Hill number as a bacterial diversity measure framework with high-throughput sequence data

Abstract

Bacterial diversity is an important parameter for measuring bacterial contributions to the global ecosystem. However, even the task of describing bacterial diversity is challenging due to biological and technological difficulties. One of the challenges in bacterial diversity estimation is the appropriate measure of rare taxa, but the uncertainty of the size of rare biosphere is yet to be experimentally determined. One approach is using the generalized diversity, Hill number (Na), to control the variability associated with rare taxa by differentially weighing them. Here, we investigated Hill number as a framework for microbial diversity measure using a taxa-accmulation curve (TAC) with soil bacterial community data from two distinct studies by 454 pyrosequencing. The reliable biodiversity estimation was obtained when an increase in Hill number arose as the coverage became stable in TACs for a ≥ 1. In silico analysis also indicated that a certain level of sampling depth was desirable for reliable biodiversity estimation. Thus, in order to attain bacterial diversity from second generation sequencing, Hill number can be a good diversity framework with given sequencing depth, that is, until technology is further advanced and able to overcome the under- and random-sampling issues of the current sequencing approaches.

Ecological Diversity: Measuring the Unmeasurable

“…Thus any diversity index can easily be converted into an effective number index. The use of effective number indices to assess changes in community diversity has become more established in ecological literature in recent years [61][62][63][64][65], as researchers recognize the advantages they bring compared to classical indices, most particularly the well-founded comparisons that they permit between different studies and even different indices.…”

Simulation-based approaches to characterize metagenome coverage as a function of sequencing effort and microbial community structure

“…The last community had 10 equally-sized groups. The abundance of the physically-distinct DNA 399 fragments in each group was based on the function form of a lognormal community [35] which has been 400 observed in microbial populations (e.g., [17,36]), such that: 401…”

“…Rather, our pipeline was configured to minimize As sequencing effort increased, there was an initial lag in complete-MAG equivalents followed 177 by a rapid increase in complete-MAG equivalents, and then diminishing returns at higher sequencing 178 efforts. Previous investigators modeled the response of 16S RNA gene [14][15][16], Hill's number diversity 179 [17], taxon-resolved abundance [18], and gene abundance [18] as a function of sequencing effort with 180 rarefaction curves, or collector's curves. The complete-MAG equivalents as a function of sequencing 181 effort did not match a traditional collector's curve, which lacks an initial lag.…”

Diversity patterns of benthic bacterial communities along the salinity continuum of the Humber estuary (UK)

“…These techniques offer an opportunity to investigate microbial communities in more depth. However, challenges remain as the very large datasets produced reveal the extremely diverse nature of microbiota, which is difficult to evaluate rigorously with the traditional mathematical and statistical approaches to biodiversity estimation (Buttigieg & Ramette 2014, Oulas et al 2015, Kang et al 2016). Hill numbers (D q ) are a unified and index-independent diversity concept; they were developed by Hill (1973) and were reintroduced to ecologists by Jost (2006Jost ( , 2007.…”

“…Hill numbers (D q ) are a unified and index-independent diversity concept; they were developed by Hill (1973) and were reintroduced to ecologists by Jost (2006Jost ( , 2007. They have been proposed as a unified framework for measuring bacterial diversity in order to control the variability associated with rare taxa, sampling issues and other biases associated with experimental procedures (Chao et al 2014, Kang et al 2016.…”