Airborne Mycobacterium avium infection in a group of red‐shanked douc langurs (Pygathrix nemaeus nemaeus)

Background This report describes an airborne Mycobacterium avium (MA)‐infection in two red‐shanked douc langurs (Pygathrix nemaeus nemaeus) from Cologne zoo. Methods The two individuals and their tissues were investigated clinically (including x‐rays), in pathology, in pathohistology, in classical bacteriology and by polymerase chain reaction (PCR). Results Clinically, one individual displayed emaciation and a positive reaction in an intrapalpebral testing for M. bovis/MA. The other individual was without any symptoms and did not show any reaction in the intrapalpebral test. In x‐ray photos of the lungs, calcified nodules were detected. In pathology, calcified and necrotic nodules were observed within the lungs and the bronchial lymph nodes. In pathohistology, both classical tuberculous granulomas, and few acid fast rods were seen in Ziehl‐Neelsen‐stain. However, classical bacteriology could not demonstrate mycobacteria. In PCR, MA‐infection could be confirmed in one individual using the bronchial lymph nodes. Conclusions It was an airborne infection; however, the definite source of infection in these cases remained unclear. Animals in contact to the langurs (house sparrows and mice) as well as water used in the building are the most promising candidates. The risk for a zoonotic transmission in these cases has been calculated to be low.     

Status and Conservation of Douc Langurs (Pygathrix nemaeus) in Laos

A recent systematic survey program of protected areas in Laos documented douc langurs (Pygathrix nemaeus) widely between 14°25N and 18°38N. Their precise northern limit is unclear as security constraints prevented survey there, but the species is unlikely to occur in Laos north of 20°. All our records are of the nominate, red-shanked form, P. n. nemaeus, though in the far south, greatly reduced red on the legs suggests intergradation with another form. Our records are overwhelmingly from evergreen or semievergreen forest and from a wide altitudinal range (200–1600 m). In most sites habitat was little degraded, but whether this reflects choice for such habitats, or the generally lower hunting pressure within them, is unclear. The largest population occurs over 3000 km ² of the Nam Theun basin and surroundings, encompassing the protected areas of Nakai-Nam Theun, Hin Namno and the proposed Nam Theun Extension. This is the most important population of red-shanked langurs in the world. Laos supports globally the vast majority of their conservable population. Douc langurs are threatened in Laos by habitat fragmentation increasing their vulnerability to the existing high hunting levels. They are a favored target for local consumption and for local and Vietnamese hunters and traders. Protective measures should center around implementing habitat conservation and antihunting measures in the recently-declared National Biodiversity Conservation Areas. A recent government initiative to reduce gun use in rural areas is likely to have a strong positive effect on the population. The best protection for some time will remain the inaccessibility of their habitat. Accordingly, road-building into remote forest and piecemeal clearance at its edges should thus be minimized. Cross-border attention should be given to wildlife trading, including measures to reduce market demand.     

Distribution and Conservation Status of the Red-Shanked Douc (Pygathrix nemaeus) in Lao PDR: An Update

The endangered red‐shanked douc (Pygathrix nemaeus), endemic to Lao PDR, Vietnam, and perhaps Cambodia, remains little known. The Lao population is highly threatened. To improve conservation prospects of the species there, we here update a status review from 1999. Subsequent literature (mostly not readily available to the outside scientific community) was reviewed critically. Doucs and their habitat in Lao PDR faced continuous, increasing threats in the past 10 years through large development projects and heavy hunting. Many locations with records from the 1990s were not surveyed in the last decade, so douc persistence remains uncertain in them. Given the poor status of the species in Vietnam and Cambodia, the Lao population is surely the world's largest and the best hope for the species’ global conservation. Resources for conserving species are very limited in the country, urging prioritization of populations, so available resources have maximum effect. Nakai–Nam Theun and Hin Namno National Protected Areas hold the largest populations of P. nemaeus, but face great threats from hunting. Management of these areas (and secondary priority areas) should focus on control of this illegal activity. Am. J. Primatol. 74:874‐889, 2012. © 2012 Wiley Periodicals, Inc.     

