17 research outputs found
Data_Sheet_1_Random sampling associated with microbial profiling leads to overestimated stochasticity inference in community assembly.docx
Revealing the mechanisms governing the complex community assembly over space and time is a central issue in ecology. Null models have been developed to quantitatively disentangle the relative importance of deterministic vs. stochastic processes in structuring the compositional variations of biological communities. Similar approaches have been recently extended to the field of microbial ecology. However, the profiling of highly diverse biological communities (e.g., microbial communities) is severely influenced by random sampling issues, leading to undersampled community profiles and overestimated β-diversity, which may further affect stochasticity inference in community assembly. By implementing simulated datasets, this study demonstrate that microbial stochasticity inference is also affected due to random sampling issues associated with microbial profiling. The effects on microbial stochasticity inference for the whole community and the abundant subcommunities were different using different randomization methods in generating null communities. The stochasticity of rare subcommunities, however, was persistently overestimated irrespective of which randomization method was used. Comparatively, the stochastic ratio approach was more sensitive to random sampling issues, whereas the Raup–Crick metric was more affected by randomization methods. As more studies begin to focus on the mechanisms governing abundant and rare subcommunities, we urge cautions be taken for microbial stochasticity inference based on β-diversity, especially for rare subcommunities. Randomization methods to generate null communities shall also be carefully selected. When necessary, the cutoff used for judging the relative importance of deterministic vs. stochastic processes shall be redefined.</p
Additional file 1: of Gene content dissimilarity for subclassification of highly similar microbial strains
This file contains the supplementary table and figures for this paper, including Table S1, Figure S1, and Figure S2. (DOCX 262 kb
StressChip as a High-Throughput Tool for Assessing Microbial Community Responses to Environmental Stresses
Microbial
community responses to environmental stresses are critical for microbial
growth, survival, and adaptation. To fill major gaps in our ability
to discern the influence of environmental changes on microbial communities
from engineered and natural environments, a functional gene-based
microarray, termed StressChip, has been developed. First, 46 functional
genes involved in microbial responses to environmental stresses such
as changes to temperature, osmolarity, oxidative status, nutrient
limitation, or general stress response were selected and curated.
A total of 22,855 probes were designed, covering 79,628 coding sequences
from 985 bacterial, 76 archaeal, and 59 eukaryotic species/strains.
Probe specificity was computationally verified. Second, the usefulness
of functional genes as indicators of stress response was examined
by surveying their distribution in metagenome data sets. The abundance
of individual stress response genes is consistent with expected distributions
based on respective habitats. Third, the StressChip was used to analyze
marine microbial communities from the Deepwater Horizon oil spill.
That functional stress response genes were detected in higher abundance
(<i>p</i> < 0.05) in oil plume compared to nonplume samples
indicated shifts in community composition and structure, consistent
with previous results. In summary, StressChip provides a new tool
for accessing microbial community functional structure and responses
to environmental changes
Development of HuMiChip for Functional Profiling of Human Microbiomes
<div><p>Understanding the diversity, composition, structure, function, and dynamics of human microbiomes in individual human hosts is crucial to reveal human-microbial interactions, especially for patients with microbially mediated disorders, but challenging due to the high diversity of the human microbiome. Here we have developed a functional gene-based microarray for profiling human microbiomes (HuMiChip) with 36,802 probes targeting 50,007 protein coding sequences for 139 key functional gene families. Computational evaluation suggested all probes included are highly specific to their target sequences. HuMiChip was used to analyze human oral and gut microbiomes, showing significantly different functional gene profiles between oral and gut microbiome. Obvious shifts of microbial functional structure and composition were observed for both patients with dental caries and periodontitis from moderate to advanced stages, suggesting a progressive change of microbial communities in response to the diseases. Consistent gene family profiles were observed by both HuMiChip and next generation sequencing technologies. Additionally, HuMiChip was able to detect gene families at as low as 0.001% relative abundance. The results indicate that the developed HuMiChip is a useful and effective tool for functional profiling of human microbiomes.</p></div
Computational evaluation of sequence-specific (A, B, C) and group-specific probes (D, E, F) at (A) maximal sequence identities, (B) maximal stretch length and (C) minimal free energy with their closest non-target sequences, and (D) minimal sequence identities, (E) minimal stretch length and (F) maximal free energy with their group targets.
