scholarly journals Assessment of Bacterial Community Composition and Dynamics in Alfalfa Silages With and Without Lactobacillus plantarum Inoculation Using Absolute Quantification 16S rRNA Sequencing

2021 ◽  
Vol 11 ◽  
Author(s):  
Fengyuan Yang ◽  
Shanshan Zhao ◽  
Yuan Wang ◽  
Xiaomiao Fan ◽  
Yanping Wang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Lactobacillus Plantarum ◽  
Bacterial Abundance ◽  
Bacterial Community Composition ◽  
Absolute Quantification ◽  
Bacterial Composition ◽  
Bacterial Dna ◽  
Rrna Sequencing ◽  
Spearman’S Correlation ◽  
Dna Amounts

Relative quantification 16S-seq (RQS) has drawn deeper insights into bacterial community compositions in silage. However, it provides no information on dynamics of the total amount of bacterial DNA through the ensiling process and across different treatments. In this study, bacterial compositions in alfalfa silage with and without Lactobacillus plantarum inoculation after 10 and 60days of ensiling were investigated using absolute quantification 16S-seq (AQS), and bacterial composition and its interaction with fermentation properties of silage indicated by AQS and RQS were compared. Variation in total bacterial DNA amounts across different treatments and ensiling periods was illustrated by AQS. AQS indicated higher bacterial richness indices and closer correlations of these indices with fermentation properties than RQS via spearman’s correlation analyses, as well as more taxa with significance on bacterial abundance via lefse analyses. In conclusion, AQS effectively illustrated the dynamics of bacterial communities during the ensiling process.

scholarly journals Variation in the Gut Microbiota of Common Marmosets: Differences with Colony of Origin and Integration

2020 ◽  
Author(s):  
Rachel E. Cooper ◽  
Lisa M. Mangus ◽  
Jessica Lynch ◽  
Kayla Schonvisky ◽  
Justin R. Wright ◽  
...  
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Community Composition ◽  
Beta Diversity ◽  
Rectal Swab ◽  
Bacterial Community Composition ◽  
16S Rrna Sequencing ◽  
Animal Origin ◽  
Common Marmosets ◽  
Rrna Sequencing

AbstractCharacterization of the gut microbiome may aid understanding and management of natural and experimental disease states in research animals, thereby promoting reproducibility. In this study, the rectal bacterial communities of three separate common marmoset (Callithrix jacchus) breeding colonies were defined using 16S rRNA sequencing of rectal swab samples. Study animals originated from two German colonies and a United States colony (JHU). The two German cohorts, previously fed the same diet, were imported into the JHU facility; they were then isolated, transitioned onto JHU diet, and then moved into rooms housing JHU animals. To dissect the contributions of diet and integration in shaping the rectal bacterial community, samples were collected from German origin marmosets upon JHU arrival (baseline), following diet transition (100 d), and following cohousing (390 d). Baseline and 390 d samples were collected from stably maintained JHU marmosets. Bacterial community composition was distinct between all three cohorts at baseline, suggesting that factors other than primary diet confer significant differences between captive populations. Beta-diversity of the animals from the two German colonies converged by 100 d but remained distinct from JHU sample beta-diversity throughout the 390-d study, indicating that diet had greater influence on bacterial community composition than did housing animals within the same room. Our results demonstrate substantial differences in gut bacteria between different captive marmoset colonies, with persistence of these differences following husbandry standardization and housing integration. Goals of rigor and reproducibility in research underscore the need to consider microbial differences between marmosets of diverse origin.ImportanceCharacterizing gut microbial populations is expected to promote health and enhance research reproducibility in animal studies. As use of common marmosets as animal models of human diseases expands, evaluating the marmoset gut bacterial community will be critical for interpreting research findings, especially as marmosets are prone to gastrointestinal inflammation. In this study, using 16S rRNA sequencing of rectal swab samples, we compared bacterial community among three captive colonies of marmosets at baseline and following importation of cohorts from two of the colonies into the third colony. Diet history had sustained influence on bacterial community composition, while housing the animals within the same room over a period of eight months did not appear to be a major factor. These persistent differences in marmoset gut bacterial community highlight the need for careful consideration of animal origin as a variable in marmoset research studies.