Cranial morphology of the golden monkey (Rhinopithecus) and douc langur (Pygathrix nemaeus)

Because they have been less studied than most other non-human primates (partly due to the difficulties in accessing their habitat) the origins and phylogenetic relationships ofR. roxellana andR. bieti are controversial. These controversies may be clarified to some degree by adding information on the cranium. To this end, ten cranial dimensions analysed morphometrically here provide data about cranial differences among species of the genusRhinopithecus, and between species ofRhinopithecus andPygathrix nemaeus. Though more similar to each other than to any others in the same genus, the results show a significant separation betweenR. roxellana andR. bieti to the degree that they may be regarded as two different species. This confirms the conclusions of prior studies of external features, qualitative morphological characteristics and biochemical evidence (Yeet al, 1987; Zhang and Ryder, 1995; Jablonski, 1998; Penget al., 1988). The differences between these two species are mainly size-related, being highly correlated with cranial length. Other differences, probably non-size related shape differences, however, are highly correlated with cranial width. Sexual dimorphism plays a part in these findings. In relation to the other species, however, the results show that the Vietnam golden monkey (R. avunculus) has closer craniometric relationships with the douc langur (Pygathrix nemaeus) rather than with the three Chinese golden monkey species. Of these, the Gouzhou species (R. brelichi) shares more similarity withR. avunculus and is more separate fromRhinopithecus roxellana and R. bieti. The smaller differentiation between the two latter species could be due to their more recent separation following the dramatic elevation of Qinghai-Tibetan Plateau after the Middle Pleistocene.     

Comparing the effectiveness of metagenomics and metabarcoding for diet analysis of a leaf‐feeding monkey (Pygathrix nemaeus)

Faecal samples are of great value as a non‐invasive means to gather information on the genetics, distribution, demography, diet and parasite infestation of endangered species. Direct shotgun sequencing of faecal DNA could give information on these simultaneously, but this approach is largely untested. Here, we used two faecal samples to characterize the diet of two red‐shanked doucs langurs (Pygathrix nemaeus) that were fed known foliage, fruits, vegetables and cereals. Illumina HiSeq produced ~74 and 67 million paired reads for these samples, of which ~10 000 (0.014%) and ~44 000 (0.066%), respectively, were of chloroplast origin. Sequences were matched against a database of available chloroplast ‘barcodes’ for angiosperms. The results were compared with ‘metabarcoding’ using PCR amplification of the P6 loop of trnL. Metagenomics identified seven and nine of the likely 16 diet plants while six and five were identified by metabarcoding. Metabarcoding produced thousands of reads consistent with the known diet, but the barcodes were too short to identify several plant species to genus. Metagenomics utilized multiple, longer barcodes that combined had greater power of identification. However, rare diet items were not recovered. Read numbers for diet species in metagenomic and metabarcoding data were correlated, indicating that both are useful for determining relative sequence abundance. Metagenomic reads were uniformly distributed across the chloroplast genomes; thus, if chloroplast genomes were used as reference, the precision of identifications and species recovery would improve further. Metagenomics also recovered the host mitochondrial genome and numerous intestinal parasite sequences in addition to generating data useful for characterizing the microbiome.     

Seasonality of group size,feeding, and breeding in wild red‐shanked douc langurs (Lao PDR)

In Asian colobines, small one‐male groups (OMG) seem to predominate alongside all‐male groups (AMG), while larger multimale groups (MMG) are rare, but are reported for Hanuman langurs and red‐shanked douc langurs. Recently, however, it has been speculated that the genus Pygathrix could have multilevel societies based on (1) a theoretical extension of the multilevel societies found in Rhinopithecus to all odd‐nosed colobines and (2) first data for black‐shanked douc langurs. This assumes bands composed of small OMG with a skewed adult sex ratio. Band size may vary with seasonal food availability resulting in smaller bands when feeding competition is increased. To investigate the social organization of red‐shanked douc langurs and potential seasonal influences, we observed 2 unhabituated groups at Hin Namno National Protected Area, Lao PDR from March 2007 to August 2008 for 803 hr. We recorded births and performed group counts and scan sampling of feeding behavior. Most births (79% of N = 15) occurred from June–September, indicating a 4‐month peak conception season from November to February. Group size averaged 24.5 individuals (range 17–45) with 2.45 adult males (range 1–4). Although the smaller group remained at a stable size (about 18 individuals), the larger group reduced from about 45 to 25 individuals during the 7‐months long lean season, when less than 50% of the feeding time was spent on fruits. This suggests feeding competition as a potential cause of seasonal variation in group size. With 1.9 females per male the skew in adult sex ratio was much lower compared with Rhinopithecus, indicating MMG rather than multilevel societies. However, data on the spacing and interaction patterns between recognized individuals need to be collected and analyzed before the social organization can be determined. Detailed ecological data are furthermore required to investigate the basis for the seasonal changes in group size found. Am. J. Primatol. 73:1134–1144, 2011. © 2011 Wiley Periodicals, Inc.     

