Analysis of bacterial community functional diversity in late-stage shrimp (Litopenaeus vannamei) ponds using Biolog EcoPlates and PICRUSt2

Aquaculture ◽  
2021 ◽  
pp. 737288
Author(s):  
Qiong Zhao ◽  
Fengxing Xie ◽  
Fengfeng Zhang ◽  
Ke Zhou ◽  
Haibo Sun ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Functional Diversity ◽  
Litopenaeus Vannamei ◽  
Late Stage ◽  
Biolog Ecoplates

scholarly journals Bacterial community structure alterations within the colorectal cancer gut microbiome

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Mark Loftus ◽  
Sayf Al-Deen Hassouneh ◽  
Shibu Yooseph
Keyword(s):  
Colorectal Cancer ◽  
Community Structure ◽  
Bacterial Community ◽  
Gut Microbiome ◽  
Late Stage ◽  
Bacterial Community Structure ◽  
Whole Genome ◽  
Human Gut ◽  
Fecal Samples ◽  
Human Gut Microbiome

Abstract Background Colorectal cancer is a leading cause of cancer-related deaths worldwide. The human gut microbiome has become an active area of research for understanding the initiation, progression, and treatment of colorectal cancer. Despite multiple studies having found significant alterations in the carriage of specific bacteria within the gut microbiome of colorectal cancer patients, no single bacterium has been unequivocally connected to all cases. Whether alterations in species carriages are the cause or outcome of cancer formation is still unclear, but what is clear is that focus should be placed on understanding changes to the bacterial community structure within the cancer-associated gut microbiome. Results By applying a novel set of analyses on 252 previously published whole-genome shotgun sequenced fecal samples from healthy and late-stage colorectal cancer subjects, we identify taxonomic, functional, and structural changes within the cancer-associated human gut microbiome. Bacterial association networks constructed from these data exhibited widespread differences in the underlying bacterial community structure between healthy and colorectal cancer associated gut microbiomes. Within the cancer-associated ecosystem, bacterial species were found to form associations with other species that are taxonomically and functionally dissimilar to themselves, as well as form modules functionally geared towards potential changes in the tumor-associated ecosystem. Bacterial community profiling of these samples revealed a significant increase in species diversity within the cancer-associated gut microbiome, and an elevated relative abundance of species classified as originating from the oral microbiome including, but not limited to, Fusobacterium nucleatum, Peptostreptococcus stomatis, Gemella morbillorum, and Parvimonas micra. Differential abundance analyses of community functional capabilities revealed an elevation in functions linked to virulence factors and peptide degradation, and a reduction in functions involved in amino-acid biosynthesis within the colorectal cancer gut microbiome. Conclusions We utilize whole-genome shotgun sequenced fecal samples provided from a large cohort of late-stage colorectal cancer and healthy subjects to identify a number of potentially important taxonomic, functional, and structural alterations occurring within the colorectal cancer associated gut microbiome. Our analyses indicate that the cancer-associated ecosystem influences bacterial partner selection in the native microbiota, and we highlight specific oral bacteria and their associations as potentially relevant towards aiding tumor progression.

scholarly journals A Standardized Method for Estimating the Functional Diversity of Soil Bacterial Community by Biolog® EcoPlatesTM Assay—The Case Study of a Sustainable Olive Orchard

2019 ◽  
Vol 9 (19) ◽  
pp. 4035 ◽  
Author(s):  
Adriano Sofo ◽  
Patrizia Ricciuti
Keyword(s):  
Bacterial Community ◽  
Functional Diversity ◽  
Soil Bacterial Community ◽  
Step Method ◽  
Olive Orchard ◽  
Correct Definition ◽  
Standardized Method ◽  
Soil Bacterial ◽  
Sustainable Conservation

Biolog® EcoPlates™ (Biolog Inc., Hayward, CA, USA) were developed to analyse the functional diversity of bacterial communities by means of measuring their ability to oxidize carbon substrates. This technique has been successfully adopted for studying bacterial soil communities from different soil environments, polluted soils and soils subjected to various agronomic treatments. Unfortunately, Biolog® EcoPlates™ assay, especially working on soil, can be difficult to reproduce and hard to standardize due to the lack of detailed procedures and protocols. The main problems of this technique mainly regard soil preparation, bacterial inoculum densities and a correct definition of blank during the calculation of the diversity indices. On the basis of our previous research on agricultural soils, we here propose a standardized and accurate step-by-step method for estimating the functional diversity of a soil bacterial community by Biolog® EcoPlatesTM assay. A case study of soils sampled in a Mediterranean olive orchard managed accordingly to sustainable/conservation practices was reported for justifying the standardized method here used. The results of this methodological paper could be important for correctly evaluating and comparing the microbiological fertility of soils managed by sustainable/conservation or conventional/non-conservation systems.

