The gut microbiome of the Sunda pangolin (Manis javanica) reveals its adaptation to specialized myrmecophagy

Background The gut microbiomes of mammals are closely related to the diets of their hosts. The Sunda pangolin (Manis javanica) is a specialized myrmecophage, but its gut microbiome has rarely been studied. Methods Using high-throughput Illumina barcoded 16S rRNA amplicons of nine fecal samples from nine captive Sunda pangolins, we investigated their gut microbiomes. Results The detected bacteria were classified into 14 phyla, 24 classes, 48 orders, 97 families, and 271 genera. The main bacterial phyla were Firmicutes (73.71%), Proteobacteria (18.42%), Actinobacteria (3.44%), and Bacteroidetes (0.51%). In the PCoA and neighbor-net network (PERMANOVA: pangolins vs. other diets, weighted UniFrac distance p < 0.01, unweighted UniFrac distance p < 0.001), the gut microbiomes of the Sunda pangolins were distinct from those of mammals with different diets, but were much closer to other myrmecophages, and to carnivores, while distant from herbivores. We identified some gut microbiomes related to the digestion of chitin, including Lactococcus, Bacteroides, Bacillus, and Staphylococcus species, which confirms that the gut microbiome of pangolins may help them to digest chitin. Significance The results will aid studies of extreme dietary adaption and the mechanisms of diet differentiation in mammals, as well as metagenomic studies, captive breeding, and ex situ conservation of pangolins.

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First Captive Breeding Program for the Endangered Pyrenean Sculpin (Cottus hispaniolensis Bacescu-Master, 1964)

Water ◽

10.3390/w12112986 ◽

2020 ◽

Vol 12 (11) ◽

pp. 2986

Author(s):

Joan Manubens ◽

Oriol Comas ◽

Núria Valls ◽

Lluís Benejam

Keyword(s):

Captive Breeding ◽

Ex Situ Conservation ◽

Breeding Program ◽

Ex Situ ◽

Major Influence ◽

Freshwater Species ◽

Non Profit ◽

Captive Breeding Program ◽

Critical Phases ◽

Conservation Plans

The strong decline of freshwater fish species in Europe implies that further ex-situ conservation plans should be implemented in the near future. The present study reflects our experience with the Pyrenean sculpin (Cottus hispaniolensis Bacescu-Mester, 1964)—a small cottid endemic to the Hispano-French Garona River basin. In recent years, the Spanish Pyrenean sculpin population has reached a limit situation. Because of that, the non-profit association ADEFFA—with support from the public administration—started the first captive breeding program for this species in 2006. Fourteen years later, this study presents the results and evaluates the different steps of the program, with the aim of discussing and improving the ex-situ conservation plans for this and other cold freshwater species. There is a description and a comparison between six consecutive phases during the captive breeding process: nesting behaviour, courtship, egg fixation, parental care (incubation), hatching and survival during juvenile development. The purposes of this project are to: (1) identify the most determining phases for a successful captive breeding; (2) identify the factors that had a major influence to the success of the critical phases; and (3) increase the number of the offspring. This study is based on thirty-three wild individuals collected from Garona River (Val d’Aran, Spanish Pyrenees). During the program, twelve couples spawned in captive conditions, with around 2300 eggs laid. Eight couples bred successfully, with 751 hatched individuals and 608 juveniles reared. The analysis of each step of the captive breeding does not reveal significant differences between phases, so it can be concluded that they are all critical at the same level. In the literature, similar study-cases of captive breeding programs identify incubation and survival phases as the most critical. Consequently, the management made for this project has probably allowed to overcome in part the main impediments described in other similar programs.

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Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing

10.1101/753053 ◽

2019 ◽

Author(s):

Creciana Maria Endres ◽

Ícaro Maia Santos de Castro ◽

Laura Delpino Trevisol ◽

Michele Bertoni Mann ◽

Ana Paula Muterle Varela ◽

...

Keyword(s):

Public Health ◽

16S Rrna ◽

High Throughput ◽

Bacterial Communities ◽

Value Added ◽

Rrna Gene ◽

Unifrac Distance ◽

Organoleptic Characteristics ◽

Significant Difference

AbstractThe production of sheep’s milk cheese has grown in recent years since it is a high value-added product with excellent properties. As such, it is necessary to provide data on the microbiota and organoleptic characteristics of this product, as well as the influence of these microorganisms on public health. Thus, the aim of the present study was to characterize the microbial community of different types of sheep cheeses using high-throughput sequencing of the 16S rRNA gene. The study was conducted with four groups of cheese: colonial, fresh, feta, and pecorino (n = 5 samples per group). The high-throughput 16S rRNA amplicon sequencing revealed 55 operational taxonomic units in the 20 samples, representing 9 genera of the two bacterial phyla Firmicutes and Proteobacteria. The predominant genera in the samples were Streptococcus and Lactobacillus. When evaluating alpha diversity by the indexes of Simpson, Chao1, Shannon, and Skew no significant differences were observed between the groups. Evaluating of the beta diversity using Bray-Curtis dissimilarity, the group of colonial cheeses presented a significant difference when compared to the feta (q = 0.030) and pecorino groups (q = 0.030). Additionally, the fresh group differed from the pecorino group (q = 0.030). The unweighted Unifrac distance suggests that the colonial cheese group differed from the others. Moreover, the feta cheese group differed from the fresh group. The distance-weighted Unifrac suggests that no significance exists between the groups. According to this information, the microbiota characterization of these cheese groups was useful in demonstrating the bacterial communities belonging to each group, its effects on processing, elaboration, maturation, and public health.

