scholarly journals Improved normalization of species count data in ecology by scaling with ranked subsampling (SRS): application to microbial communities

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9593 ◽  
Author(s):  
Lukas Beule ◽  
Petr Karlovsky
Keyword(s):  
Population Structure ◽  
Community Structure ◽  
Species Composition ◽  
Microbial Communities ◽  
Count Data ◽  
Alpha Diversity ◽  
Shannon Index ◽  
Current Standard ◽  
Library Size ◽  
Relative Abundances

Background Analysis of species count data in ecology often requires normalization to an identical sample size. Rarefying (random subsampling without replacement), which is the current standard method for normalization, has been widely criticized for its poor reproducibility and potential distortion of the community structure. In the context of microbiome count data, researchers explicitly advised against the use of rarefying. Here we introduce a normalization method for species count data called scaling with ranked subsampling (SRS) and demonstrate its suitability for the analysis of microbial communities. Methods SRS consists of two steps. In the scaling step, the counts for all species or operational taxonomic units (OTUs) are divided by a scaling factor chosen in such a way that the sum of scaled counts equals the selected total number of counts Cmin. The relative frequencies of all OTUs remain unchanged. In the subsequent ranked subsampling step, non-integer count values are converted into integers by an algorithm that minimizes subsampling error with regard to the population structure (relative frequencies of species or OTUs) while keeping the total number of counts equal Cmin. SRS and rarefying were compared by normalizing a test library representing a soil bacterial community. Common parameters of biodiversity and population structure (Shannon index H’, species richness, species composition, and relative abundances of OTUs) were determined for libraries normalized to different size by rarefying as well as SRS with 10,000 replications each. An implementation of SRS in R is available for download (https://doi.org/10.20387/BONARES-2657-1NP3). Results SRS showed greater reproducibility and preserved OTU frequencies and alpha diversity better than rarefying. The variance in Shannon diversity increased with the reduction of the library size after rarefying but remained zero for SRS. Relative abundances of OTUs strongly varied among libraries generated by rarefying, whereas libraries normalized by SRS showed only negligible variation. Bray–Curtis index of dissimilarity among replicates of the same library normalized by rarefying revealed a large variation in species composition, which reached complete dissimilarity (not a single OTU shared) among some libraries rarefied to a small size. The dissimilarity among replicated libraries normalized by SRS remained negligibly low at each library size. The variance in dissimilarity increased with the decreasing library size after rarefying, whereas it remained either zero or negligibly low after SRS. Conclusions Normalization of OTU or species counts by scaling with ranked subsampling preserves the original community structure by minimizing subsampling errors. We therefore propose SRS for the normalization of biological count data.

scholarly journals Responses of Bacterial and Fungal Community Structure to Different Rates of 1,3-Dichloropropene Fumigation

2019 ◽  
Vol 3 (3) ◽  
pp. 212-223 ◽  
Author(s):  
Yuan Zeng ◽  
Zaid Abdo ◽  
Amy Charkowski ◽  
Jane E. Stewart ◽  
Kenneth Frost
Keyword(s):  
Community Structure ◽  
Microbial Communities ◽  
Management Practices ◽  
Soil Microbial Communities ◽  
Alpha Diversity ◽  
Potato Production ◽  
Crop Species ◽  
Soil Microbial Community Structure ◽  
Soil Microbial ◽  
Sample Depth

1,3-Dichloropropene (1,3-D) is a well-known nematicidal soil fumigant on many crop species. Currently, little is known about its impact on soil microbial communities using culture-free methods. In this study, we investigated changes in soil bacterial and fungal diversity and composition at two depths (30.5 and 61 cm) in response to management practices of applying 1,3-D at four different rates (103, 122, 140, and 187 liters/ha) relative to an untreated control in potato production fields using 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. A total of 12,783 operational taxonomic units (OTUs) for 16S and 1,706 OTUs for ITS were obtained. Sequencing revealed that Proteobacteria, Firmicutes, Actinobacteria, and Ascomycota were dominant phyla in soils. Comparing alpha diversity of microbial communities at the different chemical rates with untreated plots showed that bacterial communities in plots treated with 1,3-D fumigation at 140 liters/ha were richer, which was supported by higher richness indices. Other diversity indices and overall soil microbial community structure were not significantly influenced by any rates of 1,3-D fumigation, although higher bacterial and fungal richness and diversity were observed in posttreatment soils and/or at 30.5 cm. Of the identified microbial families, the differential abundance of 45 bacterial and 24 fungal families was affected by sample depth, 1,3-D rate, or the interaction of sample depth and 1,3-D. The bacterial family Enterobacteriaceae, which includes species that specialize in decay of complex carbohydrates, increased in abundance post-1,3-D fumigation, and the fungal family Ophiocordycipitaceae, which includes nematode and insect pathogens, decreased, suggesting that the nematode and soil insect death caused by fumigation may selectively impact specific fungal and bacterial families.

