Cutaneous Communities Research Articles

Comparison of high‐throughput sequencing methods for bacterial microbiota profiling in catfish aquaculture

AbstractObjectiveBacterial community profiling in aquaculture can be useful for monitoring environmental conditions that may lead to disease outbreaks, understanding the impact of dietary treatments on fish health, and identifying microbes that have potential as probiotics. Microbiota characterization is commonly performed with high‐throughput sequencing using short‐read platforms (i.e., Illumina) targeting variable regions of the bacterial 16S ribosomal RNA (rRNA) gene. Long‐read platforms (i.e., Oxford Nanopore Technologies [ONT]) enable sequencing of full‐length 16S rRNA genes. While short‐read platforms are highly accurate, long‐read platforms sacrifice sequence quality in exchange for longer read lengths.MethodsHerein, a typical short‐read approach (Illumina MiSeq; V4 region of 16S rRNA gene) was compared with two near‐full‐length 16S rRNA gene ONT protocols (ONT Custom and ONT 16S). Sequencing was performed on a mock community composed of fish‐relevant bacteria, in addition to samples (digesta, gill, skin) obtained from 10 hybrid catfish (female Channel Catfish Ictalurus punctatus × male Blue Catfish I. furcatus) and their environment (pond and holding tank). Fish were euthanized with either an overdose of MS‐222 or cranial concussion and subsequent pithing to enable comparisons of these sequencing protocols in the context of a realistic experimental design.ResultThe ONT Custom protocol best recapitulated the theoretical composition of the mock community, followed by the ONT 16S and Illumina MiSeq protocols. Phylum‐level composition was consistent within sample type across sequencing methods. However, at lower levels there were biases for several taxa, particularly in pond samples. Euthanasia method also appeared to introduce differences, primarily on the cutaneous communities. The three sequencing methods consistently identified significant differences between euthanasia methods, with Illumina MiSeq revealing the greatest differences. While all strategies performed comparably for digesta, skin, and water samples, the ONT strategies underperformed for gill samples.ConclusionDepending on application, results indicate that near‐full‐length 16S rRNA gene nanopore sequencing is a viable option for aquaculture microbiota studies.

The Role of Yeasts in Human Health: A Review.

The microbiome consists mostly of bacteria, but new evidence and developments in sequencing methods have shown that fungi play an important role in human health and in the stability of the microbiota. Scientific knowledge about the role of commensal fungi in intestinal, oral, vaginal and cutaneous communities has been increasing; however, more studies are still needed to better understand their action in these niches. To date, fungal research focuses primarily on opportunistic diseases caused by fungal species, leaving unclear the possible role of fungi as an integral part of the microbiota. Although they are much less abundant than bacteria, fungi such as species belonging to the genus Candida, Malassezia, Rhodotorula and Cryptococcus are some of the yeasts that have been in the focus of the scientific community because they inhabit various niches. In this review, we have summarized the current information about the yeasts that inhabit the human body, including some of the diseases that they can cause when the microbiota becomes unstable.

Human skin microbiota in health and disease: The cutaneous communities' interplay in equilibrium and dysbiosis: The cutaneous communities' interplay in equilibrium and dysbiosis.

Cutaneous microbial composition is driven by the microenvironment of the skin, as well as by internal and external factors. Local changes in the microenvironment can affect the configuration of the community, which may lead toward an imbalance of microbiota. Alterations in the microbial profile are common in both inflammatory skin diseases and chronic infections. A shift in balance within the microbiota, toward limited variation and a greater abundance of specific pathogens, may further worsen the pathogenicity of the diseases. These alterations may be prevented by topical treatment of probiotic solutions stimulating a balanced multispecies community. Compositional variations may further constitute potential biomarkers to predict flares or monitor efficacy during therapy. New approaches such as machine learning may contribute to this prediction of microbial alterations prior to the development of chronic infections and flares. This review provides insight into the composition and distribution of a healthy community of microorganisms in the skin and draws parallels with the community in chronic infections and chronic inflammatory skin diseases such acne vulgaris and Hidradenitis Suppurativa. We discuss the potential role of specific species in the pathogenesis and the possible prevention of disease exacerbation.

The normal flora of the skin in different age groups.

SUMMARY. An investigation of the incidence and distribution of aerobic organisms included in the cutaneous community in 410 persons is described. These subjects were divided by age into 4 groups: infants, children, adults and geriatrics. The age of the individual was found to influence the bacterial flora found on the skin. Coagulase negative staphylococci and micrococci occurred frequently in virtually all sites in each person sampled. Other major Inhabitants of the skin were, in the infants, streptococci, in the adults, diphtheroids and in the old people, diphtheroids and streptococci. The flora was very varied in the children with Sarcina, diphtheroids, spore forming bacilli and Gram-negative bacilli frequently found in large numbers.