scholarly journals Microbiome Changes of Endemic Lake Baikal Sponges during Bleaching Syndrome Development

Diversity ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 653
Author(s):  
Valeria Itskovich ◽  
Oxana Kaluzhnaya ◽  
Olga Glyzina ◽  
Ragothaman Prathiviraj ◽  
George Seghal Kiran ◽  
...  
Keyword(s):  
Lake Baikal ◽  
Bacterial Community Composition ◽  
General Tendency ◽  
Bacterial Symbionts ◽  
Microbial Composition ◽  
Freshwater Sponges ◽  
Bacterial Composition ◽  
Rrna Sequencing ◽  
Baikalospongia Intermedia ◽  
First Time

The sponge (Porifera) microbiome is an indicator of both natural and anthropogenic stressors. Studying Baikal sponge microbial communities could help reveal if there is a connection between bacterial symbionts and a mass sponge bleaching event that was recently detected; 16S rRNA sequencing was performed among healthy and diseased freshwater sponges of Lubomirskia baikalensis and Baikalospongia intermedia, which were collected from Lake Baikal, Russia. A phylum-based taxonomic classification showed that Chlorophyta, Acidobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria were most abundant across samples. When comparing healthy and diseased L. baikalensis samples, large variations in microbial composition were found at the phylum level. Comparative analyses, which were performed for the first time for B. intermedia, showed a decrease in Chlorophyta (unicellular green algae) and an increase in Bacteroidetes and Cyanobacteria in diseased specimens. At the genus level, the Opitutus (Verrucomicrobia), Planctomyces, and Nitrospira content increased in all diseased sponges, which reflected a general tendency toward an increase in Cyanobacteria in diseased sponges. Comparative analysis of the diseased and healthy sponge metagenomes showed that diseased sponges underwent various nonspecific changes in bacterial composition. The bacterial community composition is probably influenced by sponge type and degree of disease affection.

scholarly journals Lactic Acid Bacteria Influence Silage Fermentation Characteristics and Bacterial Community Composition of Oat in Cold Region

2021 ◽  
Author(s):  
Qiming Cheng ◽  
Liangyin Chen ◽  
Yulian Chen ◽  
Ping Li ◽  
Chao Chen
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Bacterial Community ◽  
Lactobacillus Plantarum ◽  
Community Composition ◽  
Acid Content ◽  
Bacterial Community Composition ◽  
Cold Region ◽  
Phenyllactic Acid ◽  
Silage Fermentation

Abstract Background: Lactic acid bacteria have been proposed for the control of undesirable fermentation and subsequently aerobic deterioration due to their ability to produce antimicrobial metabolites in silage mass. To investigate the effect of specific LAB on silage fermentation characteristics and bacterial community composition of oat in cold region, silages were treated without additives (CK) or with three LAB strains (LB, Lactobacillus buchneri; nLP, low temperature tolerant Lactobacillus planrtarum; pLP, phenyllactic acid-producing Lactobacillus plantarum), and then stored at ambient temperature (< 20 ℃) for 30, 60 and 90 days. Results: Compared with CK, inoculation of LAB decreased final pH value, butyric acid content, ammonia-N of total N and dry matter loss of silage. Treatments with nLP and pLP increased (P < 0.05) lactic acid content, whereas LB increased (P < 0.05) acetic acid content of silage. Lactobacillus and Leuconstoc dominated in the silages with relative abundance of 68.29~96.63%. A prolonged storage period enhanced growth of Leuconstoc in pLP treated silage. In addition, pLP increased (P < 0.05) aerobic stability of silage as compared with nLP. Conclusions: In conclusion, inoculation of LAB improved silage fermentation and/or delayed aerobic deterioration by shifting bacterial community composition during ensiling. Phenyllactic acid-producing Lactobacillus plantarum as an inoculant exhibited potential for high quality silage production.

