scholarly journals The gut bacterial diversity of sheep associated with different breeds in Qinghai province

2020 ◽  
Author(s):  
Jianjun Chang ◽  
Xiaoting Yao ◽  
Chenxiang Zuo ◽  
Yuxu Qi ◽  
Dekun Chen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
The Other ◽  
Principal Coordinates Analysis ◽  
Qinghai Province ◽  
Microbiome Composition ◽  
Sheep Breeds ◽  
Principal Coordinates ◽  
Tibetan Sheep ◽  
Nmds Analysis

Abstract Background: Gut microbiota play important roles in their co-evolution with mammals. However, little is understood about gut bacterial community of Tibetan sheep compared with other sheep breeds. In this study, we investigated the gut bacterial community in 4 different sheep breeds living in the Qinghai-Tibetan Plateau (QTP) of China using high-throughput sequencing (HTS) technique. Results: The results suggested that bacterial community abundance and breeds diversity of Tibetan sheep (TS) were significantly lower than that of the other three breeds of sheep [Dorset sheep (DrS), Dorper sheep (DrS) and Small Tail Han sheep (STHS)] (p < 0.05). Principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) analysis indicated that microbiome composition of TS was significantly different from that of other three sheep breeds (p < 0.01). Firmicutes was the most predominant microbial phylum in the gut, followed by Bacteroidetes. The gut bacterial community of TS showed higher proportions of phylum Spirochaetes, Proteobacteria and Verrucomicrobia, compared to the other three sheep breeds, but the Deferribacteres was absent in TS. At the genus level, Treponema, Succinivibrio, 5-7N15 and Prevotella showed significantly higher abundance in TS than in the other three sheep breeds (p < 0.05). Conclusions: In this study, we first employed HTS to understand the gut microbiomes among different sheep breeds in QTP of China.

scholarly journals The gut bacterial diversity of sheep associated with different breeds in Qinghai province

2020 ◽  
Author(s):  
Jianjun Chang ◽  
Xiaoting Yao ◽  
Chenxiang Zuo ◽  
Yuxu Qi ◽  
Dekun Chen ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
The Other ◽  
Principal Coordinates Analysis ◽  
Qinghai Province ◽  
Microbiome Composition ◽  
Sheep Breeds ◽  
Principal Coordinates ◽  
Tibetan Sheep ◽  
Nmds Analysis

Abstract Background: Gut microbiota play important roles in their co-evolution with mammals. However, little is understood about gut bacterial community of Tibetan sheep compared with other sheep breeds. In this study, we investigated the gut bacterial community in 4 different sheep breeds living in the Qinghai-Tibetan Plateau (QTP) of China using high-throughput sequencing (HTS) technique. Results: The results suggested that bacterial community abundance and breeds diversity of Tibetan sheep (TS) were significantly lower than that of the other three breeds of sheep [Dorset sheep (DrS), Dorper sheep (DrS) and Small Tail Han sheep (STHS)] (p < 0.05). Principal coordinates analysis (PCoA) and nonmetric multidimensional scaling (NMDS) analysis indicated that microbiome composition of TS was significantly different from that of other three sheep breeds (p < 0.01). Firmicutes was the most predominant microbial phylum in the gut, followed by Bacteroidetes. The gut bacterial community of TS showed higher proportions of phylum Spirochaetes, Proteobacteria and Verrucomicrobia, compared to the other three sheep breeds, but the Deferribacteres was lacked in TS. At the genus level, Treponema, Succinivibrio, 5-7N15 and Prevotella showed significantly higher abundance in TS than in the other three sheep breeds (p < 0.05). Conclusions: In this study, we first employed HTS to fully understand the gut microbiomes among different sheep breeds in QTP of China.