scholarly journals Biomass and activity soil microorganisms in grazing and secondary forests areasA

2016 ◽  
Vol 8 (1) ◽  
pp. 107-113
Author(s):  
Rodolfo WingChing-Jones ◽  
Lidieth Uribe Lorío
Keyword(s):  
Microbial Activity ◽  
Functional Diversity ◽  
Soil Microorganisms ◽  
Carbon Deposition ◽  
Secondary Forest ◽  
Shannon Index ◽  
Secondary Forests ◽  
Biolog Ecoplates ◽  
Three Samples ◽  
Carbon Substrates

Sustainable livestock production generates benefits for the environment, such as water capture, increased biodiversity and carbon dioxide capture. To measure these factors in a tropical setting, in 2007 we took three samples of a milk production system in Turrialba, Cartago, Costa Rica, in areas with permanent African Star grass cover (under grazing) and a secondary forest with 15 years of regeneration. We estimated carbon content in the microbial biomass, microbial activity (breathing technique), carbon usage profile (BIOLOG ECOPLATES®) and functional diversity of microorganisms (Shannon index). Biomass carbon in the pasture was 3,3 times higher than in the forest, but microbial activity was similar. Carbon use rate ranged from 22,22 to 85,19% in the pasture (higher in the forest: 29,63 to 92,59%). In both areas growth correlated with incubation time, but the forest had more biodiversity. Pasture areas are favored by carbon deposition to the rhizosphere, while the variety of vegetation in the forest allows greater functional diversity in the use of carbon substrates. 

scholarly journals Comparison of bacterial community structures in digestive tract between healthy and disease whiteleg shrimp (Litopenaeus vannamei) in Soc Trang, Vietnam

2018 ◽  
Vol 16 (3) ◽  
pp. 543-551
Author(s):  
Tran Trung Thanh ◽  
Nathan Bott ◽  
Le Hoang Duc ◽  
Dang Thi Hoang Oanh ◽  
Nguyen Trung Nam ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Litopenaeus Vannamei ◽  
Penaeus Monodon ◽  
Gut Bacteria ◽  
Shrimp Pond ◽  
Sequencing Method ◽  
Gradient Gel Electrophoresis ◽  
The Stability ◽  
Generation Sequencing

Gut bacteria comprise a complex bacterial community related to many functions in a host. The stability of gut bacteria plays important models in the health and immunology of a host. Many studies on intestine bacteria constructed via cultivation and Denaturation Gradient Gel Electrophoresis (DDGE) methods have proved a limited efficiency. In order to tackle these drawbacks, the next generation sequencing method was developed on 16S-rRNA-based sequences (Metabarcoding). The composition of bacterial communities was revealed based on the analysis of 16S rRNA sequences of intestine bacteria in Litopenaeus vannamei ponds in comparison with microbial communities in a Penaeus monodon pond and a muscle of shrimp. These results showed that the dominant phyla of intestine bacteria in Litopenaeus vannamei were Proteobacteria (49.3–57.4%), Firmicutes (15.6–34.4%) and Bacteroidetes (0.1–16.9%). Rhizobium(0.4%-26.1%), Vibrio(0–23.9%) and Spongiimonas(0–16,7%) were dominant genera in Litopenaeus vannamei gut. A higher proportion of Fusobacterium (10%), a shrimp pathogen group, was found in a disease shrimp pond (ST4) in comparison with a low growth shrimp pond (ST3) (0%) and a healthy shrimp pond (ST1) (0.6%). Vibrio was marked as shrimp pathogen genus accounted for 22.3% of total genera in ST4 in comparison with 2.4% in ST3 and 3.5% in ST1. Interestingly, a higher percentage of Vibrio rotiferianus (7.98%) was found in ST4 compared to ST3 (1%) and ST1 (0%). Fusobacterium and Vibrio will be the objects for the next experiments to discover shrimp pathogens specifically.

scholarly journals Microbial Ecology of Artisanal Feta and Kefalograviera Cheeses, Part I: Bacterial Community and Its Functional Characteristics with Focus on Lactic Acid Bacteria as Determined by Culture-Dependent Methods and Phenotype Microarrays