Insight into the correlation between biochar amendment and shifts in bacterial community 4 years after a single incorporation in soybean- and maize-planted soils in northeastern China

2019 ◽  
Vol 65 (5) ◽  
pp. 353-364
Author(s):  
Huixue Liu ◽  
Yafang Wang ◽  
Haizhu Jiang ◽  
Dayu Sun ◽  
Fan Yang
Keyword(s):  
Bacterial Community ◽  
Bacterial Abundance ◽  
Bacterial Community Composition ◽  
Soil Microbiome ◽  
Crop Species ◽  
Composition And Structure ◽  
Soil Bacterial ◽  
And Shifts ◽  
Insight Into ◽  
Biochar Amendment

To date, there have been few reports examining the correlation between biochar treatments, crop species, and microbiome shifts. In this study, shifts in the soil bacterial community were investigated 4 years after a single incorporation of biochar in soils planted with soybeans and maize. Clear changes in the bacterial community composition and structure were detected in the soybean-planted soil amended with low-titer biochar (7.89 t/ha), whereas such changes in the maize-planted soil were not observed at the same biochar amendment rate, suggesting a more sensitive influence on the bacterial community in the soybean-planted soil than that in the maize-planted soil. Bacterial abundance in the maize-planted soil was reduced significantly with increasing biochar addition (15.78 and 47.34 t/ha), which was probably due to the inhibitory substances originating from biochar. Both the bacterial community and biomarkers in soil under biochar amendment varied with planted crops, bacterial communities responding differently to biochar amendment. All these results suggested that biochar might influence the bacterial community in maize- and soybean-growing soils under different mechanisms. Our findings should be valuable for an in-depth understanding of the potential mechanism of soil microbiome changes following biochar incorporation and for biochar application in agriculture.

scholarly journals Dynamics of the Fermentation Products, Residual Non-structural Carbohydrates, and Bacterial Communities of Wilted and Non-wilted Alfalfa Silage With and Without Lactobacillus plantarum Inoculation

2022 ◽  
Vol 12 ◽  
Author(s):  
Fengyuan Yang ◽  
Yanping Wang ◽  
Shanshan Zhao ◽  
Changsong Feng ◽  
Xiaomiao Fan
Keyword(s):  
Bacterial Community ◽  
Lactobacillus Plantarum ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
Water Soluble ◽  
Soluble Carbohydrates ◽  
Fermentation Products ◽  
Fermentation Quality ◽  
Alfalfa Silage

The aim of this study was to investigate effects of wilting and Lactobacillus plantarum inoculation on the dynamics of the fermentation products, residual non-structural carbohydrates, and bacterial communities in alfalfa silage. Fresh and wilted alfalfa were ensiled with and without L. plantarum for 10, 30, 60, and 90 days. A high-throughput sequencing method for absolute quantification of 16S rRNA was adopted to determine the bacterial community composition at different ensiling periods. For the wilted silage, the bacterial community, pH value, and ammonia nitrogen concentration remained stable in the silage at 30 days. L. plantarum inoculation accelerated lactic acid fermentation and altered the predominant genus in the wilted silage as compared with the non-inoculated group. For the non-wilted group, fast consumption of water-soluble carbohydrates (WSCs) was observed at 10 days in the non-inoculated silage along with rapid growth of undesirable Hafnia. L. plantarum inoculation inhibited growth of Hafnia at 10 days in the non-wilted silage. Clostridia fermentation occurred in the non-wilted silage at 90 days, as indicated by an increased pH, formation of butyric acid (BA), and apparent abundance of genera belonging to Clostridia. L. plantarum inoculation inhibited BA accumulation and growth of Garciella in the non-wilted silage at 90 days as compared with the non-wilted silage without inoculation, but had little effect on the growth of Clostridium sensu stricto. Overall, the high moisture content of the non-wilted alfalfa silage led to rapid consumption of WSCs and growth of harmful microorganisms at the early stage of ensiling, resulting in poor fermentation quality. Wilting and L. plantarum inoculation both improved fermentation quality and inhibited the growth of spoilage microorganisms in alfalfa silage, while L. plantarum inoculation alone failed to achieve optimum fermentation quality of non-wilted alfalfa silage.

scholarly journals Implications of Seed Vault Storage Strategies for Conservation of Seed Bacterial Microbiomes

