scholarly journals Identifying biases and their potential solutions in human microbiome studies

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Jacob T. Nearing ◽  
André M. Comeau ◽  
Morgan G. I. Langille
Keyword(s):  
Microbial Communities ◽  
Human Body ◽  
Human Microbiome ◽  
Sample Collection ◽  
Sequencing Technology ◽  
Microbial Composition ◽  
Significant Bias ◽  
Typical Sequence ◽  
Entire Experiment ◽  
The Impact

AbstractAdvances in DNA sequencing technology have vastly improved the ability of researchers to explore the microbial inhabitants of the human body. Unfortunately, while these studies have uncovered the importance of these microbial communities to our health, they often do not result in similar findings. One possible reason for the disagreement in these results is due to the multitude of systemic biases that are introduced during sequence-based microbiome studies. These biases begin with sample collection and continue to be introduced throughout the entire experiment leading to an observed community that is significantly altered from the true underlying microbial composition. In this review, we will highlight the various steps in typical sequence-based human microbiome studies where significant bias can be introduced, and we will review the current efforts within the field that aim to reduce the impact of these biases.

Dynamic simulations of microbial communities under perturbations: opportunities for microbiome engineering

2020 ◽  
Author(s):  
Beatriz García-Jiménez ◽  
Jorge Carrasco ◽  
Joaquín Medina ◽  
Mark D Wilkinson
Keyword(s):  
Microbial Communities ◽  
Biological Knowledge ◽  
Sample Collection ◽  
Biomedical Knowledge ◽  
Microbial Composition ◽  
Dynamic Simulations ◽  
Soil Microbial ◽  
Types Of Information ◽  
The Impact

Abstract Background : There are few large longitudinal microbiome studies, and fewer that include controlled, well-annotated perturbations between sampling-points. Thus, there are few opportunities to employ data-driven computational analyses of perturbed microbial communities over time. Results : Our novel computational system simulates the dynamics of microbial communities under perturbations using genome-scale metabolic models (GEMs). Perturbations include modifications to a) the nutrients available in the medium, allowing modelling of prebiotics; and/or b) the microorganisms present in the community to model, for example, probiotics or pathogen infection. These simulations generate the quantity and types of information required by MDPbiome, an AI system which builds predictive models suggesting the perturbation(s) required to engineer microbial communities to a desired state. We call this novel combination of technologies "MDPbiomeGEM"'. We demonstrate, in a Crohn’s disease microbiome, that MDPbiomeGEM correctly models the influence of both prebiotic fiber and a probiotic, resulting in a recommendation to consume inulin to recover from dysbiosis, consistent with prior biomedical knowledge. When used to model the soil microbiome's ability to degrade the herbicide Atrazine, differing recommendations arise depending on the highly variable state of the initial soil microbial composition, highlighting the relevance of both phosphate and microbes (i.e. Halobacillus sp. and H.stevensii ) in a directed microbiome engineering strategy, consistent with previously published observations. Conclusions : MDPbiomeGEM generates large volumes of longitudinal data of complex microbial communities experiencing perturbations. Machine learning on these data reveal patterns consistent with existing biological knowledge, supporting the validity of the approach. MDPbiomeGEM could save research resources by optimizing sample collection in metagenomics studies through identification of "informative" scenarios/time-points, or by predicting optimal in-vitro culture formulations for generating performant synthetic microbial communities. Finally, MDPbiomeGEM outputs include detailed information about the metabolic state of the community, which can be used to further interpret the impact of perturbations, and potentially could be used to predict novel metabolic biomarkers of a microbiome's state.

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

2017 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

2017 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P <0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

scholarly journals Computational Modeling of the Human Microbiome

2020 ◽  
Vol 8 (2) ◽  
pp. 197
Author(s):  
Shomeek Chowdhury ◽  
Stephen S. Fong
Keyword(s):  
Computational Modeling ◽  
Human Health ◽  
Large Scale ◽  
Human Microbiome ◽  
Human Microbiome Project ◽  
Microbial Composition ◽  
Site Specific ◽  
Microbiome Research ◽  
High Level ◽  
The Impact

