In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.

Worlds within worlds: evolution of the vertebrate gut microbiota

Microbial keratinases have become biotechnologically important since they target the hydrolysis of highly rigid, strongly cross-linked structural polypeptide “keratin” recalcitrant to the commonly known proteolytic enzymes trypsin, pepsin and papain. These enzymes are largely produced in the presence of keratinous substrates in the form of hair, feather, wool, nail, horn etc. during their degradation. The complex mechanism of keratinolysis involves cooperative action of sulfitolytic and proteolytic systems. Keratinases are robust enzymes with a wide temperature and pH activity range and are largely serine or metallo proteases. Sequence homologies of keratinases indicate their relatedness to subtilisin family of serine proteases. They stand out among proteases since they attack the keratin residues and hence find application in developing cost-effective feather by-products for feed and fertilizers. Their application can also be extended to detergent and leather industries where they serve as specialty enzymes. Besides, they also find application in wool and silk cleaning; in the leather industry, better dehairing potential of these enzymes has led to the development of greener hair-saving dehairing technology and personal care products. Further, their prospective application in the challenging field of prion degradation would revolutionize the protease world in the near future.

Microbial keratinases and their prospective applications: an overview.

Keratinases are exciting proteolytic enzymes that display the capability to degrade the insoluble protein keratin. These enzymes are produced by diverse microorganisms belonging to the Eucarya, Bacteria, and Archea domains. Keratinases display a great diversity in their biochemical and biophysical properties. Most keratinases are optimally active at neutral to alkaline pH and 40–60°C, but examples of microbial keratinolysis at alkalophilic and thermophilic conditions have been well documented. Several keratinases have been associated to the subtilisin family of serine-type proteases by analysis of their protein sequences. Studies with specific substrates and inhibitors indicated that keratinases are often serine or metalloproteases with preference for hydrophobic and aromatic residues at the P1 position. Keratinolytic enzymes have several current and potential applications in agroindustrial, pharmaceutical, and biomedical fields. Their use in biomass conversion into biofuels may address the increasing concern on energy conservation and recycling.

Biochemical features of microbial keratinases and their production and applications.

Noninvasive genetic approaches continue to improve studies in molecular ecology, conservation genetics and related disciplines such as forensics and epidemiology. Noninvasive sampling allows genetic studies without disturbing or even seeing the target individuals. Although noninvasive genetic sampling has been used for wildlife studies since the 1990s, technological advances continue to make noninvasive approaches among the most used and rapidly advancing areas in genetics. Here, we review recent advances in noninvasive genetics and how they allow us to address important research and management questions thanks to improved techniques for DNA extraction, preservation, amplification and data analysis. We show that many advances come from the fields of forensics, human health and domestic animal health science, and suggest that molecular ecologists explore literature from these fields. Finally, we discuss how the combination of advances in each step of a noninvasive genetics study, along with fruitful areas for future research, will continually increase the power and role of noninvasive genetics in molecular ecology and conservation genetics.

https://www.fs.fed.us/rm/pubs_other/rmrs_2009_beja_pereira_a001.pdf

Advancing ecological understandings through technological transformations in noninvasive genetics.

Reproductive Success, T.H. Clutton-Brock (Ed.). The University of Chicago Press, Chicago (1988), ix

A novel feather-degrading microorganism was isolated from poultry waste, producing a high keratinolytic activity when cultured on broth containing native feather. Complete feather degradation was achieved during cultivation. The bacterium presents potential use for biotechnological processes involving keratin hydrolysis. Chryseobacterium sp. strain kr6 was identified based on morphological and biochemical tests and 16S rRNA sequencing. The bacterium presented optimum growth at pH 8.0 and 30 degrees C; under these conditions, maximum feather-degrading activity was also achieved. Maximum keratinase production was reached at 25 degrees C, while concentration of soluble protein was similar at both 25 and 30 degrees C. Reduction of disulfide bridges was also observed, increasing with cultivation time. The keratinase of strain kr6 was active on azokeratin and azocasein as substrates, and presented optimum pH and temperature of 7.5 and 55 degrees C, respectively. The keratinase activity was inhibited by 1,10-phenanthroline, EDTA, Hg(2+), and Cu(2+) and stimulated by Ca(2+).

Characterization of a new keratinolytic bacterium that completely degrades native feather keratin.

