Relative Abundance Of Several Species Research Articles

Abstract 2800: Shotgun metagenomics of COPD-associated lung cancer tissue microbiome

Abstract The gut microbiome plays a crucial role in the development of multiple chronic diseases. Several solid tumors including lung cancer are also implicated in the gut microbiome in cancer initiation and progression, possibly affecting signaling pathways in the tumor microenvironment. However, the microbiome in the peripheral lung tissue is unexplored and their relationship to the lung tumor microenvironment is still unknown. Thus, to explore the relationship between the microbiome and the tumor microenvironment of lung cancer, we performed shotgun metagenomic sequencing of the lung cancer tissue, especially in lung cancer patients accompanied by chronic obstructive pulmonary disease (COPD). We confirmed the presence of a diverse microbiome in peripheral lung cancer tissue. Next, we focused on individual species. We observed significant differences in the relative abundance of several species between COPD and non-COPD patients, and cancer and non-cancer tissue. Then, we focused on the metagenomic diversity between samples. The number of species in COPD patients and cancer tissue were decreased. And the bacterial total abundance in each sample were observed similar trend. On the other hand, alpha diversity in each sample were showed different trend to them. In the analysis of beta diversity using Principal Coordinate Analysis (PCoA), clusters were formed in each group. These findings suggest that microbiome imbalance known as dysbiosis in the peripheral lung tissue may affect the tumor microenvironment resulting in cancer progression. Citation Format: Atsushi Matsuoka, Kazuhiko Shien, Shuta Tomida, Daisuke Mizuno, Masayoshi Ohki, Ryo Yoshichika, Tomohiro Higashihara, Naohiro Hayashi, Fumiaki Mukohara, Mao Yoshikawa, Ken Suzawa, Hiromasa Yamamoto, Shinichi Toyooka. Shotgun metagenomics of COPD-associated lung cancer tissue microbiome [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2800.

An Oligosaccharide Rich Diet Increases Akkermansia spp. Bacteria in the Equine Microbiota.

Some oligosaccharides induce growth of anti-inflammatory bacterial species and induce regulatory immunity in humans as well as animals. We have shown that the equine gut microbiota and the immune-microbial homeostasis largely stabilize within the first 50 days of life. Furthermore, we have previously established that certain bacterial species in the equine gut correlated with regulatory immunity. Accordingly, we hypothesized that an oligosaccharide rich diet fed to foals during the first 50 days would increase the abundance of bacterial species associated with regulatory immunity, and that this would influence immune responses in the foals. Eight pregnant mares and their foals were fed an oligosaccharide rich diet from 4 weeks before expected parturition until 49 days post-partum. Six mares and foals served as control. Fecal microbiota from mares and foals was characterized using 16S rRNA gene amplicon high throughput sequencing. On Day 49 the test foals had significantly higher abundances of Akkermansia spp. Blood sampled from the foals in the test group on Day 7, 28, and 49 showed non-significant increases in IgA, and decreases in IgG on Day 49. In BALB/cBomTac mice inoculated with gut microbiota from test and control foals we found increased species richness, increased relative abundance of several species identified as potentially anti-inflammatory in horses, which were unclassified Clostridiales, Ruminococcaceae, Ruminococcus, Oscilospira, and Coprococcus. We also found increased il10 expression in the ileum if inoculated with test foal microbiota. We conclude that an oligosaccharide diet fed to foals in the “window of opportunity,” the first 50 days of life, increases the abundance of anti-inflammatory species in the microbiota with potentially anti-inflammatory effects on regulatory immunity.

