scholarly journals Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4781 ◽  
Author(s):  
Andrian P. Gajigan ◽  
Aletta T. Yñiguez ◽  
Cesar L. Villanoy ◽  
Maria Lourdes San Diego-McGlone ◽  
Gil S. Jacinto ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Surface Waters ◽  
Taxonomic Diversity ◽  
The Philippines ◽  
Marine Biodiversity ◽  
Rrna Gene ◽  
Marine Microorganisms ◽  
Marine Microbes ◽  
Comprehensive Picture ◽  
Rrna Gene Sequencing

Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.

scholarly journals Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

2021 ◽  
Vol 9 (8) ◽  
pp. 1721
Author(s):  
Christian O’Dea ◽  
Roger Huerlimann ◽  
Nicole Masters ◽  
Anna Kuballa ◽  
Cameron Veal ◽  
...  
Keyword(s):  
16S Rrna ◽  
Gut Microbiota ◽  
Microbial Diversity ◽  
Surface Waters ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Faecal Contamination ◽  
Hypervariable Regions ◽  
Geographical Regions ◽  
V3 Region

Animal faecal contamination of surface waters poses a human health risk, as they may contain pathogenic bacteria or viruses. Of the numerous animal species residing along surface waterways in Australia, macropod species are a top contributor to wild animals’ faecal pollution load. We characterised the gut microbiota of 30 native Australian Eastern Grey Kangaroos from six geographical regions (five kangaroos from each region) within South East Queensland in order to establish their bacterial diversity and identify potential novel species-specific bacteria for the rapid detection of faecal contamination of surface waters by these animals. Using three hypervariable regions (HVRs) of the 16S rRNA gene (i.e., V1–V3, V3–V4, and V5–V6), for their effectiveness in delineating the gut microbial diversity, faecal samples from each region were pooled and microbial genomic DNA was extracted, sequenced, and analysed. Results indicated that V1-V3 yielded a higher taxa richness due to its larger target region (~480 bp); however, higher levels of unassigned taxa were observed using the V1-V3 region. In contrast, the V3–V4 HVR (~569 bp) attained a higher likelihood of a taxonomic hit identity to the bacterial species level, with a 5-fold decrease in unassigned taxa. There were distinct dissimilarities in beta diversity between the regions, with the V1-V3 region displaying the highest number of unique taxa (n = 42), followed by V3–V4 (n = 11) and V5–V6 (n = 8). Variations in the gut microbial diversity profiles of kangaroos from different regions were also observed, which indicates that environmental factors may impact the microbial development and, thus, the composition of the gut microbiome of these animals.

scholarly journals Diversity and biogeography of Woesearchaeota: A comprehensive analysis of multi-environment data

2020 ◽  
Author(s):  
Jing Xiao ◽  
Yu Zhang ◽  
Wanning Chen ◽  
Yanbing Xu ◽  
Rui Zhao ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Core Genome ◽  
Environmental Parameters ◽  
Taxonomic Diversity ◽  
Genomic Diversity ◽  
Metabolic Reconstruction ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Rrna Gene Sequencing ◽  
Comprehensive Study

AbstractWoesearchaeota is a newly proposed archaeal phylum frequently detected in various environments. Due to the limited systematical study, little is known about their distribution, taxonomy, and metabolism. Here, we conducted a comprehensive study for Woesearchaeota with 16S ribosomal RNA (rRNA) gene sequencing data of 27,709 samples and metagenomic whole genome sequencing (WGS) data of 1,266 samples. We find that apart from free-living environments, Woesearchaeota also widely distribute in host-associated environments. And host-associated environmental parameters greatly affect their distribution. 81 Woesearchaeota genomes, including 33 genomes firstly reconstructed in this project, were assigned to 59 Woesearchaeota species, suggesting their high taxonomic diversity. Comparative analysis indicated that Woesearchaeota have an open pan-genome with small core genome. Metabolic reconstruction showed that particular metabolic pathway absence in specific environments, demonstrated the metabolic diversity of Woesearchaeota varies in differences environments. These results have placed host-associated environments into the global biogeography of Woesearchaeota and have demonstrated their genomic diversity for future investigation of adaptive evolution.

scholarly journals Divergent Microbiota Dynamics along the Coastal Marine Ecosystem of Puerto Rico

2020 ◽  
Vol 11 (2) ◽  
pp. 45-55
Author(s):  
Clifford Louime ◽  
Frances Vazquez-Sanchez ◽  
Dieunel Derilus ◽  
Filipa Godoy-Vitorino
Keyword(s):  
Puerto Rico ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Marine Ecosystem ◽  
Geographical Area ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Marine Microorganisms ◽  
Coastal Marine Ecosystem ◽  
Coastal Marine

