Marinibacterium, Klebsiella, Alteromonas, Aestuaribacter, Shimia, Stenotrophomonas, and Ruegeria. Microbiota profiling based on a metagenomic approach was integrated with screening assessment for pathogenicity, antagonistic activity with Vibrio parahaemolyticus Vp5, antibiotic resistance, and digestive enzyme activities. As their assessment activity, several screened culturable bacteria were 19 of these 84 isolates. Three isolates with high activities (P < 0.05) found as novel indigenous probiotics were Shewanella algae A1, Shewanella algae A3, and Vibrio diabolicus UB3. Integrating metagenomic and screening methods was a new signature for the isolating novel indigenous probiotics in Pacific white shrimp.
Collapse
Affiliation(s)
- Sutanti Sutanti
- Department of Aquaculture, Faculty of Fisheries and Marine Sciences, Bogor Agricultural University, Campus IPB Dramaga Bogor, West Java, 16680, Indonesia; National Research and Innovation Agency, BJ Habibie Building, MH Thamrin Street No.8, Central Jakarta, 10340, Indonesia.
| | - Sukenda Sukenda
- Department of Aquaculture, Faculty of Fisheries and Marine Sciences, Bogor Agricultural University, Campus IPB Dramaga Bogor, West Java, 16680, Indonesia.
| | - Widanarni Widanarni
- Department of Aquaculture, Faculty of Fisheries and Marine Sciences, Bogor Agricultural University, Campus IPB Dramaga Bogor, West Java, 16680, Indonesia.
| | - Alimuddin Alimuddin
- Department of Aquaculture, Faculty of Fisheries and Marine Sciences, Bogor Agricultural University, Campus IPB Dramaga Bogor, West Java, 16680, Indonesia.
| | - Ratu Siti Aliah
- National Research and Innovation Agency, BJ Habibie Building, MH Thamrin Street No.8, Central Jakarta, 10340, Indonesia.
| |
Collapse
|
3
|
Duan Y, Nan Y, Xiao M, Yang Y. Toxicity of three microcystin variants on the histology, physiological and metabolism of hepatopancreas and intestinal microbiota of Litopenaeus vannamei. Comp Biochem Physiol C Toxicol Pharmacol 2024; 280:109904. [PMID: 38508355 DOI: 10.1016/j.cbpc.2024.109904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/10/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Microcystins (MCs) are prevalent harmful contaminants within shrimp aquaculture systems, exhibiting a diverse array of variants. Gut microbiota can engage in mutual interactions with the host through the gut-liver axis. In this study, the shrimp Litopenaeus vannamei were subjected to three different variants of MCs (LR, YR, RR) at a concentration of 1 μg/L each, and elucidated the alterations in both intestinal microbiota and hepatopancreas physiological homeostasis. The results showed that all three variants of MCs prompted histological alterations in the hepatopancreas, induced elevated levels of oxidative stress biomarkers (H2O2, T-SOD, and CAT), disturbed the transcription levels of immune-related genes (Crus, ALF, and Lys), along with an increase in apoptotic genes (Casp-3 and P53). Furthermore, the metabolic profiles of the hepatopancreas were perturbed, particularly in amino acid metabolism such as "lysine degradation" and "β-alanine metabolism"; the mTOR and FoxO signaling were also influenced, encompassing alterations in the transcription levels of related genes. Additionally, the alterations were observed in the intestinal microbiota's diversity and composition, particularly potential beneficial bacteria (Alloprevotella, Bacteroides, Collinsella, Faecalibacterium, and Prevotellaceae UCG-001), which exhibited a positive correlation with the metabolite berberine. These findings reveal that the three MCs variants can impact the health of the shrimp by interfering with the homeostasis of intestinal microbial and hepatopancreas physiology.
Collapse
Affiliation(s)
- Yafei Duan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya 572018, PR China.
| | - Yuxiu Nan
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Meng Xiao
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China
| | - Yukai Yang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, PR China; Shenzhen Base of South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shenzhen 518121, PR China
| |
Collapse
|
4
|
Liu Z, Wang P, Li J, Luo X, Zhang Y, Huang X, Zhang X, Li W, Qin Q. Comparative metagenomic analysis of microbial community compositions and functions in cage aquaculture and its nearby non-aquaculture environments. Front Microbiol 2024; 15:1398005. [PMID: 38841063 PMCID: PMC11150647 DOI: 10.3389/fmicb.2024.1398005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 06/07/2024] Open
Abstract
In the context of burgeoning global aquaculture, its environmental repercussions, particularly in marine ecosystems, have gained significant attentions. Cage aquaculture, a prominent method, has been observed to significantly influence marine environments by discharging substantial amounts of organic materials and pollutants. It is also one of the important reasons for water eutrophication. This study investigated the impacts of cage aquaculture on microbial diversity and functional potential using metagenomics. Specifically, a comparison was made of the physicochemical indicators and microbial diversity between three grouper aquaculture cage nets in Lingshui Xincun Port and three nearby non-aquaculture area surface waters. We found that compared to non-aquaculture areas, the eutrophication indicators in aquaculture environments significantly increased, and the abundances of Vibrio and Pseudoalteromonas in aquaculture environments significantly rose. Additionally, microbial functional genes related to carbon, nitrogen, and sulfur metabolisms were also found to be significantly affected by aquaculture activities. The correlation analysis between microbial populations and environmental factors revealed that the abundances of most microbial taxa showed positive correlations with dissolved inorganic nitrogen, soluble reactive phosphorus, NH4+, and negative correlations with dissolved oxygen. Overall, this study elucidated the significant impacts of aquaculture-induced eutrophication on the diversity and functions of planktonic bacterial communities.
Collapse
Affiliation(s)
- Zetian Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jialing Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xiaoqing Luo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ya Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xiaohong Huang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Xin Zhang
- School of Marine Biology and Fisheries, Hainan University, Haikou, Hainan, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
| | - Qiwei Qin
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Marine Sciences, South China Agricultural University, Guangzhou, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| |
Collapse
|
5
|
Raza B, Zheng Z, Zhu J, Yang W. A Review: Microbes and Their Effect on Growth Performance of Litopenaeus vannamei (White Leg Shrimps) during Culture in Biofloc Technology System. Microorganisms 2024; 12:1013. [PMID: 38792842 PMCID: PMC11123971 DOI: 10.3390/microorganisms12051013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
In the modern era of Aquaculture, biofloc technology (BFT) systems have attained crucial attention. This technology is used to reduce water renewal with the removal of nitrogen and to provide additional feed. In BFT, microorganisms play a crucial role due to their complex metabolic properties. Pathogens can be controlled through multiple mechanisms using probiotics, which can promote host development and enhance the quality of the culture environment. During culturing in a biofloc technology system, the supplementation of microalgae and its accompanying bacteria plays a beneficial role in reducing nitrogenous compounds. This enhances water quality and creates favorable environmental conditions for specific bacterial groups, while simultaneously reducing the dependency on carbon sources with higher content. The fluctuations in the bacterial communities of the intestine are closely associated with the severity of diseases related to shrimp and are used to evaluate the health status of shrimp. Overall, we will review the microbes associated with shrimp culture in BFT and their effects on shrimp growth. We will also examine the microbial impacts on the growth performance of L. vannamei in BFT, as well as the close relationship between probiotics and the intestinal microbes of L. vannamei.
Collapse
Affiliation(s)
| | | | | | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo 315832, China; (B.R.); (Z.Z.); (J.Z.)
| |
Collapse
|
6
|
Dayang Najwa AB, Elexson N, Dalene L, Teng ST. Vibrio Species and Cyanobacteria: Understanding Their Association in Local Shrimp Farm Using Canonical Correspondence Analysis (CCA). MICROBIAL ECOLOGY 2024; 87:51. [PMID: 38488929 PMCID: PMC10943157 DOI: 10.1007/s00248-024-02356-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/29/2024] [Indexed: 03/17/2024]
Abstract
In aquatic environments, Vibrio and cyanobacteria establish varying relationships influenced by environmental factors. To investigate their association, this study spanned 5 months at a local shrimp farm, covering the shrimp larvae stocking cycle until harvesting. A total of 32 samples were collected from pond A (n = 6), pond B (n = 6), effluent (n = 10), and influent (n = 10). Vibrio species and cyanobacteria density were observed, and canonical correspondence analysis (CCA) assessed their correlation. CCA revealed a minor correlation (p = 0.847, 0.255, 0.288, and 0.304) between Vibrio and cyanobacteria in pond A, pond B, effluent, and influent water, respectively. Notably, Vibrio showed a stronger correlation with pH (6.14-7.64), while cyanobacteria correlated with pH, salinity (17.4-24 ppt), and temperature (30.8-31.5 °C), with salinity as the most influential factor. This suggests that factors beyond cyanobacteria influence Vibrio survival. Future research could explore species-specific relationships, regional dynamics, and multidimensional landscapes to better understand Vibrio-cyanobacteria connections. Managing water parameters may prove more efficient in controlling vibriosis in shrimp farms than targeting cyanobacterial populations.
Collapse
Affiliation(s)
- Awg Baki Dayang Najwa
- Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Nillian Elexson
- Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia.
| | - Lesen Dalene
- Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| | - Sing Tung Teng
- Faculty of Resource Science and Technology, University Malaysia Sarawak, 94300, Kota Samarahan, Sarawak, Malaysia
| |
Collapse
|
7
|
Yang S, Dong M, Lu H, Cai Z, Ge M, Xing J, Huang H, Huang Y, Sun G, Zhou S, Xu M. Explaining nitrogen turnover in sediments and water through variations in microbial community composition and potential function. CHEMOSPHERE 2023; 344:140379. [PMID: 37827459 DOI: 10.1016/j.chemosphere.2023.140379] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 09/20/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023]
Abstract
Anthropogenic activities greatly impact nitrogen (N) biogeochemical cycling in aquatic ecosystems. High N concentrations in coastal aquaculture waters threaten fishery production and aquaculture ecosystems and have become an urgent problem to be solved. Existing microbial flora and metabolic potential significantly regulate N turnover in aquatic ecosystems. To clarify the contribution of microorganisms to N turnover in sediment and water, we investigated three types of aquaculture ecosystems in coastal areas of Guangdong, China. Nitrate nitrogen (NO3--N) was the dominant component of total nitrogen in the sediment (interstitial water, 90.4%) and water (61.6%). This finding indicates that NO3--N (1.67-2.86 mg/L and 2.98-7.89 mg/L in the sediment and water) is a major pollutant in aquaculture ecosystems. In water, the relative abundances of assimilation nitrogen reduction and aerobic denitrifying bacteria, as well as the metabolic potentials of nitrogen fixation and dissimilated nitrogen in fish monoculture, were only 61.0%, 31.5%, 47.5%, and 27.2% of fish and shrimp polyculture, respectively. In addition, fish-shrimp polyculture reduced NO3--N content (2.86 mg/L) compared to fish monoculture (7.89 mg/L), which was consistent with changes in aerobic denitrification and nitrate assimilation, suggesting that polyculture could reduce TN concentrations in water bodies and alleviate nitrogen pollution risks. Further analysis via structural equation modeling (SEM) revealed that functional pathways (36% and 31%) explained TN changes better than microbial groups in sediment and water (13% and 11%), suggesting that microbial functional capabilities explain TN better than microbial community composition and other factors (pH, O2, and aquaculture type). This study enhances our understanding of nitrogen pollution characteristics and microbial community and functional capabilities related to sediment-water nitrogen turnover in three types of aquaculture ecosystems, which can contribute to the preservation of healthy coastal ecosystems.
