P705 Evaluation of the impact of different commercially available DNA extraction kits and laboratories for assessing bacterial community structure in fecal samples – implications for IBD research

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.

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The impact of host rock geochemistry on bacterial community structure in oligotrophic cave environments

International Journal of Speleology ◽

10.5038/1827-806x.36.2.5 ◽

2007 ◽

Vol 36 (2) ◽

pp. 93-104 ◽

Cited By ~ 66

Author(s):

Hazel Barton ◽

Nicholas Taylor ◽

Michael Kreate ◽

Austin Springer ◽

Stuart Oehrle ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Host Rock ◽

Bacterial Community Structure ◽

The Impact

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Responses of Soil Organic Carbon Sequestration Potential and Bacterial Community Structure in Moso Bamboo Plantations to Different Management Strategies in Subtropical China

Forests ◽

10.3390/f9100657 ◽

2018 ◽

Vol 9 (10) ◽

pp. 657 ◽

Cited By ~ 4

Author(s):

Chuanbao Yang ◽

Zheke Zhong ◽

Xiaoping Zhang ◽

Fangyuan Bian ◽

Xuhua Du

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Management Strategies ◽

Moso Bamboo ◽

Mineralization Rate ◽

Bamboo Forest ◽

C Mineralization ◽

Sequestration Potential ◽

The Impact

Moso bamboo is one of the fastest-growing plants in the world. The objective of this study was to investigate the impact of converting secondary broadleaf evergreen forests (CK) to Moso bamboo plantations, and the impact of different management strategies, including no disturbance (M0), extensive management (M1), and intensive management (M2), on the soil organic carbon (SOC) sequestration potential, and relevant characteristics of the soil bacterial community. Our results showed that, in comparison with CK, M0 and M1 had significantly higher SOC and recalcitrant organic materials (aliphatic and aromatic compounds), and a lower C mineralization rate, whereas M2 had the opposite effects. The conversion from CK to Moso bamboo plantation significantly decreased the relative abundance of Acidobacteria in both the topsoil and subsoil soil layers. Compared with CK, M0 led to the enrichment of bacteria such as Alphaproteobacteria, Chloroflexi, and Bacteroidetes, which are involved in the decomposition of organic matter and the formation of humus and are, therefore, potentially beneficial for increasing the SOC. Furthermore, the ratio of the microbial biomass C (MBC) to total organic C (TOC), C mineralization rate, and bacterial diversity increased from M0 to M2, i.e., with an increase in the disturbance intensity. These findings indicate that the conversion of secondary broadleaf forest to bamboo forest alter the soil bacterial community structure. Reducing disturbance in bamboo forest management strategies should be actively taken up to improve the SOC, and maintain sustainable development in the forest industry.

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Corexit 9500 Enhances Oil Biodegradation and Changes Active Bacterial Community Structure of Oil-Enriched Microcosms

Applied and Environmental Microbiology ◽

10.1128/aem.03462-16 ◽

2017 ◽

Vol 83 (10) ◽

Cited By ~ 46

Author(s):

Stephen M. Techtmann ◽

Mobing Zhuang ◽

Pablo Campo ◽

Edith Holder ◽

Michael Elk ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Microbial Communities ◽

