Several studies have demonstrated differences among strains of probiotic bacteria with regard to their survival in acid environment. Probiotics must survive in gastric acids to reach the small intestine and colonize the host for appropriate prevention and management of several gastrointestinal diseases. To improve the survival rates of probiotic microorganisms during gastric transit, microencapsulation is considered to be a promising process. A variety of polymers are commonly used for microencapsulation. Thus, there is a widespread interest in the improvement of the physical and mechanical stability of the polymers use in probiotics encapsulation. In addition, there is a developing trend toward the use of milk proteins as encapsulation device. To fulfill many demands of a successful probiotics encapsulation, different techniques have been applied to increase the resistance of these sensitive microorganisms against gastric conditions. Therefore, the objective of this study is to review the effect of microencapsulation on survival of probiotics in an in vitro model simulating gastric transit.

There is an ever-growing need to control antibiotic-resistance owing to alarming resistance to commonly available antimicrobial agents for which contemporary and alternative approaches are being explored. The present study assessed the antibacterial activity of bacteriocins from lactic acid bacteria (LAB) from lesser known traditionally fermented products of India for their synergistic potential with common antibiotics against clinical β-lactamases producing pathogens. A total of 84 isolates of LAB were screened for their antibacterial efficacy against Streptococcus pyogenes, Enterococcus faecalis, Escherichia coli, Klebsiella pneumoniae and Bacillus cereus as well as against clinical pathogens harbouring β-lactamase genes such as blaCTX-M,blaVIM,blaIMP, blaSHV and blaNDM. Synergistic activity of bacteriocins were determined in combination with antibiotics namely, cefotaxime, polymyxin B, imipenem and tigecycline. Purified bacteriocins from Lactobacillus, Pediococcus and Enterococcus inhibited the growth of β-lactamase harbouring clinical pathogens which significantly higher inhibitions when compared with antibiotics alone. Minimum inhibitory concentration of the extracts ranged from 6.66 to 26.66 mg/ml and 10 to 33.33 mg/ml for Pediococcus pentosaceus LU11 and Lactobacillus plantarum LS6. The bacteriocinogenic activity of LAB opens scope for bioprospection of antibacterial components in the current struggle against increasing pandrug resistance and slowing down the expansion of multi-drug resistance.

Tempeh is a type of traditional fermented food in Indonesia. The fermentation can be performed by Rhizopus microsporus as a main microorganism. However, Bacillus spp. is found in abundance in tempeh production. Nevertheless, information regarding the diversity of Bacillus spp. in tempeh production has not been reported yet. Therefore, the aim of this investigation was to study the genetic diversity of Bacillus spp. in tempeh production based on the 16S ribosomal RNA sequence. In this study, about 22 of 24 fresh tempeh from Jakarta, Bogor, and Tangerang were used. A total of 52 protease-producing Bacillus spp. isolates were obtained. Based on 16S ribosomal RNA results, all 52 isolates were identified to be similar to B. pumilus, B. subtilis, B. megaterium, B. licheniformis, B. cereus, B. thuringiensis, B. amyloliquefaciens, Brevibacillus brevis, and Bacillus sp. All the identified isolates were divided into two large clusters: 1) a cluster of B. cereus, B. thuringiensis, Bacillus sp., and B. brevis and 2) a cluster of B. pumilus, B. subtilis, B. megaterium, B. licheniformis, and B. amyloliquefaciens. Information about the Bacillus spp. role in determining the quality of tempeh has not been reported and this is a preliminary study of Bacillus spp. from tempeh.

Turmeric (Curcuma longa L.) is a medicinal plant that is commonly used as spice and preservative. Many types of endophytic fungi have been reported as being associated with medicinal plants and able to synthesize secondary metabolites. In this study, endophytic fungi were isolated from all plant parts of turmeric plants. Identification of the endophytic fungi was done using morphological characteristics and sequencing of the internal transcribed spacer (ITS) region of ribosomal DNA. The dual culture method was used for screening antibacterial activity of the endophytic fungi against Morganella morganii, a common histamine-producing bacteria. The disc diffusion method was used to test the ability of water fractions of selected endophytic fungi to inhibit M. morganii growth. Two-dimensional thin layer chromatography was used to determine the fungal extract inhibition activity on histamine formation. In total, 11 endophytic fungi were successfully isolated and identified as Arthrobotrys foliicola, Cochliobolus kusanoi, Daldinia eschscholzii, Fusarium oxysporum, Fusarium proliferatum, Fusarium solani, Fusarium verticillioides, Phanerochaete chrysosporium, and Phaeosphaeria ammophilae. Five isolates showed inhibition activity against M. morganii in the dual culture tests. Based on the disc diffusion assay, A. foliicola and F. verticillioides inhibited the growth of M. morganii as a histamine-producing bacteria, and inhibiting histamine formation in fish. The best effects in inhibiting growth of the histamine-producing bacteria and histamine formation inhibition in fish were produced with F. verticillioides water fraction at 0°C incubation.

Methylmercury has been generally known as a toxic heavy metal for both human and environment. Bacterial-based bioremediation of heavy metal is suggested as an ecofriendly and low-cost bioremediation process. There was limited information regarding the role of lactic acid bacteria (LAB) as detoxification agent for methylmercury addressed for human body. West Sekotong, West Lombok, Indonesia, is one of the newly developed artisanal and small-scale gold mining site with high mercury contamination level. This present study was aimed to isolate the human origin methylmercury-resistant LAB and further evaluate their ability to absorb methylmercury. Methylmercury absorption assay was conducted in broth media. The remaining and absorbed methylmercury was measured using the gas chromatography flame ionization detector. A total of 56 methylmercury-resistant LAB isolates were isolated from 37 feces and 19 breast milk samples from 19 volunteers in West Sekotong. Of them, 10 isolates were further selected based on several basic probiotic characteristics and subjected to methylmercury removal assay. The selected isolates showed different methylmercury absorption ability ranged between 17.375 and 51.597 μg/g of wet mass of cell after incubated for 24 hours. Two isolates from feces showing the best removal activity were identified as Enterococcus durans and one isolates from breast milk as Enterococcus faecium based on the sequences of 16s rDNA.