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Determinant Factors of Successful Ex Situ Conservation of Lesser Bird of Paradise [Paradisaea minor Shaw, 1809]

Buletin Plasma Nutfah ◽

10.21082/blpn.v25n1.2019.p13-24 ◽

2019 ◽

Vol 25 (1) ◽

pp. 13

Author(s):

Ken Dara Cita ◽

Jarwadi Budi Hernowo ◽

Burhanuddin Masy'ud

Keyword(s):

Statistical Analysis ◽

Captive Breeding ◽

Ex Situ Conservation ◽

Habitat Destruction ◽

Ex Situ ◽

Social Aspect ◽

Biological Aspect ◽

Illegal Hunting ◽

Determinant Factors ◽

Breeding Technique

<p>Recently, the population of the lesser bird of paradise (Paradisaea minor Shaw, 1809) has been decreasing due to illegal hunting, illegal trading, and habitat destruction. Meanwhile, ex situ conservation efforts of this bird are lacked and very low in the success of breeding. The aims of this research were to identify and analyze the component that determines the successful ex situ conservation of the lesser bird of paradise. The study was conducted from March until May 2016 in the TMII Bird Park, Mega Bird and Orchid Farm (MBOF), Ragunan Zoo, Bandung Zoo, and Al Wabra Wildlife Preservation (AWWP) in Qatar. Data<br />included an internal and external biological aspect of species, captive breeding technique, and social aspect, and were analyzed by Principle Component Analysis (PCA). The statistical analysis resulted that there were five determinant factors of successful ex situ conservation of lesser bird of paradise which the first determinant factors were maturity, diet, and ability of animal keeper.</p>

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Systematic Bias Introduced by Genomic DNA Template Dilution in 16S rRNA Gene-Targeted Microbiota Profiling in Human Stool Homogenates

mSphere ◽

10.1128/msphere.00560-17 ◽

2018 ◽

Vol 3 (2) ◽

Cited By ~ 7

Author(s):

Francesco Multinu ◽

Sean C. Harrington ◽

Jun Chen ◽

Patricio R. Jeraldo ◽

Stephen Johnson ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Genomic Dna ◽

Rrna Gene ◽

Microbial Composition ◽

Unifrac Distance ◽

Β Diversity ◽

Unweighted Unifrac ◽

Stool Samples ◽

Community Representation

ABSTRACT Variability in representation of microbial communities can be caused by differences in microbial composition or artifacts introduced at sample collection or processing. Alterations in community representation introduced by variations in starting DNA concentrations have not been systematically investigated in stool samples. The goal of this study was to evaluate the effect of the genomic DNA (gDNA) concentration in the resulting 16S rRNA gene library composition and compare its effect to other sample processing variables in homogenized human fecal material. Compared to a gDNA input of 1 ng/μl, inputs of ≤1.6 × 10 −3 ng/μl resulted in a marked decrease in the concentration of the 16S rRNA gene amplicon ( P < 0.001). Low gDNA concentrations (≤1.6 × 10 −3 ng/μl) were also associated with a decrease ( P < 0.001) in the number of operational taxonomic units and significant divergence in β-diversity profiles (unweighted UniFrac distance, P < 0.001), as characterized by an overestimation of Proteobacteria and underestimation of Firmicutes . Even a gDNA concentration of 4 × 10 −2 ng/μl showed a significant impact on the β-diversity profile (unweighted UniFrac distance, P = 0.03). Overall, the gDNA concentration explained 22.4% to 38.1% of the microbiota variation based on various β-diversity measures ( P < 0.001). By comparison, the DNA extraction methods and PCR volumes tested did not significantly affect the microbial composition profile, and the PCR cycling method explained less than 3.7% of the microbiota variation (weighted UniFrac distance, P = 0.03). The 16S rRNA gene yield and the microbial community representation of human homogenized stool samples are significantly altered by gDNA template concentrations of ≤1.6 × 10 −3 ng/μl. In addition, data from studies with a gDNA input of ≤4 × 10 −2 ng/μl should be interpreted with caution. IMPORTANCE The genomic DNA input for stool samples utilized for microbiome composition has not been determined. In this study, we determined the reliable threshold level under which conclusions drawn from the data may be compromised. We also determined the type of microbial bias introduced by less-than-ideal genomic input.

