Rumen Fermentation—Microbiota—Host Gene Expression Interactions to Reveal the Adaptability of Tibetan Sheep in Different Periods

As an important ruminant on the Qinghai-Tibet Plateau, Tibetan sheep can maintain their population reproduction rate in the harsh high-altitude environment of low temperature and low oxygen, which relies on their special plateau adaptations mechanism that they have formed for a long time. Microbiomes (known as “second genomes”) are closely related to the nutrient absorption, adaptability, and health of the host. In this study, rumen fermentation characteristics, the microbiota, and rumen epithelial gene expression of Tibetan sheep in various months were analyzed. The results show that the rumen fermentation characteristics of Tibetan sheep differed in different months. The total SCFAs (short-chain fatty acids), acetate, propionate, and butyrate concentrations were highest in October and lowest in June. The CL (cellulase) activity was highest in February, while the ACX (acid xylanase) activity was highest in April. In addition, the diversity and abundance of rumen microbes differed in different months. Bacteroidetes (53.4%) and Firmicutes (27.4%) were the dominant phyla. Prevotella_1 and Rikenellaceae_RC9_gut_group were the dominant genera. The abundance of Prevotella_1 was highest in June (27.8%) and lowest in December (17.8%). In addition, the expression of CLAUDIN4 (Claudin-4) and ZO1 (Zonula occludens 1) was significantly higher in April than in August and December, while the expression of SGLT1 (Sodium glucose linked transporter 1) was highest in August. Correlation analysis showed that there were interactions among rumen fermentation characteristics, the microbiota, and host gene expression, mainly by adjusting the amino acid metabolism pathway and energy metabolism pathway to improve energy utilization. At the same time, we adjusted the balance of the rumen “core microbiota” to promote the development of rumen and maintain the homeostasis of rumen environment, which makes Tibetan sheep better able to adapt to the harsh environment in different periods of the Qinghai-Tibet Plateau.

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Interactions Among Rumen Fermentation Characteristics, the Microbiota, and Host Gene Expression in Response to Ambient Temperature Fluctuations in Tibetan Sheep

10.21203/rs.3.rs-572098/v1 ◽

2021 ◽

Author(s):

Weibing Lv ◽

Xiu Liu ◽

Yuzhu Sha ◽

Hao Shi ◽

Hong Wei ◽

...

Keyword(s):

Gene Expression ◽

Ambient Temperature ◽

High Altitude ◽

Rumen Fermentation ◽

Host Gene ◽

Tibet Plateau ◽

Host Gene Expression ◽

Microbial Composition ◽

Fermentation Products ◽

Tibetan Sheep

Abstract Background: As an important ruminant on the Qinghai-Tibet Plateau, Tibetan sheep can maintain their population reproduction rate in the harsh high-altitude environment of low temperature and low oxygen, which is related to their special adaptations to the plateau. Microbes (known as “second genomes”) play an important role in the host adaptations. However, there have been no reports on the effects of the interactions among rumen fermentation, the microbiota, and host gene expression on the adaptation of Tibetan sheep to high altitude.Results: Rumen fermentation characteristics, the microbiota, and rumen epithelial gene expression of Tibetan sheep in various months (February, April, June, August, October, and December) were analyzed. The results show that the rumen fermentation characteristics of Tibetan sheep differed in different months. The total SCFA, acetate, propionate, and butyrate concentrations were highest in Oct and lowest in Jun. The Cellulase (CL) activity was highest in Feb (when it was significantly higher than in Aug and Oct), while the acidic xylanase (ACX) activity was highest in Apr, followed by Jun (and it was significantly higher in both Apr and Jun than in Feb, Aug, and Oct). In addition, the diversity and abundance of rumen microbes differed in different months. Bacteroidetes (53.4%) and Firmicutes (27.4%) were the dominant phyla. Prevotella_1 and Rikenellaceae_RC9_gut_group were the dominant genera. The abundance of Prevotella_1 was highest in Jun (27.8%) and lowest in Dec (17.8%). Random forest analysis showed that Lachnospiraceae_NK3A20_group and Rikenellaceae_RC9_gut_group played important roles in rumen microbial composition in different months. In addition, the expression of CLAUDIN4 and ZO1 (ruminal epithelial barrier-related genes) was significantly higher in Apr than in Aug and Dec, while the expression of SGLT1 (nutrient absorption-related gene) was highest in Aug, but were significantly lower than CLAUDIN4 and ZO1 expression in the corresponding month. Correlation analysis showed that there were interactions among rumen fermentation characteristics.Conclusions: There was a certain correlation between rumen fermentation products, the microbiota, and host gene expression. The microbiota, and host gene expression, and the host adjusted the rumen fermentation and microbiota structure according to changes in ambient temperature, to adapt to the plateau environment.