scholarly journals Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract Background The effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance. Results Four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm conditions exerted an important influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information. Conclusions This study reveals that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.

Microbial community structure and function prediction of two typical biocrusts in the Mu Us Sandland, Northwest China

2021 ◽  
Author(s):  
Chang Tian ◽  
Jiao Xi ◽  
Mengchen Ju ◽  
Yahong Li ◽  
Qi Guo ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Organic Carbon ◽  
Fungal Community ◽  
High Throughput Sequencing ◽  
Shannon Index ◽  
Operational Taxonomic Units ◽  
Relative Abundances ◽  
Bacteria And Fungi ◽  
Moss Crust

<p>Biocrusts (Biological soil crusts) are a living ground cover widely distributed in arid and semi-arid regions worldwide and provide important ecological functions in ecosystems. As an important part of biocrusts, the microorganisms in the formation and succession of biocrusts should not be underestimated. However, the microbial processes among different types of biocrusts are poorly understood. We used high-throughput sequencing to identify soil bacteria and fungal community in two types of biocrusts, lichen crust and moss crust, in the Mu Us Sandland. The aims were to explore the composition, diversity, and ecological function of the microbial community in two types of biocrusts. Our study found that (1) The diversity of bacterial and fungal communities was significantly different between the two types of biocrusts. The Shannon index (6.18) of fungi in moss crust was higher than that (5.75) in lichen crust, and the operational taxonomic units of bacteria and fungi in moss crust were also higher than those in lichen crust by 3.22% and 30.61%, respectively. The bacteria and fungi community structure in two types of biocrusts were significantly different, while the differences were not significant. (2) In the microbiomes of lichen and moss biocrusts, Actinomycetes, Cyanobacteria, and Proteobacteria, the sum of which accounted for 68.01% in lichen crust and 59.88% in moss crust at operational taxonomic units level, were dominant phylum of bacteria, while the dominant phylum of fungi was mainly Ascomycota. Microcoleus (11.10%) and Exophiala (7.37%) were dominant genera in lichen crust, while the dominant genus in moss crust was RB41 (5.16%). (3) The pH, soil dissolved organic carbon, and soil organic carbon were the top three factors that correlated with both bacterial and fungal community structures. (4) The metabolic function of the bacterial community in two types of biocrusts was quite different. The relative abundances of metabolic pathways in moss crust, such as chemoheterotrophy, ureolysis, aromatic compound degradation, and nitrate reduction, were significantly higher than those in lichen crust, however, the relative abundances of cyanobacteria, oxygenic photoautotrophy, photoautotrophy, and phototrophy were significantly lower (ANOVA, P<0.05). Altogether, our study suggests that the biocrust types have significant effects on the pH, taxonomic, and metabolic diversity, providing a theoretical basis for improving the physicochemical properties of the surface soil in the desertification land ecosystem.</p>

scholarly journals Comparing the Bacterial Community in the Gastrointestinal Tracts Between Growth-Retarded and Normal Yaks on the Qinghai–Tibetan Plateau

2020 ◽  
Vol 11 ◽  
Author(s):  
Jian Ma ◽  
Yixiao Zhu ◽  
Zhisheng Wang ◽  
Xiong Yu ◽  
Rui Hu ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Growth Retardation ◽  
Alpha Diversity ◽  
Shannon Index ◽  
Principal Coordinates Analysis ◽  
Bacterial Composition ◽  
Opposite Trend ◽  
Principal Coordinates ◽  
Bacterial Structure ◽  
Relative Abundances

