Exploring the cockatiel (Nymphicus hollandicus) fecal microbiome, bacterial inhabitants of a worldwide pet

BackgroundCockatiels (Nymphicus hollandicus) were originally endemic to Australia; now, they are popular pets with a global distribution. It is now possible to conduct detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals. These studies show that bacteria are an essential part of the metabolic capacity of animals. There are few studies on bird microbiomes, and, to the best of our knowledge, this is the first report on the cockatiel microbiome.MethodsIn this paper, we analyzed the gut microbiome from fecal samples of three healthy adult cockatiels by massive sequencing of the 16S rRNA gene. Additionally, we compared the cockatiel fecal microbiomes with those of other bird species, including poultry and wild birds.ResultsThe vast majority of the bacteria found in cockatiels wereFirmicutes, whileProteobacteriaandBacteroideteswere poorly represented. A total of 19,280 different OTUs were detected, of which 8,072 belonged to theErysipelotrichaceaefamily.DiscussionIt is relevant to study cockatiel the microbiomes of cockatiels owing to their wide geographic distribution and close human contact. This study serves as a reference for cockatiel bacterial diversity. Despite the large OTU numbers, the diversity is not even and is dominated byFirmicutesof theErysipelotrichaceaefamily. Cockatiels and other wild birds are almost depleted ofBacteroidetes, which happen to be abundant in poultry-related birds, and this is probably associated with the intensive human manipulation of poultry bird diets. Some probable pathogenic bacteria, such asClostridiumandSerratia,appeared to be frequent inhabitants of the fecal microbiome of cockatiels, whereas other potential pathogens were not detected.

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Cockatiel (Nymphicus hollandicus) gut microbiomes, bacterial inhabitants of a worldwide distributed pet

10.7287/peerj.preprints.2292 ◽

2016 ◽

Author(s):

Luis David Alcaraz ◽

Apolinar M. Hernández ◽

Mariana Peimbert

Keyword(s):

Pathogenic Bacteria ◽

Ribosomal Gene ◽

Wild Birds ◽

Intestinal Microbiome ◽

Pet Birds ◽

Human Contact ◽

Poultry Birds ◽

Nymphicus Hollandicus ◽

Massive Sequencing ◽

Uncultivable Bacteria

Background. Cockatiels (Nymphicus hollandicus) were originally endemic to Australia, but they are nowadays popular worldwide pet birds. It is now possible to make detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals, these studies showed that bacteria are an essential part of the capacity and metabolic status of animals. There are few studies of bird microbiomes and to date this is the first reported cockatiel microbiome work. Methods. In this paper we analyzed the gut microbiome of 3 healthy adult cockatiel birds by massive sequencing of 16S ribosomal gene. Additionally, we show a comparison with other poultry, and wild birds microbiomes and their taxa profiles Results. The vast majority of the Cockatiel’s bacteria found were Firmicutes, while Proteobacteria and Bacteroidetes are poorly represented. 19,280 different OTUs were detected, of which 8,072 belong to the Erysipelotrichaceae family. Discussion. Cockatiels wide geographic distribution, and close human contact makes relevant to study their microbiomes, this study gives a baseline for their bacterial diversity. Cockatiels microbiomes diversity are dominated by Firmicutes of the Erysipelotrichaceae family. Cockatiels, and other wild birds are almost depleted of Bacteroidetes which happen to be abundant in poultry birds and this is probably related with the intensive human manipulation of poultry bird diets. Some pathogenic bacteria like Clostridium colinum, and Serratia marcescens are inhabitants of the cockatiel’s microbiome while other pathogens are not elements of healthy cockatiel’s microbiota, although the specimens collected were perfectly healthy at the time.

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Cockatiel (Nymphicus hollandicus) gut microbiomes, bacterial inhabitants of a worldwide distributed pet

10.7287/peerj.preprints.2292v1 ◽

2016 ◽

Author(s):

Luis David Alcaraz ◽

Apolinar M. Hernández ◽

Mariana Peimbert

Keyword(s):

Pathogenic Bacteria ◽

Ribosomal Gene ◽

Wild Birds ◽

Intestinal Microbiome ◽

Pet Birds ◽

Human Contact ◽

Poultry Birds ◽

Nymphicus Hollandicus ◽

Massive Sequencing ◽

Uncultivable Bacteria

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Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome

Scientific Reports ◽

10.1038/s41598-021-83875-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zhen Han ◽

Peter S. Thuy-Boun ◽

Wayne Pfeiffer ◽

Vincent F. Vartabedian ◽

Ali Torkamani ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Human Microbiome ◽

Host Immunity ◽

Rrna Gene ◽

Metabolic Labeling ◽

Selective Labeling ◽

Fecal Microbiome ◽

Acetylneuraminic Acid ◽

Intestinal Mucus ◽

Microbial Systems

AbstractN-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.