Collapse
Affiliation(s)
- Shan Yang
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Meijun Dong
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Huibin Lu
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Zhipeng Cai
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Meng Ge
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Jia Xing
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Haobin Huang
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Youda Huang
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Guoping Sun
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Shaofeng Zhou
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Meiying Xu
- Guangdong Environmental Protection Key Laboratory of Microbiology and Ecological Safety, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| |
Collapse
|
8
|
Waiho K, Abd Razak MS, Abdul Rahman MZ, Zaid Z, Ikhwanuddin M, Fazhan H, Shu-Chien AC, Lau NS, Azmie G, Ishak AN, Syahnon M, Kasan NA. A metagenomic comparison of clearwater, probiotic, and Rapid BFT TM on Pacific whiteleg shrimp, Litopenaeus vannamei cultures. PeerJ 2023; 11:e15758. [PMID: 37790619 PMCID: PMC10542392 DOI: 10.7717/peerj.15758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/26/2023] [Indexed: 10/05/2023] Open
Abstract
Biofloc technology improves water quality and promote the growth of beneficial bacteria community in shrimp culture. However, little is known about the bacteria community structure in both water and gut of cultured organisms. To address this, the current study characterised the metagenomes derived from water and shrimp intestine samples of novel Rapid BFTTM with probiotic and clearwater treatments using 16S V4 region and full length 16S sequencing. Bacteria diversity of water and intestine samples of Rapid BFTTM and probiotic treatments were similar. Based on the 16S V4 region, water samples of >20 μm biofloc had the highest abundance of amplicon sequence variant (ASV). However, based on full length 16S, no clear distinction in microbial diversity was observed between water samples and intestine samples. Proteobacteria was the most abundant taxon in all samples based on both 16S V4 and full length 16S sequences. Vibrio was among the highest genus based on 16S V4 region but only full length 16S was able to discern up to species level, with three Vibrios identified-V. harveyi, V. parahaemolyticus and V. vulnificus. Vibrio harveyi being the most abundant species in all treatments. Among water samples, biofloc water samples had the lowest abundance of all three Vibrios, with V. vulnificus was present only in bioflocs of <20 μm. Predicted functional profiles of treatments support the beneficial impacts of probiotic and biofloc inclusion into shrimp culture system. This study highlights the potential displacement of opportunistic pathogens by the usage of biofloc technology (Rapid BFTTM) in shrimp culture.
Collapse
Affiliation(s)
- Khor Waiho
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden, Penang, Malaysia
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, Guangdong, China
| | - Muhammad Syafiq Abd Razak
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
- Zaiyadal Aquaculture Sdn. Bhd., Shah Alam, Selangor, Malaysia
| | | | - Zainah Zaid
- Zaiyadal Aquaculture Sdn. Bhd., Shah Alam, Selangor, Malaysia
| | - Mhd Ikhwanuddin
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, Guangdong, China
- Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia
| | - Hanafiah Fazhan
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden, Penang, Malaysia
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, Guangdong, China
| | - Alexander Chong Shu-Chien
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden, Penang, Malaysia
- School of Biological Sciences, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Minden, Penang, Malaysia
| | - Ghazali Azmie
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Ahmad Najmi Ishak
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Mohammad Syahnon
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
- Centre of Research and Field Service (CRaFS), Universiti Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia
| | - Nor Azman Kasan
- Higher Institution Centre of Excellence (HICoE), Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus, Malaysia
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, Guangdong, China
| |
Collapse
|
9
|
Lalitha N, Ronald BSM, Chitra MA, Jangam AK, Katneni VK, Suganya PN, Senthilnayagam H, Senthilkumar TMA, Muralidhar M. Exploration of the candidate beneficial bacteria for Penaeus vannamei culture by core microbiome analysis using amplicon sequencing. Lett Appl Microbiol 2023; 76:ovad087. [PMID: 37541955 DOI: 10.1093/lambio/ovad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/28/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Globally, Penaeus vannamei is the vital species in aquaculture production. Beneficial bacterial exploration of gut, sediment, and water were investigated in P. vannamei culture using Illumina Miseq sequencing of 16S RNA V3-V4 hypervariable regions. Predominant phyla identified were Proteobacteria, Tenericutes, Bacteroidetes in gut; Proteobacteria, Bacteroidetes, Planctomycetes in sediment and Cyanobacteria, Proteobacteria, and Planctomycetes in water. In total, 46 phyla, 509 families and 902 genera; 70 phyla, 735 families and 1255 genera; 55 phyla, 580 families and 996 genera were observed in gut, sediment and water, respectively. Diversity of microbial communities in respect of observed Operational Taxonomic Units, diversity indices (Shannon and Simpson), richness index (Chao1) were significantly high P (<0.05) in 60 DoC in gut and 30 DoC in sediment. Beta diversity indicated separate clusters for bacterial communities in gut, sediment and water samples and formation of distinct community profiles. Core microbiome in P. vannamei rearing ponds over a time consisted of 9, 21, and 20 OTUs in gut, rearing water and sediment, respectively. This study helps to intervene with suitable beneficial microbes to establish an aquaculture system thereby contributes to enhance the productivity, improve water quality and pond bottom condition, and control the pathogenic agents at each stage of the culture.
Collapse
Affiliation(s)
- Natarajan Lalitha
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India
| | | | - Murugesan Ananda Chitra
- Centre for Animal Health Studies, Madhavaram Milk Colony, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600051, India
| | - Ashok Kumar Jangam
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Vinaya Kumar Katneni
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Panjan Nathamuni Suganya
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| | - Hemalatha Senthilnayagam
- Madras Veterinary College, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600007, India
| | | | - Moturi Muralidhar
- ICAR-Central Institute of Brackishwater Aquaculture, Aquatic Animal Health and Environment Division, Chennai 600028, India
| |
Collapse
|
10
|
Foysal MJ. Host habitat shapes the core gut bacteria of decapod crustaceans: A meta-analysis. Heliyon 2023; 9:e16511. [PMID: 37274665 PMCID: PMC10238905 DOI: 10.1016/j.heliyon.2023.e16511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 06/06/2023] Open
Abstract
Gut microbiota is an essential determinant factor that drives the physiological, immunological, and metabolic functions of animals. A few meta-analysis studies identified crucial information about the gut microbiota of vertebrate animals in different habitats including fish while no report is yet available for the commercially cultured decapod crustaceans (DC). This meta-analysis investigated the gut microbiota of 11 commercially cultured DC species from five different groups-crab, crayfish, lobster, prawn, and shrimp to gain an overview of microbial diversity and composition and to find out core genera under two different host habitats: freshwater and saltwater. The analysis of 627 Illumina datasets from 25 published studies revealed selective patterns of diversity and compositional differences among groups and between freshwater and saltwater culture systems. The study found a salinity-dependent heterogeneous response of gut microbiota, specifically Vibrio in saltwater for white shrimp, a species that can be cultured with and without salt. Overall, the genera reared in freshwater showed higher diversity in the gut microbial communities than those reared in saltwater. An overwhelming abundance of Candidatus Bacilloplasma and Vibrio were identified for species cultured in freshwater and saltwater system, respectively and these two species were identified as the main core genera for nine out of 11 DC species, except freshwater prawn and river prawn. Together, these results demonstrate the effectiveness of the meta-analysis in identifying the robust and reproducible features of DC gut microbiota for different groups and host habitats. The diversity information curated here could be used as a reference for future studies to differentiate various DC species under two different rearing environments.
Collapse
|
11
|
Diwan A, Harke SN, Panche AN. Host-microbiome interaction in fish and shellfish: An overview. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2023; 4:100091. [PMID: 37091066 PMCID: PMC10113762 DOI: 10.1016/j.fsirep.2023.100091] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/28/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
The importance of the gut microbiome in the management of various physiological activities including healthy growth and performance of fish and shellfish is now widely considered and being studied in detail for potential applications in aquaculture farming and the future growth of the fish industry. The gut microbiome in all animals including fish is associated with a number of beneficial functions for the host, such as stimulating optimal gastrointestinal development, producing and supplying vitamins to the host, and improving the host's nutrient uptake by providing additional enzymatic activities. Besides nutrient uptake, the gut microbiome is involved in strengthening the immune system and maintaining mucosal tolerance, enhancing the host's resilience against infectious diseases, and the production of anticarcinogenic and anti-inflammatory compounds. Because of its significant role, the gut microbiome is very often considered an "extra organ," as it plays a key role in intestinal development and regulation of other physiological functions. Recent studies suggest that the gut microbiome is involved in energy homeostasis by regulating feeding, digestive and metabolic processes, as well as the immune response. Consequently, deciphering gut microbiome dynamics in cultured fish and shellfish species will play an indispensable role in promoting animal health and aquaculture productivity. It is mentioned that the microbiome community available in the gut tract, particularly in the intestine acts as an innovative source of natural product discovery. The microbial communities that are associated with several marine organisms are the source of natural products with a diverse array of biological activities and as of today, more than 1000 new compounds have been reported from such microbial species. Exploration of such new ingredients from microbial species would create more opportunities for the development of the bio-pharma/aquaculture industries. Considering the important role of the microbiome in the whole life span of fish and shellfish, it is necessary to understand the interaction process between the host and microbial community. However, information pertaining to host-microbiome interaction, particularly at the cellular level, gene expression, metabolic pathways, and immunomodulation mechanisms, the available literature is scanty. It has been reported that there are three ways of interaction involving the host-microbe-environment operates to maintain homeostasis in the fish and shellfish gut i.e. host intrinsic factors, the environment that shapes the gut microbiome composition, and the core microbial community present in the gut system itself has equal influence on the host biology. In the present review, efforts have been made to collect comprehensive information on various aspects of host-microbiome interaction, particularly on the immune system and health maintenance, management of diseases, nutrient uptake, digestion and absorption, gene expression, and metabolism in fish and shellfish.
Collapse
Affiliation(s)
- A.D. Diwan
- Institute of Biosciences and Technology, Mahatma Gandhi Mission (MGM) University, Aurangabad, 431003, Maharashtra, India
- Corresponding author at: MGM Institute of Biosciences and Technology, MGM University, N-6, CIDCO, Aurangabad 431003, Maharashtra, India.
| | - Sanjay N Harke
- Institute of Biosciences and Technology, Mahatma Gandhi Mission (MGM) University, Aurangabad, 431003, Maharashtra, India
| | - Archana N Panche
- Novo Nordisk Centre for Biosustainability, Technical University of Denmark, B220 Kemitorvet, 2800 Kgs, Lyngby, Denmark
| |
Collapse
|
12
|
Chaudhari HG, Prajapati S, Wardah ZH, Raol G, Prajapati V, Patel R, Shati AA, Alfaifi MY, Elbehairi SEI, Sayyed RZ. Decoding the microbial universe with metagenomics: a brief insight. Front Genet 2023; 14:1119740. [PMID: 37197021 PMCID: PMC10183756 DOI: 10.3389/fgene.2023.1119740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
A major part of any biological system on earth involves microorganisms, of which the majority are yet to be cultured. The conventional methods of culturing microbes have given fruitful outcomes yet have limitations. The curiosity for better understanding has led to the development of culture-independent molecular methods that help push aside the roadblocks of earlier methods. Metagenomics unifies the scientific community in search of a better understanding of the functioning of the ecosystem and its component organisms. This approach has opened a new paradigm in advanced research. It has brought to light the vast diversity and novelty among microbial communities and their genomes. This review focuses on the development of this field over time, the techniques and analysis of data generated through sequencing platforms, and its prominent interpretation and representation.