Microhistological analysis of ancient camelid dung from the southern Argentinean Puna: Past vegetation composition and diet

Identification of plant micro-remains in ancient dung is a tool used infrequently in archaeological studies to infer past vegetation diversity and herbivore diet. Through the microhistological analysis of dung of South American camelids from two micro-sectors of a rockshelter archaeological site in the Puna of Catamarca (Argentina), we identified plant micro-remains to illuminate our knowledge of the environment and the use of camelids during the late Holocene (540 ± 40 years BP). Grasses were the main plant category found in dung samples of both micro-sectors, followed by sedges (Cyperaceae), shrubs and annual herbs. However, relative abundance of several species and vegetation type varied between samples. Differences were also detected in the abundance of species from vegas (high Andean wetlands) and open areas. Our results could be explained by several factors, such as the season of the year in which dung was produced, differences in foraging habitats and foraging behavior of camelid species. Our work underscores the importance of microhistology as a useful tool for future paleoenvironmental studies. This method, combined with other reconstruction techniques (pollen, stable isotopes and macro-vegetation remains), has the potential to provide insights of paleovegetation histories and the use of wildlife by hunter-gatherers of the Southern Puna during the entire Holocene.

Salivary Microbiome Diversity in Caries-Free and Caries-Affected Children.

Dental caries (tooth decay) is an infectious disease. Its etiology is not fully understood from the microbiological perspective. This study characterizes the diversity of microbial flora in the saliva of children with and without dental caries. Children (3–4 years old) with caries (n = 20) and without caries (n = 20) were recruited. Unstimulated saliva (2 mL) was collected from each child and the total microbial genomic DNA was extracted. DNA amplicons of the V3-V4 hypervariable region of the bacterial 16S rRNA gene were generated and subjected to Illumina Miseq sequencing. A total of 17 phyla, 26 classes, 40 orders, 80 families, 151 genera, and 310 bacterial species were represented in the saliva samples. There was no significant difference in the microbiome diversity between caries-affected and caries-free children (p > 0.05). The relative abundance of several species (Rothia dentocariosa, Actinomyces graevenitzii, Veillonella sp. oral taxon 780, Prevotella salivae, and Streptococcus mutans) was higher in the caries-affected group than in the caries-free group (p < 0.05). Fusobacterium periodonticum and Leptotrichia sp. oral clone FP036 were more abundant in caries-free children than in caries-affected children (p < 0.05). The salivary microbiome profiles of caries-free and caries-affected children were similar. Salivary counts of certain bacteria such as R. dentocariosa and F. periodonticum may be useful for screening/assessing children’s risk of developing caries.

Capitalizing on opportunistic data for monitoring relative abundances of species.

With the internet, a massive amount of information on species abundance can be collected by citizen science programs. However, these data are often difficult to use directly in statistical inference, as their collection is generally opportunistic, and the distribution of the sampling effort is often not known. In this article, we develop a general statistical framework to combine such "opportunistic data" with data collected using schemes characterized by a known sampling effort. Under some structural assumptions regarding the sampling effort and detectability, our approach makes it possible to estimate the relative abundance of several species in different sites. It can be implemented through a simple generalized linear model. We illustrate the framework with typical bird datasets from the Aquitaine region in south-western France. We show that, under some assumptions, our approach provides estimates that are more precise than the ones obtained from the dataset with a known sampling effort alone. When the opportunistic data are abundant, the gain in precision may be considerable, especially for rare species. We also show that estimates can be obtained even for species recorded only in the opportunistic scheme. Opportunistic data combined with a relatively small amount of data collected with a known effort may thus provide access to accurate and precise estimates of quantitative changes in relative abundance over space and/or time.

Distribution, diversity gradients and Rapoport's elevational rule in the black scavenger flies of the Swiss Alps (Diptera: Sepsidae)

Abstract Elevational gradients influence the distribution and abundance of species drastically and can lead to variation in community composition. Although coprophagous flies are of ecological and economic importance, their biodiversity and distribution are largely neglected. We studied the impact of steep elevational gradients and geography on the distribution of sepsid flies in the Swiss Alps. Sepsidae are a family of acalyptrate flies strongly associated with decaying organic matter and vertebrate dung, and characterised by a high extent of sympatry in their breeding substrates. Historical, haphazardly sampled specimens from 116 locations covering an elevational range from 200 to 2000 m were available in ethanol collections of various Swiss museums. Nineteen species encompassing all native genera (Meroplius, Nemopoda, Saltella, Sepsis and Themira) were recorded. Local species richness increased linearly with elevation, while area‐corrected regional species richness of elevational belts increased asymptotically. Species occurring at higher altitudes had lower wing loadings and greater elevational ranges than lowland species, supporting Rapoport's elevational rule. Despite compositional similarities, the sepsid communities of the northern lowlands differed significantly from the alpine sepsid fauna. The southern lowlands were particularly differentiated in community composition due to a number of presumably thermophilic species that predominantly occur south of the Alps. Relative abundances of several species were thus strongly affected by elevation and climatic variables. We illustrate the impact of elevational gradients and geography on a community of closely related, often sympatric species, and discuss potential mechanisms of niche partitioning via temporal succession, thermal adaptation and differential resource use.

