Graphene-Based Nanomaterials Modulate Internal Biofilm Interactions and Microbial Diversity

Graphene-based nanomaterials (GBMs), such as graphene oxide (GO) and reduced graphene oxide (rGO), possess unique properties triggering high expectations for the development of new technological applications and are forecasted to be produced at industrial-scale. This raises the question of potential adverse outcomes on living organisms and especially toward microorganisms constituting the basis of the trophic chain in ecosystems. However, investigations on GBMs toxicity were performed on various microorganisms using single species that are helpful to determine toxicity mechanisms but fail to predict the consequences of the observed effects at a larger organization scale. Thus, this study focuses on the ecotoxicological assessment of GO and rGO toward a biofilm composed of the diatom Nitzschia palea associated to a bacterial consortium. After 48 and 144 h of exposure to these GBMs at 0, 0.1, 1, and 10 mg.L−1, their effects on the diatom physiology, the structure, and the metabolism of bacterial communities were measured through the use of flow cytometry, 16S amplicon sequencing, and Biolog ecoplates, respectively. The exposure to both of these GBMs stimulated the diatom growth. Besides, GO exerted strong bacterial growth inhibition as from 1 mg.L−1, influenced the taxonomic composition of diatom-associated bacterial consortium, and increased transiently the bacterial activity related to carbon cycling, with weak toxicity toward the diatom. On the contrary, rGO was shown to exert a weaker toxicity toward the bacterial consortium, whereas it influenced more strongly the diatom physiology. When compared to the results from the literature using single species tests, our study suggests that diatoms benefited from diatom-bacteria interactions and that the biofilm was able to maintain or recover its carbon-related metabolic activities when exposed to GBMs.

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Metagenomic, Metabolomic, and Functional Evaluation of Kimchi Broth Treated with Light-Emitting Diodes (LEDs)

Metabolites ◽

10.3390/metabo11080472 ◽

2021 ◽

Vol 11 (8) ◽

pp. 472

Author(s):

Yeong-Ji Oh ◽

Ye-Rin Park ◽

Jungil Hong ◽

Do-Yup Lee

Keyword(s):

Amplicon Sequencing ◽

Taxonomic Composition ◽

Metabolic Phenotype ◽

Rrna Gene ◽

Functional Evaluation ◽

Initial Condition ◽

Microbial Composition ◽

Light Emitting ◽

Blue Led ◽

Red Led

The light-emitting diode (LED) has been widely used in the food industry, and its application has been focused on microbial sterilization, specifically using blue-LED. The investigation has been recently extended to characterize the biotic and abiotic (photodynamic) effects of different wavelengths. Here, we investigated LED effects on kimchi fermentation. Kimchi broths were treated with three different colored-LEDs (red, green, and blue) or kept in the dark as a control. Multiomics was applied to evaluate the microbial taxonomic composition using 16S rRNA gene amplicon sequencing, and the metabolomic profiles were determined using liquid chromatography–Orbitrap mass spectrometry. Cell viability was tested to determine the potential cytotoxicity of the LED-treated kimchi broths. First, the amplicon sequencing data showed substantial changes in taxonomic composition at the family and genus levels according to incubation (initial condition vs. all other groups). The differences among the treated groups (red-LED (RLED), green-LED (GLED), blue-LED (BLED), and dark condition) were marginal. The relative abundance of Weissella was decreased in all treated groups compared to that of the initial condition, which coincided with the decreased composition of Lactobacillus. Compositional changes were relatively high in the GLED group. Subsequent metabolomic analysis indicated a unique metabolic phenotype instigated by different LED treatments, which led to the identification of the LED treatment-specific and common compounds (e.g., luteolin, 6-methylquinoline, 2-hydroxycinnamic acid, and 9-HODE). These results indicate that different LED wavelengths induce characteristic alterations in the microbial composition and metabolomic content, which may have applications in food processing and storage with the aim of improving nutritional quality and the safety of food.

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Glacier ice archives nearly 15,000-year-old microbes and phages

Microbiome ◽

10.1186/s40168-021-01106-w ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Zhi-Ping Zhong ◽

Funing Tian ◽

Simon Roux ◽

M. Consuelo Gazitúa ◽

Natalie E. Solonenko ◽

...

