Species-specific but not phylosymbiotic gut microbiomes of New Guinean passerine birds are shaped by diet and flight-associated gut modifications

Animal hosts have evolved intricate associations with microbial symbionts, where both depend on each other for particular functions. In many cases, these associations lead to phylosymbiosis, where phylogenetically related species harbour compositionally more similar microbiomes than distantly related species. However, evidence for phylosymbiosis is either weak or lacking in gut microbiomes of flying vertebrates, particularly in birds. To shed more light on this phenomenon, we compared cloacal microbiomes of 37 tropical passerine bird species from New Guinea using 16S rRNA bacterial gene sequencing. We show a lack of phylosymbiosis and document highly variable microbiomes. Furthermore, we find that gut bacterial community compositions are species-specific and tend to be shaped by host diet but not sampling locality, potentially driven by the similarities in habitats used by individual species. We further show that flight-associated gut modifications, coupled with individual dietary differences, shape gut microbiome structure and variation, contributing to the lack of phylosymbiosis. These patterns indicate that the stability of symbiosis may depend on microbial functional diversity rather than taxonomic composition. Furthermore, the more variable and fluid host–microbe associations suggest probable disparities in the potential for coevolution between bird host species and microbial symbionts.

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Ecological Perturbations Impact Species-Specific Gene Expression of the Oral Microbiota

10.21203/rs.3.rs-104582/v1 ◽

2020 ◽

Author(s):

Daniel Belstrøm ◽

Florentin Constancias ◽

Daniela I Drautz-Moses ◽

Stephan C Schuster ◽

Mark Veleba ◽

...

Keyword(s):

Gene Expression ◽

Carbohydrate Metabolism ◽

Taxonomic Composition ◽

Bacterial Activity ◽

Oral Microbiota ◽

Bacterial Gene ◽

Bacterial Gene Expression ◽

Oral Site ◽

Species Specific ◽

The Impact

Abstract Background: The purpose of the present investigation was to use the oral cavity as an in-vivo model to study the impact of internal and external perturbations on bacterial biofilm communities. We tested the hypotheses that bacterial gene expression of the healthy microbiota reflects habituation to site-specific ecological perturbations, and that the perturbation effect of chronic inflammation, i.e. periodontitis, impacts bacterial gene expression not only locally, but also at other sites of the oral cavity. Oral microbial samples were collected from three oral sites – plaque, tongue and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterization of taxonomic composition and to determine species specific bacterial activity as expressed by the ratio of messenger RNA to the corresponding genomic DNA.Results: Here we show the impact of two perturbations – oral site and periodontitis - on bacterial gene expression of the oral microbiota. The oral site was the main determinant of taxonomic composition as well as bacterial gene expression. However, bacterial activity at the three oral sites (plaque, tongue, and saliva) was significantly impacted by periodontitis, with a reduction of the carbohydrate metabolism.Conclusions: Data from the present study characterize the impact of two perturbations – oral site and periodontitis - on bacterial gene expression of the oral microbiota. The oral site was the main determinant of taxonomic composition as well as bacterial gene expression. However, presence of periodontitis had impact on bacterial activity of both plaque but also on tongue and the salivary microbiota. Collectively, data suggest that periodontitis associates with impaired carbohydrate metabolism of the oral microbiota. Future longitudinal and interventional studies are warranted to evaluate the potential pathogenic role of impaired bacterial carbohydrate metabolism not only in periodontitis, but also in other diseases with low grade inflammation, such as type 2 diabetes mellitus.

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PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

10.1101/484832 ◽

2018 ◽

Author(s):

Sean P. Gordon ◽

Joshua J. Levy ◽

John P. Vogel

Keyword(s):

Repetitive Dna ◽

Dna Sequences ◽

Related Species ◽

Software Package ◽

Gc Content ◽

Individual Species ◽

Closely Related Species ◽

As Species ◽

Pooled Dna ◽

Species Specific

AbstractExisting methods for assigning sequences to individual species from pooled DNA samples rely on differences in genome properties like GC content or sequences from related species. These approaches do not work for closely related species where gross features are indistinguishable and related genomes are lacking. We describe a method and associated software package that uses rapidly evolving repetitive DNA to circumvent these limitations. By using short, repetitive, DNA sequences as species-specific signals we separated closely related genomes without any prior knowledge. This approach is ideal for separating the subgenomes of polyploid species with unsequenced or unknown progenitor genomes.

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Periodontitis associates with species-specific gene expression of the oral microbiota

npj Biofilms and Microbiomes ◽

10.1038/s41522-021-00247-y ◽

2021 ◽

Vol 7 (1) ◽

Author(s):

Daniel Belstrøm ◽

Florentin Constancias ◽

Daniela I. Drautz-Moses ◽

Stephan C. Schuster ◽

Mark Veleba ◽

...

