scholarly journals Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

mSystems ◽  
2018 ◽  
Vol 3 (2) ◽  
Author(s):  
Isabelle Laforest-Lapointe ◽  
Marie-Claire Arrieta

ABSTRACTHuman-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.

Diversity ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 201 ◽  
Author(s):  
Carlos Rochera ◽  
Antonio Camacho

Here we present a comprehensive review of the diversity revealed by research in limnology and microbial ecology conducted in Byers Peninsula (Livingston Island, South Shetland Islands, Antarctica) during the last two decades. The site constitutes one of the largest ice-free areas within the Antarctic Peninsula region. Since it has a high level of environmental protection, it is less human-impacted compared to other sites within the South Shetland archipelago. The main investigations in Byers Peninsula focused on the physical and chemical limnology of the lakes, ponds, rivers, and wetlands, as well as on the structure of their planktonic and benthic microbial communities, and on the functional ecology of the microbial food webs. Lakes and ponds in Byers range along a productivity gradient that extends from the less productive lakes located upland to the eutrophic coastal lakes. Their planktonic assemblages include viruses, bacteria, a metabolically diverse community of protists (i.e., autotrophs, heterotrophs, and mixotrophs), and a few metazooplankton species. Most of the studies conducted in the site demonstrate the strong influence of the physical environment (i.e., temperature, availability of light, and water) and nutrient availability in structuring these microbial communities. However, top-down biotic processes may occur in summer, when predation by zooplankton can exert a strong influence on the abundance of protists, including flagellates and ciliated protozoa. As a consequence, bacterioplankton could be partly released from the grazing pressure exerted by these protists, and proliferates fueled by external nutrient subsidies from the lake’s catchment. As summer temperatures in this region are slightly above the melting point of water, biotic processes, such as those related to the productivity of lakes during ice-free periods, could become even more relevant as warming induced by climate change progresses. The limnological research carried out at the site proves that Byers Peninsula deserves special attention in the framework of the research in extreme environments. Together with nearby sites, such as Signy Island, Byers Peninsula comprises a featuring element of the Maritime Antarctic region that represents a benchmark area relative to the global distribution and diversity of aquatic microorganisms.


2021 ◽  
Vol 11 ◽  
Author(s):  
Jung-A Ryu ◽  
Eiseul Kim ◽  
Mi-Ju Kim ◽  
Shinyoung Lee ◽  
Sung-Ran Yoon ◽  
...  

Gochujang is a Korean fermented hot pepper paste beneficial to human health by providing various nutrients. In this study, its physicochemical characteristics were identified, and its microbial communities were analyzed by high-throughput sequencing. The interrelationship between physicochemical characteristics and microbial composition was investigated to reveal the properties of gochujang before and after fermentation. After fermentation, all samples showed decreased salt concentration, pH, and reducing sugar content, while the acidity and amino-type nitrogen increased. The water content, salt concentration, amino-type nitrogen, and reducing sugar differed according to the batches of samples. Bacillus, Aerosakkonema, and Enterococcus were identified as the predominant bacterial genera. Furthermore, Aerosakkonema was the most abundant genus before fermentation; however, it was replaced by Bacillus as it decreased after fermentation. For the fungi, Aspergillus dominated before fermentation, whereas Zygosaccharomyces and Millerozyma dominated after fermentation. The high level of amino-type nitrogen in gochujang was related to the relative abundance of B. haynesii/B. licheniformis before fermentation. Additionally, the high abundance of Z. rouxii after fermentation was related to the flavor of gochujang. This comprehensive analysis of the microbial community associated with the physicochemical properties of gochujang could help in understanding the factors affecting the quality of the product.


2021 ◽  
Vol 12 ◽  
Author(s):  
Lauren M. Lui ◽  
Erica L.-W. Majumder ◽  
Heidi J. Smith ◽  
Hans K. Carlson ◽  
Frederick von Netzer ◽  
...  

Over the last century, leaps in technology for imaging, sampling, detection, high-throughput sequencing, and -omics analyses have revolutionized microbial ecology to enable rapid acquisition of extensive datasets for microbial communities across the ever-increasing temporal and spatial scales. The present challenge is capitalizing on our enhanced abilities of observation and integrating diverse data types from different scales, resolutions, and disciplines to reach a causal and mechanistic understanding of how microbial communities transform and respond to perturbations in the environment. This type of causal and mechanistic understanding will make predictions of microbial community behavior more robust and actionable in addressing microbially mediated global problems. To discern drivers of microbial community assembly and function, we recognize the need for a conceptual, quantitative framework that connects measurements of genomic potential, the environment, and ecological and physical forces to rates of microbial growth at specific locations. We describe the Framework for Integrated, Conceptual, and Systematic Microbial Ecology (FICSME), an experimental design framework for conducting process-focused microbial ecology studies that incorporates biological, chemical, and physical drivers of a microbial system into a conceptual model. Through iterative cycles that advance our understanding of the coupling across scales and processes, we can reliably predict how perturbations to microbial systems impact ecosystem-scale processes or vice versa. We describe an approach and potential applications for using the FICSME to elucidate the mechanisms of globally important ecological and physical processes, toward attaining the goal of predicting the structure and function of microbial communities in chemically complex natural environments.


