Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia.

Human body microbes interact with the host, forming microbial communities that are in continual flux during the aging process. Previous studies have mostly focused on surveying a single body habitat to determine the age-related variation in the bacterial and fungal communities. A more comprehensive understanding of the variation in the human microbiota and mycobiota across multiple body habitats related to aging is still unclear. To obtain an integrated view of the spatial distribution of microbes in a specific Mediterranean population across a wide age range, we surveyed the bacterial and fungal communities in the skin, oral cavity, and gut in the young, elderly, and centenarians in Sardinia using 16S rRNA gene and internal transcribed spacer 1 (ITS1) sequencing. We found that the distribution and correlation of bacterial and fungal communities in Sardinians were largely determined by body site. In each age group, the bacterial and fungal communities found in the skin were significantly different in structure. In the oral cavity, age had a marginal impact on the structures of the bacterial and fungal communities. Furthermore, the gut bacterial communities in centenarians clustered separately from those of the young and elderly, while the fungal communities in the gut habitat could not be separated by host age.IMPORTANCE Site-specific microbial communities are recognized as important factors in host health and disease. To better understand how the human microbiota potentially affects and is affected by its host during the aging process, the fundamental issue to address is the distribution of microbiota related to age. Here, we show an integrated view of the spatial distribution of microbes in a specific Mediterranean population (Sardinians) across a wide age range. Our study indicates that age plays a critical role in shaping the human microbiota in a habitat-dependent manner. The dynamic age-related microbiota changes we observed across multiple body sites may provide possibilities for modulating microbe communities to maintain or improve health during aging.

Wu L ，Zeng T ，Deligios M ，Milanesi L ，Langille MGI ，Zinellu A ，Rubino S ，Carru C ，Kelvin DJ ... -  《mSphere》

The gut mycobiome of the Human Microbiome Project healthy cohort.

Nash AK ，Auchtung TA ，Wong MC ，Smith DP ，Gesell JR ，Ross MC ，Stewart CJ ，Metcalf GA ，Muzny DM ，Gibbs RA ，Ajami NJ ，Petrosino JF ... -  《Microbiome》

Determinants and Interactions of Oral Bacterial and Fungal Microbiota in Healthy Chinese Adults.

Cheung MK ，Chan JYK ，Wong MCS ，Wong PY ，Lei P ，Cai L ，Lan L ，Ho WCS ，Yeung ACM ，Chan PKS ，Chen Z ... -  《Microbiology Spectrum》

Early gut mycobiota and mother-offspring transfer.

Schei K ，Avershina E ，Øien T ，Rudi K ，Follestad T ，Salamati S ，Ødegård RA ... -  《Microbiome》

Mycobiome: Approaches to analysis of intestinal fungi.

Massively parallel sequencing (MPSS) of bacterial 16S rDNA has been widely used to characterize the microbial makeup of the human and mouse gastrointestinal tract. However, techniques for fungal microbiota (mycobiota) profiling remain relatively under-developed. Compared to 16S profiling, the size and sequence context of the fungal Internal Transcribed Spacer 1 (ITS1), the most common target for mycobiota profiling, are highly variable. Using representative gastrointestinal tract fungi to build a known "mock" library, we examine how this sequence variability affects data quality derived from Illumina Miseq and Ion Torrent PGM sequencing pipelines. Also, while analysis of bacterial 16S profiles is facilitated by the presence of high-quality well-accepted databases of bacterial 16S sequences, such an accepted database has not yet emerged to facilitate fungal ITS sequence characterization, and we observe that redundant and inconsistent ITS1 sequence representation in publically available fungal reference databases affect quantitation and annotation of species in the gut. To address this problem, we have constructed a manually curated reference database optimized for annotation of gastrointestinal fungi. This targeted host-associated fungi (THF) database contains 1817 ITS1 sequences representing sequence diversity in genera previously identified in human and mouse gut. We observe that this database consistently outperforms three common ITS database alternatives on comprehensiveness, taxonomy assignment accuracy and computational efficiency in analyzing sequencing data from the mouse gastrointestinal tract.

Tang J ，Iliev ID ，Brown J ，Underhill DM ，Funari VA ... -  《-》