The impact of microorganisms on human health has long been acknowledged and studied, but recent advances in research methodologies have enabled a new systems-level perspective on the collections of microorganisms associated with humans, the human microbiome. Large-scale collaborative efforts such as the NIH Human Microbiome Project have sought to kick-start research on the human microbiome by providing foundational information on microbial composition based upon specific sites across the human body. Here, we focus on the four main anatomical sites of the human microbiome: gut, oral, skin, and vaginal, and provide information on site-specific background, experimental data, and computational modeling. Each of the site-specific microbiomes has unique organisms and phenomena associated with them; there are also high-level commonalities. By providing an overview of different human microbiome sites, we hope to provide a perspective where detailed, site-specific research is needed to understand causal phenomena that impact human health, but there is equally a need for more generalized methodology improvements that would benefit all human microbiome research.

scholarly journals Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e4178 ◽  
Author(s):  
Taha Soliman ◽  
Sung-Yin Yang ◽  
Tomoko Yamazaki ◽  
Holger Jenke-Kodama
Keyword(s):  
Next Generation Sequencing ◽  
Microbial Communities ◽  
Dna Extraction ◽  
Dna Isolation ◽  
Soil Microbial Communities ◽  
Next Generation ◽  
Microbial Composition ◽  
Okinawa Island ◽  
The Impact ◽  
Generation Sequencing

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil®DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin®Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA;P < 0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

scholarly journals Circulating 16S RNA in Biofluids: Extracellular Vesicles as Mirrors of Human Microbiome?

2020 ◽  
Vol 21 (23) ◽  
pp. 8959
Author(s):  
Veronica Ricci ◽  
Davide Carcione ◽  
Simone Messina ◽  
Gualtiero I. Colombo ◽  
Yuri D’Alessandra
Keyword(s):  
Extracellular Vesicles ◽  
Human Body ◽  
Human Microbiome ◽  
Microbial Composition ◽  
Gold Standard Method ◽  
Rna Molecules ◽  
Detection And Identification ◽  
16S Rna ◽  
Principal Tool ◽  
Generation Sequencing

The human body is inhabited by around 1013 microbes composing a multicomplex system, termed microbiota, which is strongly involved in the regulation and maintenance of homeostasis. Perturbations in microbiota composition can lead to dysbiosis, which has been associated with several human pathologies. The gold-standard method to explore microbial composition is next-generation sequencing, which involves the analysis of 16S rRNA, an indicator of the presence of specific microorganisms and the principal tool used in bacterial taxonomic classification. Indeed, the development of 16S RNA sequencing allows us to explore microbial composition in several environments and human body districts and fluids, since it has been detected in “germ-free” environments such as blood, plasma, and urine of diseased and healthy subjects. Recently, prokaryotes showed to generate extracellular vesicles, which are known to be responsible for shuttling different intracellular components such as proteins and nucleic acids (including 16S molecules) by protecting their cargo from degradation. These vesicles can be found in several human biofluids and can be exploited as tools for bacterial detection and identification. In this review, we examine the complex link between circulating 16S RNA molecules and bacteria-derived vesicles.

scholarly journals Metabolome–Microbiome Crosstalk and Human Disease

Metabolites ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 181 ◽  
Author(s):  
Kathleen A. Lee-Sarwar ◽  
Jessica Lasky-Su ◽  
Rachel S. Kelly ◽  
Augusto A. Litonjua ◽  
Scott T. Weiss
Keyword(s):  
Human Body ◽  
Disease Risk ◽  
Human Microbiome ◽  
Treatment Strategies ◽  
Human Microbiome Project ◽  
Combined Use ◽  
Microbiome Data ◽  
The Impact ◽  
Active Investigation ◽  
Human Intestinal Tract

In this review, we discuss the growing literature demonstrating robust and pervasive associations between the microbiome and metabolome. We focus on the gut microbiome, which harbors the taxonomically most diverse and the largest collection of microorganisms in the human body. Methods for integrative analysis of these “omics” are under active investigation and we discuss the advances and challenges in the combined use of metabolomics and microbiome data. Findings from large consortia, including the Human Microbiome Project and Metagenomics of the Human Intestinal Tract (MetaHIT) and others demonstrate the impact of microbiome-metabolome interactions on human health. Mechanisms whereby the microbes residing in the human body interact with metabolites to impact disease risk are beginning to be elucidated, and discoveries in this area will likely be harnessed to develop preventive and treatment strategies for complex diseases.