Collapse
Affiliation(s)
- Hiral G. Chaudhari
- Shri Alpesh N. Patel PG Institute of Science and Research, Sardar Patel University, Anand, Gujarat, India
| | - Shobha Prajapati
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Zuhour Hussein Wardah
- Shri Alpesh N. Patel PG Institute of Science and Research, Sardar Patel University, Anand, Gujarat, India
| | - Gopal Raol
- Shri R. P. Arts, Shri K.B. Commerce, and Smt. BCJ Science College, Khambhat, Gujarat, India
| | - Vimalkumar Prajapati
- Division of Microbial and Environmental Biotechnology, Aspee Shakilam Biotechnology Institute, Navsari Agricultural University, Surat, Gujarat, India
- *Correspondence: Vimalkumar Prajapati,
| | - Rajesh Patel
- Department of Biosciences, Veer Narmad South Gujarat University, Surat, Gujarat, India
| | - Ali A. Shati
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammad Y. Alfaifi
- Biology Department, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | | | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandal's S I Patil Arts, G B Patel Science and STKV Sangh Commerce College, Shahada, India
| |
Collapse
|
13
|
Abidin Z, Huang HT, Hu YF, Chang JJ, Huang CY, Wu YS, Nan FH. Effect of dietary supplementation with Moringa oleifera leaf extract and Lactobacillus acidophilus on growth performance, intestinal microbiota, immune response, and disease resistance in whiteleg shrimp (Penaeus vannamei). FISH & SHELLFISH IMMUNOLOGY 2022; 127:876-890. [PMID: 35810967 DOI: 10.1016/j.fsi.2022.07.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
This study investigated the effect of the moringa (Moringa oleifera) leaf extract and Lactobacillus acidophilus individually or combined on growth performance, enzyme activity, intestinal and hepatopancreatic histology, intestinal microbiota, immune response, and resistance against Vibrio alginolyticus and Vibrio parahaemolyticus in whiteleg shrimp (Penaeus vannamei). Six diets were formulated: three diets without L. acidophilus containining 0 (control, ME0), 2.5 (ME2.5), and 5.0 g/kg of moringa (ME5.0) and the same three diets containing L. acidophilus at 1 × 107 CFU/g of diet (ME0+P, ME2.5 + P, and ME5.0 + P, respectively). Growth performance was measured after 60 days of the rearing period. On the final day, the shrimp were sampled to assess enzyme activity, intestinal and hepatopancreatic histology, and gut microbiota. Shrimp hemocytes were examined on Days 0, 1, 2, 4, 7, 14, 21, and 28 to measure the immune response in terms of the total hemocyte count, phenoloxidase activity, phagocytosis, and superoxide anion production. Furthermore, the shrimp were challenged with V. alginolyticus and V. parahaemolyticus. The results revealed that ME2.5 + P significantly increased (P < 0.05) final weight, weight gain, specific growth rate, enzyme activities, and villi height compared with ME2.5 and control. Wall thickness was increased in the shrimp fed diet supplemented with moringa and L. acidophilus compared with the control shrimp. Hepatopancreatic histology revealed that R cells were more abundant in the shrimp fed diet containing moringa and L. acidophilus compared with those fed diet containing moringa alone (P < 0.05) at the same concentration. High-throughput sequencing analysis indicated that the dietary supplementation with moringa and L. acidophilus affected the gut microbiota composition. All gene functions, members of KEGG level 2, related to metabolism were increased in diet supplemented with moringa with or without L. acidophilus compared with the control group. The immune assay revealed that the total hemocyte count, phenoloxidase activity, phagocytic rate, superoxide anion production, and immune-related gene expression (including those of prophenoloxidase II, alpha-2-macroglobulin, penaeidin2, antilipopolysaccharide factor, crustin, lysozyme, glutathione peroxidase, and superoxide dismutase) were higher in the experimental groups than in the control group on several observed days; however, the increases were observed more often in the ME2.5 + P group than in the other treatment groups. Furthermore, the ME2.5 + P group exhibited a significantly higher survival rate (P < 0.05) in the challenge test against V. alginolyticus and V. parahaemolyticus. In conclusion, supplementation with dietary moringa and L. acidophilus at ME2.5 + P improved growth performance, immune system, and resistance against Vibrio in the shrimp.
Collapse
Affiliation(s)
- Zaenal Abidin
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Huai-Ting Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Yeh-Fang Hu
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Jui-Jen Chang
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan; Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Chih-Yang Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan
| | - Yu-Sheng Wu
- Department of Aquaculture, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Fan-Hua Nan
- Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan.
| |
Collapse
|
14
|
Foysal MJ, Nguyen TTT, Sialumano M, Phiri S, Chaklader MR, Fotedar R, Gagnon MM, Tay A. Zeolite mediated processing of nitrogenous waste in the rearing environment influences gut and sediment microbial community in freshwater crayfish (Cherax cainii) culture. CHEMOSPHERE 2022; 298:134276. [PMID: 35278449 DOI: 10.1016/j.chemosphere.2022.134276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Zeolite is known to uptake toxic metals and filter nitrogenous waste from aquaculture effluents. The present study aimed to investigate the impacts of zeolite in three different applications namely, dietary zeolite (DZ), suspended zeolite (SZ) in the water column, and a combination of both (DZSZ) relative to unexposed freshwater crayfish, marron (control). At the end of the 56-days trial, the impact was assessed in terms of characterization of microbial communities in the culture environment and the intestine of marron. Alongside the microbial communities, the innate immune response of marron was also evaluated. The 16S rRNA data showed that marrons exposed to the suspended zeolite had a significant increase of bacterial diversity in the gut, including the restoration of marron core operational taxonomic units (OTUs), relative to other forms of exposures (DZ, DZSZ) and the control. Suspended zeolite alone also increased the number of unshared OTUs and genera, and improved predicted metabolic functions for the biosynthesis and digestion of proteins, amino acids, fatty acids, and hormones. In the tank sediment, the shift of microbial communities was connected more strongly with the time of experiment than the type of zeolite exposure. In the second case, only control marron had a different microbial ordination in terms of rare taxa present in the community. Nevertheless, the modulation in the gut environment was found more prominent in DZ, relative to modulation in the tank sediments. The taxa-environment correlation identified Rhodoferax as the most potential bacteria in removing nitrogenous waste from the rearing environment. Further analysis showed that SZ resulted in the upregulation of genes associated with the innate immune response of marron. Overall results suggest that SZ can be used to enrich microbial communities in the gut and tank sediments and better immune performance of marron.
Collapse
Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh.
| | - Thi Thu Thuy Nguyen
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Experimental Biology, Research Institute for Aquaculture No. 2, Ho Chi Minh City, Viet Nam.
| | - Mavis Sialumano
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Veterinary Services, Ministry of Fisheries and Livestock, Zambia
| | - Simon Phiri
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Veterinary Services, Ministry of Fisheries and Livestock, Zambia
| | - Md Reaz Chaklader
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia; Department of Primary Industries and Regional Development, Fleet Street, Fremantle, WA, Australia
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | | | - Alfred Tay
- Marshall Centre for Infectious Disease Research and Training, University of Western Australia, WA, Australia
| |
Collapse
|
15
|
Hsu JCK, Huang HT, Lin HJ, Chou HY, Huang PY, Prachumwat A, Chen LL. Applying Modified VP53A Recombinant Protein as an Anti-White Spot Syndrome Virus Biological Agent in Litopenaeus vannamei Farming. Viruses 2022; 14:v14071353. [PMID: 35891334 PMCID: PMC9324474 DOI: 10.3390/v14071353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/20/2022] [Accepted: 06/20/2022] [Indexed: 02/01/2023] Open
Abstract
Shrimp farming is an important economic activity. However, due to the spread of pathogens, shrimp aquaculture is becoming increasingly difficult. Many studies have confirmed that white spot syndrome virus (WSSV) recombinant proteins can inhibit viral infection. Among them, VP53 recombinant protein has been found to reduce mortality upon WSSV challenge. This study was conducted in Kaohsiung, Taiwan and reports the first field feeding trial to demonstrate that WSSV recombinant proteins can improve shrimp survival rates at a farming scale. Prior to the feeding trial, the shrimp were confirmed to be slightly infected with WSSV, Vibrio parahaemolyticus strains causing acute hepatopancreatic necrosis disease (AHPND), non-AHPND V. parahaemolyticus strains, and Enterocytozoon hepatopenaei (EHP), which are common pathogens that shrimp farmers often face. The shrimp were then divided into two groups: a control group (C group) fed with a commercial diet and a protein group (P group) fed with the same commercial feed with VP53 recombinant protein. Our findings indicated that the survival rate and expression of immune genes of the P group were higher than those of the C group. The intestinal microbiota of the two groups were also analysed. Collectively, our results confirmed that the recombinant WSSV envelope protein derivative can be used as an effective anti-virus biological agent in shrimp farms.
Collapse
Affiliation(s)
- Jeff Chia-Kai Hsu
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 20224, Taiwan;
- Innocreate Bioscience Co., Ltd., Zhonghe District, New Taipei City 23557, Taiwan
| | - Huai-Ting Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.H.); (H.-Y.C.)
| | - Han-Jia Lin
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan;
| | - Hsin-Yiu Chou
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan; (H.-T.H.); (H.-Y.C.)
| | - Po-Yu Huang
- Department of Life Science, National Taitung University, Taitung 95092, Taiwan;
| | - Anuphap Prachumwat
- Aquatic Animal Health Research Team, Integrative Aquaculture Biotechnology Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (A.P.); (L.-L.C.)
| | - Li-Li Chen
- Institute of Marine Biology, National Taiwan Ocean University, Keelung 20224, Taiwan;
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
- Correspondence: (A.P.); (L.-L.C.)
| |
Collapse
|
16
|
Reyes G, Betancourt I, Andrade B, Panchana F, Román R, Sorroza L, Trujillo LE, Bayot B. Microbiome of Penaeus vannamei Larvae and Potential Biomarkers Associated With High and Low Survival in Shrimp Hatchery Tanks Affected by Acute Hepatopancreatic Necrosis Disease. Front Microbiol 2022; 13:838640. [PMID: 35615516 PMCID: PMC9125206 DOI: 10.3389/fmicb.2022.838640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND) is an emerging bacterial disease of cultured shrimp caused mainly by Vibrio parahaemolyticus, which harbors the lethal PirAB toxin genes. Although Penaeus vannamei (P. vannamei) postlarvae are susceptible to AHPND, the changes in the bacterial communities through the larval stages affected by the disease are unknown. We characterized, through high-throughput sequencing, the microbiome of P. vannamei larvae infected with AHPND-causing bacteria through the larval stages and compared the microbiome of larvae collected from high- and low-survival tanks. A total of 64 tanks from a commercial hatchery were sampled at mysis 3, postlarvae 4, postlarvae 7, and postlarvae 10 stages. PirAB toxin genes were detected by PCR and confirmed by histopathology analysis in 58 tanks. Seven from the 58 AHPND-positive tanks exhibited a survival rate higher than 60% at harvest, despite the AHPND affectation, being selected for further analysis, whereas 51 tanks exhibited survival rates lower than 60%. A random sample of 7 out of these 51 AHPND-positive tanks was also selected. Samples collected from the selected tanks were processed for the microbiome analysis. The V3–V4 hypervariable regions of the 16S ribosomal RNA (rRNA) gene of the samples collected from both the groups were sequenced. The Shannon diversity index was significantly lower at the low-survival tanks. The microbiomes were significantly different between high- and low-survival tanks at M3, PL4, PL7, but not at PL10. Differential abundance analysis determined that biomarkers associated with high and low survival in shrimp hatchery tanks affected with AHPND. The genera Bacillus, Vibrio, Yangia, Roseobacter, Tenacibaculum, Bdellovibrio, Mameliella, and Cognatishimia, among others, were enriched in the high-survival tanks. On the other hand, Gilvibacter, Marinibacterium, Spongiimonas, Catenococcus, and Sneathiella, among others, were enriched in the low-survival tanks. The results can be used to develop applications to prevent losses in shrimp hatchery tanks affected by AHPND.