Calcified macroalgae and their bacterial community in relation to larval settlement and metamorphosis of reef-building coral Pocillopora damicornis

2020 ◽  
Vol 97 (1) ◽  
Author(s):  
Fangfang Yang ◽  
Jiahao Mo ◽  
Zhangliang Wei ◽  
Lijuan Long
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Larval Settlement ◽  
Pocillopora Damicornis ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Coral Reef Ecosystems ◽  
Settlement And Metamorphosis ◽  
Invertebrate Larvae

ABSTRACT Calcified macroalgae play an important role in the settlement and metamorphosis of invertebrate larvae in coral reef ecosystems. However, little is known about the algal-associated bacterial communities and their effects on larval settlement. In this study, the responses of larvae of the coral Pocillopora damicornis to calcified algae (Porolithon onkodes, Halimeda cylindracea, Halimeda opuntia and Amphiroa fragilissima) were evaluated. The results revealed that Por. onkodes and H. cylindracea significantly enhanced the rates of settlement and metamorphosis, whereas fewer larvae settled on Am. fragilissima and H. opuntia. Amplicon pyrosequencing of the V3–V4 region of 16S rDNA was applied to investigate the relationship between algal bacterial community and larval settlement. Principal coordinates analysis demonstrated that the bacterial community composition of H. opuntia was more similar to that of Am. fragilissima, but clearly distinct from those of H. cylindracea and Por. onkodes. Furthermore, the relative abundances of bacteria were highly diverse among different algae. H. opuntia had higher percentages of Thalassobius, Pelagibius and SM1A02, whereas the abundances of Mycoplasma and Suttonella were significantly higher in H. cylindracea than other algae. Our results showed that larval settlement/metamorphosis was strongly correlated with the bacterial community composition and with the relative abundance of a few operational taxonomic units.

scholarly journals Altitude influences microbial diversity and herbage fermentation in the rumen of yaks

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Qingshan Fan ◽  
Metha Wanapat ◽  
Tianhai Yan ◽  
Fujiang Hou
Keyword(s):  
Bacterial Community ◽  
Microbial Diversity ◽  
Volatile Fatty Acids ◽  
Rumen Fluid ◽  
Energy Requirement ◽  
Tibet Plateau ◽  
Limited Information ◽  
Principal Coordinates Analysis ◽  
Rumen Microbiota ◽  
Principal Coordinates

Abstract Background Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level. Results The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks. Conclusions Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.

scholarly journals Metagenomic Characterization Reveals Pronounced Seasonality in the Diversity and Structure of the Phyllosphere Bacterial Community in a Mediterranean Ecosystem

2019 ◽  
Vol 7 (11) ◽  
pp. 518 ◽  
Author(s):  
Despoina Vokou ◽  
Savvas Genitsaris ◽  
Katerina Karamanoli ◽  
Katerina Vareli ◽  
Marina Zachari ◽  
...  
Keyword(s):  
Bacterial Community ◽  
High Throughput Sequencing ◽  
Bacterial Colonization ◽  
The Other ◽  
Mediterranean Ecosystem ◽  
Seasonal Differences ◽  
Operational Taxonomic Units ◽  
Seasonal Environment ◽  
Habitat Specialists ◽  
Taxonomic Groups

We explore how the phyllosphere microbial community responds to a very seasonal environment such as the Mediterranean. For this, we studied the epiphytic bacterial community of a Mediterranean ecosystem in summer and winter, expecting to detect seasonal differences at their maximum. With high-throughput sequencing (HTS), we detected the operational taxonomic units (OTUs) present in the phyllosphere and also in the surrounding air. The epiphytic community is approximately five orders of magnitude denser than the airborne one and is made almost exclusively by habitat specialists. The two communities differ considerably but Proteobacteria and Actinobacteria are dominant in both. Of the five most abundant phyllosphere OTUs, two were closely related to Sphingomonas strains, one to Methylobacterium and the other two to Rhizobiales and Burkholderiales. We found the epiphytic community to become much richer, more distinct, even and diverse, denser and more connected in summer. In contrast, there was no difference in the level of bacterial colonization of the phyllosphere between the two seasons, although there were seasonal differences for individual taxonomic groups: Firmicutes, Gemmatimonadetes and Chlroroflexi had a higher participation in summer, whereas the major Proteobacteria classes presented reverse patterns, with Betaproteobacteria increasing in summer at the expense of the prominent Alphaproteobacteria.

scholarly journals Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host

2020 ◽  
Author(s):  
Laura C. Rosenwald ◽  
Michael I. Sitvarin ◽  
Jennifer A. White
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Strain ◽  
High Throughput Sequencing ◽  
Cytoplasmic Incompatibility ◽  
The Other ◽  
Bacterial Endosymbionts ◽  
Different Strains

AbstractMany arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally-inherited symbiont from the genera Wolbachia, Rickettsia, and Rickettsiella. The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella. We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella-infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella, or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally-inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia.