Keyword(s):

Gene Expression ◽

Carbohydrate Metabolism ◽

Taxonomic Composition ◽

Bacterial Activity ◽

Oral Microbiota ◽

Low Grade ◽

Subgingival Plaque ◽

Bacterial Gene ◽

Bacterial Gene Expression ◽

Species Specific

AbstractThe purpose of the present investigation was to characterize species-specific bacterial activity of the oral microbiota in periodontitis. We tested the hypotheses that chronic inflammation, i.e., periodontitis, associates with bacterial gene expression of the oral microbiota. Oral microbial samples were collected from three oral sites—subgingival plaque, tongue, and saliva from patients with periodontitis and healthy controls. Paired metagenomics and metatranscriptomics were used to perform concomitant characterization of taxonomic composition and to determine species-specific bacterial activity as expressed by the ratio of specific messenger RNA reads to their corresponding genomic DNA reads. Here, we show the association of periodontitis with bacterial gene expression of the oral microbiota. While oral site was the main determinant of taxonomic composition as well as bacterial gene expression, periodontitis was significantly associated with a reduction of carbohydrate metabolism of the oral microbiota at three oral sites (subgingival plaque, tongue, and saliva). Data from the present study revealed the association of periodontitis with bacterial gene expression of the oral microbiota. Conditions of periodontitis was associated with bacterial activity of local subgingival plaque, but also on tongue and the salivary microbiota. Collectively, data suggest that periodontitis associates with impaired carbohydrate metabolism of the oral microbiota. Future longitudinal and interventional studies are warranted to evaluate the potential pathogenic role of impaired bacterial carbohydrate metabolism not only in periodontitis but also in other diseases with low-grade inflammation, such as type 2 diabetes mellitus.

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Die Brutvogelfauna eines Nadelwaldes der nördlichen Voralpen nach dem Sturm Lothar

Schweizerische Zeitschrift fur Forstwesen ◽

10.3188/szf.2017.0059 ◽

2017 ◽

Vol 168 (2) ◽

pp. 59-66

Author(s):

Pierre Mollet ◽

René Hardegger ◽

Res Altwegg ◽

Pius Korner ◽

Simon Birrer

Keyword(s):

Forest Succession ◽

Coniferous Forest ◽

Bird Species ◽

Individual Species ◽

Mountain Forest ◽

Breeding Bird ◽

Point Counts ◽

Federal Institute ◽

Central Switzerland ◽

Bird Fauna

Breeding bird fauna in a coniferous forest in the northern Prealps after storm Lothar In a 70-hectare large coniferous forest located on the northern edge of the Alps in central Switzerland, Canton of Obwalden, at an altitude of 1260 to 1550 metres above sea level, we surveyed the local breeding bird fauna in 2002 and 2013 by means of point counts as well as additional area searches for rare species. In December 1999, hurricane Lothar caused two large windthrow areas and several smaller areas with scattered throws in the survey range. We found a total of 48 breeding bird species, which is a very diverse species composition for a mountain forest. In the eleven years between surveys, a decline in distribution or abundance was recorded for four species, while seven species showed an increase; a further four species showed no change. For the remaining species, the data sets were too small to reliably estimate changes. A comparison with forest structure data provided by the Swiss Federal Institute of Forest, Snow and Landscape Research WSL revealed that for five bird species, the changes in distribution or abundance could be explained at least partially by forest succession. In order to obtain realistic distribution and abundance values in this kind of breeding bird survey, it is essential to collect large enough samples and to consider the detection probability of each individual species using appropriate statistical methods.

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Avian Community Response to Midrotation Herbicide Release and Prescribed Burning in Conservation Reserve Program Plantations

Southern Journal of Applied Forestry ◽

10.1093/sjaf/32.3.111 ◽

2008 ◽

Vol 32 (3) ◽

pp. 111-119 ◽

Cited By ~ 9

Author(s):

Brandon Sladek ◽

L. Burger ◽

Ian Munn

Keyword(s):

Loblolly Pine ◽

Prescribed Burning ◽

Conservation Reserve Program ◽

Volume Growth ◽

Bird Species ◽

Community Response ◽

Individual Species ◽

Avian Community ◽

Disturbance Regimes ◽

Pinus Spp

Abstract Former agricultural lands converted to pine (Pinus spp.) plantations in the Conservation Reserve Program (CRP) have potential to provide early successional (ES) habitat for many regionally declining pine/grassland and shrub-successional bird species if actively managed with appropriate disturbance regimes. One such regime is use of the selective herbicide Imazapyr (Arsenal Applicators Concentrate) and prescribed burning, which is permitted on CRP lands and cost share payments are available. This study quantified combined effects of Imazapyr and prescribed fire on the breeding season avian community characteristics and pine volume growth in thinned, midrotation afforested loblolly pine (Pinus taedaL.) plantations in Mississippi. Herbicide treatments were applied in fall of 2002 and winter burns were conducted during winter and early spring of 2002–2003. ES bird species richness was significantly greater in the treated plots compared with controls for both 2003 and 2004. Ten individual species exhibited treatment effects. These responses by ES bird species indicate that midrotation CRPplantations can provide needed ES habitat if treated with appropriate disturbance regimes.