Collapse
Affiliation(s)
- Guillermo Reyes
- Centro Nacional de Acuicultura e Investigaciones Marinas (CENAIM), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
- Facultad de Ciencias de la Vida (FCV), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
- *Correspondence: Guillermo Reyes,
| | - Irma Betancourt
- Centro Nacional de Acuicultura e Investigaciones Marinas (CENAIM), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
| | - Betsy Andrade
- Centro Nacional de Acuicultura e Investigaciones Marinas (CENAIM), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
| | - Fanny Panchana
- Centro Nacional de Acuicultura e Investigaciones Marinas (CENAIM), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
| | - Rubén Román
- Centro Nacional de Acuicultura e Investigaciones Marinas (CENAIM), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
| | - Lita Sorroza
- Facultad de Ciencias Agropecuarias, Universidad Técnica de Machala, Machala, Ecuador
| | - Luis E. Trujillo
- Industrial Biotechnology Research Group, Center for Nanoscience and Nanotechnology (CENCINAT), Universidad de las Fuerzas Armadas (ESPE), Sangolquí, Ecuador
| | - Bonny Bayot
- Centro Nacional de Acuicultura e Investigaciones Marinas (CENAIM), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
- Facultad de Ingeniería Marítima y Ciencias del Mar (FIMCM), Escuela Superior Politécnica del Litoral (ESPOL), Guayaquil, Ecuador
- Bonny Bayot,
| |
Collapse
|
17
|
Soo TCC, Bhassu S. Biochemical indexes and gut microbiota testing as diagnostic methods for
Penaeus monodon
health and physiological changes during AHPND infection with food safety concerns. Food Sci Nutr 2022; 10:2694-2709. [PMID: 35959249 PMCID: PMC9361443 DOI: 10.1002/fsn3.2873] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Tze Chiew Christie Soo
- Animal Genetics and Genome Evolutionary Laboratory (AGAGEL) Department of Genetics and Microbiology Faculty of Science Institute of Biological Sciences University of Malaya Kuala Lumpur Malaysia
| | - Subha Bhassu
- Animal Genetics and Genome Evolutionary Laboratory (AGAGEL) Department of Genetics and Microbiology Faculty of Science Institute of Biological Sciences University of Malaya Kuala Lumpur Malaysia
- Terra Aqua Laboratory Centre for Research in Biotechnology for Agriculture (CEBAR) Research Management and Innovation Complex University of Malaya Kuala Lumpur Malaysia
| |
Collapse
|
18
|
Soto-Rodriguez SA, Lozano-Olvera R, Ramos-Clamont Montfort G, Zenteno E, Sánchez-Salgado JL, Vibanco-Pérez N, Aguilar Rendón KG. New Insights into the Mechanism of Action of PirAB from Vibrio Parahaemolyticus. Toxins (Basel) 2022; 14:toxins14040243. [PMID: 35448852 PMCID: PMC9030326 DOI: 10.3390/toxins14040243] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/06/2023] Open
Abstract
PirAB toxins secreted by Vibrio parahaemolyticus (Vp) harbor the pVA1 virulence plasmid, which causes acute hepatopancreatic necrosis disease (AHPND), an emerging disease in Penaeid shrimp that can cause 70–100% mortality and that has resulted in great economic losses since its first appearance. The cytotoxic effect of PirABVp on the epithelial cells of the shrimp hepatopancreas (Hp) has been extensively documented. New insights into the biological role of the PirBVp subunit show that it has lectin-like activity and recognizes mucin-like O-glycosidic structures in the shrimp Hp. The search for toxin receptors can lead to a better understanding of the infection mechanisms of the pathogen and the prevention of the host disease by blocking toxin–receptor interactions using a mimetic antagonist. There is also evidence that Vp AHPND changes the community structure of the microbiota in the surrounding water, resulting in a significant reduction of several bacterial taxa, especially Neptuniibacter spp. Considering these findings, the PirABvp toxin could exhibit a dual role of damaging the shrimp Hp while killing the surrounding bacteria.
Collapse
Affiliation(s)
- Sonia A. Soto-Rodriguez
- Laboratorio de Bacteriología, Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad de Acuacultura y Manejo Ambiental, Av. Sábalo-Cerritos S/N A.P. 711, Mazatlán 82112, Sinaloa, Mexico; (R.L.-O.); (K.G.A.R.)
- Correspondence:
| | - Rodolfo Lozano-Olvera
- Laboratorio de Bacteriología, Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad de Acuacultura y Manejo Ambiental, Av. Sábalo-Cerritos S/N A.P. 711, Mazatlán 82112, Sinaloa, Mexico; (R.L.-O.); (K.G.A.R.)
| | - Gabriela Ramos-Clamont Montfort
- Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo 83304, Sonora, Mexico;
| | - Edgar Zenteno
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacan, Mexico City 04510, Mexico, Mexico; (E.Z.); (J.L.S.-S.)
| | - José Luis Sánchez-Salgado
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Coyoacan, Mexico City 04510, Mexico, Mexico; (E.Z.); (J.L.S.-S.)
| | - Norberto Vibanco-Pérez
- Laboratorio de Investigación en Biología Molecular e Inmunología, Unidad Académica de Ciencias Químico Biológicas y Farmacéuticas, Universidad Autónoma de Nayarit, Ciudad de la Cultura, Tepic 63190, Nayarit, Mexico;
| | - Karla G. Aguilar Rendón
- Laboratorio de Bacteriología, Centro de Investigación en Alimentación y Desarrollo, A.C. Unidad de Acuacultura y Manejo Ambiental, Av. Sábalo-Cerritos S/N A.P. 711, Mazatlán 82112, Sinaloa, Mexico; (R.L.-O.); (K.G.A.R.)
| |
Collapse
|
19
|
Zhou Y, Leung MHY, Tong X, Lee JYY, Lee PKH. City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:15051-15062. [PMID: 34738808 DOI: 10.1021/acs.est.1c03941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Currently, there is a lack of understanding on the variations of the indoor airborne microbiotas of different building types within a city, and how operational taxonomic unit (OTU)- and amplicon sequence variant (ASV)-based analyses of the 16S rRNA gene sequences affect interpretation of the indoor airborne microbiota results. Therefore, in this study, the indoor airborne bacterial microbiotas between commercial buildings, residences, and subways within the same city were compared using both OTU- and ASV-based analytic methods. Our findings suggested that indoor airborne bacterial microbiota compositions were significantly different between building types regardless of the bioinformatics method used. The processes of ecological drift and random dispersal consistently played significant roles in the assembly of the indoor microbiota across building types. Abundant taxa tended to be more centralized in the correlation network of each building type, highlighting their importance. Taxonomic changes between the microbiotas of different building types were also linked to changes in their inferred metabolic function capabilities. Overall, the results imply that customized strategies are necessary to manage indoor airborne bacterial microbiotas for each building type or even within each specific building.
Collapse
Affiliation(s)
- You Zhou
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marcus H Y Leung
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Xinzhao Tong
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Justin Y Y Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Patrick K H Lee
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
20
|
Murphy TR, Xiao R, Brooks ML, Rader BA, Hamilton-Brehm SD. Aquaculture production of hatchling Hawaiian Bobtail Squid (Euprymna scolopes) is negatively impacted by decreasing environmental microbiome diversity. J Appl Microbiol 2021; 132:1724-1737. [PMID: 34724303 PMCID: PMC9299211 DOI: 10.1111/jam.15350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/16/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]
Abstract
Aims The Hawaiian Bobtail Squid (Euprymna scolopes) is a model organism for investigating host–symbiont relationships. The current scientific focus is on the microbiome within E. scolopes, while very little is known about the microbiome of the tanks housing E. scolopes. We examined the hypothesis that bacterial communities and geochemistry within the squid tank environment correlate with the production of viable paralarval squid. Methods and Results Total DNA was extracted from sediment and filtered water samples from ‘productive’ squid cohorts with high embryonic survival and paralarval hatching, ‘unproductive’ cohorts with low embryonic survival and paralarval hatching. As a control total DNA was extracted from environmental marine locations where E. scolopes is indigenous. Comparative analysis of the bacterial communities by the 16S rRNA gene was performed using next generation sequencing. Thirty‐eight differentially abundant genera were identified in the adult tank waters. The majority of the sequences represented unclassified, candidate or novel genera. The characterized genera included Aquicella, Woeseia and Ferruginibacter, with Hyphomicrobium and Rhizohapis were found to be more abundant in productive adult tank water. In addition, nitrate and pH covaried with productive cohorts, explaining 67% of the bacterial populations. The lower abundance of nitrate‐reducing bacteria in unproductive adult tank water could explain detected elevated nitrate levels. Conclusions We conclude that microbiome composition and water geochemistry can negatively affect E. scolopes reproductive physiology in closed tank systems, ultimately impacting host‐microbe research using these animals. Significance and Impact of study These results identify the tight relationship between the microbiome and geochemistry to E. scolopes. From this study, it may be possible to design probiotic counter‐measures to improve aquaculture conditions for E. scolopes.
Collapse
Affiliation(s)
- Trevor R Murphy
- School of Biological Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Rui Xiao
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA
| | - Marjorie L Brooks
- School of Biological Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Bethany A Rader
- School of Biological Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| | - Scott D Hamilton-Brehm
- School of Biological Sciences, Southern Illinois University Carbondale, Carbondale, Illinois, USA
| |
Collapse
|
21
|
Zhang W, Zhu Z, Chen J, Qiu Q, Xiong J. Quantifying the Importance of Abiotic and Biotic Factors Governing the Succession of Gut Microbiota Over Shrimp Ontogeny. Front Microbiol 2021; 12:752750. [PMID: 34691004 PMCID: PMC8531273 DOI: 10.3389/fmicb.2021.752750] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/31/2021] [Indexed: 02/01/2023] Open
Abstract
Intensive studies have evaluated abiotic factors in shaping host gut microbiota. In contrast, little is known on how and to what extent abiotic (geochemical variables) and biotic (i.e., surrounding microbes, younger shrimp, and age) factors assemble the gut microbiota over shrimp ontogeny. Considering the functional importance of gut microbiota in improving host fitness, this knowledge is fundamental to sustain a desirable gut microbiota for a healthy aquaculture. Here, we characterized the successional rules of both the shrimp gut and rearing water bacterial communities over the entire shrimp farming. Both the gut and rearing water bacterial communities exhibited the time decay of similarity relationship, with significantly lower temporal turnover rate for the gut microbiota, which were primarily governed by shrimp age (days postlarval inoculation) and water pH. Gut commensals were primary sourced (averaged 60.3%) from their younger host, rather than surrounding bacterioplankton (19.1%). A structural equation model revealed that water salinity, pH, total phosphorus, and dissolve oxygen directly governed bacterioplankton communities but not for the gut microbiota. In addition, shrimp gut microbiota did not simply mirror the rearing bacterioplankton communities. The gut microbiota tended to be governed by variable selection over shrimp ontogeny, while the rearing bacterioplankton community was shaped by homogeneous selection. However, the determinism of rare and stochasticity of abundant subcommunities were consistent between shrimp gut and rearing water. These findings highlight the importance of independently interpreting host-associated and free-living communities, as well as their rare and abundant subcommunities for a comprehensive understanding of the ecological processes that govern microbial successions.