Soil Research ◽  
2020 ◽  
Vol 58 (1) ◽  
pp. 35
Author(s):  
Lin Gao ◽  
Rui Wang ◽  
Jiaming Gao ◽  
Fangming Li ◽  
Guanghua Huang ◽  
...  

To clarify the differences between microbial communities resident in disease suppressive soil (DSS) and disease conducive soil (DCS) in tobacco cultivation, representative soil samples were collected from tobacco plantations in Shengjiaba, China, and the structure and diversity of the resident bacterial and fungal communities were analysed using high-throughput sequencing technology. Our results showed a greater number of operational taxonomic units associated with bacteria and fungi in DSS than in DCS. At the phylum level, abundances of Chloroflexi, Saccharibacteria, Firmicutes, and Planctomycetes in DSS were lower than in DCS, but abundance of Gemmatimonadetes was significantly higher. Abundances of Zygomycota and Chytridiomycota were higher in DSS than DCS, but abundance of Rozellomycota was significantly lower. At the genus level, abundances of 18 bacterial and nine fungal genera varied significantly between DSS and DCS. Relative abundances of Acidothermus, Microbacterium, Curtobacterium, and Colletotrichum were higher in DCS than DSS. The Shannon and Chao1 indices of DSS microbial communities were higher than those of DCS communities. High microbial diversity reduces the incidence of soil-borne diseases in tobacco plantations and promotes the formation of DSSs.


BMC Biology ◽  
2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Jillian L. Waters ◽  
Ruth E. Ley

Abstract The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.


2014 ◽  
Vol 955-959 ◽  
pp. 276-280
Author(s):  
Rui Fang Du ◽  
Jing Yu Li ◽  
Jian Li Liu ◽  
Ji Zhao Zhao

The major goal of microbial ecology is to study the structure and function of complex microbial communities. Various bioinformatics software were employed to handle a large number of genomic information emerged by using high throughput sequencing. This paper summarizes application of bioinformatics in microbial ecology and their corresponding software used in α, β-diversity studies; and finally expounds the important roles in establishment of four synthesis databases.


Author(s):  
Bugero N.V. ◽  
Ilyina N.A. ◽  
Aleksandrova S.M.

In addition to the classical pathogens, which are well understood and well identified, new pathogens with the potential to spread epidemiologically are being identified. Some of these little-known organisms are the simplest Blastocystis spp. blastocystostosis. The clinical significance of Blastocystis spp. and its pathogenicity are still under discussion. This parasite belongs to a group of single-celled eukaryotic organisms living in the colon of the human intestine. Blastocystis spp. is known to be found both in people with reduced immune status and in individuals without any clinical manifestation. It has been established that a sufficiently high degree of invasiveness is observed in persons with gastrointestinal tract diseases, dermatosis, allergic reactions, in patients with carriers of the human immunodeficiency virus, etc. Possessing persistence factors, protozoa blastocysts contribute to the inactivation of host defensive mechanisms, providing a stable anthogonistic effect. In recent years, many works have been devoted to the characteristics of the persistent properties of Blastocystis spr., however, individual properties of blastocysts, in particular, anticytokine activity (ACA), have not yet been studied. In this regard, the work studied the anticytokine activity of microorganisms isolated from healthy subjects and patients with gastrointestinal tract diseases. A high prevalence of the studied characteristic in the subjects was shown. The expression of anticytokine activity in the obtained isolates of blastocysts was the highest in the group of persons with gastric ulcer disease, which decreased in the order of duodenal ulcer, chronic cholecystitis, chronic gastritis, etc. The data obtained in this work on the high level of ACA expression in blastocyst isolates obtained from individuals with gastrointestinal diseases as compared with the control group enables to conclude that their exometabolites may influence the local cytokine balance [1], which supports the inflammatory process.


Gut Microbes ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 1-13
Author(s):  
Julia Moor ◽  
Tsering Wüthrich ◽  
Suzanne Aebi ◽  
Nadezda Mostacci ◽  
Gudrun Overesch ◽  
...  

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