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Faculty Opinions recommendation of Transcriptome analysis of a cnidarian-dinoflagellate mutualism reveals complex modulation of host gene expression.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1014151.370912 ◽

2006 ◽

Author(s):

Nico M van Straalen

Keyword(s):

Gene Expression ◽

Transcriptome Analysis ◽

Host Gene ◽

Host Gene Expression ◽

Complex Modulation

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Publisher Correction: Exogenously overexpressed intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis

Scientific Reports ◽

10.1038/s41598-020-79079-3 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Zhang-Wei Liu ◽

Nan Zhao ◽

Yin-Na Su ◽

Shan-Shan Chen ◽

Xin-Jian He

Keyword(s):

Gene Expression ◽

Histone Modification ◽

Noncoding Rnas ◽

Long Noncoding Rnas ◽

Host Gene ◽

Host Gene Expression

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Research on the Influence of Energy Utilization and Economic Development on Human Well-Being in Qinghai-Tibet Plateau

Sustainability ◽

10.3390/su13010196 ◽

2020 ◽

Vol 13 (1) ◽

pp. 196

Author(s):

Mengmeng Meng ◽

Weiguo Fan ◽

Jianchang Lu ◽

Xiaobin Dong ◽

Hejie Wei

Keyword(s):

Economic Development ◽

Well Being ◽

Resource Acquisition ◽

Energy Utilization ◽

Western China ◽

Tibet Plateau ◽

Four Dimensions ◽

Generalized Matrix ◽

Qinghai Tibet Plateau ◽

Means Of Production

Qinghai-Tibet Plateau is a typical resource-rich but economically backward region in western China, and it is of great urgency to improve human well-being. Combined with previous scholars’ research and the characteristics of Qinghai-Tibet Plateau, this paper constructs an index system of human well-being including four dimensions: income and consumption, means of production, means of subsistence, and resource acquisition ability. Then, it uses generalized matrix method estimations to measure the influence of energy utilization and economic development on human well-being and makes a regression analysis on the influence of energy utilization and economic development on human well-being in various provinces in this region. It is found that per capita GDP and coke utilization promote the well-being of all dimensions, while the urban registered unemployment rate only promotes the well-being of means of subsistence. The utilization of gasoline and natural gas promotes income and consumption and inhibits the means of subsistence and resource acquisition ability, but they have opposite effects on means of production. The impacts of energy utilization and economic development in different provinces on human well-being are different. This study is of great significance to the related research aiming at improving people’s livelihood and promoting regional development.

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Regulation of host gene expression during nodule development in soybeans

Nitrogen Fixation ◽

10.1007/978-1-4684-6432-0_60 ◽

1990 ◽

pp. 701-708 ◽

Cited By ~ 2

Author(s):

C. Sengupta-Gopalan ◽

E. Estabrook ◽

H. Gambliel ◽

W. Nirunsuksiri ◽

H. Richter

Keyword(s):

Gene Expression ◽

Host Gene ◽

Nodule Development ◽

Host Gene Expression

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Wolbachia infection may improve learning and memory capacity of Drosophila by altering host gene expression through microRNA

Insect Biochemistry and Molecular Biology ◽

10.1016/j.ibmb.2018.11.007 ◽

2019 ◽

Vol 106 ◽

pp. 47-54 ◽

Cited By ~ 3

Author(s):

Jie Bi ◽

Ya Zheng ◽

Rui-Fang Wang ◽

Hui Ai ◽

Paula R. Haynes ◽

...

Keyword(s):

Gene Expression ◽

Learning And Memory ◽

Wolbachia Infection ◽

Memory Capacity ◽

Host Gene ◽

Host Gene Expression

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Immune Gene Expression Covaries with Gut Microbiome Composition in Stickleback

mBio ◽

10.1128/mbio.00145-21 ◽

2021 ◽

Vol 12 (3) ◽

Author(s):

Lauren E. Fuess ◽

Stijn den Haan ◽

Fei Ling ◽

Jesse N. Weber ◽

Natalie C. Steinel ◽

...