Clinical Insights from Metagenomic Analysis of Sputum Samples from Patients with Cystic Fibrosis

As DNA sequencing becomes faster and cheaper, genomics-based approaches are being explored for their use in personalized diagnoses and treatments. Here, we provide a proof of principle for disease monitoring using personal metagenomic sequencing and traditional clinical microbiology by focusing on three adults with cystic fibrosis (CF). The CF lung is a dynamic environment that hosts a complex ecosystem composed of bacteria, viruses, and fungi that can vary in space and time. Not surprisingly, the microbiome data from the induced sputum samples we collected revealed a significant amount of species diversity not seen in routine clinical laboratory cultures. The relative abundances of several species changed as clinical treatment was altered, enabling the identification of the climax and attack communities that were proposed in an earlier work. All patient microbiomes encoded a diversity of mechanisms to resist antibiotics, consistent with the characteristics of multidrug-resistant microbial communities that are commonly observed in CF patients. The metabolic potentials of these communities differed by the health status and recovery route of each patient. Thus, this pilot study provides an example of how metagenomic data might be used with clinical assessments for the development of treatments tailored to individual patients.

Insect visitation rates and foraging patterns differ in androdioecious and hermaphrodite-only populations of Laguncularia racemosa (Combretaceae) in Florida

Abstract:Insect-pollinated Laguncularia racemosa has a variable breeding system; some populations are androdioecious, with male and hermaphroditic plants, while others lack male plants. We observed the foraging behaviours of insects in three androdioecious and three hermaphrodite-only populations of L. racemosa in Florida. In each population, insect visitation rates were estimated from 30–108 timed intervals. We recorded the number of flowers visited by 144–224 insects during foraging bouts made to 15–40 male and hermaphroditic plants. Male plants in androdioecious populations had significantly more visitors than hermaphroditic plants, increasing the number of vectors carrying pollen from male plants. Further, many insects visited few flowers during foraging bouts, which should increase outcrossing frequency. According to mathematical models, male plants benefit from these combined factors. Plants in hermaphrodite-only populations had significantly more visitors than hermaphroditic plants in androdioecious populations. Proportionately more insects visited many flowers during foraging bouts in hermaphrodite-only versus androdioecious populations. The increased likelihood of geitonogamous self-pollination could help explain the lack of male plants in hermaphrodite-only populations. Differences in pollinator assemblages and the relative abundances of several species were responsible for differences in foraging behaviours: Apis mellifera, Bombus sp., Melissodes sp., Xylocopa sp., Euodynerus sp. and a calliphorid species.

Diversity and Habitat Use of Neotropical Harvestmen (Arachnida: Opiliones) in a Costa Rican Rainforest

In tropical rain forests, harvestmen assemblages are extremely diverse, with richness often exceeding 25 species. In the neotropics, there are published accounts of harvestmen faunas in South America rainforests (especially Amazonia), but relatively little is known about the community ecology of harvestmen in tropical forests of Central America. In this paper, we provide the first insights into the diverse assemblage of harvestmen inhabiting a wet forest at La Selva Biological Station, Costa Rica. Over five field seasons, we recorded 38 species. During our 2009 field season, we examined variation in species abundance, richness, and composition between adjacent successional forests (young secondary, mature secondary, and primary forests) as well as between distinct habitats (ground/litter layer and shrub/tree layer). Based on night samples (but not day), our results indicate that there are only minor differences in species composition and relative abundance between the forest ages, but no differences in richness. The ground/litter layer and shrub/tree layer habitats differed markedly in species composition, species richness, and relative abundance of several species. Our analysis of covariance supports the hypothesis that leg length is related to climbing behavior for several species belonging to Eupnoi and Laniatores.