<p>Computational evaluation of sequence-specific (A, B, C) and group-specific probes (D, E, F) at (A) maximal sequence identities, (B) maximal stretch length and (C) minimal free energy with their closest non-target sequences, and (D) minimal sequence identities, (E) minimal stretch length and (F) maximal free energy with their group targets.</p
Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer
To further understand the diversity
and dynamics of SRB in response
to substrate amendment, we sequenced genes coding for the dissimilatory
sulfite reductase (<i>dsrA</i>) in groundwater samples collected
after an emulsified vegetable oil (EVO) amendment, which sustained
UÂ(VI)-reducing conditions for one year in a fast-flowing aquifer.
EVO amendment significantly altered the composition of groundwater
SRB communities. Sequences having no closely related-described species
dominated (80%) the indigenous SRB communities in nonamended wells.
After EVO amendment, <i>Desulfococcus</i>, <i>Desulfobacterium</i>, and <i>Desulfovibrio</i>, known for long-chain-fatty-acid,
short-chain-fatty-acid and H<sub>2</sub> oxidation and UÂ(VI) reduction,
became dominant accounting for 7 ± 2%, 21 ± 8%, and 55 ±
8% of the SRB communities, respectively. Succession of these SRB at
different bioactivity stages based on redox substrates/products (acetate,
SO<sub>4</sub><sup>–2</sup>, UÂ(VI), NO<sub>3</sub><sup>–</sup>, FeÂ(II), and MnÂ(II)) was observed. <i>Desulfovibrio</i> and <i>Desulfococcus</i> dominated SRB communities at
4–31 days, whereas <i>Desulfobacterium</i> became
dominant at 80–140 days. By the end of the experiment (day
269), the abundance of these SRB decreased but the overall diversity
of groundwater SRB was still higher than non-EVO controls. Up to 62%
of the SRB community changes could be explained by groundwater geochemical
variables, including those redox substrates/products. A significant
(<i>P</i> < 0.001) correlation was observed between groundwater
UÂ(VI) concentrations and <i>Desulfovibrio</i> abundance.
Our results showed that the members of SRB and their dynamics were
correlated significantly with slow EVO biodegradation, electron donor
production and maintenance of UÂ(VI)-reducing conditions in the aquifer
Comparative analysis of functional gene profiles as revealed by HuMiChip (total signal intensity) and NGS platforms (relative abundance): A) human gut samples.
<p>B) human oral samples.</p
Saliva Microbiota Carry Caries-Specific Functional Gene Signatures
<div><p>Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as <i>Diaminopimelate epimerase</i>, <i>Prephenate dehydrogenase</i>, <i>Pyruvate-formate lyase</i> and <i>N-acetylmuramoyl-L-alanine amidase</i> were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis.</p></div
Summary of designed probes and covered coding sequence information of HuMiChip based on gene categories.
<p>*Gene families targeting human microbiomes are selected from KEGG pathway database, and may participate in multiple pathways. The total number of probes and covered coding sequences is based on non-redundant genes included in all pathways, but it is not calculated as the sum of all sub-categories.</p
Response ratio analyses of changes of gene abundances based on categories.
<p>A) Moderate periodontitis patients vs. healthy individuals; B) Advanced periodontitis patients vs. healthy individuals. Error bar symbols plotted at the right of dashed line indicated increased relative abundances in moderate/advanced periodontitis patients, while error bar symbols plotted at the left of dashed line indicated decreased relative abundances in healthy individuals.</p