Collapse
Affiliation(s)
- Wenqian Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zidong Zhu
- School of Biochemical Engineering, Jingzhou Institute of Technology, Jingzhou, China
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qiongfen Qiu
- School of Marine Sciences, Ningbo University, Ningbo, China
| | - Jinbo Xiong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, China.,School of Marine Sciences, Ningbo University, Ningbo, China
| |
Collapse
|
22
|
Patil PK, Vinay TN, Ghate SD, Baskaran V, Avunje S. 16 S rRNA gene diversity and gut microbial composition of the Indian white shrimp (Penaeus indicus). Antonie van Leeuwenhoek 2021; 114:2019-2031. [PMID: 34536184 DOI: 10.1007/s10482-021-01658-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/09/2021] [Indexed: 01/15/2023]
Abstract
The endemic Indian white shrimp (Penaeus indicus) is an economically important crustacean species, distributed in the Indo-West Pacific region. Knowledge of its gut microbial composition helps in dietary interventions to ensure improved health and production. Here we analyzed V3-V4 hypervariable regions of the 16 S rRNA gene to examine intestinal microbiota in wild and domesticated farmed P. indicus. The study revealed that Proteobacteria, Fusobacteria, Tenericutes, and Bacteroidetes, were the dominant phyla in both the groups although there were differences in relative abundance. The dominant genera in case of the wild group were Photobacterium (29.5 %) followed by Propionigenium (13.9 %), Hypnocyclicus (13.7 %) and Vibrio (11.1 %); while Vibrio (46.5 %), Catenococcus (14 %), Propionigenium (10.3 %) and Photobacterium (8.7 %) were dominant in the farmed group. The results of the study suggest the role of environment on the relative abundance of gut bacteria. This is the first report characterizing gut microbial diversity in P. indicus, which can be used to understand the role of gut microbiota in health, nutrition, reproduction, and growth.
Collapse
Affiliation(s)
- Prasanna Kumar Patil
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | | | - Sudeep Darbhe Ghate
- Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to be University), Mangalore, India
| | - Viswanathan Baskaran
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| | - Satheesha Avunje
- ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, Chennai, 600028, India
| |
Collapse
|
23
|
Distribution of Vibrio parahaemolyticus in Farmed Shrimp Penaeus vannamei, Farm Water and Sediment. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2021. [DOI: 10.22207/jpam.15.3.57] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The halophilic marine bacterium Vibrio parahaemolyticus is a zoonotic pathogen associated with wild-caught and farmed shrimp. The bacterium is an important cause of gastroenteritis associated with the consumption of raw or undercooked seafood. In the present study, the prevalence and human pathogenic potential of Vibrio parahaemolyticus in Penaeus vannamei (tissue and hepatopancreas) and the farm environment (water and sediment) was investigated by conventional culture and molecular techniques. The total Vibrio counts of P. vannamei ranged from <1 CFU/mL in hemolymph to 7.61 log CFU/g in the hepatopancreas. The sediment samples consistently showed the counts of 6-7 log CFU/g, while the pond water had Vibrio counts in the range of 2-3 log CFU/ml. Of 120 Vibrio isolates identified, 87 were confirmed as V. parahaemolyticus based on the toxR and tlh gene-specific PCR. The virulence marker gene tdh was not detected in any of the isolates, while the trh gene was detected in 3 (3.6%) isolates. Although the incidence of pathogenic V. parahaemolyticus in farmed P. vannamei is low, the high numbers of total vibrios and V. parahaemolyticus demand constant monitoring of animals and the farm environment for human pathogenic strains of V. parahaemolyticus.
Collapse
|
24
|
Prathiviraj R, Rajeev R, Fernandes H, Rathna K, Lipton AN, Selvin J, Kiran GS. A gelatinized lipopeptide diet effectively modulates immune response, disease resistance and gut microbiome in Penaeus vannamei challenged with Vibrio parahaemolyticus. FISH & SHELLFISH IMMUNOLOGY 2021; 112:92-107. [PMID: 33675990 DOI: 10.1016/j.fsi.2021.02.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/28/2021] [Accepted: 02/28/2021] [Indexed: 06/12/2023]
Abstract
Penaeus vannamei is one of the most economically vital shrimp globally, but infectious diseases have hampered its proper production and supply. As antibiotics pose a huge threat to the environment and humankind, it is essential to seek an alternative strategy to overcome infection and ensure proper culture and production. The present study investigates the effect of an anti-infective biosurfactant derivative lipopeptide MSA31 produced by a marine bacterium on the growth performance, disease resistance, and the gut microbiome of P. vannamei when challenged with pathogenic Vibrio parahaemolyticus SF14. The shrimp were fed with a commercial and lipopeptide formulated diet for 60 days and the growth performance was analyzed. The lipopeptide fed shrimp group showed enhanced growth performance and specific growth rate with improved weight gain than the control group. The challenge experiment showed that the survival rate was significant in the lipopeptide fed group compared to the control group. The results revealed 100% mortality in the control group at the end of 12 h of challenge, while 50% of the lipopeptide diet-fed group survived 24 h, which indicates the enhanced disease resistance in shrimp fed with a lipopeptide diet. The test group also showed higher levels of digestive and immune enzymes, which suggests that the lipopeptide diet could positively modulate the digestive and immune activity of the shrimp. The gut microbiome profiling by Illumina high-throughput sequencing revealed that the most abundant genera in the lipopeptide diet-fed group were Adhaeribacter, Acidothermus, Brevibacillus, Candidatus, Mycobacterium, Rodopila, and Streptomyces, while opportunistic pathogens such as Streptococcus, Escherichia, Klebsiella, Neisseria, Rhizobium, and Salmonella were abundant in the control diet-fed shrimp. Also, lipopeptide diet-fed shrimp were found to have a high abundance of ammonia and nitrogen oxidizing bacteria, which are essential pollutant degraders. Therefore, the study reveals that the dietary supplementation of lipopeptide in shrimp aquaculture could positively modulate the gut microbiome and enhance the shrimp's overall health and immunity in an eco-friendly manner.
Collapse
Affiliation(s)
- R Prathiviraj
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | - Riya Rajeev
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | - Henrietta Fernandes
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | - K Rathna
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | - Anuj Nishanth Lipton
- Curtin Malaysia Research Institute, Curtin University, CDT 250, 98009, Miri, Sarawak, Malaysia
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry, 605014, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India.
| |
Collapse
|
25
|
Frühe L, Dully V, Forster D, Keeley NB, Laroche O, Pochon X, Robinson S, Wilding TA, Stoeck T. Global Trends of Benthic Bacterial Diversity and Community Composition Along Organic Enrichment Gradients of Salmon Farms. Front Microbiol 2021; 12:637811. [PMID: 33995296 PMCID: PMC8116884 DOI: 10.3389/fmicb.2021.637811] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/23/2021] [Indexed: 01/04/2023] Open
Abstract
The analysis of benthic bacterial community structure has emerged as a powerful alternative to traditional microscopy-based taxonomic approaches to monitor aquaculture disturbance in coastal environments. However, local bacterial diversity and community composition vary with season, biogeographic region, hydrology, sediment texture, and aquafarm-specific parameters. Therefore, without an understanding of the inherent variation contained within community complexes, bacterial diversity surveys conducted at individual farms, countries, or specific seasons may not be able to infer global universal pictures of bacterial community diversity and composition at different degrees of aquaculture disturbance. We have analyzed environmental DNA (eDNA) metabarcodes (V3-V4 region of the hypervariable SSU rRNA gene) of 138 samples of different farms located in different major salmon-producing countries. For these samples, we identified universal bacterial core taxa that indicate high, moderate, and low aquaculture impact, regardless of sampling season, sampled country, seafloor substrate type, or local farming and environmental conditions. We also discuss bacterial taxon groups that are specific for individual local conditions. We then link the metabolic properties of the identified bacterial taxon groups to benthic processes, which provides a better understanding of universal benthic ecosystem function(ing) of coastal aquaculture sites. Our results may further guide the continuing development of a practical and generic bacterial eDNA-based environmental monitoring approach.
Collapse
Affiliation(s)
- Larissa Frühe
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Verena Dully
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Nigel B Keeley
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Research, Bergen, Norway
| | - Olivier Laroche
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | - Xavier Pochon
- Biosecurity, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Shawn Robinson
- St. Andrews Biological Station, Department of Fisheries and Oceans, St. Andrews, NB, Canada
| | | | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
26
|
García-López R, Cornejo-Granados F, Lopez-Zavala AA, Cota-Huízar A, Sotelo-Mundo RR, Gómez-Gil B, Ochoa-Leyva A. OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters. Genes (Basel) 2021; 12:genes12040564. [PMID: 33924545 PMCID: PMC8070570 DOI: 10.3390/genes12040564] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/03/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.
Collapse
Affiliation(s)
- Rodrigo García-López
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
| | - Alonso A. Lopez-Zavala
- Departamento de Ciencias Químico Biológicas, Universidad de Sonora (UNISON), Blvd., Rosales y Luis, Encinas, Hermosillo, Sonora 83000, Mexico;
| | - Andrés Cota-Huízar
- Camarones el Renacimiento S.P.R. de R.I. Justino Rubio 26, Colonia Ejidal, Higuera de Zaragoza, Sinaloa 81330, Mexico;
| | - Rogerio R. Sotelo-Mundo
- Laboratorio de Estructura Biomolecular, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora 83304, Mexico;
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo, A.C. Mazatlán, Sinaloa 82100, Mexico;
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología (IBT), Universidad Nacional, Autónoma de México (UNAM) Avenida Universidad #2001, Colonia Chamilpa, Cuernavaca, Morelos 62210, Mexico; (R.G.-L.); (F.C.-G.)
- Correspondence: ; Tel.: +52-777-3291614
| |
Collapse
|
27
|
Sabu EA, Gonsalves MJ, Sreepada RA, Shivaramu MS, Ramaiah N. Evaluation of the Physiological Bacterial Groups in a Tropical Biosecured, Zero-Exchange System Growing Whiteleg Shrimp, Litopenaeus vannamei. MICROBIAL ECOLOGY 2021; 81:335-346. [PMID: 32880700 DOI: 10.1007/s00248-020-01575-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
To elucidate the individual and multiple roles of physiological bacterial groups involved in biogeochemical cycles of carbon, nitrogen, phosphorus and sulfur, the changes in the abundance of aerobic bacteria (heterotrophs, methane oxidizers, ammonia oxidizers, sulfur oxidizers, phosphate solubilizers, phosphate accumulators) and anaerobic bacteria (total anaerobes, nitrate reducers, denitrifiers and sulfate reducers) were investigated in a biosecured, zero-exchange system stocked with whiteleg shrimp, Litopenaeus vannamei for one production cycle. Key water quality parameters during the 96-day production cycle fell within the normal range for L. vannamei culture. Results of Spearman's correlation matrix revealed that different sets of variables correlated at varying levels of significance of the interrelationships between bacterial abundances and water quality parameters. The three nitrogenous species (ammonia, nitrite and nitrate) strongly influenced the physiological bacterial groups' abundance. The strong relationship of bacterial groups with phytoplankton biomass and abundance clearly showed the trophic interconnections in nutrient exchange/recycling. Canonical correspondence analysis performed to assess the total variation revealed that the three dissolved nitrogen species followed by salinity, temperature, phytoplankton biomass and pH collectively accounted for as much as 82% of the total variation. In conclusion, the results of the study revealed that the major drivers that interweaved biogeochemical cycles are the three dissolved nitrogen species, which microbially mediated various aerobic-anaerobic assimilation/dissimilation processes in the pond ecosystem. Considering the pond microbial ecology becoming an important management tool where applied research could improve the economic and environmental sustainability of the aquaculture industry, the findings of the present study are practically relevant.