Seasonal variation in structure and function of gut microbiota in Pomacea canaliculata

Gut microbiota is associated with host health and its environmental adaption, influenced by seasonal variation. Pomacea canaliculata is one of the world''s 100 worst invasive alien species. Here, we used high‐throughput sequencing of the 16S rRNA gene to analyze the seasonal variation of gut microbiota of P. canaliculata. The results suggested that the predominant gut microbial phyla of P. canaliculata included Firmicutes and Proteobacteria, which helped digest plant food and accumulate energy. The gut microbiota of P. canaliculata in summer group showed the highest diversity, whereas the winter group possessed the lowest, probably due to the shortage of food resources of P. canaliculata in winter. Principal coordinate analysis analysis based on unweighted unifrac and weighted unifrac indicated that the composition of gut microbiota of P. canaliculata significantly varied across seasons. Bacteroidetes tended to be enriched in summer by linear discriminant analysis effect size analysis. Actinobacteria and Cyanobacteria were extremely abundant in autumn, while Fusobacteria and Cetobacterium enriched in winter. In conclusion, the structure of the gut microbiota of P. canaliculata was significantly different among seasons, which was beneficial to the environment adaptation and the digestion and metabolism of food during different periods.     

Observational methods to measure behaviors of captive cotton‐top tamarins (Saguinus oedipus)

The purpose of this study was to identify efficient sampling methods for establishing accurate activity budgets for zoo animals. Seven cotton‐top tamarins (Saguinus oedipus) from two zoos were videotaped for multiple 90 min sessions, 3 to 4 days per week for 12 weeks. An activity budget was constructed for each animal using a continuous sampling method to analyze 30 hr of video recording of each animal. These master datasets, reflecting actual behavior, were re‐sampled using interval sampling lengths of 0.25, 0.5, 1, 2, 4, 5, 7, 10, 15 and 20 min, and cluster sampling protocols (periodic sessions of continuous sampling) of 10 min×3, 15 min×2, 20 min×1, 15 min×1 and 10 min×1 (min×repetitions/90 min sample period) to construct additional activity budgets for each animal. The Canberra similarity index was used to determine the statistical relationship between these activity budgets and those based on the master datasets. As interval length increased, there was a consequent decrease in the accuracy of the associated activity budgets as compared with the master dataset. No cluster sampling protocols yielded activity budgets as accurate as the four shortest interval lengths, but all cluster sampling protocols were more accurate than the three longest interval lengths. All the tested protocols varied in ability to accurately portray animal behavior. Overall, interval sampling provided superior behavioral representations at lower observer input. Results from this study will potentially facilitate the standardization of behavior monitoring protocols at zoos. Zoo Biol 29:416–431, 2010. © 2009 Wiley‐Liss, Inc.     

The role of gut microbes in satisfying the nutritional demands of adult and juvenile wild,black howler monkeys (Alouatta pigra)

In all mammals, growth, development, pregnancy, and lactation increase nutritional demands. Although primate field studies tend to focus on shifts in activity and diet as mechanisms to compensate for these demands, differences in digestive efficiency also are likely to be important. Because the gut microbiota can impact host digestive efficiency, we examined differences in activity budget, diet, and the gut microbial community among adult male (N = 4), adult female (N = 4), and juvenile (N = 5) wild black howler monkeys (Alouatta pigra) across a ten‐month period in Palenque National Park, Mexico to determine how adult females and juveniles compensate for increased nutritional demands. Results indicate that adult females and juveniles consumed more protein and energy than adult males. Adult males, adult females, and juveniles also possessed distinct gut microbial communities, unrelated to diet. Juveniles exhibited a gut microbiota characterized by bacteria from the phylum Firmicutes, such as Roseburia and Ruminococcus, and demonstrated high fecal volatile fatty acid content, suggesting increased microbial contributions to host energy balances. Adult females possessed a higher Firmicutes to Bacteroidetes ratio, also suggesting increased energy production, and their gut microbiota was characterized by Lactococcus, which has been associated with folate biosynthesis. On the basis of these patterns, it appears that the gut microbiota differentially contributes to howler monkey nutrition during reproduction and growth. Determining the nutritional and energetic importance of shifts in activity, diet, and the gut microbiota in other nonhuman primate taxa, as well as humans, will transform our understanding of these life history processes and the role of host‐microbe relationships in primate evolution. Am J Phys Anthropol 155:652–664, 2014. © 2014 Wiley Periodicals, Inc.     

Suppurative peritonitis by Klebsiella pneumoniae in captive gold‐handed tamarin (Saguinus midas midas)

This report describes an outbreak of suppurative peritonitis caused by Klebsiella pneumoniae in an adult female of captive golden‐handed tamarin (Saguinus midas midas). Two virulent and multidrug‐resistant strains were isolated and classified through MLST as ST60 and ST1263. The microbiological diagnosis works as a support tool for preventive measures.     