Understanding the different factors shaping the spatial and temporal distribution of marine microorganisms is fundamental in predicting their responses to future environmental disturbances. There has been, however, little effort to characterize the microbial diversity including the microbiome dynamics among regions in the Caribbean Sea. Toward this end, this study was designed to gain some critical insights into microbial diversity within the coastal marine ecosystem off the coast of Puerto Rico. Using Illumina MiSeq, the V4 region of the 16S rRNA gene was sequenced with the goal of characterizing the microbial diversity representative of different coastal sites around the island of Puerto Rico. This study provided valuable insights in terms of the local bacterial taxonomic abundance, α and β diversity, and the environmental factors shaping microbial community composition and structure. The most dominant phyla across all 11 sampling sites were the Proteobacteria, Bacteroidetes, and Planctomycetes, while the least dominant taxonomic groups were the NKB19, Tenericutes, OP3, Lentisphaerae, and SAR406. The geographical area (Caribbean and Atlantic seas) and salinity gradients were the main drivers shaping the marine microbial community around the island. Despite stable physical and chemical features of the different sites, a highly dynamic microbiome was observed. This highlights Caribbean waters as one of the richest marine sources for a microbial biodiversity hotspot. The data presented here provide a basis for further temporal evaluations aiming at deciphering microbial taxonomic diversity around the island, while determining how microbes adapt to changes in the climate.

scholarly journals Passenger-surface microbiome interactions in the subway of Mexico City

2020 ◽  
Author(s):  
Daniela Vargas-Robles ◽  
Carolina Gonzalez-Cedillo ◽  
Apolinar M. Hernandez ◽  
Luis D. Alcaraz ◽  
Mariana Peimbert
Keyword(s):  
Microbial Diversity ◽  
Mexico City ◽  
16S Rrna Gene Sequencing ◽  
Surface Cleaning ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Usage Frequency ◽  
Rrna Gene Sequencing ◽  
Passenger Behavior ◽  
Effect Of Surface

AbstractInteraction between hands and the environment permits the interchange of microorganisms. The Mexico City subway is used daily by millions of passengers that get in contact with its surfaces. In this study, we used 16S rRNA gene sequencing to characterize the microbiomes of frequently touched surfaces, also comparing regular and women-only wagons. We also explored the effect of surface cleaning on microbial resettling. Finally, we studied passenger behavior and characterized microbial changes after traveling.Most passengers (99%), showed some type of surface interaction during a wagon trip, mostly with the hands (92%). We found microbiome differences associated with surfaces, probably reflecting diverse surface materials and usage frequency. The platform floor was the most bacterial diverse surface, while the stair handrail and pole were the least diverse ones. After pole cleaning, the resettling of microbial diversity was fast (5-30 minutes); however, it did not resemble the initial composition.After traveling, passengers significantly increased their hand microbial diversity and converged to a similar microbial composition among passengers. Additionally, passenger hand microbiomes resembled subway surfaces in diversity and also in the frequency of potentially pathogenic taxa. However, microbial fingerprints were preserved within passengers after traveling.

scholarly journals Urine and Fecal Microbiota in a Canine Model of Bladder Cancer

2021 ◽  
Author(s):  
Ryan Mrofchak ◽  
Christopher Madden ◽  
Morgan V Evans ◽  
William C Kisseberth ◽  
Deepika Dhawan ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Tumor Development ◽  
16S Rrna Gene Sequencing ◽  
Canine Model ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Fecal Samples ◽  
Robust Model ◽  
Rrna Gene Sequencing ◽  
Future Work

Introduction: Urothelial carcinoma (UC) is the tenth most diagnosed cancer in humans worldwide. Dogs are a robust model for invasive UC as tumor development and progression is similar in humans and dogs. Recent studies on urine microbiota in humans revealed alterations in microbial diversity and composition in individuals with UC; however, the potential role of microbiota in UC has yet to be elucidated. Dogs could be valuable models for this research, but microbial alterations in dogs with UC have not been evaluated. Objective: The objective of this this pilot study was to compare the urine and fecal microbiota of dogs with UC (n = 7) and age-, sex-, and breed-matched healthy controls (n = 7). Methods: DNA was extracted from mid-stream free-catch urine and fecal samples using Qiagen Bacteremia and PowerFecal kits, respectively. 16S rRNA gene sequencing was performed followed by sequence processing and analyses (QIIME 2 and R). Results: Canine urine and fecal samples were dominated by taxa similar to those found in humans. Significantly decreased microbial diversity (Kruskal-Wallis: Shannon, p = 0.048) and altered bacterial composition were observed in the urine but not feces of dogs with UC (PERMANOVA: Unweighted UniFrac, p = 0.011). The relative abundances of Fusobacterium was also increased, although not significantly, in the urine and feces of dogs with UC. Conclusion: This study characterizes urine and fecal microbiota in dogs with UC, and it provides a foundation for future work exploring host-microbe dynamics in UC carcinogenesis, prognosis, and treatment.

scholarly journals Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use

2018 ◽  
Vol 9 ◽  
pp. 215265671878951 ◽  
Author(s):  
Vijay R. Ramakrishnan ◽  
Justin Holt ◽  
Leah F. Nelson ◽  
Diana Ir ◽  
Charles E. Robertson ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
16S Rrna Gene Sequencing ◽  
Mometasone Furoate ◽  
Simultaneous Increase ◽  
Rrna Gene ◽  
Independent Sequence ◽  
Intranasal Steroids ◽  
Culture Independent ◽  
Current Article ◽  
Rrna Gene Sequencing