The role of ammonia-oxidizing bacteria and archaea was evaluated using amoA gene in a freshwater recirculating system. Broken earthen pot pieces (BEP) were used as filter bed material. Five archaeal and four bacterial operational taxonomic units were retrieved from amoA genes. Shannon-Weiner and Simpson indices were higher in archaeal amoA sequence compared with the bacteria. Subtype diversity ratio and subtype diversity variance were 0.522 and 0.008, respectively, for archaea and 0.403 and 0.015, respectively, for bacteria. In archaea, 50% amoA sequences showed 99%–100% similarity with the known sequences of ammonia monooxygenase subunit A of uncultured archaeon clones and thaumarchaeote. In bacteria, 84% sequences showed 99% similarity with amoA sequences of different uncultured bacterial clone and Nitrosomonadaceae. Absolute quantification showed that the abundance of archaea was 12-fold higher compared with bacteria. In this recirculating system, ammonia-oxidizing archaea and bacteria played a major role; BEP supported the growth of these ammonia-oxidizing microorganisms.

Different plantation forests possibly harbor different bird communities. This study was aimed to reveal responses of bird community to the different plantation (Schima wallichii, Agathis loranthifolia, Pinus merkusii, and mixed plantation), identify species shared in all plantation, and species confined to a particular plantation. The study site was plantation forests, using the point count method for 64 effective hours. There were 40 bird species (maximum prediction 52) in all forest plantations and each type had 26–31 species. Number of individuals, species density, and diversity index in Schima plantation were higher, followed by Agathis, Pinus, and mixed plantations. Mixed plantation could have harbored more species based on the prediction by Chao. Although there were some differences in tree species, tree sizes, and tree heights, the response of bird composition in all plantations was not differed (93–81% similarity) probably because of the short distances among the forests, the abundance of food insects, and the same late-successional stages. There were 15 (37.5%) widely distributed species in all forest types. Eight species were confined only to a specific forest type. Four species were considered true confined species, namely Javan sunbird (Schima forest), Grey-cheeked bulbul (in Pinus), Crescent-chested babbler (Agathis), and Mountain white-eye (Agathis).

Many health related problems such as cardiovascular diseases are associated with the formation of excessive clot in the blood (thrombus). Approaches in cardiovascular disease treatment are preventing the formation or removing the thrombus. The present thrombolytic agents can be classified as plasminogen activators, fibrinolytic enzyme which directly degrades fibrinogen or fibrin and heparin type which act as thrombin inhibitor. Recently, microbial fibrinolytic enzymes of food origin receive more attention that leads to escalating efforts to explore traditional fermented foods as the natural sources. We have successfully isolated microorganism from Indonesian fermented soybean tofu dregs “Oncom” that secretes fibrinolytic enzyme. The microorganism identified as Stenotrophomonas sp. is unique because most of the reported fibrinolytic microorganism belongs to Bacillus sp. This isolate was found to produce extracellular fibrinolytic enzyme which could degrade fibrinogen and fibrin directly as determined by fibrinogen zymography and fibrin plate methods. More importantly, the 30-kD purified enzymes was found to demonstrate not only fibrin and fibrinogen degradation capabilities, but also acted as thrombin inhibitor as determined using specific substrates for thrombin. This is the first report of a fibrinolytic enzyme that demonstrates additional synergistic activities. This finding accentuates the importance of further development of the enzyme into a powerful agent to treat the thrombus-related disease effectively.

Molt is one of the biological processes in the life of birds that requires high energy. Therefore, it usually occurs when food is abundant. However, molt and breeding overlap have been recorded in the tropics. There are very few studies on bird molting patterns in Indonesia. This study aimed at describing molt in birds that inhabit a human-dominated habitat in Bogor Agricultural University Campus in Bogor, West Java. Molt of primary feathers of adult birds were checked during bird monitoring using mist nets from August 2010 to December 2013. Occurrence of brood patch as indicator of breeding stage was also recorded. Molt data were obtained from 230 adult birds from 29 species. Molts occurred from February to December, with most birds having active molts in July and October. Breeding occurred in March, April, July, and October, with the peak of breeding occurring in March. Molt and breeding overlap were identified only in three species, i.e. Eurasian Tree Sparrow (Passer montanus), Horsfield's Babbler (Malacocincla sepiarium), and Scarlet-headed Flowerpecker (Dicaeum trochileum). This study suggests that resources in the study site are available for conservation of bird community in human-dominated habitat. However, further research is needed to assess food availability and bird breeding success.

Mangrove forests an intertidal mudflat in the eastern coastal region of Deli Serdang are important habitats for migratory shorebirds. Land-use change and forest conversion threaten this important stopover point for migrating species. The lack of data and information of shorebirds habitats in this area limits conservation efforts and further threatens the survival of these species. The objective of this study is to investigate trends in habitat use by migratory shorebirds. Field work was conducted during migration season starting from October 2014 until April 2015. The presence of migratory shorebirds was assessed using binoculars and a monocular. Scan sampling was used to describe habitat use by shorebirds. The difference in behaviour among habitat was analyzed using analysis of variance. There were 30 species of shorebirds distributed across seven different habitat types in our study area. The most widely used habitat by shorebirds was mudflats, followed by marshes and plantations. This study revealed that mudflat habitat has high potential in supporting the existence of migratory shorebirds in this area.