Keyword(s):

Climate Change ◽

Ice Core ◽

Ice Cores ◽

Single Species ◽

Amplicon Sequencing ◽

Future Climate Change ◽

Climate Conditions ◽

Glacier Ice ◽

Sampling Procedures ◽

Functional Genome

Abstract Background Glacier ice archives information, including microbiology, that helps reveal paleoclimate histories and predict future climate change. Though glacier-ice microbes are studied using culture or amplicon approaches, more challenging metagenomic approaches, which provide access to functional, genome-resolved information and viruses, are under-utilized, partly due to low biomass and potential contamination. Results We expand existing clean sampling procedures using controlled artificial ice-core experiments and adapted previously established low-biomass metagenomic approaches to study glacier-ice viruses. Controlled sampling experiments drastically reduced mock contaminants including bacteria, viruses, and free DNA to background levels. Amplicon sequencing from eight depths of two Tibetan Plateau ice cores revealed common glacier-ice lineages including Janthinobacterium, Polaromonas, Herminiimonas, Flavobacterium, Sphingomonas, and Methylobacterium as the dominant genera, while microbial communities were significantly different between two ice cores, associating with different climate conditions during deposition. Separately, ~355- and ~14,400-year-old ice were subject to viral enrichment and low-input quantitative sequencing, yielding genomic sequences for 33 vOTUs. These were virtually all unique to this study, representing 28 novel genera and not a single species shared with 225 environmentally diverse viromes. Further, 42.4% of the vOTUs were identifiable temperate, which is significantly higher than that in gut, soil, and marine viromes, and indicates that temperate phages are possibly favored in glacier-ice environments before being frozen. In silico host predictions linked 18 vOTUs to co-occurring abundant bacteria (Methylobacterium, Sphingomonas, and Janthinobacterium), indicating that these phages infected ice-abundant bacterial groups before being archived. Functional genome annotation revealed four virus-encoded auxiliary metabolic genes, particularly two motility genes suggest viruses potentially facilitate nutrient acquisition for their hosts. Finally, given their possible importance to methane cycling in ice, we focused on Methylobacterium viruses by contextualizing our ice-observed viruses against 123 viromes and prophages extracted from 131 Methylobacterium genomes, revealing that the archived viruses might originate from soil or plants. Conclusions Together, these efforts further microbial and viral sampling procedures for glacier ice and provide a first window into viral communities and functions in ancient glacier environments. Such methods and datasets can potentially enable researchers to contextualize new discoveries and begin to incorporate glacier-ice microbes and their viruses relative to past and present climate change in geographically diverse regions globally.

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Inference based PICRUSt accuracy varies across sample types and functional categories

10.1101/655746 ◽

2019 ◽

Cited By ~ 3

Author(s):

Shan Sun ◽

Roshonda B. Jones ◽

Anthony A. Fodor

Keyword(s):

16S Rrna ◽

Gene Prediction ◽

Amplicon Sequencing ◽

Taxonomic Composition ◽

Inference Models ◽

16S Rrna Amplicon Sequencing ◽

Gene Profiles ◽

Metagenome Sequencing ◽

The Cost ◽

Functional Profiles

AbstractBackgroundDespite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon sequencing. Methods have been developed to predict the functional profiles of microbial communities based on their taxonomic composition, and PICRUSt is the most widely used of these techniques. In this study, we evaluated the performance of PICRUSt by comparing the significance of the differential abundance of functional gene profiles predicted with PICRUSt to those from shotgun metagenome sequencing across different environments.ResultsWe selected 7 datasets of human, non-human animal and environmental (soil) samples that have publicly available 16S rRNA and shotgun metagenome sequences. As we would expect based on previous literature, strong Spearman correlations were observed between gene compositions predicted with PICRUSt and measured with shotgun metagenome sequencing. However, these strong correlations were preserved even when the sample labels were shuffled. This suggests that simple correlation coefficient is a highly unreliable measure for the performance of algorithms like PICRUSt. As an alternative, we compared the performance of PICRUSt predicted genes to metagenome genes in inference models associated with metadata within each dataset. With this method, we found reasonable performance for human datasets, with PICRUSt performing better for inference on genes related to “house-keeping” functions. However, the performance of PICRUSt degraded sharply outside of human datasets when used for inference.ConclusionWe conclude that the utility of PICRUSt for inference with the default database is likely limited outside of human samples and that development of tools for gene prediction specific to different non-human and environmental samples is warranted.