Bacterial Community Structure ◽

Oil Spills ◽

Content Type ◽

Corexit 9500 ◽

Oil Biodegradation ◽

Degrading Bacteria ◽

The Impact

ABSTRACT To better understand the impacts of Corexit 9500 on the structure and activity levels of hydrocarbon-degrading microbial communities, we analyzed next-generation 16S rRNA gene sequencing libraries of hydrocarbon enrichments grown at 5 and 25°C using both DNA and RNA extracts as the sequencing templates. Oil biodegradation patterns in both 5 and 25°C enrichments were consistent with those reported in the literature (i.e., aliphatics were degraded faster than aromatics). Slight increases in biodegradation were observed in the presence of Corexit at both temperatures. Differences in community structure were observed between treatment conditions in the DNA-based libraries. The 25°C consortia were dominated by Vibrio, Idiomarina, Marinobacter, Alcanivorax, and Thalassospira species, while the 5°C consortia were dominated by several species of the genera Flavobacterium, Alcanivorax, and Oleispira. Most of these genera have been linked to hydrocarbon degradation and have been observed after oil spills. Colwellia and Cycloclasticus, known aromatic degraders, were also found in these enrichments. The addition of Corexit did not have an effect on the active bacterial community structure of the 5°C consortia, while at 25°C, a decrease in the relative abundance of Marinobacter was observed. At 25°C, Thalassospira, Marinobacter, and Idiomarina were present at higher relative abundances in the RNA than DNA libraries, suggesting that they were active in degradation. Similarly, Oleispira was greatly stimulated by the addition of oil at 5°C. IMPORTANCE While dispersants such as Corexit 9500 can be used to treat oil spills, there is still debate on the effectiveness on enhancing oil biodegradation and its potential toxic effect on oil-degrading microbial communities. The results of this study provide some insights on the microbial dynamics of hydrocarbon-degrading bacterial populations in the presence of Corexit 9500. Operational taxonomic unit (OTU) analyses indicated that several OTUs were inhibited by the addition of Corexit. Conversely, a number of OTUs were stimulated by the addition of the dispersant, many of which were identified as known hydrocarbon-degrading bacteria. The results highlight the value of using RNA-based methods to further understand the impact of dispersant on the overall activity of different hydrocarbon-degrading bacterial groups.

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Shift of anammox bacterial community structure along the Pearl Estuary and the impact of environmental factors

Journal of Geophysical Research Oceans ◽

10.1002/2014jc010554 ◽

2015 ◽

Vol 120 (4) ◽

pp. 2869-2883 ◽

Cited By ~ 16

Author(s):

Bingbing Fu ◽

Jiwen Liu ◽

Hongmei Yang ◽

Ting Chang Hsu ◽

Biyan He ◽

...

Keyword(s):

Community Structure ◽

Environmental Factors ◽

Bacterial Community ◽

Bacterial Community Structure ◽

The Impact

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Influence of hydrological factors on bacterial community structure in a tropical monsoonal estuary in India

10.21203/rs.3.rs-281357/v1 ◽

2021 ◽

Author(s):

Parvathi Ammini ◽

Michela R Catena ◽

Jasna Vijayan ◽

Nikhil Phadke ◽

Nikhita Gogate

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Communities ◽

Bacterial Community Structure ◽

Salinity Gradient ◽

Pearson Correlation ◽

Temporal Variations ◽

Spatial And Temporal Variation ◽

Physico Chemical ◽

The Impact

Abstract In the present study, we analysed variations in bacterial community structure along a salinity gradient in a tropical monsoonal estuary (Cochin estuary, CE), on the southwest coast of India, using Illumina next-generation sequencing (NGS). Water samples were collected from eight different locations thrice a year, to assess the variability in the bacterial community structure and to determine the physico-chemical factors influencing the bacterial diversity. Proteobacteria was the most dominant phyla in the estuary followed by Bacteroidetes, Cyanobacteria, Actinobacteria, and Firmicutes. Statistical analysis indicated significant variations in bacterial communities between freshwater, mesohaline and euryhaline regions, as well as between the monsoon (wet) and non-monsoon (dry) periods. Non-metric multidimensional scaling (NMDS) analysis demonstrated that the bacterial communities cluster according to different salinity regimes of the estuary. Canonical Correspondence analysis (CCA) showed a clear spatial and temporal variation in the distribution of bacterial communities in the CE. Abundance of Betaproteobacteria was high in the freshwater regions, while Gammaproteobacteria, Alphaproteobacteria and Epsilonproteobactera were more abundant in mesohaline and euryhaline regions of the estuary. Correlagram based on Pearson correlation analysis demonstrated the impact of different physico-chemical variables on the distribution of dominant phyla, class and genera. Spatial and temporal variations in bacterial community structure could be due to regional variations in environmental conditions imparted by allochthonous inputs, monsoonal rainfall, and tidal influence.

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