Collapse
Affiliation(s)
- Elaine A Sabu
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Taleigao Plateau, Goa, 403 206, India
| | - Maria Judith Gonsalves
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India.
| | - R A Sreepada
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
| | - Mamatha S Shivaramu
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
- Department of Food Protectants & Infestation Control, CSIR-Central Food Technological Research Institute, Mysuru, Karnataka, 570 020, India
| | - N Ramaiah
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, Goa, 403 004, India
| |
Collapse
|
28
|
Ting ASY, Zoqratt MZHM, Tan HS, Hermawan AA, Talei A, Khu ST. Bacterial and eukaryotic microbial communities in urban water systems profiled via Illumina MiSeq platform. 3 Biotech 2021; 11:40. [PMID: 33479595 PMCID: PMC7794265 DOI: 10.1007/s13205-020-02617-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/26/2020] [Indexed: 01/04/2023] Open
Abstract
Microbial communities from a lake and river flowing through a highly dense urbanized township in Malaysia were profiled by sequencing amplicons of the 16S V3-V4 and 18S V9 hypervariable rRNA gene regions via Illumina MiSeq. Results revealed that Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes were the dominant prokaryotic phyla; whereas, eukaryotic communities were predominantly of the SAR clade and Opisthokonta. The abundance of Pseudomonas and Flavobacterium in all sites suggested the possible presence of pathogens in the urban water systems, supported by the most probable number (MPN) values of more than 1600 per 100 mL. Urbanization could have impacted the microbial communities as transient communities (clinical, water-borne and opportunistic pathogens) coexisted with common indigenous aquatic communities (Cyanobacteria). It was concluded that in urban water systems, microbial communities vary in their abundance of microbial phyla detected along the water systems. The influences of urban land use and anthropogenic activities influenced the physicochemical properties and the microbial dynamics in the water systems. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02617-3.
Collapse
Affiliation(s)
- Adeline Su Yien Ting
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 46150 Bandar Sunway, Selangor Darul Ehsan Malaysia
| | - Muhammad Zarul Hanifah Md Zoqratt
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor Malaysia
| | - Hock Siew Tan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Andreas Aditya Hermawan
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Amin Talei
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| | - Soon Thiam Khu
- School of Engineering, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Malaysia
| |
Collapse
|
29
|
Determining Soil Microbial Communities and Their Influence on Ganoderma Disease Incidences in Oil Palm ( Elaeis guineensis) via High-Throughput Sequencing. BIOLOGY 2020; 9:biology9120424. [PMID: 33260913 PMCID: PMC7760618 DOI: 10.3390/biology9120424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/04/2023]
Abstract
Simple Summary Biological and physicochemical soil factors involved in the incidence of the basal stem rot (BSR) disease in an oil palm (Elaeis guineensis) plantation in Malaysia were characterized. Blenheim soil with a low BSR disease incidence and Bernam soil with high BSR disease incidence were analyzed and observed to have differences in composition and diversity of soil prokaryotic and eukaryotic communities. Blenheim soil with a high pH and calcium was shown to have higher prokaryotic and eukaryotic diversity compared to Bernam soil. High abundances of rare metabolically diverse and versatile bacterial taxa, bacterial taxa that increased with the introduction of biocontrol agents, potential disease-suppressive bacteria, and bacterivorous flagellates were observed in Blenheim soil. In contrast, Bernam soil was predominantly characterized by potential disease-inducible bacterial taxa. A combination of both abiotic and biotic elements might be essential in driving disease-suppressive soil microbiome toward Ganoderma BSR in Blenheim soil. Abstract Basal stem rot (BSR), caused by Ganoderma boninense, is the most devastating oil palm disease in South East Asia, costing US$500 million annually. Various soil physicochemical parameters have been associated with an increase in BSR incidences. However, very little attention has been directed to understanding the relationship between soil microbiome and BSR incidence in oil palm fields. The prokaryotic and eukaryotic microbial diversities of two coastal soils, Blenheim soil (Typic Quartzipsamment—calcareous shell deposits, light texture) with low disease incidence (1.9%) and Bernam soil (Typic Endoaquept—non-acid sulfate) with high disease incidence (33.1%), were determined using the 16S (V3–V4 region) and 18S (V9 region) rRNA amplicon sequencing. Soil physicochemical properties (pH, electrical conductivity, soil organic matter, nitrogen, phosphorus, cation exchange capacity, exchangeable cations, micronutrients, and soil physical parameters) were also analyzed for the two coastal soils. Results revealed that Blenheim soil comprises higher prokaryotic and eukaryotic diversities, accompanied by higher pH and calcium content. Blenheim soil was observed to have a higher relative abundance of bacterial taxa associated with disease suppression such as Calditrichaeota, Zixibacteria, GAL15, Omnitrophicaeota, Rokubacteria, AKYG587 (Planctomycetes), JdFR-76 (Calditrichaeota), and Rubrobacter (Actinobacteria). In contrast, Bernam soil had a higher proportion of other bacterial taxa, Chloroflexi and Acidothermus (Actinobacteria). Cercomonas (Cercozoa) and Calcarisporiella (Ascomycota) were eukaryotes that are abundant in Blenheim soil, while Uronema (Ciliophora) and mammals were present in higher abundance in Bernam soil. Some of the bacterial taxa have been reported previously in disease-suppressive and -conducive soils as potential disease-suppressive or disease-inducible bacteria. Furthermore, Cercomonas was reported previously as potential bacterivorous flagellates involved in the selection of highly toxic biocontrol bacteria, which might contribute to disease suppression indirectly. The results from this study may provide valuable information related to soil microbial community structures and their association with soil characteristics and soil susceptibility to Ganoderma.
Collapse
|
30
|
Tepaamorndech S, Nookaew I, Higdon SM, Santiyanont P, Phromson M, Chantarasakha K, Mhuantong W, Plengvidhya V, Visessanguan W. Metagenomics in bioflocs and their effects on gut microbiome and immune responses in Pacific white shrimp. FISH & SHELLFISH IMMUNOLOGY 2020; 106:733-741. [PMID: 32858186 DOI: 10.1016/j.fsi.2020.08.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 05/20/2023]
Abstract
Biofloc systems generate and accumulate microbial aggregates known as bioflocs. The presence of bioflocs has been shown to change gut bacterial diversity and stimulate innate immunity in shrimp. The microbial niche of bioflocs may therefore have the potential to drive shifts in the shrimp gut microbiota associated with stimulation of innate immunity. We performed shotgun metagenomic analysis and 16S rRNA-based amplicon sequencing to characterize complex bacterial members in bioflocs and the shrimp digestive tract, respectively. Moreover, we determined whether biofloc-grown shrimp with discrete gut microbiomes had an elevation in local immune-related gene expression and systemic immune activities. Our findings demonstrated that the bacterial community in bioflocs changed dynamically during Pacific white shrimp cultivation. Metagenomic analysis revealed that Vibrio comprised 90% of the biofloc population, while Pseualteromonas, Photobacterium, Shewanella, Alteromonas, Bacillus, Lactobacillus, Acinetobacter, Clostridium, Marinifilum, and Pseudomonas were also detected. In the digestive tract, biofloc-grown shrimp maintained the presence of commensal bacteria including Vibrio, Photobacterium, Shewanella, Granulosicoccus, and Ruegeria similar to control shrimp. However, Vibrio and Photobacterium were significantly enriched and declined, respectively, in biofloc-grown shrimp. The presence of bioflocs upregulated immune-related genes encoding serine proteinase and prophenoloxidase in digestive organs which are routinely exposed to gut microbiota. Biofloc-grown shrimp also demonstrated a significant increase in systemic immune status. As a result, the survival rate of biofloc-grown shrimp was substantially higher than that of the control shrimp. Our findings suggested that the high relative abundance of vibrios in bioflocs enriched the number of vibrios in the digestive tract of biofloc-grown shrimp. This shift in gut microbiota composition may be partially responsible for local upregulation of immune-related gene expression in digestive organs and systemic promotion of immune status in circulating hemolymph.
Collapse
Affiliation(s)
- Surapun Tepaamorndech
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Phahonyothin Rd., Pathumthani, 12120, Thailand.
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Shawn M Higdon
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Pannita Santiyanont
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Metavee Phromson
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Kanittha Chantarasakha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Wuttichai Mhuantong
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Vetthachai Plengvidhya
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Phahonyothin Rd., Pathumthani, 12120, Thailand
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Phahonyothin Rd., Pathumthani, 12120, Thailand
| |
Collapse
|
31
|
Qu YF, Wu YQ, Zhao YT, Lin LH, Du Y, Li P, Li H, Ji X. The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota. PeerJ 2020; 8:e10271. [PMID: 33194431 PMCID: PMC7603792 DOI: 10.7717/peerj.10271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/08/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle (Chinemys reevesii) and the invasive red-eared slider turtle (Trachemys scripta elegans) are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected. METHODS We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform. RESULTS The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in C. reevesii, whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in T. s. elegans. In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in T. s. elegans than in C. reevesii, as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in T. s. elegans than in C. reevesii, presumably suggesting an enhanced potential to colonize new habitats in the former species.
Collapse
Affiliation(s)
- Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yan-Qing Wu
- National Key Laboratory of Environmental Protection and Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, Jiangsu, China
| | - Yu-Tian Zhao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Yu Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, Hainan, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| |
Collapse
|
32
|
Intestinal Tract Microbe Communities Associated with Horseshoe Crabs from Beibu Gulf, China. Curr Microbiol 2020; 77:3330-3338. [PMID: 32926183 DOI: 10.1007/s00284-020-02140-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/21/2020] [Indexed: 10/23/2022]
Abstract
Until now, there has been little research on the intestinal microbial community of horseshoe crabs. To fill this gap, we investigated the microbiome composition of the Chinese horseshoe crab, Tachypleus tridentatus, and the mangrove horseshoe crab, Carcinoscorpius rotundicauda. We sequenced the 16S rRNA gene of intestinal bacterial species and compared the microbial community structure and diversity. Next, we show that the total effective bacterial sequence was 36,865 reads, and the average annotated operational taxonomic unit (OTU) number was 240. Through hierarchical clustering analysis and principal coordinate analysis samples from two horseshoe crab species, we found that the intestinal flora of the same horseshoe crab species was relatively concentrated, while the microbiome of a different horseshoe crab species were significantly separated. Cluster analysis showed that two samples, one from Chinese horseshoe crabs and one from mangrove horseshoe crabs, had similar microbial community structure, while other samples were relatively discrete. The gut microbiota of the mangrove horseshoe crab were dominated by the phyla Tenericutes (42.71%), Firmicutes (24.27%), and Proteobacteria (20.39%), while the top three phyla in the Chinese horseshoe crab intestinal tract were Tenericutes (57.19%), Proteobacteria (22.14%), and Bacteroidetes (7.38%). To intuitively understand the similarity and overlap of the OTU composition of each group, we performed Venn diagram analysis. The two species shared 284 OTUs, accounting for 81.8% of the total. This indicates that although there is high similarity between mangrove and Chinese horseshoe crab in gastrointestinal microbial community structure, there are also some differences, which deserve further discussion.
Collapse
|
33
|
Panteli N, Mastoraki M, Nikouli E, Lazarina M, Antonopoulou E, Kormas KA. Imprinting statistically sound conclusions for gut microbiota in comparative animal studies: A case study with diet and teleost fishes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100738. [PMID: 32896688 DOI: 10.1016/j.cbd.2020.100738] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Despite the technical progress in high-throughput sequencing technologies, defining the sample size which is capable of yielding representative inferences in metabarcoding analysis still remains debatable. The present study addresses the influence of individual variability in assessing dietary effects on fish gut microbiota parameters and estimates the biological sample size that is sufficient to imprint a statistically secure outcome. European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata) were fed three alternative animal protein diets and a fishmeal control diet. Gut microbiota data from 12 individuals per diet, derived from Illumina sequencing of the V3-V4 region of the 16S rRNA gene, were randomized in all possible combinations of n-1 individuals. Results in this study showcased that increasing the sample size can limit the prevalence of individuals with high microbial load on the outcome and can ensure the statistical confidence required for an accurate validation of dietary-induced microbe shifts. Inter-individual variability was evident in the four dietary treatments where consequently misleading inferences arose from insufficient biological replication. These findings have critical implications for the design of future metabarcoding studies and highlight the urgency in selecting an adequate sample size able to safely elucidate the dietary effects on fish gut microbial communities.