In ruminants, the bacterial community in the gastrointestinal tract (GIT) has an essential role in healthy growth. Examining the bacterial composition in the GIT between growth-retarded and normal yaks could improve our understanding of the role of microorganisms in yaks with growth retardation. In this study, eight male yaks with growth retardation were used as the growth-retarded yak (GRY) group, and another eight male growth normal yaks (GNYs) with the same breed and age were used as the GNY group. We compared the bacterial community in the rumen, duodenum, jejunum, ileum, cecum, and colon between GRY and GNY groups based on the 16S ribosomal RNA gene sequencing. Alpha-diversity revealed that the Shannon index in the duodenum and ileum of the GNY group was higher (P < 0.05) than that of the GRY group. However, the opposite trend was found in the jejunum and cecum. The principal coordinates analysis (PCoA) showed that the bacterial structure in all segments of GIT differed from each other between two groups. In the rumen, the relative abundances of Ruminococcaceae NK4A214 group, Ruminococcaceae UCG-014, and Treponema 2 were higher (P < 0.05) in the GNY group as compared with the GRY group. However, the Christensenellaceae R-7 group exhibited an opposite trend. In the jejunum, compared with the GNY group, the unclassified Chitinophagaceae was enriched significantly (P < 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P < 0.05) in the GNY group. In the ileum, the relative abundances of the Rikenellaceae RC9 gut group and Prevotellaceae UCG-004 were higher (P < 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P < 0.05) relative abundance of Prevotellaceae UCG-003 as compared with the GRY group. In the colon, the relative abundances of Treponema 2 and unclassified Lachnospiraceae were slightly higher (0.05 < P < 0.10) in the GNY group than those in the GRY group. Overall, these results improve our knowledge about the bacterial composition in the GIT of growth-retarded and normal yaks, and regulating the bacterial community may be an effective solution to promote the compensatory growth of GRYs.

scholarly journals Soil microbial community composition in a paddy field with different fertilization managements

2021 ◽  
pp. 1-11
Author(s):  
Limin Wang ◽  
Dongfeng Huang
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Soil Properties ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Alpha Diversity ◽  
Phosphorus Fertilization ◽  
Bacterial Phyla ◽  
P Fertilizer

Microbes play vital roles in soil quality; however, their response to N (nitrogen) and P (phosphorus) fertilization in acidic paddy soils of subtropical China remains poorly understood. Here, a 10-year field experiment was conducted to evaluate the effects of different fertilization treatments on microbial communities by Illumina MiSeq sequencing. The results showed that different fertilization treatments did not exert a significant effect on microbial alpha diversity, but altered soil properties, and thus affected microbial community composition. The microbial communities in the T1 (optimized N and P fertilizer) and T2 (excessive N fertilizer) treated soils differed from those in the T0 (no N and P fertilizer) and T3 (excessive P fertilizer) treated soils. In addition, the bacterial phyla Proteobacteria, Chloroflexi, and Acidobacteria, and the fungal phyla Ascomycota and Basidiomycota dominated all the fertilized treatments. Soil total potassium (TK) concentration was the most important factor driving the variation in bacterial community structure under different fertilization regimes, while the major factors shaping fungal community structure were soil TN and NO3–-N (nitrate N). These findings indicate that optimization of N and P application rates might result in variations in soil properties, which changed the microbial community structure in the present study.

scholarly journals Dietary Patterns and Gut Microbiome Composition in a Large Population-Based Cohort

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 514-514
Author(s):  
Zhangling Chen ◽  
Djawad Radjabzadeh ◽  
Arfan Ikram ◽  
Andre Uitterlinden ◽  
Robert Kraaij ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Diet Quality ◽  
Gut Microbiome ◽  
Linear Models ◽  
Large Population ◽  
Alpha Diversity ◽  
Population Based ◽  
Shannon Index ◽  
Food Groups ◽  
Microbiome Composition

