A polyphasic study was designed to determine the taxonomic provenance of a strain, isolate PRKS01-29T, recovered from an Indonesian sand dune and provisionally assigned to the Streptomyces violaceusniger clade. Genomic, genotypic and phenotypic data confirmed this classification. The isolate formed an extensively branched substrate mycelium which carried aerial hyphae that differentiated into spiral chains of rugose ornamented spores, contained LL-as the wall diaminopimelic acid, MK-9 (H6, H8) as predominant isoprenologues, phosphatidylethanolamine as the diagnostic phospholipid and major proportions of saturated, iso- and anteiso- fatty acids. Whole-genome sequences generated for the isolate and Streptomyces albiflaviniger DSM 41598T and Streptomyces javensis DSM 41764T were compared with phylogenetically closely related strains, the isolate formed a branch within the S. violaceusniger clade in the resultant phylogenomic tree. Whole-genome sequences data showed that isolate PRKS01-29T was most closely related to the S. albiflaviniger strain but was distinguished from the latter and from other members of the clade using combinations of phenotypic properties and average nucleotide identity and digital DNA:DNA hybridization scores. Consequently, it is proposed that isolate PRKS01-29T (= CCMM B1303T = ICEBB-02T = NCIMB 15210T) should be classified in the genus Streptomyces as Streptomyces sabulosicollis sp. nov. It is also clear that streptomycetes which produce spiral chains of rugose ornamented spores form a well-defined monophyletic clade in the Streptomyces phylogenomic tree., the taxonomic status of which requires further study. The genome of the type strain of S. sabulosicollis contains biosynthetic gene clusters predicted to produce new natural products.

A polyphasic study was undertaken to establish the position of a Streptomyces strain, isolate PRKS01-65T, recovered from sand dune soil collected at Parangkusumo, Yogyakarta Province, Java, Indonesia. A combination of chemotaxonomic, cultural and morphological properties confirmed its position in the genus of Streptomyces . Comparative 16S rRNA gene sequence analyses showed that the isolate was most closely related to Streptomyces leeuwenhoekii C34T (99.9 % similarity) and loosely associated with the type strains of Streptomyces chiangmaiensis (98.7 % similarity) and Streptomyces glomeratus (98.9 % similarity). Multilocus sequence analyses based on five conserved housekeeping gene alleles confirmed the close relationship between the isolate and S. leeuwenhoekii C34T, although both strains belonged to a well-supported clade that encompassed the type strains of S. glomeratus , Streptomyces griseomycini , Streptomyces griseostramineus , Streptomyces labedae , Streptomyces lomondensis and Streptomyces spinoverrucosus . A comparison of the draft genome sequence generated for the isolate with corresponding whole genome sequences of its closest phylogenomic neighbours showed that it formed a well-separated lineage with S. leeuwenhoekii C34T. These strains can also be distinguished using a combination of phenotypic properties and by average nucleotide identity and digital DNA–DNA hybridization similarities of 94.3 and 56 %, values consistent with their classification in different species. Based on this wealth of data it is proposed that isolate PRKS01-65T (=NCIMB 15211T=CCMM B1302T=ICEBB-03T) be classified as Streptomyces harenosi sp. nov. The genome of the isolate contains several biosynthetic gene clusters with the potential to produce new natural products.

Coffee is an important commodity and one of the most popular beverages in the world. Over 2.25 billion cups of coffee are consumed in the world every day (Ponte 2002). In 2012, Indonesia ranked third after Brazil and Vietnam in the global production of green coffee beans (USDA 2012). Five species of coffee that are commonly cultivated in the world include Coffea arabica, C. canephora, C. robusta, C. liberica, and C. excelsa (Doyle et al., 2001). In Indonesia C. robusta and C. arabica are the species mostly planted (Neilson, 2008). Due to its high market demand, coffee processing has developed to produce various flavors to satisfy the consumers. One type of coffee that is increasingly popular is luwak coffee (Kopi Luwak) which is produced exclusively by the Indonesian palm civet or luwak (Paradoxurus hermaphrodites ssp.). Luwak is a small mammal (Carnivora, Viverridae) living in the rain forests of Java and Sumatera, although its various subspecies are intensely distributed in South East Asia (Patou 2010). The distinctive taste of this coffee has been recognized since coffee plantation started in Indonesia during the Dutch colonial era. The luwak eats fruits, including coffee fruits or coffee cherries. Only the best and mature coffee cherries would be eaten by the luwak. This process will produce coffee with distinctive flavor. The price of luwak coffee is relatively high because only a small quantity of this coffee is produced (Marcone 2004). Once ingested by luwak, coffee cherries will pass through its entire digestive system. This process removes the outer layers of the fruit. After digestion, the remaining coffee beans were collected from the forest floor, cleaned, roasted, and ground; with the same process as the harvested coffee beans. Thus the unique flavor of Kopi Luwak comes from the digestion process in luwak, which includes mechanical, biochemical, and fermentation processes (Marcone 2004). Microorganisms, especially bacteria, are closely associated with the digestive process in monogastric animals (Kraatz 2010). Several studies have been conducted to determine the types of bacteria involved in the fermentation process, for example by trying to isolate the bacteria from faeces of civet and the luwak's coffee beans (Fauzi 2014). Currently, there is no information about the bacterial diversity in parts of Luwak coffee is a highly-priced coffee produced exclusively by the palm civet or luwak (Paradoxurus hermaphrodites ssp.). The purpose of this study was to determine the diversity of culturable bacteria in the gastro intestinal tract of luwak. The bacterial isolates were phenotypically characterized by their morphology and molecularly by analysis of their 1 500 bp 16s rDNA sequence. The results showed that Enterobacter cloacae and Lactobacillus brevis were found all over luwak's digestive tract. E. cloacae was the most common species. The most diverse bacterial population was found in small intestine. Seven bacterial genera were successfully identified from the small intestine and colon, compared to only ...

A Micromonospora strain, isolate MT25T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including 1H-15N HSQC and 1H-15N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25T (NCIMB 15245T, TISTR 2834T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.