scholarly journals Microbial Species that Initially Colonize the Human Gut at Birth or in Early Childhood Can Stay in Human Body for Lifetime

2021 ◽  
Author(s):  
Weizhong Li ◽  
Karen E. Nelson
Keyword(s):  
Early Childhood ◽  
Human Body ◽  
Rare Variants ◽  
Human Microbiome ◽  
Sample Collection ◽  
Human Gut ◽  
Significant Difference ◽  
And Function ◽  
Changes Over Time ◽  
Prevalent Species

AbstractIn recent years, many studies have described the composition and function of the human microbiome at different body sites and suggested a role for the microbiome in various diseases and health conditions. Some studies, using longitudinal samples, have also suggested how the microbiome changes over time due to disease, diet, development, travel, and other environmental factors. However, to date, no study has demonstrated whether the microorganisms established at birth or in early childhood, either transmitted from parents or obtained from the environment, can stay in the human body until adult or senior age. To directly answer this question is difficult, because microbiome samples at childhood and at later adulthood for the same individual will need to be compared and the field is not old enough to have allowed for that type of sample collection. Here, using a metagenomic approach, we analyzed 1004 gut microbiome samples from senior adults (65 ± 7.8 years) from the TwinsUK cohort. Our data indicate that many species in the human gut acquired in early childhood can stay for a lifetime until senior ages. We identified the rare genomic variants (single nucleotide variation and indels) for 27 prevalent species with enough sequencing coverage for confident genomic variant identification. We found that for some species, twin pairs, including both monozygotic (MZ) and dizygotic (DZ) twins, share significantly more rare variants than unrelated subject pairs. But no significant difference is found between MZ and DZ twin pairs. These observations strongly suggest that these species acquired in early childhood remained in these persons until senior adulthood.

scholarly journals Mass-immigration determines the assembly of activated sludge microbial communities

2021 ◽  
Vol 118 (27) ◽  
pp. e2021589118
Author(s):  
Giulia Dottorini ◽  
Thomas Yssing Michaelsen ◽  
Sergey Kucheryavskiy ◽  
Kasper Skytte Andersen ◽  
Jannie Munk Kristensen ◽  
...  
Keyword(s):  
Activated Sludge ◽  
Microbial Communities ◽  
Abundant Species ◽  
Partial Least Square ◽  
Least Square ◽  
Partial Least Square Regression ◽  
Similar Process ◽  
Microbial Composition ◽  
Species Abundances ◽  
The Impact

The assembly of bacterial communities in wastewater treatment plants (WWTPs) is affected by immigration via wastewater streams, but the impact and extent of bacterial immigrants are still unknown. Here, we quantify the effect of immigration at the species level in 11 Danish full-scale activated sludge (AS) plants. All plants have different source communities but have very similar process design, defining the same overall environmental growth conditions. The AS community composition in each plant was strongly reflected by the corresponding influent wastewater (IWW) microbial composition. Most species in AS across the plants were detected and quantified in the corresponding IWW, allowing us to identify their fate in the AS: growing, disappearing, or surviving. Most of the abundant species in IWW disappeared in AS, so their presence in the AS biomass was only due to continuous mass-immigration. In AS, most of the abundant growing species were present in the IWW at very low abundances. We predicted the AS species abundances from their abundance in IWW by using a partial least square regression model. Some species in AS were predicted by their own abundance in IWW, while others by multiple species abundances. Detailed analyses of functional guilds revealed different prediction patterns for different species. We show, in contrast to the present understanding, that the AS microbial communities were strongly controlled by the IWW source community and could be quantitatively predicted by taking into account immigration. This highlights a need to revise the way we understand, design, and manage the microbial communities in WWTPs.

scholarly journals Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

2021 ◽  
Vol 12 ◽  
Author(s):  
Ludek Sehnal ◽  
Elizabeth Brammer-Robbins ◽  
Alexis M. Wormington ◽  
Ludek Blaha ◽  
Joe Bisesi ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Aquatic Ecosystems ◽  
Marine Mammals ◽  
Integrative Approach ◽  
Aquatic Animal ◽  
Gastrointestinal Microbiota ◽  
Microbial Composition ◽  
Aquatic Vertebrates ◽  
And Function ◽  
The Impact

Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.

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