2022 ◽  
Vol 10 (1) ◽  
pp. 161
Author(s):  
Markella Tsigkrimani ◽  
Magdalini Bakogianni ◽  
Spiros Paramithiotis ◽  
Loulouda Bosnea ◽  
Eleni Pappa ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Bacterial Community ◽  
Microbial Communities ◽  
Carbon Sources ◽  
Rrna Gene ◽  
Ripening Stage ◽  
Biolog Ecoplates ◽  
Feta Cheese ◽  
Main Carbon Source ◽  
Early Ripening

Artisanal cheesemaking is still performed using practices and conditions derived from tradition. Feta and Kefalograviera cheeses are very popular in Greece and have met worldwide commercial success. However, there is a lack of knowledge regarding their lactic acid microecosystem composition and species dynamics during ripening. Thus, the aim of the present study was to assess the microecosystem as well as the autochthonous lactic acid microbiota during the ripening of artisanal Feta and Kefalograviera cheeses. For that purpose, raw sheep’s milk intended for cheesemaking, as well as Feta and Kefalograviera cheeses during early and late ripening were analyzed, and the lactic acid microbiota was identified using the classical phenotypic approach, clustering with PCR-RAPD and identification with sequencing of the 16S-rRNA gene, as well as with the Biolog GEN III microplates. In addition, the functional properties of the bacterial community were evaluated using the Biolog EcoPlates, which consists of 31 different carbon sources. In general, concordance between the techniques used was achieved. The most frequently isolated species from raw sheep’s milk were Enteroroccus faecium, Lactiplantibacillus plantarum and Pediococcus pentosaceus. The microecosystem of Feta cheese in the early ripening stage was dominated by Lp. plantarum and E. faecium, whereas, in late ripening, the microecosystem was dominated by Weissella paramesenteroides. The microecosystem of Kefalograviera cheese in the early ripening stage was dominated by Levilactobacillus brevis and E. faecium, and in late ripening by W. paramesenteroides and E. faecium. Finally, Carbohydrates was the main carbon source category that metabolized by all microbial communities, but the extent of their utilization was varied. Kefalograviera samples, especially at early ripening, demonstrated higher metabolic activity compared to Feta cheese. However, dominating species within microbial communities of the cheese samples were not significantly different.

scholarly journals Probiotic modulation of the gut bacterial community of juvenile Litopenaeus vannamei challenged with Vibrio parahaemolyticus CAIM 170

2017 ◽  
Vol 43 (4) ◽  
pp. 766-775
Author(s):  
Irasema E. Luis-Villaseñor ◽  
Domenico Voltolina ◽  
Bruno Gomez-Gil ◽  
Felipe Ascencio ◽  
Ángel I. Campa-Córdova ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Litopenaeus Vannamei ◽  
Vibrio Parahaemolyticus ◽  
Single Strand Conformation Polymorphism ◽  
Positive Control ◽  
Negative Control ◽  
Rrna Gene ◽  
Protective Effects ◽  
Probiotic Treatment ◽  
Significant Difference

The protective effects of two probiotic mixtures was studied using the fingerprints of the bacterial community of Litopenaeus vannamei juveniles exposed to probiotics and challenged with Vibrio parahaemolyticus CAIM 170. Fingerprints were constructed using 16S rRNA gene and the PCR-SSCP (Single strand conformation polymorphism) technique, and the probiotics used were an experimental Bacillus mixture (Bacillus tequilensis YC5-2 + B. endophyticus C2-2 and YC3-B) and the commercial probiotic Alibio. The DNA for PCR-SSCP analyses was extracted directly from the guts of shrimps treated for 20 days with the probiotics and injected with 2.5×105 CFU g-1 of V. parahaemolyticus one week after suspension of the probiotic treatment. Untreated shrimps served as positive (injected with V. parahaemolyticus) and negative (not injected) controls Analysis of the bacterial community carried out after inoculation and 12 and 48 h later confirmed that V. parahaemolyticus was present in shrimps of the positive control , but not in the negative control or treated with the probiotic mixtures. A significant difference in the diversity of the bacterial community was observed between times after infection. The band patterns in 0-12 h were clustered into a different group from that determined after 48 h, and suggested that during bacterial infection the guts of whiteleg shrimp were dominated by gamma proteobacteria represented by Vibrio sp. and Photobacterium sp. Our results indicate that the experimental and the commercial mixtures are suitable to modulate the bacterial community of L. vannamei and could be used as a probiotic to control vibriosis in juvenile shrimp.

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