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Anatomy of the Male Reproductive Organs of Javan Pangolin (Manis javanica)

10.31219/osf.io/q4z6k ◽

2019 ◽

Author(s):

Yusrizal Akmal ◽

Chairun Nisa ◽

Savitri Novelina

Keyword(s):

Reproductive Biology ◽

Captive Breeding ◽

Ex Situ Conservation ◽

Morphological Characteristics ◽

Reproductive Organs ◽

Ex Situ ◽

Wild Animals ◽

Market Demand ◽

Illegal Hunting ◽

Male Reproductive Organs

Pangolin is an animal that has special attention by CITES since 1985. This is due to increase of market demand, especially from China. It causes the illegal hunting is increasing, so that alleged wild population decreases dramatically. Overcoming of decreasing of the pangolin populations in the wild, could be anticipated by captive breeding. The information about the status of the reproductive biology of wild animals is very important for implementation of ex situ conservation activities. One of the aspects of the reproductive biology of wild animals is knowledge of the anatomy and physiology of the reproductive organs both males and females.Nowdays, data on morphological characteristics of male reproductive organs of pangolin (M. javanica) still limited. The data obtained of this study is new information in reproductive biology, especially on the morphological characteristics of the male reproductive organs of pangolin (M. javanica). In addition, the information can be the data base that is important in the effort to support ex situ conservation.

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Casting the Net Widely for Change in Animal Welfare: The Plight of Birds in Zoos, Ex Situ Conservation, and Conservation Fieldwork

Animals ◽

10.3390/ani12010031 ◽

2021 ◽

Vol 12 (1) ◽

pp. 31

Author(s):

Gisela Kaplan

Keyword(s):

At Risk ◽

Captive Breeding ◽

New Technologies ◽

Ex Situ Conservation ◽

Field Studies ◽

Ex Situ ◽

Species At Risk ◽

Avian Behavior ◽

Urgent Task ◽

Welfare Model

This paper discusses paradoxes in our relationship to and treatment of birds in captive and conservation contexts. The paper identifies modern and new challenges that arise from declining bird numbers worldwide. Such challenges have partly changed zoos into providers of insurance populations specifically for species at risk of extinction. They have also accelerated fieldwork projects, but by using advanced technological tools and in increasing numbers, contradictorily, they may cause serious harm to the very birds studied for conservation purposes. In practice, very few avian species have any notable protection or guarantee of good treatment. The paper first deals with shortcomings of identifying problematic avian behavior in captive birds. It then brings together specific cases of field studies and captive breeding for conservation in which major welfare deficits are identified. Indeed, the paper argues that avian welfare is now an urgent task. This is not just because of declining bird numbers but because of investment in new technologies in field studies that may have introduced additional stressors and put at risk bird survival. While the paper documents a substantial number of peer-reviewed papers criticizing practices counter to modern welfare standards, they have by and large not led to changes in some practices. Some solutions are suggested that could be readily implemented and, to my knowledge, have never been considered under a welfare model before.

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Ex situ conservation genetics: a review of molecular studies on the genetic consequences of captive breeding programmes for endangered animal species

Biodiversity and Conservation ◽

10.1007/s10531-011-0074-4 ◽

2011 ◽

Vol 20 (9) ◽

pp. 1843-1861 ◽

Cited By ~ 113

Author(s):

Kathrin A. Witzenberger ◽

Axel Hochkirch

Keyword(s):

Conservation Genetics ◽

Animal Species ◽

Captive Breeding ◽

Ex Situ Conservation ◽

Ex Situ ◽

Molecular Studies ◽

Breeding Programmes

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Captive breeding and ex situ conservation

Primate Ecology and Conservation ◽

10.1093/acprof:oso/9780199659449.003.0017 ◽

2013 ◽

pp. 294-322 ◽

Cited By ~ 1

Author(s):

Dean Gibson ◽

Colleen McCann

Keyword(s):

Captive Breeding ◽

Ex Situ Conservation ◽

Ex Situ

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The Public Perception towards the Development of Deer Breeding in Bandar Lampung

Jurnal Sylva Lestari ◽

10.23960/jsl27244-254 ◽

2019 ◽

Vol 7 (2) ◽

pp. 244

Author(s):

Bainah Sari Dewi ◽

Akhmad Kamaluddin ◽

Yoshua Gdemakarti

Keyword(s):

Public Perception ◽

Captive Breeding ◽

Ex Situ Conservation ◽

Natural Habitat ◽

Breeding Habitat ◽

Ex Situ ◽

The Public ◽

In Captivity ◽

Management And Development ◽

Community Supports

The existence of the deer population that continue to decline in its natural habitat need conservation efforts, such as through ex-situ conservation. Deer captive breeding is one of the ex-situ conservation efforts to ensure the sustainability of wildlife from the threat of extinction. This research aims to know the public perception towards the management and development of captive deer in an effort to improve the conservation of deer was ex-situ. This research was conducted in October – November 2018 in three stations of the captive breeding of sambar deer (Cervus unicolor) and timor deer (Cervus timorensis) in University of Lampung and timor deer (Cervus timorensis) breeding in Tahura Wan Abdul Rachman through interviews to respondents and then the data collected were analyzed descriptively. The results showed a positive public perception towards the development of captive breeding. The results also showed the community supports on the development of deer captive breeding, the management of captive breeding, habitat suitability characteristics, the existence of species and species treatment in captivity, and the development of deer captive as object conservation-based tourism. Keywords: captive reeding, perception, deer

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