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Structural and functional approaches to describe polychaete assemblages: ecological implications for estuarine ecosystems

Marine and Freshwater Research ◽

10.1071/mf10277 ◽

2011 ◽

Vol 62 (8) ◽

pp. 918 ◽

Cited By ~ 23

Author(s):

Wagner F. Magalhães ◽

Francisco Barros

Keyword(s):

Environmental Variability ◽

Salinity Gradient ◽

Single Species ◽

Taxonomic Composition ◽

Feeding Guilds ◽

High Plasticity ◽

Benthic Assemblages ◽

Feeding Guild ◽

And Function ◽

Trophic Role

Polychaete assemblages are of special interest when studying dynamic environments such as estuaries because of their high plasticity in life strategies to cope with environmental variability. We tested the hypothesis that polychaete feeding guilds would be more related to environmental characteristics than to taxonomic composition. Polychaetes were sampled on two different occasions along three tropical estuarine systems in north-eastern Brazil. Different polychaete taxa replaced one another along the entire salinity gradient and the overall pattern from high- to low-salinity regions was from high species and feeding-guild diversities to dominance by a single species or a feeding group. We suggest that the relationships between structure and function of polychaete assemblages might provide a measure of the resilience of estuarine conditions; estuaries with a high redundancy in the trophic role of polychaetes might recover faster from disturbance and retain more natural ecological functions than those estuaries with low or no redundancy, because more species would have the capacity to expand their niches to compensate for the loss of neighbouring species. Integrative approaches allying species composition to their trophic role need to be thoroughly investigated to help understand such complex temporal and spatial organisation of benthic assemblages in estuaries.

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Inference based accuracy of metagenome prediction tools varies across sample types and functional categories

10.21203/rs.2.20233/v1 ◽

2020 ◽

Author(s):

Shan Sun ◽

Roshonda B. Jones ◽

Anthony A. Fodor

Keyword(s):

16S Rrna ◽

Gene Prediction ◽

Amplicon Sequencing ◽

Taxonomic Composition ◽

Inference Models ◽

Prediction Tools ◽

16S Rrna Amplicon Sequencing ◽

Metagenome Sequencing ◽

The Cost ◽

Functional Profiles

Abstract Background: Despite recent decreases in the cost of sequencing, shotgun metagenome sequencing remains more expensive compared with 16S rRNA amplicon sequencing. Methods have been developed to predict the functional profiles of microbial communities based on their taxonomic composition. In this study, we evaluated the performance of three commonly used metagenome prediction tools (PICRUSt, PICRUSt2 and Tax4Fun) by comparing the significance of the differential abundance of predicted functional gene profiles to those from shotgun metagenome sequencing across different environments. Results: We selected 7 datasets of human, non-human animal and environmental (soil) samples that have publicly available 16S rRNA and shotgun metagenome sequences. As we would expect based on previous literature, strong Spearman correlations were observed between predicted gene compositions and gene relative abundance measured with shotgun metagenome sequencing. However, these strong correlations were preserved even when the abundance of genes were permuted across samples. This suggests that simple correlation coefficient is a highly unreliable measure for the performance of metagenome prediction tools. As an alternative, we compared the performance of genes predicted with PICRUSt, PICRUSt2 and Tax4Fun to sequenced metagenome genes in inference models associated with metadata within each dataset. With this approach, we found reasonable performance for human datasets, with the metagenome prediction tools performing better for inference on genes related to “house-keeping” functions. However, their performance degraded sharply outside of human datasets when used for inference. Conclusion: We conclude that the utility of PICRUSt, PICRUSt2 and Tax4Fun for inference with the default database is likely limited outside of human samples and that development of tools for gene prediction specific to different non-human and environmental samples is warranted.

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On the robustness of inference of association with the gut microbiota in stool, swab and mucosal tissue samples

10.1101/2021.02.04.429844 ◽

2021 ◽

Author(s):

Shan Sun ◽

Xiangzhu Zhu ◽

Xiang Huang ◽

Harvey J. Murff ◽

Reid M. Ness ◽

...