AIMS: To characterize a new feather-degrading bacterium. METHODS AND RESULTS: The strain kr10 producing a high keratinolytic activity when cultured on native feather broth was identified as Microbacterium sp., based on phenotypical characteristics and 16S rDNA sequence. The bacterium presented optimum growth and feather-degrading activity at pH 7.0 and 30 degrees C. Complete feather degradation was achieved during cultivation. The keratinase was partially purified by gel filtration chromatography. It was optimally active at pH 7.0 and 55 degrees C. The enzyme was inhibited by 1,10-phenanthroline, EDTA, p-chloromercuribenzoic acid, 2-mercaptoethanol and metal ions like Hg(2+), Cu(2+) and Zn(2+). SIGNIFICANCE AND IMPACT OF THE STUDY: A new Microbacterium sp. strain was characterized presenting high feather-degrading activity, which appears to be associated to a metalloprotease-type keratinase. This micro-organism has enormous potential for use in biotechnological processes involving keratin hydrolysis.

https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1472-765X.2004.01558.x

Characterization of a protease of a feather‐degrading Microbacterium species

The aim of this study was to determine the diversity of cultivable bacteria able to degrade feathers and present in soil under temperate climate. We obtained 33 isolates from soil samples, which clustered in 13 ARDRA groups. These isolates were able to grow on solid medium with pigeon feathers as sole carbon and nitrogen source. One representative isolate of each ARDRA group was selected for identification and feather degradation tests. The phylogenetic analysis of 16S rDNA gene fragments revealed that only 4 isolates were gram positives. Two other isolates belonged to the Cytophaga–Flavobacterium group, and the remaining to Proteobacteria. High keratinolysis activity was found for strains related to Bacillus, Cytophagales, Actinomycetales, and Proteobacteria. The 13 selected strains showed variable efficiency in degrading whole feathers and 5 strains were able to degrade maximum 40% to 98% of the whole feathers. After 4 weeks incubation, five strains grown on milled feathers produced more than 0.5 U keratinase per mL. Keratinase activities across the 13 strains were positively correlated with the percentage of feather fragmentation and protein concentration.

High Diversity among Feather-Degrading Bacteria from a Dry

The aim of this study was to determine the diversity of cultivable bacteria able to degrade feathers and present in soil under temperate climate. We obtained 33 isolates from soil samples, which clustered in 13 ARDRA groups. These isolates were able to grow on solid medium with pigeon feathers as sole carbon and nitrogen source. One representative isolate of each ARDRA group was selected for identification and feather degradation tests. The phylogenetic analysis of 16S rDNA gene fragments revealed that only 4 isolates were gram positives. Two other isolates belonged to the Cytophaga-Flavobacterium group, and the remaining to Proteobacteria. High keratinolysis activity was found for strains related to Bacillus, Cytophagales, Actinomycetales, and Proteobacteria. The 13 selected strains showed variable efficiency in degrading whole feathers and 5 strains were able to degrade maximum 40% to 98% of the whole feathers. After 4 weeks incubation, five strains grown on milled feathers produced more than 0.5 U keratinase per mL. Keratinase activities across the 13 strains were positively correlated with the percentage of feather fragmentation and protein concentration.

High diversity among feather-degrading bacteria from a dry meadow soil.

Despite their potential ecological and evolutionary importance, factors shaping the composition of bacterial communities in wild vertebrate populations remain poorly understood. The goal of this study was to examine the relative contributions of environmental factors and genetic factors (e.g. species and common origin) to the variation of cloacal bacterial assemblages in wild bird nestlings. We conducted a partial cross-fostering experiment with two passerine species, the great tit Parus major and the blue tit P caeruleus, sharing similar habitats and breeding biology. Nestlings of the two species were exchanged four days after hatching and cloacal bacteria were sampled nine days later. The structure of cloacal bacterial communities was determined by Ribosomal Intergenic Spacer Analysis. Our results showed that each nestling displayed a unique bacterial community. Furthermore, nestlings raised in the same nest shared significantly similar bacterial communities. The similarity of bacterial community was higher among heterospecific siblings raised within the same nest than between biological siblings raised in separate nests. Effects of common origin between species could not be detected and, if present, were dominated by nest-based short-term environmental effects. Our results show that growth conditions within nests and individually based endogenous factors have significant effects on cloacal bacteria assemblages and could affect post-fledging condition.

Françoise S. Lucas

Papers

Characterization of a new keratinolytic bacterium that completely degrades native feather keratin.

Characterization of a protease of a feather‐degrading Microbacterium species

High Diversity among Feather-Degrading Bacteria from a Dry

High diversity among feather-degrading bacteria from a dry meadow soil.

Environmental factors shape cloacal bacterial assemblages in great tit Parus major and blue tit P. caeruleus nestlings