Plecoptera response to acidification in several headwater streams in the Vosges Mountains (northeastern France)

Plecoptera are among the most threatened aquatic invertebrates in industrialised countries as they are very sensitive to many types of pollution. On the contrary, stoneflies are largely considered as tolerant to acidification in comparison with many other macroinvertebrate groups. However, an understanding of Plecoptera responses to acidification is lacking due firstly to the complexity of most Nemouroidea specific determinations at larval instars and secondly to the poor Plecoptera diversity in North European countries, where most studies on acidification impact were performed. In the present study, we assess the response of Plecoptera species and species assemblages to freshwater acidification by collecting adults, allowing specific determination. Significant relationships were observed between richness and several chemical parameters. The relative abundance of several species was also significantly correlated to pH and acid neutralizing capacity (ANC). The results highlight the importance of species determination to assess the effects of acidification. Direct effects, i.e. ecotoxicological effects, were not the only factor leading to the erosion of Plecoptera diversity. Finally, this study tends to demonstrate that this order of aquatic insects is more severely affected by freshwater acidification than commonly believed.

Response of Vegetation on Subantarctic Macquarie Island to Reduced Rabbit Grazing

The responses of vascular plant species to a reduction in grazing pressure were monitored as part of a rabbit-control program on Macquarie Island. The initial response of the vegetation was more luxuriant growth with changes in abundance recorded after 2–3 years. After 8–10 years the relative abundance of several species had changed while species not previously recorded had appeared on study sites and others had disappeared. Of the 32 species recorded on study sites, 11 species (Agrostis magellanica, Deschampsia chapmanii, Festuca contracta, Juncus scheuchzerioides, Luzula crinita, Pleurophyllum hookeri, Poa annua, P. foliosa, Stilbocarpa polaris and Uncinia spp. (two species)) were found to form the major portion of the rabbits’ diet while another four species (Acaena magellanica, Cerastium fontanum, Isolepis aucklandica, Polystichum vestitum) were moderately grazed. The other species were either rarely grazed or occurred too infrequently to assess. Of the 25 species that were recorded over 30 times, 17 were considered to have benefited from the introduction of rabbits.

Macroinvertebrate Colonization of the Intertidal Habitat of a Dredge Spoil Island in North Florida

Macroinvertebrate colonization of the intertidal habitat of a dredge spoil island was studied for one year by collecting triplicate 0.0625-m2 x 10-cm core samples of substratum from four stations established relative to the slope of the habitat. Fauna first colonized the subtidal site, and after lapses of time appeared respectively at low, mid and high-tide stations. The total abundance and diversity of the assemblage increased significantly in the latter half of the year mainly due to the appearance of late colonizers at low and mid-tide stations. The temporal abundance patterns at the four stations were variable. Several species that initially appeared at low tide station later aggregated at other stations. While no discrete species groups formed at each station, the relative abundances of several species were related to tidal exposure gradient. This phenomenon was reflected in the species dominance hierarchy at the four stations and spatial distributions in the intertidal zone. Equilibrium between extinction and immigration rates of species did not occur within the year. The intertidal assemblages as a whole did not show stability of species composition or species abundance.

Seabirds and Fishing Vessels: Co-Occurrence and Attraction

Seabirds in many areas of the world feed on fish, crustaceans and other organic matter discarded from fishing vessels working over continental shelves or other fishing grounds (Rees 1963, Grindley 1967, Jenkins 1971, Bartle 1974, Jehl 1974, Summerhayes et al. 1974). Our observations off the coast of Washington (Wahl 1975) have enabled us to quantitatively examine such behavior in terms of the effect of fisheries discards on the dispersion of different seabird species, and the relative importance of different types of vessels to different species. In this paper we compare and evaluate the relative abundances of several species recorded in the vicinity of fishing vessels with those recorded, on the same day, away from fishing vessels. The results of these analyses are discussed in relation to our observations of the feeding behavior of the different species at fishing vessels.