2021 ◽  
Vol 12 ◽  
Author(s):  
Ankush Chandel ◽  
Ross Mann ◽  
Jatinder Kaur ◽  
Sally Norton ◽  
Jacqueline Edwards ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Storage Temperature ◽  
Plant Genetic Resources ◽  
Bacterial Community Composition ◽  
Seed Storage ◽  
Storage Condition ◽  
Storage Conditions ◽  
Bacterial Composition ◽  
Subsequent Storage ◽  
The Impact

Global seed vaults are important, as they conserve plant genetic resources for future breeding to improve crop yield and quality and to overcome biotic and abiotic stresses. However, little is known about the impact of standard storage procedures, such as seed drying and cold storage on the seed bacterial community, and the ability to recover seed-associated bacteria after storage. In this study, soybean [Glycine max (L.) Merr.] seeds were analyzed to characterize changes in the bacterial community composition and culturability under varying storage conditions. The G. max bacterial microbiome was analyzed from undried seed, dried seed, and seed stored for 0, 3, 6, and 14months. Storage temperatures consisted of −20°C, 4°C, and room temperature (RT), with −20°C being commonly used in seed storage vaults globally. The seed microbiome of G. max was dominated by Gammaproteobacteria under all conditions. Undried seed was dominated by Pantoea (33.9%) and Pseudomonas (51.1%); however, following drying, the abundance of Pseudomonas declined significantly (0.9%), Pantoea increased significantly (73.6%), and four genera previously identified including Pajaroellobacter, Nesterenkonia, env.OPS_17, and Acidibacter were undetectable. Subsequent storage at RT, 4, or −20°C maintained high-abundance Genera at the majority of time points, although RT caused greater fluctuations in abundances. For many of the low-abundance Genera, storage at −20°C resulted in their gradual disappearance, whereas storage at 4°C or RT resulted in their more rapid disappearance. The changes in seed bacterial composition were reflected by cultured bacterial taxa obtained from the stored G. max seed. The main taxa were largely culturable and had similar relative abundance, while many, but not all, of the low-abundance taxa were also culturable. Overall, these results indicate that the initial seed drying affects the seed bacterial composition, suggesting that microbial isolation prior to seed drying is recommended to conserve these microbes. The standard seed storage condition of −20°C is most suitable for conservation of the bacterial seed microbiome, as this storage temperature slows down the loss of seed bacterial diversity over longer time periods, particularly low-abundance taxa.

scholarly journals Effect of Lactobacillus plantarum Inoculation on Chemical Composition, Fermentation, and Bacterial Community Composition of Ensiled Sweet Corn Whole Plant or Stover

Fermentation ◽  
2022 ◽  
Vol 8 (1) ◽  
pp. 24
Author(s):  
Zhi-Yuan Ma ◽  
Emilio Ungerfeld ◽  
Zhu Ouyang ◽  
Xiao-Ling Zhou ◽  
Xue-Feng Han ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Lactobacillus Plantarum ◽  
Nutritive Value ◽  
Sweet Corn ◽  
Starch Content ◽  
Bacterial Community Composition ◽  
Water Soluble ◽  
Soluble Carbohydrates ◽  
Whole Plant ◽  
Genus Lactobacillus

Sweet corn is a feed resource with a high content of water-soluble carbohydrates (WSC) available for ruminant production. This study was conducted to investigate the effect of inoculation with Lactobacillus plantarum on fermentation and nutritional quality of sweet corn silage. Sweet corn whole plant (WP) and sweet corn stover (CS) were ensiled in mini silos with or without inoculation of L. plantarum. Proximate composition and fermentation variables, and composition of the bacterial community, were evaluated before ensiling and at the end of the first, second, and third month after ensiling. There was fiber degradation in CS silage after three months of ensilage, but not in WP silage. Inoculation of WP silage, but not of CS silage, with L. plantarum, increased starch content. The relative abundance of genus Lactobacillus was increased by inoculation with L. plantarum by 14.2% and 82.2% in WP and CS silage, respectively. Inoculation with L. plantarum was not necessary to achieve adequate fermentation of either WP or CS silage, as the abundance of native lactic acid bacteria in both materials seemed suitable for adequate fermentation. That said, increased starch content in WP resulting from inoculation with L. plantarum can increase the nutritive value of WP for ruminants.