Collapse
Affiliation(s)
- Nikolas Panteli
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Maria Mastoraki
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Eleni Nikouli
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| | - Maria Lazarina
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Efthimia Antonopoulou
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece.
| | - Konstantinos A Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 384 46 Volos, Greece
| |
Collapse
|
34
|
Uengwetwanit T, Uawisetwathana U, Arayamethakorn S, Khudet J, Chaiyapechara S, Karoonuthaisiri N, Rungrassamee W. Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp ( Penaeus monodon) with different growth performance. PeerJ 2020; 8:e9646. [PMID: 32864208 PMCID: PMC7430268 DOI: 10.7717/peerj.9646] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/12/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the correlation between shrimp growth and their intestinal bacteria would be necessary to optimize animal's growth performance. Here, we compared the bacterial profiles along with the shrimp's gene expression responses and metabolites in the intestines between the Top and the Bottom weight groups. Black tiger shrimp (Penaeus monodon) were collected from the same population and rearing environments. The two weight groups, the Top-weight group with an average weight of 36.82 ± 0.41 g and the Bottom-weight group with an average weight of 17.80 ± 11.81 g, were selected. Intestines were aseptically collected and subjected to microbiota, transcriptomic and metabolomic profile analyses. The weighted-principal coordinates analysis (PCoA) based on UniFrac distances showed similar bacterial profiles between the two groups, suggesting similar relative composition of the overall bacterial community structures. This observed similarity was likely due to the fact that shrimp were from the same genetic background and reared under the same habitat and diets. On the other hand, the unweighted-distance matrix revealed that the bacterial profiles associated in intestines of the Top-weight group were clustered distinctly from those of the Bottom-weight shrimp, suggesting that some unique non-dominant bacterial genera were found associated with either group. The key bacterial members associated to the Top-weight shrimp were mostly from Firmicutes (Brevibacillus and Fusibacter) and Bacteroidetes (Spongiimonas), both of which were found in significantly higher abundance than those of the Bottom-weight shrimp. Transcriptomic profile of shrimp intestines found significant upregulation of genes mostly involved in nutrient metabolisms and energy storage in the Top-weight shrimp. In addition to significantly expressed metabolic-related genes, the Bottom-weight shrimp also showed significant upregulation of stress and immune-related genes, suggesting that these pathways might contribute to different degrees of shrimp growth performance. A non-targeted metabolome analysis from shrimp intestines revealed different metabolic responsive patterns, in which the Top-weight shrimp contained significantly higher levels of short chain fatty acids, lipids and organic compounds than the Bottom-weight shrimp. The identified metabolites included those that were known to be produced by intestinal bacteria such as butyric acid, 4-indolecarbaldehyde and L-3-phenyllactic acid as well as those produced by shrimp such as acyl-carnitines and lysophosphatidylcholine. The functions of these metabolites were related to nutrient absorption and metabolisms. Our findings provide the first report utilizing multi-omics integration approach to investigate microbiota, metabolic and transcriptomics profiles of the host shrimp and their potential roles and relationship to shrimp growth performance.
Collapse
Affiliation(s)
- Tanaporn Uengwetwanit
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Umaporn Uawisetwathana
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Sopacha Arayamethakorn
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Juthatip Khudet
- Shrimp Genetic Improvement Center, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Sage Chaiyapechara
- Aquaculture Service Development Research Team, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Nitsara Karoonuthaisiri
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| | - Wanilada Rungrassamee
- Microarray Research Team, National Center for Genetic Engineering and Biotechnology, Pathum Thani, Thailand
| |
Collapse
|
35
|
de Souza Valente C, Rodiles A, Freire Marques MR, Merrifield DL. White spot syndrome virus (WSSV) disturbs the intestinal microbiota of shrimp (Penaeus vannamei) reared in biofloc and clear seawater. Appl Microbiol Biotechnol 2020; 104:8007-8023. [PMID: 32789745 DOI: 10.1007/s00253-020-10816-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/13/2020] [Accepted: 08/05/2020] [Indexed: 01/18/2023]
Abstract
White spot syndrome virus (WSSV) is one of the most virulent pathogens afflicting shrimp farming. Understanding its influence on shrimp intestinal microbiota is paramount for the advancement of aquaculture, since gut dysbiosis can negatively impact shrimp development, physiology, and immunological response. Thereupon, the data presented herein assesses the influence of WSSV infection and different rearing systems on the intestinal microbiota of Penaeus vannamei. Our study aimed to describe and correlate the composition of shrimp (Penaeus vannamei) gut microbiota, when reared in biofloc and clear seawater, before and (48 h) after WSSV experimental infection. Shrimp were kept in two different systems (biofloc and clear seawater) and experimentally infected with WSSV. Intestine and water samples were characterized by 16S rRNA gene sequencing, before and after viral infection. We observed (i) WSSV induced higher mortality among shrimp reared in biofloc; (ii) WSSV led to a loss of intestinal microbiota heterogeneity, at the genus level, in shrimp kept in clear seawater; (iii) there was a prevalence of Cetobacterium and Bacillus in the intestine of shrimp from both systems; (iv) WSSV did not cause significant changes in intestinal microbiota diversity or richness; (v) regardless of the type of system and time of infection, intestinal microbiota was dissimilar to that of the surrounding water, despite being influenced by the type of system. Therefore, WSSV infection leads to punctual dysbiotic changes in shrimp microbiota, although the virus is sufficiently virulent to cause high mortalities even in well-managed systems, such as a balanced experimental biofloc system. KEY POINTS: • WSSV infection leads to a perturbed gut microbiota in shrimp. • WSSV infection greater impacts microbiota of shrimp reared in CSW than those in BFT. • WSSV infection caused higher mortality levels in shrimp reared in BFT than in CSW. • Rearing system influences shrimp gut microbiota composition. Graphical abstract.
Collapse
Affiliation(s)
- Cecília de Souza Valente
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry, Department of Biochemistry, Federal University of Santa Catarina, Florianopolis, SC, Brazil.
| | - Ana Rodiles
- School of Biological & Marine Sciences, Faculty of Science & Engineering, University of Plymouth, Plymouth, UK.,Lallemand Animal Nutrition, Lallemand SAS, 31702, Blagnac, France
| | - Maria Risoleta Freire Marques
- Laboratory of Biomarkers of Aquatic Contamination and Immunochemistry, Department of Biochemistry, Federal University of Santa Catarina, Florianopolis, SC, Brazil
| | - Daniel Lee Merrifield
- School of Biological & Marine Sciences, Faculty of Science & Engineering, University of Plymouth, Plymouth, UK
| |
Collapse
|
36
|
Pérez-Cobas AE, Gomez-Valero L, Buchrieser C. Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses. Microb Genom 2020; 6:mgen000409. [PMID: 32706331 PMCID: PMC7641418 DOI: 10.1099/mgen.0.000409] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/30/2020] [Indexed: 12/23/2022] Open
Abstract
Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.
Collapse
Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| | - Laura Gomez-Valero
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| | - Carmen Buchrieser
- Institut Pasteur, Biologie des Bactéries Intracellulaires, Paris, France and CNRS UMR 3525, 675724, Paris, France
| |
Collapse
|
37
|
Yan CZY, Austin CM, Ayub Q, Rahman S, Gan HM. Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes. FEMS Microbiol Lett 2020; 366:5582596. [PMID: 31589302 DOI: 10.1093/femsle/fnz211] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
The Malaysian and global shrimp aquaculture production has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND) typically caused by Vibrio parahaemolyticus harboring the pVA plasmid containing the pirAVp and pirBVp genes, which code for Photorhabdus insect-related (Pir) toxin. The limited genomic resource for V. parahaemolyticus strains from Malaysian aquaculture farms precludes an in-depth understanding of their diversity and evolutionary relationships. In this study, we isolated shrimp-associated and environmental (rearing water) V. parahaemolyticus from three aquaculture farms located in Northern and Central Malaysia followed by whole-genome sequencing of 40 randomly selected isolates on the Illumina MiSeq. Phylogenomic analysis and multilocus sequence typing (MLST) reveal distinct lineages of V. parahaemolyticus that harbor the pirABVp genes. The recovery of pVA plasmid backbone devoid of pirAVp or pirABVp in some V. parahaemolyticus isolates suggests that the toxin genes are prone to deletion. The new insight gained from phylogenomic analysis of Asian V. parahaemolyticus, in addition to the observed genomic instability of pVa plasmid, will have implications for improvements in aquaculture practices to diagnose, treat or limit the impacts of this disease.
Collapse
Affiliation(s)
- Chrystine Zou Yi Yan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Christopher M Austin
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3220 Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong 3220, Victoria, Australia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, Jalan Lagoon Selatan, 47500 Bandar Sunway, Selangor Darul Ehsan, Malaysia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, 3220 Victoria, Australia.,Deakin Genomics Centre, Deakin University, Geelong 3220, Victoria, Australia
| |
Collapse
|
38
|
Intestinal Microbiota Analyses of Litopenaeus vannamei During a Case of Atypical Massive Mortality in Northwestern Mexico. Curr Microbiol 2020; 77:2312-2321. [PMID: 32524276 DOI: 10.1007/s00284-020-02079-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/04/2020] [Indexed: 10/24/2022]
Abstract
This study investigated the intestinal microbial community structure of Litopenaeus vannamei at six different stages during shrimp farming. Our goal was to elucidate the bacterial profile and the changes in the relative abundance of taxa during an atypical massive mortality event in Sonora, Mexico. High-throughput sequencing of the 16S rRNA gene and denaturing gradient gel electrophoresis showed that Vibrionaceae was persistent with high relative abundances in the intestine from cultivated shrimp during all the studied stages. The massive mortality observed at day 63 could be related to an overabundance of different Operational Taxonomic Units (OTUs) of Vibrio, Shewanella and Clostridium. Principal coordinate analysis (PCoA) showed variations in microbial structure at different culture times. These findings suggest that OTUs of different taxa contributed to the community switch from healthy to diseased individuals, questioning the hypothesis that single bacterial species is the cause of disease outbreaks. This study provided data to improve the understanding of disease outbreaks during shrimp farming.
Collapse
|
39
|
Holt CC, Bass D, Stentiford GD, van der Giezen M. Understanding the role of the shrimp gut microbiome in health and disease. J Invertebr Pathol 2020; 186:107387. [PMID: 32330478 DOI: 10.1016/j.jip.2020.107387] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/05/2020] [Accepted: 04/17/2020] [Indexed: 02/08/2023]
Abstract
With rapid increases in the global shrimp aquaculture sector, a focus on animal health during production becomes ever more important. Animal productivity is intimately linked to health, and the gut microbiome is becoming increasingly recognised as an important driver of cultivation success. The microbes that colonise the gut, commonly referred to as the gut microbiota or the gut microbiome, interact with their host and contribute to a number of key host processes, including digestion and immunity. Gut microbiome manipulation therefore represents an attractive proposition for aquaculture and has been suggested as a possible alternative to the use of broad-spectrum antibiotics in the management of disease, which is a major limitation of growth in this sector. Microbiota supplementation has also demonstrated positive effects on growth and survival of several different commercial species, including shrimp. Development of appropriate gut supplements, however, requires prior knowledge of the host microbiome. Little is known about the gut microbiota of the aquatic invertebrates, but penaeid shrimp are perhaps more studied than most. Here, we review current knowledge of information reported on the shrimp gut microbiota, highlighting the most frequently observed taxa and emphasizing the dominance of Proteobacteria within this community. We discuss involvement of the microbiome in the regulation of shrimp health and disease and describe how the gut microbiota changes with the introduction of several economically important shrimp pathogens. Finally, we explore evidence of microbiome supplementation and consider its role in the future of penaeid shrimp production.
