Deciphering Diversity Indices for a Better Understanding of Microbial Communities

( Bo-ra Kim ),( Jiwon Shin ),( Robin B. Guevarra ),( Jun Hyung Lee ),( Doo Wan Kim ),( Kuk-hwan Seol ),( Ju-hoon Lee ),( Hyeun Bum Kim ),( Richard E. Isaacson ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.12

The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using culture-independent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

경작지토양에서 미생물제제가 미생물의 다양성과 고추의 생육에 미치는 영향

안창환 ( Chang Hwan An ),임종희 ( Jong Hui Lim ),김요환 ( Yo Hwan Kim ),정병권 ( Byung Kwon Jung ),김진원 ( Jin Won Kim ),김상달 ( Sang Dal Kim ) 한국미생물생명공학회 ( 구 한국산업미생물학회 ) 2012 한국미생물·생명공학회지 Vol.40 No.1

We investigated the effects on soil microbial diversity and the growth promotion of red pepper resulting from inoculation with a microbial agent composed of Bacillus subtilis AH18, B. licheniformis K11 and Pseudomonas fluorescens 2112 in a red pepper farming field. Photosynthetic bacteria, Trichoderma spp., Azotobacter spp., Actinomycetes, nitrate oxidizing bacteria, nitrite oxidizing bacteria, nitrogen fixing bacteria, denitrifying bacteria, phosphate solubilizing bacteria, cellulase producing bacteria, and urease producing bacteria are all indicator microbes of healthy soil microbial diversity. The microbial diversity of the consortium microbial agent treated soil was seen to be 1.1 to 14 times greater than soils where other commercial agent treatments were used, the latter being the commercial agent AC-1, and chemical fertilizer. The yield of red pepper in the field with the treated consortium microbial agent was increased by more than 15% when compared to the other treatments. Overall, the microbial diversity of the red pepper farming field soil was improved by the consortium microbial agent, and the promotion of growth and subsequent yield of red pepper was higher than soils where the other treatments were utilized.

Green manure amendment enhances microbial activity and diversity in antibiotic-contaminated soil

Caban, Jiff Randy,Kuppusamy, Saranya,Kim, Jang Hwan,Yoon, Young-Eun,Kim, Song Yeob,Lee, Yong Bok Elsevier 2018 Applied soil ecology Vol.129 No.-

<P><B>Abstract</B></P> <P>The impacts of antibiotics on soil microbial activity and community structure are poorly understood. It is also important to identify strategies to reduce the problems that antibiotics inflict on soil biology. Hence, for the first time, this study investigated the effect of sulfathiazole (STZ) on soil microbial activity (measured in terms of dehydrogenase activity) and bacterial community structure (revealed by pyrosequencing analysis) in antibiotics contaminated soils (10 and 100 mg STZ kg<SUP>−1</SUP> soil), and treated with (in)organic amendments (NPK, compost and hairy vetch). Dehydrogenase activity was significantly higher in the hairy vetch amended soils (with and without STZ). Pyrosequencing analysis revealed a concentration dependent impact of antibiotics on soil microbial richness and diversity. <I>Proteobacteria</I> and <I>Actinobacteria</I> were present in greater proportions even in soils with a high antibiotic concentration of 100 mg kg<SUP>−1</SUP>. With 10 mg kg<SUP>−1</SUP> STZ, the effect on microbial community richness and diversity was minimal. Meanwhile, with 100 mg kg<SUP>−1</SUP> STZ, the disappearance of <I>Verrucomicrobia, Bacteroidetes and Planctomycetes</I> was observed. Even with a high antibiotic spiking concentration, a tremendous increase in the relative abundance of <I>Firmicutes</I> was seen in the hairy vetch amended soils which led to a considerably higher Gram-positive proportion than the compost and NPK treatments. We conclude that utilization of green manure (cover crop – hairy vetch) can be considered a viable strategy for safer crop production in antibiotic-contaminated soils. This is because it enhances soil microbial/enzyme activity, bacterial richness and diversity, notably the population of beneficial Gram-positive bacteria.</P>