Keyword(s):

Gene Expression ◽

Microbial Communities ◽

Gut Microbiome ◽

Alpha Diversity ◽

Host Immunity ◽

Host Gene ◽

Microbiota Composition ◽

Host Gene Expression ◽

Microbiome Composition ◽

Immune Genes

ABSTRACT Commensal microbial communities have immense effects on their vertebrate hosts, contributing to a number of physiological functions, as well as host fitness. In particular, host immunity is strongly linked to microbiota composition through poorly understood bi-directional links. Gene expression may be a potential mediator of these links between microbial communities and host function. However, few studies have investigated connections between microbiota composition and expression of host immune genes in complex systems. Here, we leverage a large study of laboratory-raised fish from the species Gasterosteus aculeatus (three-spined stickleback) to document correlations between gene expression and microbiome composition. First, we examined correlations between microbiome alpha diversity and gene expression. Our results demonstrate robust positive associations between microbial alpha diversity and expression of host immune genes. Next, we examined correlations between host gene expression and abundance of microbial taxa. We identified 15 microbial families that were highly correlated with host gene expression. These families were all tightly correlated with host expression of immune genes and processes, falling into one of three categories—those positively correlated, negatively correlated, and neutrally related to immune processes. Furthermore, we highlight several important immune processes that are commonly associated with the abundance of these taxa, including both macrophage and B cell functions. Further functional characterization of microbial taxa will help disentangle the mechanisms of the correlations described here. In sum, our study supports prevailing hypotheses of intimate links between host immunity and gut microbiome composition. IMPORTANCE Here, we document associations between host gene expression and gut microbiome composition in a nonmammalian vertebrate species. We highlight associations between expression of immune genes and both microbiome diversity and abundance of specific microbial taxa. These findings support other findings from model systems which have suggested that gut microbiome composition and host immunity are intimately linked. Furthermore, we demonstrate that these correlations are truly systemic; the gene expression detailed here was collected from an important fish immune organ (the head kidney) that is anatomically distant from the gut. This emphasizes the systemic impact of connections between gut microbiota and host immune function. Our work is a significant advancement in the understanding of immune-microbiome links in nonmodel, natural systems.

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Microbiota Modulates Host Gene Expression via MicroRNAs

Gastroenterology ◽

10.1016/s0016-5085(11)62754-6 ◽

2011 ◽

Vol 140 (5) ◽

pp. S-663 ◽

Cited By ~ 2

Author(s):

Guillaume Dalmasso ◽

Hang Thi Thu Nguyen ◽

Yutao Yan ◽

Hamed Laroui ◽

Moiz A. Charania ◽

...

Keyword(s):

Gene Expression ◽

Host Gene ◽

Host Gene Expression

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Abstract 19222: Hypoxia Regulated Circular RNAs Control Endothelial Cell Functions (Best of Basic Science Abstract)

Circulation ◽

10.1161/circ.132.suppl_3.19222 ◽

2015 ◽

Vol 132 (suppl_3) ◽

Author(s):

Andreas W Heumüller ◽

Jes-Niels Boeckel ◽

Nicolas Jaé ◽

Yuliya Ponomareva ◽

Wei Chen ◽

...

Keyword(s):

Gene Expression ◽

Endothelial Cells ◽

Network Formation ◽

Rare Event ◽

Expression Regulation ◽

Host Gene ◽

Circular Rnas ◽

Host Gene Expression ◽

Go Annotation ◽

Cell Functions

Circular RNAs (circRNAs) are non-coding RNAs generated by back-splicing. Back-splicing has been considered as a rare event, but circRNAs were recently found to be abundantly expressed among a variety of human cells and tissues. Nevertheless, the expressional regulation, processing and biological functions of circRNAs are largely unknown. Cytoplasmic circRNAs can bind and trap microRNAs, whereas nuclear circRNAs may affect host gene expression. However, the expression, regulation and functions of circRNAs in endothelial cells have not been determined so far. In this study, basal expression and regulation of circRNAs by hypoxia in human umbilical endothelial cells (HUVEC) were analyzed using deep sequencing. Among the identified 7,388 circRNAs, 2,875 had not been annotated before. We further validated the expression of 40 selected circRNAs by RT-PCR and found that the majority is resistant to RNase R digestion, lacks polyadenylation and is localized to the cytoplasm. Cloning and subsequent sequencing validated the newly generated back splice sites for selected circRNAs. Furthermore, analysis of RNA-seq data revealed that circRNAs, particularly the cytoplasmatic circular RNA cZNF292, are significantly regulated by hypoxia in HUVECs. The siRNA-mediated knockdown of HIF-1α had no effect on cZNF292 induction under hypoxia, suggesting a HIF-1α independent regulation. Most importantly, siRNA-mediated knockdown of cZNF292 significantly reduced spheroid sprouting and network formation of endothelial cells. Furthermore, knockdown of cZNF292 had no effect on its host gene expression. Exon array analysis after cZNF292 knockdown revealed a significant expressional upregulation of 167 as well as a significant expressional downregulation of 123 genes of which most were associated with metabolic processes according to GO annotation. Analysis of Ago-HITS-CLIP data revealed no putative miR-binding sites, suggesting that cZNF292 does not act as a miR-sponge. Taken together, we show for the first time the expression, regulation and function of circRNAs in endothelial cells. The circRNA cZNF292 is regulated by hypoxia and has an important angiogenic function in endothelial cells.

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