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Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos) Shown with 16S rRNA Gene-Based Microbial Community Analysis

BioMed Research International ◽

10.1155/2013/438956 ◽

2013 ◽

Vol 2013 ◽

pp. 1-5 ◽

Cited By ~ 8

Author(s):

Isamu Maeda ◽

Mohammad Shohel Rana Siddiki ◽

Tsutomu Nozawa-Takeda ◽

Naoki Tsukahara ◽

Yuri Tani ◽

...

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Pathogenic Bacteria ◽

Community Analysis ◽

Microbial Community Analysis ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Jungle Crow ◽

Corvus Macrorhynchos

Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous toEimeriasp., which belongs to the protozoan phylumApicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the generaCampylobacterandBrachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

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A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function

Microorganisms ◽

10.3390/microorganisms8121887 ◽

2020 ◽

Vol 8 (12) ◽

pp. 1887

Author(s):

Laurin Gierse ◽

Alexander Meene ◽

Daniel Schultz ◽

Theresa Schwaiger ◽

Claudia Karte ◽

...

Keyword(s):

16S Rrna ◽

Short Chain Fatty Acids ◽

Minimal Invasive ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Fecal Microbiome ◽

Longitudinal Dynamics ◽

Microbiome Composition ◽

Swine Feces ◽

And Function

Swine are regarded as promising biomedical models, but the dynamics of their gastrointestinal microbiome have been much less investigated than that of humans or mice. The aim of this study was to establish an integrated multi-omics protocol to investigate the fecal microbiome of healthy swine. To this end, a preparation and analysis protocol including integrated sample preparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integration linked microbiome composition with function, and metabolic activity with protein inventories, i.e., 16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites. 16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated by Prevotellaceae, Lactobacillaceae, Lachnospiraceae, Ruminococcaceae and Clostridiaceae. Similar microbiome compositions in feces and colon, but not ileum samples, were observed, showing that feces can serve as minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition, e.g., temporal decreased abundance of Lactobacillaceae and Streptococcaceae during the experiment, were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed a rather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associated metaproteome functions, pointing towards functional redundancy among microbiome constituents. In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomy and functionality of the intestinal microbiome of swine.

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Composition and Potential Function of Fecal Bacterial Microbiota from Six Bird Species

Birds ◽

10.3390/birds2010003 ◽

2021 ◽

Vol 2 (1) ◽

pp. 42-59

Author(s):

Jose F. Garcia-Mazcorro ◽

Cecilia Alanis-Lopez ◽

Alicia G. Marroquin-Cardona ◽

Jorge R. Kawas

Keyword(s):

Bird Species ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Mimus Polyglottos ◽

Pet Birds ◽

Psittacula Krameri ◽

Bacterial Microbiota ◽

Nymphicus Hollandicus ◽

Health And Disease ◽

The Impact

Gut microbial communities play a fundamental role in health and disease, but little is known about the gut microbiota of pet bird species. This is important to better understand the impact of microbes on birds’ health but may also be relevant in a context of zoonoses. Total genomic DNA samples from pooled fecal samples from 30 flocks (4–7 pet birds per flock) representing over 150 birds of six different species (two Passeriformes: Northern Mockingbird (Mimus polyglottos) and Zebra Finch (Taeniopygia guttata), and four Psittaciformes: Lovebird (Agapornis, different species), Cockatiel (Nymphicus hollandicus), Red-rumped Parrot (Psephotus haematonotus), and Rose-ringed Parakeet (Psittacula krameri) were used for 16S rRNA gene analysis. Several taxa were found to be different among the bird species (e.g., lowest median of Lactobacillus: 2.2% in Cockatiels; highest median of Lactobacillus: 79.4% in Lovebirds). Despite marked differences among individual pooled samples, each bird species harbored a unique fecal bacterial composition, based on the analysis of UniFrac distances. A predictive approach of metagenomic function and organism-level microbiome phenotypes revealed several differences among the bird species (e.g., a higher proportion of proteobacteria with the potential to form biofilms in samples from Northern Mockingbirds). The results provide a useful catalog of fecal microbes from pet birds and encourage more research on this unexplored topic.