Rumen bacterial diversity of Tibetan sheep (Ovis aries) associated with different forage types on the Qinghai-Tibetan Plateau

2019 ◽  
Vol 65 (12) ◽  
pp. 859-869 ◽  
Author(s):  
Xiongxiong Cui ◽  
Zhaofeng Wang ◽  
Tianhai Yan ◽  
Shenghua Chang ◽  
Hong Wang ◽  
...  
Keyword(s):  
Tibetan Plateau ◽  
Bacterial Community ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Diet Group ◽  
Ovis Aries ◽  
Bacterial Composition ◽  
Rumen Microbiome ◽  
Tibetan Sheep ◽  
Native Pasture

Diet is the great determinant of bacterial composition in the rumen. However, little is known about the rumen bacterial community of Tibetan sheep living in the special ecological environment of the Qinghai-Tibetan Plateau (QTP) of China. In the present study, we used high-throughput sequencing to investigate the rumen bacterial community of Tibetan sheep associated with two primary diets: alpine pasture diet (a continuation of the sheep’s natural grazing diet) and oat (Avena sativa) hay diet on the QTP. The results showed that bacterial community richness and species diversity of the oat hay diet group were significantly greater than that of the native pasture diet group (p < 0.05). Principal co-ordinate analysis and analysis of similarities revealed that the bacterial community of the oat hay diet group was distinctly different from that of the native pasture diet group (p < 0.05). Bacteroidetes and Firmicutes were the predominant microbial phyla in the rumen. The rumen of oat-hay-fed sheep had higher proportions of Proteobacteria and novel bacteria species than the rumen of native-pasture-fed sheep. Actinobacteria, an uncommon bacterial phylum, occurred only in the oat-hay-fed group. At the genus level, Komagataeibacter, Ruminococcaceae_UCG-014, and Ruminococcaceae_NK4A214 showed significantly higher relative abundance in the oat-hay-fed sheep than in the native-pasture-fed sheep (p < 0.05). This study is the first of the QTP to employ high-throughput sequencing to examine the influence of diet on the rumen microbiome of Tibetan sheep.

scholarly journals Endosymbiotic Rickettsiella causes cytoplasmic incompatibility in a spider host

2020 ◽  
Vol 287 (1930) ◽  
pp. 20201107 ◽  
Author(s):  
Laura C. Rosenwald ◽  
Michael I. Sitvarin ◽  
Jennifer A. White
Keyword(s):  
Bacterial Community ◽  
High Throughput ◽  
Bacterial Strain ◽  
High Throughput Sequencing ◽  
Cytoplasmic Incompatibility ◽  
The Other ◽  
Bacterial Endosymbionts ◽  
Different Strains

Many arthropod hosts are infected with bacterial endosymbionts that manipulate host reproduction, but few bacterial taxa have been shown to cause such manipulations. Here, we show that a bacterial strain in the genus Rickettsiella causes cytoplasmic incompatibility (CI) between infected and uninfected hosts. We first surveyed the bacterial community of the agricultural spider Mermessus fradeorum (Linyphiidae) using high throughput sequencing and found that individual spiders can be infected with up to five different strains of maternally inherited symbiont from the genera Wolbachia , Rickettsia , and Rickettsiella . The Rickettsiella strain was pervasive, found in all 23 tested spider matrilines. We used antibiotic curing to generate uninfected matrilines that we reciprocally crossed with individuals infected only with Rickettsiella . We found that only 13% of eggs hatched when uninfected females were mated with Rickettsiella -infected males; in contrast, at least 83% of eggs hatched in the other cross types. This is the first documentation of Rickettsiella , or any Gammaproteobacteria, causing CI. We speculate that induction of CI may be much more widespread among maternally inherited bacteria than previously appreciated. Further, our results reinforce the importance of thoroughly characterizing and assessing the inherited microbiome before attributing observed host phenotypes to well-characterized symbionts such as Wolbachia .

