scholarly journals Sea Cucumber Intestinal Regeneration Reveals Deterministic Assembly of the Gut Microbiome

2020 ◽  
Vol 86 (14) ◽  
Author(s):  
Brooke L. Weigel
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Gut Microbiome ◽  
Sea Cucumber ◽  
Animal Health ◽  
Experimental System ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Microbial Community Assembly ◽  
Microbiome Assembly

ABSTRACT The gut microbiome has far-reaching effects on host organism health, so understanding the processes that underlie microbial community assembly in the developing gut is a current research priority. Here, a holothurian (also known as sea cucumber; phylum Echinodermata) host is explored as a promising model system for studying the assembly of the gut microbiome. Holothurians have a unique capacity for evisceration (expulsion of the internal organs), followed by rapid regeneration of the gut, decoupling host ontogeny from gut tissue development and permitting experimental manipulation of the gut microbiome in mature host individuals. Here, evisceration was induced in the sea cucumber Sclerodactyla briareus, and regenerating stomach and intestine microbiomes were characterized before and on days 0, 13, 17, and 20 after evisceration using Illumina sequencing of 16S rRNA genes. Regenerating stomach and intestine tissues had microbial communities significantly different from those of mature tissues, with much higher alpha diversity and evenness of taxa in regenerating tissues. Despite immersion in a diverse pool of sediment and seawater microbes in flowthrough seawater aquaria, regenerating gut microbiomes differed at each stage of regeneration and displayed a highly similar community structure among replicates, providing evidence for deterministic host selection of a specific microbial consortium. Moreover, regenerating gut tissues acquired a microbiome that likely conferred energetic and immune advantages to the sea cucumber host, including microbes that can fix carbon and degrade invading pathogens. IMPORTANCE The gut microbiome is pertinent to many aspects of animal health, and there is a great need for natural but tractable experimental systems to examine the processes shaping gut microbiome assembly. Here, the holothurian (sea cucumber) Sclerodactyla briareus was explored as an experimental system to study microbial colonization in the gut, as S. briareus individuals have the ability to completely eviscerate and rapidly regenerate their digestive organs. After induced evisceration, microbial community assembly was characterized over 20 days in regenerating animals. This study demonstrated that colonization of the sea cucumber gut was deterministic; despite immersion in a diverse consortium of environmental microbes, a specific subset of microbes proliferated in the gut, including taxa that likely conferred energetic and immune advantages to the host. Sea cucumbers have the potential to revolutionize our understanding of gut microbiome assembly, as rapid and repeatable gut tissue regeneration provides a promising and tractable experimental system.

scholarly journals Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades

2018 ◽  
Author(s):  
Nicholas D. Youngblut ◽  
Georg H. Reischer ◽  
William Walters ◽  
Nathalie Schuster ◽  
Chris Walzer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Gut Microbiome ◽  
Evolutionary History ◽  
Environmental Filtering ◽  
Microbiome Diversity ◽  
Host Diet ◽  
Host Phylogeny ◽  
Microbe Interactions ◽  
Microbial Community Assembly

AbstractMultiple factors modulate microbial community assembly in the gut, but the magnitude of each can vary substantially across studies. This may be in part due to a heavy reliance on captive animals, which can have very different gut microbiomes versus their wild counterparts. In order to better resolve the influence of evolution and diet on gut microbiome diversity, we generated a large and highly diverse animal distal gut 16S rRNA microbiome dataset, which comprises 80 % wild animals and includes members of Mammalia, Aves, Reptilia, Amphibia, and Actinopterygii. We decoupled the effects of host evolutionary history and diet on gut microbiome diversity and show that each factor explains different aspects of diversity. Moreover, we resolved particular microbial taxa associated with host phylogeny or diet, and we show that Mammalia have a stronger signal of cophylogeny versus non-mammalian hosts. Additionally, our results from ecophylogenetics and co-occurrence analyses suggest that environmental filtering and microbe-microbe interactions differ among host clades. These findings provide a robust assessment of the processes driving microbial community assembly in the vertebrate intestine.

scholarly journals Terrestrial connectivity, upstream aquatic history and seasonality shape bacterial community assembly within a large boreal aquatic network

2021 ◽  
Author(s):  
Masumi Stadler ◽  
Paul A. del Giorgio
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Microbial Community Composition ◽  
Potential Effect ◽  
Species Selection ◽  
Rrna Genes ◽  
Microbial Succession ◽  
Dna And Rna ◽  
Microbial Community Assembly ◽  
16 S Rrna