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Occurrence of Mycoplasma spp. in wild birds: phylogenetic analysis and potential factors affecting distribution

Scientific Reports ◽

10.1038/s41598-021-96577-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Anna Sawicka-Durkalec ◽

Olimpia Kursa ◽

Łukasz Bednarz ◽

Grzegorz Tomczyk

Keyword(s):

Phylogenetic Analysis ◽

Feeding Habits ◽

Bird Species ◽

Ecological Factors ◽

Wild Birds ◽

Rrna Gene ◽

Factors Affecting ◽

Pcr Products ◽

Commercial Poultry ◽

Potential Factors

AbstractDifferent Mycoplasma species have been reported in avian hosts. However, the majority of studies focus on one particular species of Mycoplasma or one host. In our research, we screened a total of 1141 wild birds representing 55 species, 26 families, and 15 orders for the presence of mycoplasmas by conventional PCR based on the 16S rRNA gene. Selected PCR products were sequenced to perform the phylogenetic analysis. All mycoplasma-positive samples were tested for M. gallisepticum and M. synoviae, which are considered the major pathogens of commercial poultry. We also verified the influence of ecological characteristics of the tested bird species including feeding habits, habitat types, and movement patterns. The presence of Mycoplasma spp. was confirmed in 498 birds of 29 species, but none of the tested birds were positive for M. gallisepticum or M. synoviae. We found possible associations between the presence of Mycoplasma spp. and all investigated ecological factors. The phylogenetic analysis showed a high variability of Mycoplasma spp.; however, some clustering of sequences was observed regarding particular bird species. We found that wild migratory waterfowl, particularly the white-fronted goose (Anser albifrons) and mallard (Anas platyrhynchos) could be reservoirs and vectors of mycoplasmas pathogenic to commercial waterfowl.

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PSVI-22 Fecal microbiome of dairy calves fed with different liquid diets

Journal of Animal Science ◽

10.1093/jas/skaa278.751 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 431-431

Author(s):

Gercino F Virgínio Júnior ◽

Marina Coelho ◽

Marcos Silva ◽

Horácio Montenegro ◽

Luiz Coutinho ◽

...

Keyword(s):

Animal Health ◽

Illumina Miseq ◽

Diversity Indices ◽

Liquid Diet ◽

Intestinal Microbiome ◽

Milk Replacer ◽

Rrna Gene ◽

Fecal Microbiome ◽

Bacterial Phyla ◽

Whole Milk

Abstract Feeding a liquid diet to the newborn calf has considerable implications for the development of the intestinal microbiota, as its composition can shift population to a highly adapted microbiota. Milk acidification may positively affect microorganisms that are beneficial to the intestine health. The present study evaluated 15 Holstein calves housed in tropical shelters, fed one of the three liquid diets: I – whole milk (n = 5), II – milk replacer (22.9 % CP; 18.5 % fat; diluted to 14% solids; n = 5) and III - whole milk acidified to pH 4.5 with formic acid (n = 5). All animals received 6 L of liquid diet, divided into two meals, being weaned at the 8th week of age. After weaning, all calves were group housed and fed with starter concentrate and coast-cross hay ad libitum. To evaluate the microbioma, fecal samples were collected at birth (0) and at weeks 1, 2, 4, 8 and 10. The microbial community was determined by sequencing V3 and V4 region amplicons of the 16S rRNA gene that was amplified by PCR and sequenced by the Illumina MiSeq platform. The diversity indices and evenness were higher for whole milk when compared to milk replacer (P < 0,05), with no difference for acidified whole milk. Animal age affected all indices. Time 0 had higher richness and diversity (P < 0,001), while weeks 1 and 2 had the lowest (P < 0,001). Thirty-eight bacterial phyla were identified, and the most abundant in were Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria and Firmicutes C. It is possible to modify the microbiome by changing the liquid diet. However, differences according to calf age may show the best time for possible interventions in the diet to manipulate the intestinal microbiome to improve animal health and performance.

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Gut Microbiome Composition and Metabolomic Profiles of Wild and Captive Chinese Monals (Lophophorus Lhuysii)

10.21203/rs.3.rs-32587/v1 ◽

2020 ◽

Author(s):

Dandan Jiang ◽

Xin He ◽

Marc Valitutto ◽

Li Chen ◽

Qin Xu ◽

...