Abstract Objectives Effects of diet on health and disease risk may be mediated by changes in gut microbiome composition. Our aim was to examine associations between intake of food groups and overall diet quality with gut microbiome composition in a large population-based cohort. Methods We analyzed data of 1130 participants (median age 57 years) from the Rotterdam Study, a population-based cohort study in the Netherlands. We measured dietary intake using a 389-item FFQ, and assessed adherence to dietary guidelines for 14 food groups and combined into a diet quality score. We assessed gut microbiome composition using 16S rRNA gene sequencing. Data were available for 11 phyla, 19 classes, 25 orders, 44 families, and 184 genera. Alpha diversity was quantified by Shannon index and Richness, and beta diversity was qualified by Bray-Curtis distance. We used linear models to examine associations with Shannon index and Richness, Adonis function to examine variations of Bray-Curtis distance, and Multivariate Association with Linear Models to examine associations with gut microbial communities. Models were adjusted for technical covariates, energy intake, age, sex, physical activity, education, smoking and BMI. Results After adjustment, higher diet quality was associated with more alpha diversity and explained part of the variation in beta diversity (P < 0.001). Overall diet quality was associated with relative abundance of four families (Erysipelotrichaceae, Ruminococcaceae, Lachnospiraceae, Christensenellaceae), and 15 genera (Torques group, RuminococcaceaeUCG002, RuminococcaceaeUCG003, RuminococcaceaeUCG005, RuminococcaceaeUCG010, Xylanophilum group, Blautia, RuminococcaceaeNK4A214 group, Eligens group, Coprococcus3, Senegalimassilia, Lachnospira, Halliigroup, ChristensenellaceaeR7 group, Ventriosum group) (adjusted p: q < 0.05). Results were not explained by any single food group. Higher intake of fruits, vegetables, whole grains, and tea, and lower intake of red meat and alcohol were all related to microbiome composition. Replication analyses are ongoing. Conclusions Better overall diet quality may improve overall gut microbial diversity. Furthermore, diet quality may influence abundance of certain gut microbial communities, several of which have previously been linked to lower risk of metabolic and inflammatory diseases. Funding Sources N/A.

scholarly journals Taxonomic and Functional Composition of Soil Mycobiome of Two Agricultural Sites in Khartoum State, Sudan

2021 ◽  
Author(s):  
Marwa H. E. Elnaiem ◽  
Takeshi Taniguchi ◽  
Marmar El Siddig
Keyword(s):  
Land Use ◽  
Community Structure ◽  
Fungal Community ◽  
Alpha Diversity ◽  
Shannon Index ◽  
Fungal Community Composition ◽  
Fungal Community Structure ◽  
Land Use Types ◽  
Diverse Groups ◽  
First Time

Abstract Fungi are one of the most diverse groups of organisms and considered as one of the least-explored biodiversity resources. Soil fungal community was investigated in two agricultural sites in Khartoum state, Sudan, during two seasons. A total of 42 soil samples were collected, their physicochemical properties were determined, then subjected to metabarcoding and metagenomic analyses. fungal community composition, diversity and microbial trophic modes were determined utilizing R software packages. From both sites, a total of 15 different phyla were detected, out of them, 11 were the most abundant and frequent. Ascomycota was the dominant phylum (86.54% total abundance), followed by the Basidiomycota (8.29%). The dominant class was Sordariomycetes (41.02%), followed by Dothideomycetes (19.80%). Aspergillus (6.2%), Curvularia (6.0%), Neurospora (5.8%) and Fusarium (4.9%) were the most abundant genera. Deniquelata for the first time being recorded in Sudan. Apha diversity measures revealed sample richness ranging from 71 to 361 ASVs, and Shannon index ranging from 2.794 to 5.087. The two sites had significantly different alpha diversity. Land-use types were also significantly different in their diversity regardless of site. Season had no effect on alpha diversity of soil fungal communities. Beta diversity analysis indicated significant differences between the two sites and the different land-use types. No significant differences in the community structure recorded between the two seasons. The dominant trophic mode among the assigned ASVs in soil mycobiome was saprotroph mode (22.11%). Results of this study reveals that fungal community structure is affected by site and land-use type. It gives a comprehensive database for the mycobiome of the agricultural soil in Khartoum state.

scholarly journals Study of Periplaneta Americana Microbial Community Structure and Diversity by 16S rRNA High-Throughput Sequencing

2017 ◽  
Vol 2 (4) ◽  
pp. 350
Author(s):  
Zhuang Zhi Chen ◽  
Xiu Mei Wu ◽  
Yong Mei Shen ◽  
Cheng Gong Li ◽  
Kai Ge Xu ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
16S Rrna ◽  
Microbial Communities ◽  
High Throughput ◽  
Microbial Community Structure ◽  
Periplaneta Americana ◽  
High Throughput Sequencing ◽  
Shannon Index

