<commit_before>---
title: Introduction
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The background to the work.

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<div>\[ \sum_{i=0}^{\infty}\pi_i=\sum_{i=0}^{\infty}\rho^i\pi_0=\frac{\pi_0}{1-\rho}=1 \]</div><commit_msg>Update 02-introduction.md<commit_after>---
title: Introduction
---
The background to the work.

The giant panda (Ailuropoda melanoleura), one of the most endangered mammals with only ~2000 adult survived and less 10 new-born captive children each year in the southwestern China, is widely interested by its carnivore-like gastrointestine but herbivore-like diet that gives them a high risk of extinction (Zhan et al. 2006; Wei et al. 2015). For this mammal, a short and relatively simple digestive tract of as typical carnivore without a rumen for fermentation makes this mammal processing bamboo with a low digestibility (only ~17%), and thus they have to consuming a lot of bamboo (~12.5 kg) and time (up to 14 h) to ensure the least nutrition each day (Jin et al. 2007; Jin et al. 2011; Wei et al. 2015). Recently, the advent of high-throughput sequencing technologies has led to a turning point in our understanding of this animal intestinal microbial colonization. Several researches revealed the constructions and part potential functions of gut flora for this mammal by metagenomics procedure (Zhu et al. 2011; Tun et al. 2014; Li et al. 2015; Xue et al. 2015), which were more comprehensive and accurate than early culture-dependent studies (Hirayama et al. 1989; Williams et al. 2013) or traditional molecular approaches (Wei et al. 2007; Fang et al. 2012). However, with increasing projects we found there are large community variations between the different researches below, for example, <NAME>, et al. (Li et al. 2015) identified gut microbiota were contrary to Tun HM, et al. (Tun et al. 2014) with much lower diversity and dominated mainly by class Streptococcus but not Gammaproteobacteria.
As we know, there is a close symbiotic relationship between host diet and intestinal microbiome (Ley et al. 2008a; Ley et al. 2008b). Age and season are both widely considered as mainly factors affecting animal diet components that could lead to a significantly structural transformation in the intestinal flora, and thus affecting the microbiota functions (Lozupone et al. 2012). For the age element, a significant diet transition generally happens in different growth stages of animal. For example, infant mammals are commonly fed by milk, but with the growing of age and weight the diet changes to their adult specific food (Zivkovic et al. 2011). Similarly, seasonal shift will also result animals changing their primary diet sources or prefer different species of local food (Morehouse and Boyce 2011; Blumenthal et al. 2012). We can easily foresee that these two important variations of diet could significantly affect intestinal flora of pandas both in structure and function, and result the community gaps between different studies below. Like other mammals, the giant panda is not born to bamboo but has diet transition period, generally 0.5-2 years old, of which main diet changes from milk to their adult specific food bamboo and thus is the key period for the high-fiber diet adaptation, in the meantime this period lasts 1.5 years that covered different seasons. Therefore, the diet transition period of the giant panda could be an excellent opportunity to study the specific variety relation of gut microbiota to find out which element has more weight to shape the community and to play functions for the adaptation of the bamboo diet.
Metagenomics based approaches (including 16S rRNA gene amplicon sequencing and whole-metagenome shotgun) are usually desired to demonstrate the microbiota community and their potential functions currently (Franzosa et al. 2015; Yoon et al. 2015). However, given such a long range of microbial gut community issues that remain to be addressed by metagenomic methods, e.g. the proportion of microbiota is not as same as their activities, and the potentially functional genes in their genomes may not totally present the pronounced ability. Ribosomal RNA (rRNA) is a key factor regulating ribosome synthesis, which plays central roles in controlling and coordinating cell growth, division and differentiation, and generally is on behalf of the cell activity (Yu and Zhang 2012; Franzosa et al. 2014). Therefore, we believe that metatranscriptomics is a better way to future investigate the activities of gut microbiota and explore the cellulose adaptation of this mammal as a complementary method. In this work, we use both of metagenomic and metatranscriptomic approaches analyzed the characterizations of community structures and functions of the giant panda intestinal microbiome during the diet transition period in the meantime covered the seasons of summer and winter. Characterization of gut microbiota in the special moment of the giant panda as well as detection of their cellulose digesting activities in our work will provide a series of mechanistic insights into the digestion and utilization in different diet transformation on bamboo food both in genetic and in transcriptional levels, and thus contribute to the reproduction, protection and reintroduction projects of the giant panda.
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