Use of Terminal Restriction Length Polymorphism (T-RFLP) Analysis to Evaluate Uncultivable Microbial Community Structure of Soil

Chauhan, Puneet Singh,Shagol, Charlotte C.,Yim, Woo-Jong,Tipayno, Sherlyn C.,Kim, Chang-Gi,Sa, Tong-Min Korean Society of Soil Science and Fertilizer 2011 한국토양비료학회지 Vol.44 No.1

Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

Use of Terminal Restriction Length Polymorphism (T-RFLP) Analysis to Evaluate Uncultivable Microbial Community Structure of Soil

Puneet Singh Chauhan,Charlotte C. Shagol,Woojong Yim,Sherlyn C. Tipayno,Chang-Gi Kim,Tongmin Sa 한국토양비료학회 2011 한국토양비료학회지 Vol.44 No.1

Various environmental ecosystems are valuable sources for microbial ecology studies, and their analyses using recently developed molecular ecological approaches have drawn significant attention within the scientific community. Changes in the microbial community structures due to various anthropogenic activities can be evaluated by various culture-independent methods e.g. ARISA, DGGE, SSCP, T-RFLP, clone library, pyrosequencing, etc. Direct amplification of total community DNA and amplification of most conserved region (16S rRNA) are common initial steps, followed by either fingerprinting or sequencing analysis. Fingerprinting methods are relatively quicker than sequencing analysis in evaluating the changes in the microbial community. Being an efficient, sensitive and time- and cost effective method, T-RFLP is regularly used by many researchers to access the microbial diversity. Among various fingerprinting methods T-RFLP became an important tool in studying the microbial community structure because of its sensitivity and reproducibility. In this present review, we will discuss the important developments in T-RFLP methodology to distinguish the total microbial diversity and community composition in the various ecosystems.

Comparative evaluation of microbial diversity and metabolite profiles in <i>doenjang</i>, a fermented soybean paste, during the two different industrial manufacturing processes

Lee, Sunmin,Lee, Sarah,Singh, Digar,Oh, Ji Young,Jeon, Eun Jung,Ryu, Hyung SeoK,Lee, Dong Wan,Kim, Beom Seok,Lee, Choong Hwan Elsevier 2017 Food chemistry Vol.221 No.-

<P><B>Abstract</B></P> <P>Two different <I>doenjang</I> manufacturing processes, the industrial process (IP) and the modified industrial process (mIP) with specific microbial assortments, were subjected to metabolite profiling using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). The multivariate analyses indicated that both primary and secondary metabolites exhibited distinct patterns according to the fermentation processes (IP and mIP). Microbial community analysis for <I>doenjang</I> using denaturing gradient gel electrophoresis (DGGE), exhibited that both bacteria and fungi contributed proportionally for each step in the process viz., soybean, steaming, drying, <I>meju</I> fermentation, cooling, brining, and aging. Further, correlation analysis indicated that <I>Aspergillus</I> population was linked to sugar metabolism, <I>Bacillus</I> spp. with that of fatty acids, whereas <I>Tetragenococcus</I> and <I>Zygosaccharomyces</I> were found associated with amino acids. These results suggest that the components and quality of <I>doenjang</I> are critically influenced by the microbial assortments in each process.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The mIP showed similar metabolite profiles compared to IP despite reduced time. </LI> <LI> Microbial assortments regulate differential metabolite profiles in each process. </LI> <LI> <I>Doenjang</I> quality was synchronous with microbial metabolic diversity. </LI> </UL> </P>

Molecular Analysis of Prokaryotic Diversity in the Deep Subsurface of the Former Homestake Gold Mine, South Dakota, USA

Gurdeep Rastogi,Larry D. Stetler,Brent M. Peyton,Rajesh K. Sani 한국미생물학회 2009 The journal of microbiology Vol.47 No.4