Keyword(s):

Microbial Community ◽

Gut Microbiota ◽

Community Composition ◽

Microbial Community Composition ◽

Amplicon Sequencing ◽

Taxonomic Composition ◽

Mucosal Tissue ◽

Tissue Samples ◽

16S Rrna Amplicon Sequencing ◽

Functional Profiles

AbstractThe gut microbiota plays an important role in human health and disease. Stool, swab and mucosal tissue samples have been used in individual studies to survey the microbial community but the consequences of using these different sample types are not completely understood. We previously reported differences in microbial community composition with 16S rRNA amplicon sequencing between stool, swab and mucosal tissue samples. Here, we extended the previous study to a larger cohort and performed shotgun metagenome sequencing of 1,397 stool, swab and mucosal tissue samples from 240 participants. Consistent with previous results, taxonomic composition of stool and swab samples was distinct, but still more similar to each other than mucosal tissue samples, which had a substantially different community composition, characterized by a high relative abundance of the mucus metabolizers Bacteroides and Subdoligranulum, as well as bacteria with higher tolerance for oxidative stress such as Escherichia. As has been previously reported, functional profiles were more uniform across sample types than taxonomic profiles with differences between stool and swab samples smaller, but mucosal tissue samples remained distinct from the other two types. When the taxonomic and functional profiles of different sample types were used for inference in association with host phenotypes of age, sex, body mass index (BMI), antibiotics or non-steroidal anti-inflammatory drugs (NSAIDs) use, hypothesis testing using either stool or swab gave broadly similar results, but inference performed on mucosal tissue samples gave results that were generally less consistent with either stool or swab. Our study represents an important resource for the experimental design of studies aimed to understand microbiota perturbations specific to defined micro niches within the human intestinal tract.

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Unlocking a high bacterial diversity in the coralloid root microbiome from the cycad genusDioon

10.1101/381798 ◽

2018 ◽

Cited By ~ 1

Author(s):

Pablo de Jesús Suárez-Moo ◽

Andrew P. Vovides ◽

M. Patrick Griffith ◽

Francisco Barona-Gómez ◽

Angélica Cibrián-Jaramillo

Keyword(s):

Bacterial Diversity ◽

Natural Populations ◽

Amplicon Sequencing ◽

Botanical Garden ◽

Taxonomic Composition ◽

Rrna Gene ◽

Biological Interactions ◽

Plant Growth Promoting ◽

Coralloid Roots ◽

Root Microbiome

AbstractCycads are among the few plants that have developed specialized roots to host nitrogen-fixing bacteria. We describe the bacterial diversity of the coralloid roots from sevenDioonspecies and their surrounding rhizosphere and soil. Using 16S rRNA gene amplicon sequencing, we found that all coralloid roots are inhabited by a broad diversity of bacterial groups, including cyanobacteria and Rhizobiales among the most abundant groups. The diversity and composition of the endophytes are similar in the six Mexican species ofDioonthat we evaluated, suggesting a recent divergence ofDioonpopulations and/or similar plant-driven restrictions in maintaining the coralloid root microbiome. Botanical garden samples and natural populations have a similar taxonomic composition, although the beta diversity differed between these populations. The rhizosphere surrounding the coralloid root serves as a reservoir and source of mostly diazotroph and plant growth-promoting groups that colonize the coralloid endosphere. In the case of cyanobacteria, the endosphere is enriched withNostocspp andCalothrixspp that are closely related to previously reported symbiont genera in cycads and other early divergent plants. The data reported here provide an in-depth taxonomic characterization of the bacterial community associated with coralloid root microbiome. The functional aspects of the endophytes, their biological interactions, and their evolutionary history are the next research step in this recently discovered diversity within the cycad coralloid root microbiome.

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Multiomic Approach to Analyze Infant Gut Microbiota: Experimental and Analytical Method Optimization

Biomolecules ◽

10.3390/biom11070999 ◽

2021 ◽

Vol 11 (7) ◽

pp. 999

Author(s):

Helena Torrell ◽

Adrià Cereto-Massagué ◽

Polina Kazakova ◽

Lorena García ◽

Héctor Palacios ◽

...