Keyword(s):

Gut Microbiome ◽

Bacterial Species ◽

Bird Species ◽

Alpha Diversity ◽

Integrated Approach ◽

Rrna Gene ◽

Metabolomic Profile ◽

Liquid Chromatograph ◽

Fecal Microbiome ◽

Microbiome Composition

Abstract Background：The Chinese monal (Lophophorus lhuysii) is an endangered bird species, with a wild population restricted to the mountains of southwest China, and only one known captive population in the world. We investigated the fecal microbiota and metabolomics of wild and captive Chinese monals to explore differences and similarities in nutritional status and digestive characteristics. An integrated approach combining 16S ribosomal rRNA (16S rRNA) gene sequencing and ultra-high performance liquid chromatograph (UHPLC) based metabolomics were used to examine the fecal microbiome composition and the metabolomic profile of Chinese monals. Results: The results showed that the alpha diversity of gut microbes in the wild group were significantly higher than that in the captive group and the core bacterial species in the two groups showed remarkable differences at all levels. Metabolomic profiling revealed a concurrent difference, mainly related to galactose, starch and sucrose metabolism, fatty acid, bile acid biosynthesis and bile secretion. Furthermore, these metabolites in difference are have a strong correlation with the main microbe in genus level.Conclusions: Various factors related to diet and environmental conditions played a crucial role in shaping the gut microbiome composition and metabolomic profile. Through this study, we have established a baseline for a normal gut microbiome and metabolomic profile for wild Chinese monals, thus allowing us to evaluate if differences seen in captive specimens has an impact on their overall health and reproduction.

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Production, Storage Stability, and Susceptibility Testing of Reuterin and Its Impact on the Murine Fecal Microbiome and Volatile Organic Compound Profile

Frontiers in Microbiology ◽

10.3389/fmicb.2021.699858 ◽

2021 ◽

Vol 12 ◽

Author(s):

Christoph Castellani ◽

Beate Obermüller ◽

Bernhard Kienesberger ◽

Georg Singer ◽

Clemens Peterbauer ◽

...

Keyword(s):

Antimicrobial Activity ◽

Storage Stability ◽

Antimicrobial Effect ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Linear Discriminant ◽

Fecal Microbiome ◽

Alpha And Beta Diversity ◽

Volatile Organic

Background: Probiotics are generally considered as safe, but infections may rarely occur in vulnerable patients. Alternatives to live microorganisms to manage dysbiosis may be of interest in these patients. Reuterin is a complex component system exhibiting broad spectrum antimicrobial activity and a possible candidate substance in these cases.Methods: Reuterin supernatant was cultured from Lentilactobacillus diolivorans in a bioreactor in a two-step process. Storage stability at −20°C and effect of repeated freeze-thaw cycles were assessed by high performance liquid chromatography (HPLC). Antimicrobial activity was tested against Clostridium difficile, Listeria monocytogenes, Escherichia coli, Enterococcus faecium, Staphylococcus (S.) aureus, Staphylococcus epidermidis, Streptococcus (S.) agalactiae, Propionibacterium acnes, and Pseudomonas aeruginosae. Male BALBc mice were gavage fed with reuterin supernatant (n = 10) or culture medium (n = 10). Fecal volatile organic compounds (VOC) were assessed by gas chromatography mass spectroscopy; the microbiome was examined by 16S rRNA gene sequencing.Results: The supernatant contained 13.4 g/L reuterin (3-hydroxypropionaldehyde; 3-HPA). 3-HPA content remained stable at −20°C for 35 days followed by a slow decrease of its concentration. Repeated freezing/thawing caused a slow 3-HPA decrease. Antimicrobial activity was encountered against S. aureus, S. epidermidis, and S. agalactiae. Microbiome analysis showed no differences in alpha and beta diversity markers. Linear discriminant effect size (LEfSe) analysis identified Lachnospiraceae_bacterium_COE1 and Ruminoclostridium_5_uncultured_Clostridiales_ bacterium (in the reuterin medium group) and Desulfovibrio_uncultured_ bacterium, Candidatus Arthromitus, Ruminococcae_NK4A214_group, and Eubacterium_xylanophilum_group (in the reuterin group) as markers for group differentiation. VOC analysis showed a significant decrease of heptane and increase of 3-methylbutanal in the reuterin group.Conclusion: The supernatant produced in this study contained acceptable amounts of 3-HPA remaining stable for 35 days at −20°C and exhibiting an antimicrobial effect against S. aureus, S. agalactiae, and S. epidermidis. Under in vivo conditions, the reuterin supernatant caused alterations of the fecal microbiome. In the fecal, VOC analysis decreased heptane and increased 3-methylbutanal were encountered. These findings suggest the high potential of the reuterin system to influence the intestinal microbiome in health and disease, which needs to be examined in detail in future projects.

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