Extensive variability in the gut microbiome of a highly‐specialized and critically endangered lemur species across sites

Deforestation continues to jeopardize Malagasy primates as viable habitats become smaller, more fragmented, and more disturbed. This deforestation can lead to changes in diet, microhabitat, and gene flow between populations of endangered species, and it remains unclear how these changes may affect gut microbiome (GM) characteristics. The black‐and‐white ruffed lemur (Varecia variegata), which is among Madagascar's most threatened lemur species, provides a critical model for understanding the relationships between historical and on‐going deforestation (habitat disturbance), feeding ecology, and GM composition and diversity. We studied four populations inhabiting two rainforests (relatively pristine vs. highly disturbed) in southeastern Madagascar. We conducted full‐day focal animal behavioral follows and collected fecal samples opportunistically across a three‐month period. Our results indicate that lemurs inhabiting sites characterized by habitat disturbance and low dietary diversity exhibited reduced gut microbial alpha diversity. We also show that these same factors were associated with high community dissimilarity using weighted and unweighted UniFrac metrics. Finally, an indicator species analysis showed that the most pristine site was characterized by an abundance of methanogenic archaea. While it is impossible to disentangle the relative contributions of each confounding variable presented by our sampling design, these results provide crucial information about GM variability, thereby underscoring the importance of monitoring endangered species at the population‐level.     

Bacterial community structure and function in a metal-working fluid

The diversity of bacterial populations colonizing spatially and temporally separated samples of the same metal-working fluid (MWF) formulation was investigated. Analyses were performed with a view to improve strategies for bioaugmentation of waste MWF in bioreactor systems and prevention of in-use MWF biodeterioration in engineering workshops. Significantly, complementary phenotypic, genotypic and in situ methods revealed that the bacterial communities in operationally exhausted MWFs had low diversity and were similar in species composition from different locations and uses. Of the 179 bacterial isolates studied, only 11 genera and 15 species were identified using fatty acid methyl ester (FAME) analysis, with culture independent analyses by 16S rDNA denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization being congruent with these FAME data. In order to gain some insight into functional role of detected populations, we correlated the MWF chemical composition and potential pollution load with bacterial abundance and community composition detected within samples.     

The microbiome and childhood diseases: Focus on brain‐gut axis

Many childhood diseases such as autism spectrum disorders, allergic disease, and obesity are on the increase. Although environmental factors are thought to play a role in this increase. The mechanisms at play are unclear but increasing evidence points to an interaction with the gastrointestinal microbiota as being potentially important. Recently this community of bacteria and perturbation of its colonization in early life has been linked to a number of diseases. Many factors are capable of influencing this colonization and ultimately leading to an altered gut microbiota which is known to affect key systems within the body. The impact of the microbial composition of our gastrointestinal tract on systems outside the gut is also becoming apparent. Here we highlight the factors that are capable of impacting on microbiota colonization in early‐life and the developing systems that are affected and finally how this may be involved in the manifestation of childhood diseases. Birth Defects Research (Part C) 105:296–313, 2015. © 2015 Wiley Periodicals, Inc.     

Divergence in gut microbial communities mirrors a social group fission event in a black‐and‐white colobus monkey (Colobus vellerosus)

Host behavior and social factors have increasingly been implicated in structuring the composition of gut microbial communities. In social animals, distinct microbial communities characterize different social groups across a variety of taxa, although little longitudinal research has been conducted that demonstrates how this divergence occurs. Our study addresses this question by characterizing the gut microbial composition of an African Old World monkey, the black‐and‐white colobus (Colobus vellerosus), before and after a social group fission event. Gut microbial taxonomic composition of these monkeys was profiled using the V‐4 hypervariable region of the bacterial 16S ribosomal RNA gene, and pairwise‐relatedness values were calculated for all individuals using 17 short tandem repeat loci and partial pedigree information. The two social groups in this study were found to harbor distinct microbial signatures after the fission event from which they emerged, while these communities were not divergent in the same individuals before this event. Three genera were found to differ in abundance between the two new social groups: Parabacteroides, Coprococcus, and Porphyromonadaceae. Additionally, although this fission happened partially along lines of relatedness, relatedness did not structure the differences that we found. Taken together, this study suggests that distinct gut microbial profiles can emerge in social groups in <1 year and recommends further work into more finely mapping the timescales, causes, and potentially adaptive effects of this recurring trend toward distinct group microbial signatures.