Impact of mode of delivery on the milk microbiota composition of healthy women

2015 ◽  
Vol 7 (1) ◽  
pp. 54-60 ◽  
Author(s):  
R. Cabrera-Rubio ◽  
L. Mira-Pascual ◽  
A. Mira ◽  
M. C. Collado
Keyword(s):  
Breast Milk ◽  
Biological Effects ◽  
Quantitative Polymerase Chain Reaction ◽  
Mode Of Delivery ◽  
Principal Coordinates Analysis ◽  
Microbiome Composition ◽  
Milk Samples ◽  
Principal Coordinates ◽  
Vaginal Deliveries ◽  
The Impact

Breast milk constitutes one of the most important sources of postnatal microbes. However, the influence of perinatal factors on the milk microbiome is still poorly understood. The aim of our study was to assess the impact of mode of delivery on the microbiome composition and diversity present in breast milk of healthy mothers. Mature milk samples (n=10) were taken from mothers after 1 month of exclusively breastfeeding. Microbiomes from milk samples were analyzed with 16S ribosomal RNA gene pyrosequencing and targeted quantitative polymerase chain reaction (PCR). Despite inter-individual variability in bacterial composition, The Principal Coordinates Analysis clearly separated milk microbiome from mothers with vaginal delivery (n=6) from those who undergo C-section (n=4). In addition, higher bacterial diversity and richness was found in milk samples from vaginal deliveries. Quantitative PCR data showed that higher levels of Bifidobacterium spp. were related significantly to lower levels of Staphylococcus spp. Despite the low sample size, our data suggest that mode of delivery has an important impact on milk microbiome composition. Further studies with larger sample sizes are needed to confirm these results and to understand the biological effects of C-section associated microbes on infant’s health.

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 &lt; 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 &lt; 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 &lt; 0.05) in the GRY group. However, the unclassified Peptostreptococcaceae, Christensenellaceae R-7 group, and Lachnospiraceae NK3A20 group were enriched (P &lt; 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 &lt; 0.05) in the GNY group than those in the GRY group. In the cecum, the GNY group showed a higher (P &lt; 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 &lt; P &lt; 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 Composition and Functional Characteristics and Influencing Factors of Bacterioplankton Community in the Huangshui River, China

2021 ◽  
Vol 9 (11) ◽  
pp. 2260
Author(s):  
Qianqian Zhang ◽  
Zhenbing Wu ◽  
Juan Zhao ◽  
Guojie Wang ◽  
Jingwen Hao ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Loess Plateau ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Bacterial Community Composition ◽  
The Arctic ◽  
Valuable Insight ◽  
Potential Health ◽  
Bacterioplankton Community ◽  
Principal Coordinates

Bacterial community plays a key role in environmental and ecological processes of river ecosystems. Given the special climatic and geographical conditions, studying the compositional characteristics of microorganisms in highland rivers and the relationship between such microorganisms and water physicochemical factors is important for an in-depth understanding of microbial ecological mechanisms. In the present study, high-throughput sequencing was used to investigate and study the bacterioplankton community of the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau. The results showed that the Huangshui River had significantly lower alpha diversity than the plain rivers. Despite the similarity in their environmental conditions, the main taxonomic compositions of the bacterial communities were distinct between the Huangshui River and polar regions (the Arctic and Antarctica). Proteobacteria accounted for the largest proportion (30.79–99.98%) of all the sequences, followed by Firmicutes (0–49.38%). Acidiphilium was the most numerous genera, which accounted for 0.03–86.16% of the assigned 16S reads, followed by Acidocella (0–95.9%), both belonging to Alphaproteobacteria. The diverse taxa of potential pathogens, such as Acinetobacter, Pseudomonas, and Aeromonas, were also identified. A principal coordinates analysis, coupled with a canonical correspondence analysis, showed spatial variations in the bacterial community composition. The water physical properties (e.g., Cr6+, total phosphorus, and CODMn); altitude; and land use (e.g., urban land cover and aquaculture) determined the distribution of the bacterioplankton composition. PICRUSt2 revealed that the overall functional profiles of the bacterial communities in different samples were similar, and our results suggested the potential health risks of water sources in this area. This work provided valuable insight into the composition of the plankton bacterial community and its relationship with the environmental factors in the Huangshui River in the ecotone zone of the Qinghai Plateau and Loess Plateau and a theoretical foundation for ecological health management.

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