Collapse
Affiliation(s)
- Corey C Holt
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Biosciences, University of Exeter, Stocker Road, Exeter, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom; Department of Botany, University of British Columbia, Vancouver, Canada.
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health Theme, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset DT4 8UB, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom
| | - Mark van der Giezen
- Biosciences, University of Exeter, Stocker Road, Exeter, United Kingdom; Centre for Sustainable Aquaculture Futures, University of Exeter, Stocker Road, Exeter, United Kingdom; Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway.
| |
Collapse
|
40
|
Holt CC, van der Giezen M, Daniels CL, Stentiford GD, Bass D. Spatial and temporal axes impact ecology of the gut microbiome in juvenile European lobster (Homarus gammarus). THE ISME JOURNAL 2020; 14:531-543. [PMID: 31676854 PMCID: PMC6976562 DOI: 10.1038/s41396-019-0546-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 12/25/2022]
Abstract
Microbial communities within the gut can markedly impact host health and fitness. To what extent environmental influences affect the differential distribution of these microbial populations may therefore significantly impact the successful farming of the host. Using a sea-based container culture (SBCC) system for the on-growing of European lobster (Homarus gammarus), we tracked the bacterial gut microbiota over a 1-year period. We compared these communities with lobsters of the same cohort, retained in a land-based culture (LBC) system to assess the effects of the culture environment on gut bacterial assemblage and describe the phylogenetic structure of the microbiota to compare deterministic and stochastic assembly across both environments. Bacterial gut communities from SBCCs were generally more phylogenetically clustered, and therefore deterministically assembled, compared to those reared in land-based systems. Lobsters in SBCCs displayed significantly more species-rich and species-diverse gut microbiota compared to those retained in LBC. A reduction in the bacterial diversity of the gut was also associated with higher infection prevalence of the enteric viral pathogen Homarus gammarus nudivirus (HgNV). SBCCs may therefore benefit the overall health of the host by promoting the assembly of a more diverse gut bacterial community and reducing the susceptibility to disease.
Collapse
Affiliation(s)
- Corey C Holt
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK.
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
- The National Lobster Hatchery, South Quay, Padstow, UK.
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
| | - Mark van der Giezen
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
- Centre for Organelle Research, University of Stavanger, 4021, Stavanger, Norway
| | | | - Grant D Stentiford
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, Weymouth, Dorset, DT4 8UB, UK.
- The Centre for Sustainable Aquaculture Futures, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter, UK.
- Department of Life Sciences, The Natural History Museum, Cromwell Road, Kensington, London, UK.
| |
Collapse
|
41
|
Doing More with Less: A Comparison of 16S Hypervariable Regions in Search of Defining the Shrimp Microbiota. Microorganisms 2020; 8:microorganisms8010134. [PMID: 31963525 PMCID: PMC7022540 DOI: 10.3390/microorganisms8010134] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 12/12/2022] Open
Abstract
The shrimp has become the most valuable traded marine product in the world, and its microbiota plays an essential role in its development and overall health status. Massive high-throughput sequencing techniques using several hypervariable regions of the 16S rRNA gene are broadly applied in shrimp microbiota studies. However, it is essential to consider that the use of different hypervariable regions can influence the obtained data and the interpretation of the results. The present study compares the shrimp microbiota structure and composition obtained by three types of amplicons: one spanning both the V3 and V4 hypervariable regions (V3V4), one for the V3 region only (V3), and one for the V4 region only (V4) using the same experimental and bioinformatics protocols. Twenty-four samples from hepatopancreas and intestine were sequenced and evaluated using the GreenGenes and silva reference databases for clustering and taxonomic classification. In general, the V3V4 regions resulted in higher richness and diversity, followed by V3 and V4. All three regions establish an apparent clustering effect that discriminates between the two analyzed organs and describe a higher richness for the intestine and a higher diversity for the hepatopancreas samples. Proteobacteria was the most abundant phyla overall, and Cyanobacteria was more common in the intestine, whereas Firmicutes and Actinobacteria were more prevalent in hepatopancreas samples. Also, the genus Vibrio was significantly abundant in the intestine, as well as Acinetobacter and Pseudomonas in the hepatopancreas suggesting these taxa as markers for their respective organs independently of the sequenced region. The use of a single hypervariable region such as V3 may be a low-cost alternative that enables an adequate description of the shrimp microbiota, allowing for the development of strategies to continually monitor the microbial communities and detect changes that could indicate susceptibility to pathogens under real aquaculture conditions while the use of the full V3V4 regions can contribute to a more in-depth characterization of the microbial composition.
Collapse
|
42
|
Bacterial Community Dynamics During Nursery Rearing of Pacific White Shrimp ( Litopenaeus vannamei) Revealed via High-Throughput Sequencing. Indian J Microbiol 2020; 60:214-221. [PMID: 32255854 DOI: 10.1007/s12088-019-00853-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
A 20-day trial was conducted to reveal bacterial community dynamics in a commercial nursery of larval Litopenaeus vannamei larvae. The bacterial communities in the ambient water were profiled by high-throughput sequencing of the V4-V5 hypervariable region of the 16S rRNA gene. The results indicated that the dominant bacterial phyla between the metamorphosis stage and postlarval stage were Bacteroidetes, Proteobacteria, Cyanobacteria, and Firmicutes, representing more than 80.09% of the bacterial operational taxonomic units. The relative abundance among bacterial phyla notably differed between the two stages. The relative abundance of Cyanobacteria was higher in the metamorphosis stage, while that of Bacteroidetes was higher and more stable in the postlarval stage. At the class level, the relative abundance of Sphingobacteriia and Alphaproteobacteria increased markedly in the postlarval stage, while that of Flavobacteriia decreased. Redundancy analysis showed that bacterial composition in the metamorphosis stage was positively correlated with salinity, alkalinity, and pH, while in the postlarval stage, it was positively correlated with ammonium nitrogen and nitrite nitrogen. Thus, microbial community diversity in the nursery phase varies per rearing stage.
Collapse
|
43
|
Forster D, Lentendu G, Filker S, Dubois E, Wilding TA, Stoeck T. Improving eDNA-based protist diversity assessments using networks of amplicon sequence variants. Environ Microbiol 2019; 21:4109-4124. [PMID: 31361938 DOI: 10.1111/1462-2920.14764] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/25/2019] [Accepted: 07/25/2019] [Indexed: 12/20/2022]
Abstract
Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high-throughput sequencing datasets. Amplicon sequence variants (ASVs) offer a promising alternative that may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studies. We compared the performance of a recently developed pipeline based on the algorithm DADA2 for obtaining ASVs against a pipeline based on the algorithm SWARM for obtaining OTUs. Illumina-sequencing of 29 individual ciliate species resulted in up to 11 ASVs per species, while SWARM produced up to 19 OTUs per species. To improve the congruency between species diversity and molecular diversity, we applied sequence similarity networks (SSNs) for second-level sequence grouping into network sequence clusters (NSCs). At 100% sequence similarity in SWARM-SSNs, NSC numbers decreased from 7.9-fold overestimation without abundance filter, to 4.5-fold overestimation when an abundance filter was applied. For the DADA2-SSN approach, NSC numbers decreased from 3.5-fold to 3-fold overestimation. Rand index cluster analyses predicted best binning results between 97% and 94% sequence similarity for both DADA2-SSNs and SWARM-SSNs. Depending on the ecological questions addressed in an environmental sequencing study with protists we recommend ASVs as replacement for OTUs, best in combination with SSNs.
Collapse
Affiliation(s)
- Dominik Forster
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Guillaume Lentendu
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Elyssa Dubois
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Thomas A Wilding
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, Scotland, UK
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| |
Collapse
|
44
|
Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective. mSystems 2019; 4:4/4/e00148-19. [PMID: 31239394 PMCID: PMC6593219 DOI: 10.1128/msystems.00148-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Sponges establish tight associations with both micro- and macroorganisms. However, while studies on sponge microbiomes are numerous, nothing is currently known about the microbiomes of sponge-associated polychaetes and their relationships with those of their host sponges. We analyzed the bacterial communities of symbiotic polychaetes (Haplosyllis spp.) and their host sponges (Clathria reinwardti, Amphimedon paraviridis, Neofibularia hartmani, and Aaptos suberitoides) to assess the influence of the sponges on the polychaete microbiomes. We identified both eukaryote partners by molecular (16S and COI genes) and morphological features, and we identified their microbial communities by high-throughput sequencing of the 16S rRNA gene (V4 region). We unravel the existence of six Haplosyllis species (five likely undescribed) associated at very high densities with the study sponge species in Nha Trang Bay (central Vietnam). A single polychaete species inhabited A. paraviridis and was different from the single species that inhabited A. suberitoides Conversely, two different polychaete species were found in C. reinwardti and N. hartmani, depending on the two host locations. Regardless of the host sponge, polychaete microbiomes were species specific, which is a widespread feature in marine invertebrates. More than half of the polychaete bacteria were also found in the host sponge microbiome but at contrasting abundances. Thus, the associated polychaetes seemed to be able to select, incorporate, and enrich part of the sponge microbiome, a selection that appears to be polychaete species specific. Moreover, the bacterial diversity is similar in both eukaryotic partners, which additionally confirms the influence of food (host sponge) on the structure of the polychaete microbiome.IMPORTANCE The symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own bacterial communities. Here, we study the microbiomes of sponge-polychaete associations and confirm that polychaetes feed on their host sponges. The study worms select and enrich part of the sponge microbiome to shape their own species-specific bacterial communities. Moreover, worm microbiome diversity runs parallel to that of its food host sponge. Considering our results on symbiotic polychaetes and previous studies on fishes and mammals, diet appears to be an important source of bacteria for animals to shape their species-specific microbiomes.
Collapse
|
45
|
Foysal MJ, Fotedar R, Tay CY, Gupta SK. Dietary supplementation of black soldier fly ( Hermetica illucens) meal modulates gut microbiota, innate immune response and health status of marron ( Cherax cainii, Austin 2002) fed poultry-by-product and fishmeal based diets. PeerJ 2019; 7:e6891. [PMID: 31149398 PMCID: PMC6534111 DOI: 10.7717/peerj.6891] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/01/2019] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to evaluate the dietary supplementary effects of black soldier fly (Hermetia illucens) (BSF) meal on the bacterial communities in the distal gut, immune response and growth of freshwater crayfish, marron (Cherax cainii) fed poultry-by-product meal (PBM) as an alternative protein source to fish meal (FM). A total of 64 marron were randomly distributed into 16 different tanks with a density of four marron per tank. After acclimation, a 60-days feeding trial was conducted on marron fed isonitrogenouts and isocalorific diets containing protein source from FM, PBM, and a combination of FM + BSF and PBM + BSF. At the end of the trial, weight gain and growth of marron were found independent of any dietary treatment, however, the two diets supplemented with BSF significantly (P < 0.05) enhanced haemolymph osmolality, lysozyme activity, total haemocyte counts, and protein and energy contents in the tail muscle. In addition, the analysis of microbiota and its predicted metabolic pathways via 16s rRNA revealed a significantly (P < 0.05) higher bacterial activity and gene function correlated to biosynthesis of protein, energy and secondary metabolites in PBM + BSF than other dietary groups. Diets FM + BSF and PBM + BSF were seen to be associated with an up-regulation of cytokine genes in the intestinal tissue of marron. Overall, PBM + BSF diet proved to be a superior diet in terms of improved health status, gut microbiota and up-regulated expression of cytokine genes for marron culture.
Collapse
Affiliation(s)
- Md Javed Foysal
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Department of Genetic Engineering and Biotechnology, Shahjalal University of Science & Technology, Sylhet, Bangladesh
| | - Ravi Fotedar
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia
| | - Chin-Yen Tay
- Helicobacter Research Laboratory, Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Sanjay Kumar Gupta
- School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India
| |
Collapse
|