A culture-independent molecular phylogenetic analysis was carried out to study the prokaryotic diversity in two soil samples collected from the subsurface (1.34 km depth) of the former Homestake gold mine, Lead, South Dakota, USA at two sites, the Ross shaft and number 6 Winze. Microbial community analyses were performed by cloning and sequencing of 16S rRNA genes retrieved directly from soil samples. Geochemical characterization of soils revealed high amount of toxic metals such as As, Cd, Co, Cr, Cu, Ni, Pb, Zn, and U at both the sites. Phylogenetic analyses showed that soil samples were predominantly composed of phylotypes related to phylum Proteobacteria. Other phyla detected in libraries were Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Chlorobi, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, Verrucomicrobia, and candidate divisions OP10 and TM7. The majority (>95%) of the phylotypes retrieved in the libraries were most closely related to environmental sequences from yet-uncultured bacteria representing a hitherto unidentified diversity. The archaeal communities at both the sites exhibited lower diversity and were most closely affiliated to uncultivated species within the Crenarchaeota. Results showed the existence of diverse microbial populations in deep subsurface environment of the Homestake gold mine. Statistical analyses demonstrated that each site harbored phylogenetically distinct microbial populations that were more diverse at Ross site compare to winze site.

The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing

Kim, H.B.,Isaacson, R.E. Elsevier Scientific Pub. Co 2015 Veterinary microbiology Vol.177 No.3

The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors.

DNA 염기서열 분석에 의한 떡차의 미생물 다양성 분석

백근식(Keun-Sik Baik),성치남(Chi-Nam Seong),황영민(Yeong-Min Hwang),김기안(Gee-An Kim),이나라(Na-Ra Lee),김두운(Duwoon Kim),조정용(Jeong-Yong Cho),김선재(Seon-Jae Kim),박근형(Keun-Hyung Park),문제학(Jae-Hak Moon) 한국차학회 2012 한국차학회지 Vol.18 No.3

To determine the microbiological characteristics of ddeok cha, which is known as a Korean traditional microbial-fermented tea, bacterial and fungal communities of ddeok cha were analyzed by using a pyrosequencing method. Total genomic DNAs were extracted from ddeok cha directly. Ribosomal RNA genes were amplified and sequenced using specific primers for bacteria and fungi. A total of 12,851 reads (bacteria, 8,995; fungi, 3,586) were compared with known sequences in the database. Bacteria were assigned to five phyla, 25 families, 44 genera, and 104 species, whereas fungi were to five phyla, 41 families, 51 genera, and 69 species. Almost all of the bacteria (98.63%) were Gram-negative and members of the phylum Proteobacteria, of which the predominant genus was Pantoea (89.02%) followed by Erwinia (6.13%). Almost all of the fungi (98.86%) were acomycetes such as Dothideomycetes (60.97%) and Eurotiomycetes (31.55%). In this study, we found that microflora of ddeok cha could be distinguished from the predominant microflora (Aspergillus, Penicillium and yeast, Candida) of Pu-erh tea.

Dynamic changes of bacterial communities and nitrite character during northeastern Chinese sauerkraut fermentation

Zhou, Qi,Zang, Shizhu,Zhao, Zinan,Li, Xinli 한국식품과학회 2018 Food Science and Biotechnology Vol.27 No.1

Northeastern Chinese sauerkraut is a well-known traditional fermented vegetable in China. Incomplete identification of the microorganisms' (bacteria in spontaneous fermentation) diversity and accumulation of nitrite make it difficult to normalize the fermentation process and product qualities of northeastern Chinese sauerkraut. Conventional culturing and polymerase chain reaction-denaturing gradient gel electrophoresis methods were combined to describe microbial structure and diversity. Lactobacillus, Leuconostoc, Enterobacter, Accumulibacter, Thermotoga, Pseudomonas, Clostridium, Rahnella and Citrobacter were predominant microorganisms in different fermentation periods. The pH value and nitrite concentration presented a certain relevance to the amount of lactic acid bacteria. Lactobacillus and Leuconostoc had the ability to decrease nitrite by inhibiting nitrate-reducing bacteria such as Enterobacter. Therefore, Northeastern Chinese sauerkraut should not be eaten until 4 weeks of fermentation for the safety and quality of fermented foods. Northeastern Chinese sauerkraut is rich in lactic acid bacteria, which demonstrate its ability as an excellent probiotic for applications in functional foods.