<p><strong><em>Objective: </em></strong><em>The present study probes into the microbial community structure in Periplaneta americana under different breeding conditions, using 16S rRNA high-throughput sequencing technique, in the hope of finding the microbial community structure in Periplaneta americana and their diversity under different breeding conditions. </em></p><p><strong><em>Methods:</em></strong><em> In this study, we extract the microbial metagenomic DNA of 5 groups of Periplaneta americana which under different breeding conditions. Using lllumina Miseq sequencing platform, two-terminal sequencing of V3-V4 regions of 16S rRNA were sequenced; diversity of community structure was analyzed using the softwares such as fastqc, </em><em>QIIME, </em><em>PyNAST, fasttree and R language.</em></p><p><strong><em>Results: </em></strong><em>Shannon index of samples in SG group was lower than that of the other four groups, significantly lower than that of DB group (P&lt;0.05), but not significantly different from other groups. This suggested that the intake of a mixed fodder with high sugar, high fat and high protein by Periplaneta americana can reduce the diversity of microbial communities. Our findings showed that breeding intervention with different fodders may cause differences in the contents of Bacteroidetes, Proteobacteria and Firmicutes in Periplaneta americana. Results showed that long-term intake of lots of sucrose and fat may increase the proportion of Bacteroidetes in Periplaneta americana; and long-term intake of lots of sucrose may reduce the proportion of Proteobacteria in Periplaneta americana; and long-term intake of lots of fat may reduce the proportion of Firmicutes in Periplaneta americana. Two major dominant bacterial genera in all samples were Blattabacterium and Rickettsiella. But different feeding interventions can change the proportions of Blattabacterium and Rickettsiella.</em></p><p><strong><em>Conclusion:</em></strong><em> Periplaneta americana has a complex microbial community structure. Different feeding conditions may change the microbial community structure of Periplaneta americana. An important bacterial genus in Periplaneta americana, Blattabacterium is positively correlated with the intake of sucrose- and fat-rich fodder. In the breeding process of Periplaneta americana, adding sucrose and fat to fodder may increase the content and proportion of Blattabacterium in microbial communities.</em></p>

scholarly journals Breeding farm, level of feeding and presence of antibiotics in the feed influence rabbit cecal microbiota

2020 ◽  
Author(s):  
María Velasco-Galilea ◽  
Miriam Guivernau ◽  
Miriam Piles ◽  
Marc Viñas ◽  
Oriol Rafel ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Management Practices ◽  
Alpha Diversity ◽  
Rrna Gene ◽  
Animal Performance ◽  
Production Environment ◽  
Feed Composition ◽  
Cecal Microbiota ◽  
Relative Abundances ◽  
The Impact

Abstract Background: the effect of the production environment and different management practices in rabbit cecal microbiota remains poorly understood. While previous studies have proved the impact of the age or the feed composition, research in the breeding farm and other animal management aspects, such as the presence of antibiotics in the feed or the level of feeding, is still needed. Characterization of microbial diversity and composition of growing rabbits raised under different conditions could help better understand the role these practices play in cecal microbial communities and how it may result in different animal performance.Results: four hundred twenty-five meat rabbits raised in two different facilities, fed under two feeding regimes (ad libitum or restricted) with feed supplemented or free of antibiotics, were selected for this study. A 16S rRNA gene-based assessment through the MiSeq Illumina sequencing platform was performed on cecal samples collected from these individuals at slaughter. Different univariate and multivariate approaches were conducted to unravel the influence of the different factors on microbial alpha diversity and composition at phylum, genus and OTU taxonomic levels. The animals raised in the facility harboring the most stable environmental conditions had greater, and less variable, microbial richness and diversity. Bootstrap univariate analyses of variance and sparse partial least squares-discriminant analyses endorsed that farm conditions exerted an important influence on rabbit microbiota since the relative abundances of many taxa were found differentially represented between both facilities at all taxonomic levels characterized. Furthermore, only five OTUs were needed to achieve a perfect classification of samples according to the facility where animals were raised. The level of feeding and the presence of antibiotics did not modify the global alpha diversity but had an impact on some bacteria relative abundances, albeit in a small number of taxa compared with farm, which is consistent with the lower sample classification power according to these factors achieved using microbial information.Conclusions: this study reveals that factors associated with the farm effect and other management factors, such as the presence of antibiotics in the diet or the feeding level, modify cecal microbial communities. It highlights the importance of offering a controlled breeding environment that reduces differences in microbial cecal composition that could be responsible for different animal performance.

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