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Signatures of conserved and unique molecular features in Afrotheria

Scientific Reports ◽

10.1038/s41598-020-79559-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Arangasamy Yazhini ◽

Narayanaswamy Srinivasan ◽

Sankaran Sandhya

Keyword(s):

Ribosomal Proteins ◽

Individual Species ◽

Functional Domain ◽

Nucleic Acid Binding ◽

Uncharacterized Protein ◽

Homologous Proteins ◽

Functional Roles ◽

Molecular Features ◽

Specific Proteins ◽

Species Specific

AbstractAfrotheria is a clade of African-origin species with striking dissimilarities in appearance and habitat. In this study, we compared whole proteome sequences of six Afrotherian species to obtain a broad viewpoint of their underlying molecular make-up, to recognize potentially unique proteomic signatures. We find that 62% of the proteomes studied here, predominantly involved in metabolism, are orthologous, while the number of homologous proteins between individual species is as high as 99.5%. Further, we find that among Afrotheria, L. africana has several orphan proteins with 112 proteins showing < 30% sequence identity with their homologues. Rigorous sequence searches and complementary approaches were employed to annotate 156 uncharacterized protein sequences and 28 species-specific proteins. For 122 proteins we predicted potential functional roles, 43 of which we associated with protein- and nucleic-acid binding roles. Further, we analysed domain content and variations in their combinations within Afrotheria and identified 141 unique functional domain architectures, highlighting proteins with potential for specialized functions. Finally, we discuss the potential relevance of highly represented protein families such as MAGE-B2, olfactory receptor and ribosomal proteins in L. africana and E. edwardii, respectively. Taken together, our study reports the first comparative study of the Afrotherian proteomes and highlights salient molecular features.

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Numerical electrophoretic analysis and the behavior of larval proteins among Aedes mosquitoes

Canadian Journal of Zoology ◽

10.1139/z79-123 ◽

1979 ◽

Vol 57 (5) ◽

pp. 979-982 ◽

Cited By ~ 2

Author(s):

Emmanuel C. Igbokwe

Keyword(s):

Collective Behavior ◽

Protein Complex ◽

Related Species ◽

Electrophoretic Analysis ◽

Behavioral Profile ◽

Aedes Mosquitoes ◽

Molecular Behavior ◽

Interspecific Divergence ◽

Molecular Divergence ◽

Species Specific

Species-specific patterns of larval protein electrophoregrams obtained among three species of Aedes mosquitoes were analyzed numerically. A behavioral profile was derived and illustrated for the larval protein complex of each species. Patterns of interspecific divergence in molecular behavior not detectable otherwise from the electrophoregrams were evident in the behavioral profiles of the proteins. The degree of electrophoretic correspondence obtained from the number of shared fractions among the species differs from that derived from the collective behavior of proteins. The numerical and graphic approach to the interpretation of protein electrophoregrams offers another parameter for gauging molecular divergence among related species of insects.

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Cognitive flexibility in the wild: Individual differences in reversal learning are explained primarily by proactive interference, not by sampling strategies, in two passerine bird species

Learning & Behavior ◽

10.3758/s13420-021-00505-1 ◽

2022 ◽

Author(s):

Julie Morand-Ferron ◽

Michael S. Reichert ◽

John L. Quinn

Keyword(s):

Individual Differences ◽

Proactive Interference ◽

Cognitive Flexibility ◽

Reversal Learning ◽

Bird Species ◽

Passerine Bird ◽

Sampling Strategies ◽

In The Wild ◽

Wild Individual

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Locally rare species influence grassland ecosystem multifunctionality

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2015.0269 ◽

2016 ◽

Vol 371 (1694) ◽

pp. 20150269 ◽

Cited By ~ 67

Author(s):

Santiago Soliveres ◽

Peter Manning ◽

Daniel Prati ◽

Martin M. Gossner ◽

Fabian Alt ◽

...

Keyword(s):

Land Use ◽

Rare Species ◽

Common Species ◽

Ecosystem Functions ◽

Individual Species ◽

Conservation Priorities ◽

Below Ground ◽

Species Specific ◽

The Relationship ◽

Ecosystem Multifunctionality

Species diversity promotes the delivery of multiple ecosystem functions (multifunctionality). However, the relative functional importance of rare and common species in driving the biodiversity–multifunctionality relationship remains unknown. We studied the relationship between the diversity of rare and common species (according to their local abundances and across nine different trophic groups), and multifunctionality indices derived from 14 ecosystem functions on 150 grasslands across a land-use intensity (LUI) gradient. The diversity of above- and below-ground rare species had opposite effects, with rare above-ground species being associated with high levels of multifunctionality, probably because their effects on different functions did not trade off against each other. Conversely, common species were only related to average, not high, levels of multifunctionality, and their functional effects declined with LUI. Apart from the community-level effects of diversity, we found significant positive associations between the abundance of individual species and multifunctionality in 6% of the species tested. Species-specific functional effects were best predicted by their response to LUI: species that declined in abundance with land use intensification were those associated with higher levels of multifunctionality. Our results highlight the importance of rare species for ecosystem multifunctionality and help guiding future conservation priorities.

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