Introduction A role for bacteria and other microbes has long been suspected in the chronic inflammatory sinonasal diseases. Recent studies utilizing culture-independent, sequence-based identification have demonstrated aberrant shifts in the sinus microbiota of chronic rhinosinusitis subjects, compared with ostensibly healthy controls. Examining how such microbiota shifts occur and the potential for physician-prescribed interventions to influence microbiota dynamics are the topics of the current article. Methods The nasal cavity microbiota of 5 subjects was serially examined over an 8-week period using pan-bacterial 16S rRNA gene sequencing. Four of the subjects were administered topical mometasone furoate spray, while 1 subject underwent a mupirocin decolonization procedure in anticipation of orthopedic surgery. Results Measures of microbial diversity were unaffected by intranasal treatment in 2 patients and were markedly increased in the remaining 3. The increase in microbial diversity was related to clearance of Moraxella spp. and a simultaneous increase in members of the phylum Actinobacteria. Both effects persisted at least 2 weeks beyond cessation of treatment. Transient changes in the relative abundance of several bacterial genera, including Staphylococcus and Priopionibacteria, were also observed during treatment. Conclusions The effects of intranasal steroids on the sinonasal microbiome are poorly understood, despite their widespread use in treating chronic sinonasal inflammatory disorders. In this longitudinal study, administration of intranasal mometasone furoate or mupirocin resulted in shifts in microbial diversity that persisted to some degree following treatment cessation. Further characterization of these effects as well as elucidation of the mechanism(s) underlying these changes is needed.

scholarly journals The development of gut microbiota in ostriches and its association with juvenile growth

2018 ◽  
Author(s):  
Elin Videvall ◽  
Se Jin Song ◽  
Hanna M. Bensch ◽  
Maria Strandh ◽  
Anel Engelbrecht ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Microbial Diversity ◽  
16S Rrna Gene Sequencing ◽  
Model Organisms ◽  
Rrna Gene ◽  
Juvenile Growth ◽  
Adult Fitness ◽  
Yolk Absorption ◽  
Rrna Gene Sequencing ◽  
Extinction Events

AbstractThe development of gut microbiota during ontogeny in vertebrates is emerging as an important process influencing physiology, immune system, health, and adult fitness. However, we have little knowledge of how the gut microbiome is colonised and develops in non-model organisms, and to what extent microbial diversity and specific taxa influence changes in fitness-related traits. Here, we used 16S rRNA gene sequencing to describe the successional development of the faecal microbiota in juvenile ostriches (Struthio camelus; n = 71) over their first three months of life, during which time a five-fold difference in weight was observed. We found a gradual increase in microbial diversity with age, an overall convergence in community composition among individuals, multiple colonisation and extinction events, and major taxonomic shifts coinciding with the cessation of yolk absorption. In addition, we discovered significant but complex associations between juvenile growth and microbial diversity, and identified distinct bacterial groups that had positive (Bacteroidaceae) and negative (Enterobacteriaceae, Enterococcaceae, Lactobacillaceae) correlations with the growth of individuals at specific ages. These results have broad implications for our understanding of the development of gut microbiota and its association with juvenile growth.

scholarly journals Occurrence and characterization of Trichomitus batrachorum (Protista, Trichomonadidae) from Rhinella marina (Amphibia, Bufonidae) in the Philippines

2020 ◽  
Vol 14 (1) ◽  
Keyword(s):  
Ultrastructural Study ◽  
Phylogenetic Trees ◽  
18S Rrna Gene ◽  
The Philippines ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Data Sets ◽  
Rhinella Marina ◽  
Rrna Gene Sequencing

Trichomonad isolation from amphibians is new in the Philippines as trichomonad studies in the country are few, limited only to mammals, reptiles and birds. Moreover, there are very few studies on amphibian-associated trichomonad ultrastructure and morphology. Trichomitus batrachorum (Ts. batrachorum) was isolated from Rhinella marina fecal samples and identified using SEM and TEM for ultrastructural study and 18S rRNA gene sequencing. A 37.5% prevalence of Ts. batrachorum from R. marina was observed based on in vitro culture and molecular analysis. Characteristics of this coprozoic trichomonad that provided distinctive features for classification included body size and shape, three anterior flagella and a recurrent flagellum, lamelliform undulating membrane, type A costa periodicity, V-shaped parabasal body, well-developed pelta, shape and location of organelles such as the nucleus, blepharoplast, axostyle, comb-like organelle, hydrogenosomes and the observation of a pseudocyst stage. DNA sequence analysis corroborated these results, and generated phylogenetic trees with high bootstrap support further proved the identity of the isolate. The few identified trichomonads in the Philippines exhibit the capability for adaptation to new hosts and it is possible they have zoonotic potential. These findings contribute to the existing trichomonad data sets in the country. This is the first ultrastructural study of Ts. batrachorum species isolated from a toad.

Sign in / Sign up

Export Citation Format

Share Document