scholarly journals Regional and oyster microenvironmental scale heterogeneity in the Pacific oyster bacterial community

2020 ◽  
Vol 96 (5) ◽  
Author(s):  
William L King ◽  
Nachshon Siboni ◽  
Tim Kahlke ◽  
Michael Dove ◽  
Wayne O'Connor ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Digestive Gland ◽  
Bacterial Communities ◽  
Bacterial Abundance ◽  
Pacific Oyster ◽  
Bacterial Community Composition ◽  
Geographical Location ◽  
Adductor Muscle ◽  
Tissue Type ◽  
The Pacific

ABSTRACT Different organs of a host represent distinct microenvironments resulting in the establishment of multiple discrete bacterial communities within a host. These discrete bacterial communities can also vary according to geographical location. For the Pacific oyster, Crassostrea gigas, the factors governing bacterial diversity and abundance of different oyster microenvironments are poorly understood. In this study, the factors shaping bacterial abundance, diversity and composition associated with the C. gigas mantle, gill, adductor muscle and digestive gland were characterised using 16S (V3-V4) rRNA amplicon sequencing across six discrete estuaries. Both location and tissue-type, with tissue-type being the stronger determinant, were factors driving bacterial community composition. Bacterial communities from wave-dominated estuaries had similar compositions and higher bacterial abundance despite being geographically distant from one another, possibly indicating that functional estuarine morphology characteristics are a factor shaping the oyster bacterial community. Despite the bacterial community heterogeneity, examinations of the core bacterial community identified Spirochaetaceae bacteria as conserved across all sites and samples. Whereas members of the Vulcaniibacterium, Spirochaetaceae and Margulisbacteria, and Polynucleobacter were regionally conserved members of the digestive gland, gill and mantle bacterial communities, respectively. This indicates that baseline bacterial community profiles for specific locations are necessary when investigating bacterial communities in oyster health.

scholarly journals Land use in urban areas impacts the composition of soil bacterial communities involved in nitrogen cycling. A case study from Lefkosia (Nicosia) Cyprus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Coralea Stephanou ◽  
Michalis Omirou ◽  
Laurent Philippot ◽  
Andreas M. Zissimos ◽  
Irene C. Christoforou ◽  
...  
Keyword(s):  
Land Use ◽  
Bacterial Community ◽  
Bacterial Diversity ◽  
Urban Areas ◽  
Chemical Elements ◽  
Bacterial Community Composition ◽  
Sampling Location ◽  
Land Use Management ◽  
Bacterial Composition ◽  
Bacterial Assemblages

AbstractThe different types of land-use and soil lithology in urban and peri-urban areas of modern cities compose a complex mosaic of soil ecosystems. It is largely unknown how these differences result in changes in bacterial community composition and structure as well as in functional guilds involved in N cycling. To investigate the bacterial composition and the proportion of denitrifiers in agricultural, forested, schoolyard and industrial areas, 24 samples were collected from urban and peri-urban sites of Lefkosia. Bacterial diversity and the proportion of denitrifiers were assessed by NGS and qPCR, respectively. Proteobacteria, Actinobacteria, Bacteriodetes, Chloroflexi, Acidobacteria and Planctomycetes were identified as the most dominant phyla across all sites, while agricultural sites exhibited the highest bacterial diversity. Heavy metals such as Co, Pb, V and Al were identified as key factors shaping bacterial composition in industrial and schoolyard sites, while the bacterial assemblages in agricultural and forested sites were associated with Ca. Variance partitioning analysis showed that 10.2% of the bacterial community variation was explained by land use management, 5.1% by chemical elements due to soil lithology, and 1.4% by sampling location. The proportion of denitrifiers varied with land use management. In industrial and schoolyard sites, the abundance of the nosZII bacterial community increased while nirK abundance declined. Our data showed that land use and lithology have a moderate impact on the bacterial assemblages in urban and peri-urban areas of Lefkosia. As the nosZII bacterial community is important to the N2O sink capacity of soils, it would be interesting to elucidate the factors contributing to the proliferation of the nosZII clade in these soils.

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