AbstractDuring transit from soils to the ocean, microbial communities are modified and re-assembled, generating complex patterns of ecological succession. The potential effect of upstream assembly on downstream microbial community composition is seldom considered within aquatic networks. Here, we reconstructed the microbial succession along a land-freshwater-estuary continuum within La Romaine river watershed in Northeastern Canada. We captured hydrological seasonality and differentiated the total and reactive community by sequencing both 16 S rRNA genes and transcripts. By examining how DNA- and RNA-based assemblages diverge and converge along the continuum, we inferred temporal shifts in the relative importance of assembly processes, with mass effects dominant in spring, and species selection becoming stronger in summer. The location of strongest selection within the network differed between seasons, suggesting that selection hotspots shift depending on hydrological conditions. The unreactive fraction (no/minor RNA contribution) was composed of taxa with diverse potential origins along the whole aquatic network, while the majority of the reactive pool (major RNA contribution) could be traced to soil/soilwater-derived taxa, which were distributed along the entire rank-abundance curve. Overall, our findings highlight the importance of considering upstream history, hydrological seasonality and the reactive microbial fraction to fully understand microbial community assembly on a network scale.

scholarly journals Thermodynamically Favorable Reactions Shape the Archaeal Community Affecting Bacterial Community Assembly in Oil Reservoirs

2020 ◽  
Author(s):  
Xiao-Lei Wu ◽  
Jie-Yu Zhao ◽  
Bing Hu ◽  
Yan Li ◽  
Yue-Qin Tang ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Abiotic Factors ◽  
Oil Reservoirs ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Distribution Analysis ◽  
The Core ◽  
Archaeal Communities

Abstract Background: Microbial communities exist everywhere on the earth, and play essential roles in biogeochemical cycling in all ecosystems. Understanding microbial community assembly mechanisms could improve our ability to manage microbial ecosystems for industrial, pharmaceutical, and agricultural applications. Previous studies have shown that microbial communities are shaped by deterministic or stochastic processes, but how these two processes influence the microbial community together is rarely investigated, especially in deep terrestrial ecology. Methods: Here, the microbial compositions in the production waters collected from water injection wells and oil production wells across eight oil reservoirs throughout northern China were determined using high-throughput 454 pyrosequencing of 16S rRNA genes, and analyzed by proportional distribution analysis and null model analysis. Results: In the study, a ‘core’ microbiota consisting of three bacterial genera and eight archaeal genera were found to be existent in all production water samples. Canonical correlation analysis reflected that these core archaea were significantly influenced by the abiotic factors of temperature and reservoir depth, while the core bacteria were affected by the combined impact of the core archaea and environmental factors. Considering that two of the core archaeal genera, acetoclastic methanogens and hydrogenotrophic methanogens, were enriched in low- and high-temperature oil reservoirs, respectively, it was proposed that the archaeal communities in oil reservoirs were characterized by thermodynamic constraints. Conclusions: Together, our study indicates that microbial community structures in wells of oil reservoirs are originally determined by the thermodynamic conditions, through which the core archaeal communities are shaped directly followed by the deterministic recruiting of core bacterial genera, and then the stochastically selection of some other microbial members from local environments.

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

scholarly journals Ultra-accurate microbial amplicon sequencing with synthetic long reads

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Benjamin J. Callahan ◽  
Dmitry Grinevich ◽  
Siddhartha Thakur ◽  
Michael A. Balamotis ◽  
Tuval Ben Yehezkel
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Strain Identification ◽  
Long Reads ◽  
Long Read

Abstract Background Out of the many pathogenic bacterial species that are known, only a fraction are readily identifiable directly from a complex microbial community using standard next generation DNA sequencing. Long-read sequencing offers the potential to identify a wider range of species and to differentiate between strains within a species, but attaining sufficient accuracy in complex metagenomes remains a challenge. Methods Here, we describe and analytically validate LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology that generates highly accurate long reads from standard short reads. Results LoopSeq reads are sufficiently long and accurate to identify microbial genes and species directly from complex samples. LoopSeq perfectly recovered the full diversity of 16S rRNA genes from known strains in a synthetic microbial community. Full-length LoopSeq reads had a per-base error rate of 0.005%, which exceeds the accuracy reported for other long-read sequencing technologies. 18S-ITS and genomic sequencing of fungal and bacterial isolates confirmed that LoopSeq sequencing maintains that accuracy for reads up to 6 kb in length. LoopSeq full-length 16S rRNA reads could accurately classify organisms down to the species level in rinsate from retail meat samples, and could differentiate strains within species identified by the CDC as potential foodborne pathogens. Conclusions The order-of-magnitude improvement in length and accuracy over standard Illumina amplicon sequencing achieved with LoopSeq enables accurate species-level and strain identification from complex- to low-biomass microbiome samples. The ability to generate accurate and long microbiome sequencing reads using standard short read sequencers will accelerate the building of quality microbial sequence databases and removes a significant hurdle on the path to precision microbial genomics.

scholarly journals Habitat Elevation Shapes Microbial Community Composition and Alter the Metabolic Functions in Wild Sable (Martes zibellina) Guts

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 865
Author(s):  
Lantian Su ◽  
Xinxin Liu ◽  
Guangyao Jin ◽  
Yue Ma ◽  
Haoxin Tan ◽  
...  
Keyword(s):  
Microbial Community ◽  
Environmental Factors ◽  
Microbial Communities ◽  
Community Composition ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Functional Genes ◽  
Martes Zibellina ◽  
Clear Cutting ◽  
Metabolic Functions

In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

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