Keyword(s):

16S Rrna ◽

Gut Microbiota ◽

Variable Region ◽

Amplicon Sequencing ◽

Taxonomic Composition ◽

Intestinal Microbiome ◽

Fecal Samples ◽

16S Rrna Amplicon Sequencing ◽

Method Optimization ◽

Feature Selection Approach

Background: The human intestinal microbiome plays a central role in overall health status, especially in early life stages. 16S rRNA amplicon sequencing is used to profile its taxonomic composition; however, multiomic approaches have been proposed as the most accurate methods for study of the complexity of the gut microbiota. In this study, we propose an optimized method for bacterial diversity analysis that we validated and complemented with metabolomics by analyzing fecal samples. Methods: Forty-eight different analytical combinations regarding (1) 16S rRNA variable region sequencing, (2) a feature selection approach, and (3) taxonomy assignment methods were tested. A total of 18 infant fecal samples grouped depending on the type of feeding were analyzed by the proposed 16S rRNA workflow and by metabolomic analysis. Results: The results showed that the sole use of V4 region sequencing with ASV identification and VSEARCH for taxonomy assignment produced the most accurate results. The application of this workflow showed clear differences between fecal samples according to the type of feeding, which correlated with changes in the fecal metabolic profile. Conclusion: A multiomic approach using real fecal samples from 18 infants with different types of feeding demonstrated the effectiveness of the proposed 16S rRNA-amplicon sequencing workflow.

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Turnover in life strategies recapitulates microbial succession on synthetic marine particles

10.1101/2021.11.05.466518 ◽

2021 ◽

Author(s):

Alberto Pascual-García ◽

Julia Schwartzman ◽

Tim N Enke ◽

Arion Iffland-Stettner ◽

Otto X Cordero ◽

...

Keyword(s):

Metabolic Pathways ◽

Amplicon Sequencing ◽

Trophic Chain ◽

Microbial Succession ◽

Ecological Processes ◽

Shotgun Metagenomics ◽

16S Rrna Amplicon Sequencing ◽

Environmental Selection ◽

Complex Matter ◽

Uptake Of Nutrients

Particulate organic matter (POM) in the ocean sustains diverse communities of bacteria that mediate the remineralization of organic complex matter. However, the variability of these particles and of the environmental conditions surrounding them present a challenge to the study of the ecological processes shaping particle-associated communities and their function. In this work, we utilise data from experiments in which coastal water communities were grown on synthetic particles to ask which are the most important ecological drivers of their assembly and associated traits. Combining 16S rRNA amplicon sequencing with shotgun metagenomics, together with an analysis of the full genomes of a subset of isolated strains, we were able to identify two-to-three distinct community classes, corresponding to early vs. late colonizers. We show that these classes are shaped by environmental selection (early colonizers) and facilitation (late colonizers), and find distinctive traits associated with each class. While early colonizers have a larger proportion of genes related to uptake of nutrients, motility and environmental sensing with few pathways enriched for metabolism, late colonizers devote a higher proportion of genes for metabolism, comprising a wide array of different pathways including metabolism of carbohydrates, amino acids and xenobiotics We find evidence in selected metabolic pathways for the existence of a trophic-chain topology connecting both classes. The interpretation of these traits suggests a distinction between early and late colonizers analogous to other classifications found in the literature, and we discuss connections with the classical distinction between r- and K-strategists.

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Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity

Conservation ◽

10.3390/conservation1040024 ◽

2021 ◽

Vol 1 (4) ◽

pp. 311-326

Author(s):

Cameron S. Dodd ◽

Catherine E. Grueber

Keyword(s):

Microbial Communities ◽

Environmental Changes ◽

Amplicon Sequencing ◽

Taxonomic Composition ◽

Conservation Strategies ◽

Careful Study ◽

Microbiome Composition ◽

Functional Perspective ◽

Functional Characterisation ◽

Microbiome Research

Conservation research has historically been conducted at the macro level, focusing on animals and plants and their role in the wider ecosystem. However, there is a growing appreciation of the importance of microbial communities in conservation. Most microbiome research in conservation thus far has used amplicon sequencing methods to assess the taxonomic composition of microbial communities and inferred functional capabilities from these data. However, as manipulation of the microbiome as a conservation tool becomes more and more feasible, there is a growing need to understand the direct functional consequences of shifts in microbiome composition. This review outlines the latest advances in microbiome research from a functional perspective and how these data can be used to inform conservation strategies. This review will also consider some of the challenges faced when studying the microbiomes of wild animals and how they can be overcome by careful study design and sampling methods. Environmental changes brought about by climate change or direct human actions have the potential to alter the taxonomic composition of microbiomes in wild populations. Understanding how taxonomic shifts affect the function of microbial communities is important for identifying species most threatened by potential disruption to their microbiome. Preservation or even restoration of these functions has the potential to be a powerful tool in conservation biology and a shift towards functional characterisation of gut microbiome diversity will be an important first step.

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