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Investigating the Diversity of Bacteria and Fungi in Rock Pigeon (Columba livia) Stool using Metagenomics in Sarawak, Malaysian Borneo.
Get PDFRock pigeon (Columba livia), are domesticated birds, commonly found in urban areas worldwide. Apart from being a nuisance, pigeons are associated with 110 pathogens, with most studies focused on the bacterial and fungal diversity due to its zoonotic potential. Previously, culture-dependent techniques in diversity studies were preferred, including bacterial and fungal studies of pigeon stool. However, the technique underestimates presence of unculturable bacteria and fungi, ultimately inaccurately reporting the actual diversity. To this day, only one study respectively has described on the bacterial and fungal diversity using culture-independent techniques worldwide. Additionally, any microbiome data on pigeon stool has not been reported in Malaysia previously. Thus, to fill this knowledge gap, this study aims to characterise the bacterial and fungal diversity and to identify potentially pathogenic bacteria and fungi in pigeon stool found in towns of Sarawak using high- throughput amplicon sequencing and to identify potentially pathogenic bacterial and fungal genera. Six samples consisting of fresh and dry stool samples were collected from four towns in Sarawak, and its microbial composition was identified through sequencing of the V3 – V4 16S rRNA and ITS2 rRNA regions. A total of 1381 and 481 bacterial and fungal amplicon sequence variants (ASVs), respectively, were identified in pigeon stool, with dry pigeon stool having higher bacterial and fungal ASVs than fresh pigeon stool. Firmicutes was the dominating bacterial pigeon stool contributed by the presence of probiotic bacteria such as Sporosarcina, Clostridium sensu stricto 1, Romboutsia, Lactobacillus and Anerosporobacter, reflecting the pigeon gut microbiome. Whereas, the dominance of Proteobacteria in dry pigeon stool was attributed to the presence of enteric bacteria such as Escherichia-Shigella and Enterococcus, which have been found to proliferate upon the excrement from the gastrointestinal tract. On the other hand, dominance of Ascomycota is contributed by the presence of Kazachstania and Neocucurbutaria. However, environmental fungal genera including Aspergillus, Trichosporon, Penicillium, Iodophanus, and Cephaliophora contributed to the dominance of Ascomycota in dry pigeon stool. Additionally, 18 bacterial and fungal genera, respectively, were flagged as potentially pathogenic. Of these, four and six bacterial and fungal genera, respectively, were not previously associated with pigeon stool. This study gives insight into the importance of utilising high-throughput amplicon sequencing for bacterial and fungal diversity characterisation, depicting the important role of fresh and dry pigeon stool in the environment. Additionally, the detection of additional pigeon-related potentially pathogenic pathogens in study shows that geographical location and immune status of the bird plays a role in the prevalence of microbes
Prevalence of haemosporidia in Asian Glossy Starling with discovery of misbinding of Haemoproteus-specific primer to Plasmodium genera in Sarawak, Malaysian Borneo
Get PDFBackground
Plasmodium, Haemoproteus and Leucocytozoon are three mainly studied blood parasites known to cause malarial and pseudomalarial infections in avian worldwide. Although Sarawak is a biodiversity hotspot, molecular data on blood parasite diversity in birds are absent. The objective of the study is to determine the prevalence of blood parasite in Asian Glossy Starlings (AGS), an urban bird with high population density in Sarawak and to elucidate the phylogenetic relationship with other blood parasite.
Methods
Twenty-nine carcasses of juvenile AGS that were succumbed to death due to window collision were collected around the vicinity of Universiti Malaysia Sarawak. Nested-multiplex and nested PCR targeting the Cytochrome B gene were used to detect Plasmodium and Haemoproteus, and Leucocytozoon respectively. Two primer sets were used for Haemoproteus detection to increase detection sensitivity, with one being a genus-specific primer.
Results
Fourteen samples (prevalence rate: 48.28%) were found positive for avian Plasmodium. Phylogenetic analysis divided our sequences into five lineages, pFANTAIL01, pCOLL4, pACCBAD01, pALPSIS01 and pALPSIS02, with two lineages being novel. No Haemoproteus and Leucocytozoon was found in this study. However, Haemoproteus-specific primer used amplified our Plasmodium samples, making the primer non-specific to Haemoproteus only.
Conclusion
This is the first blood parasite detection study on AGS using carcasses and blood clot as sample source in Sarawak. Due to the scarcity of longer sequences from regions with high genetic plasticity, usage of genus-specific primers should be validated with sequencing to ensure correct prevalence interpretation
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Additional file 4 of Prevalence of haemosporidia in Asian Glossy Starling with discovery of misbinding of Haemoproteus-specific primer to Plasmodium genera in Sarawak, Malaysian Borneo
No full textAdditional file 4: Figure S3. Uncropped electrophoresis gel of nested PCR of amplification of CytB gene of avian Plasmodium using Haemoproteus-specific primer set HaemF/AE982 producing amplicons of 820bp only. Cropped region presented in the manuscript is denoted by the red box and labelled as Fig. 2B
Additional file 3 of Prevalence of haemosporidia in Asian Glossy Starling with discovery of misbinding of Haemoproteus-specific primer to Plasmodium genera in Sarawak, Malaysian Borneo
No full textAdditional file 3: Figure S2. Uncropped electrophoresis gel of nested-multiplex PCR amplification of CytB gene of avian Plasmodium and Haemoproteus using primer set AE980/AE982 and AE983/AE985 producing amplicons of 580bp only. A positive amplification of Haemoproteus is indicated by the 346 bp amplicon in the positive control. Cropped region presented in the manuscript is denoted by the red box and labelled as Fig. 2A
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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