Cumulative Abundance Research Articles

Assessing the conservation status of EU forest habitats: The case of Quercus suber woodlands

In the European Union (EU), there is an urgent need to define a specific and standardized monitoring strategy for Habitat Directive (HD) forest habitats, like Quercus suber woodlands (EU habitat 9330). Such forests are an important component of western Mediterranean landscapes. In Italy, they are undergoing a relevant regression due to the decline of traditional management. Here, we tested the effectiveness of the Cumulative Abundance Profile (CAP) method in assessing the conservation status (CS) of habitat 9330 in central Italy. The CAP method compares plant communities based on their structure and species composition. Our aims were: i) to test the effectiveness of structure and species composition of the tree layer as predictors of different understories and forest habitat types; ii) to compare the results obtained using the CAP method with those deriving from traditional cover-based (CB) vegetation classification; iii) to evaluate the advantages and limitations of using the two methods to assess the CS of EU forest habitats.The similarity between 48 sampling plots was assessed analysing data through the Fuzzy C-Means clustering method. The three groups resulting from the analysis of CAP data corresponded to as many different community types, each highlighting a different CS of the habitat 9330. For the CAP-based groups, the Mantel test showed a significant correlation between the overstory and the understory composition. Besides, the indicator species analysis detected significantly distinct understories in the three groups, and hypsometric curves suggested that each one is related to soils with different fertility. The CB classification (cover data of all species) produced three clusters, too. However, according to the Adjusted Rand index, the agreement between the two classifications was low. When woods have a higher compositional and structural diversity, in CB classification many plots remain unexplained from an ecological, floristic, and conservation point of view. Compositional data, even if essential, resulted insufficient to classify and monitor the CS of highly structurally complex forest habitats. This highlights that the role of structural data in the classification and monitoring of HD forests is underrated, since they resulted to be an important proxy for forest monitoring and management. The CAP procedure could thus represent a viable standardized methodology to assess the CS of forest habitats, together with the analysis of the understory composition. Further studies applying the CAP method in other woody habitats might support the inclusion of this methodology in the guidelines for EU Habitats monitoring.

Prospective manipulation of the gut microbiome with Microbial Ecosystem Therapeutic 4 (MET4) in locoregionally advanced oropharyngeal squamous cell carcinoma (LA-OPSCC) undergoing primary chemoradiation (ROMA2).

6059 Background: Therapeutic manipulation of the gut microbiome in cancer patients (pts) is an area of active investigation. MET4 (NuBiyota) is an oral alternative to fecal transplant consisting of a mixture of human gut bacteria associated with immunotherapy (IO) response. We previously reported variation in IO-responsive taxa across stages in human papilloma virus related (HPV+) LA-OPSCC pts treated with chemoradiotherapy (CRT) (Oliva et al., ASCO 2020). ROMA-2 is the first interventional study evaluating the safety, feasibility and ecological effect of MET4, in combination with definitive CRT in HPV+ LA-OPSCC (NCT03838601). Methods: This is an investigator-initiated study of pts with HPV+ LA-OPSCC treated with standard of care CRT. MET4 is administered daily until week 4 of CRT or unacceptable toxicity. Stool samples are collected at baseline, week 4, week 8-10, and 2-months post CRT. Bacterial V4 16S rDNA was extracted from stool and sequenced. Microbiome analyses were conducted in R using DADA2, phyloseq and DESeq2. Results: As of February 11 2021, 25 pts have been enrolled. A total of 50 stool samples from the first 14 pts were collected (98% adherence) and analyzed. Baseline cohort characteristics: median age = 62.5 (range, 48-69); Stage I/II/III = 5/1/8; use of antibiotics = 1pt. 3 pts did not complete the 3-week course of MET4 treatment due to non-compliance (n = 1), withdrawal of consent (n = 1) and grade 2 diarrhea (n = 1). Other reported MET4-related adverse events (all grade 1) included bloating (n = 2), flatulence (n = 1) and belching (n = 1). No longitudinal changes in alpha-diversity were seen from baseline through follow up. Administration of MET4 resulted in a transient trend towards increased cumulative MET4 taxa relative abundance (RA) by week 4. Stage III patients demonstrated the lowest MET4 taxa RA at baseline, and the greatest increase in MET4 taxa RA from baseline to week 4. By week 4 the following taxa in all pts were increased compared to baseline: Eubacterium hallii (21.71 Log2Fold change[L2FC], padj < 0.001) and Parabacteroides johnsonii (23.67 L2FC, padj < 0.001). An increase in the following taxa was observed by weeks 8-10 compared to baseline: Akkermansia muciniphilla (3.75 L2FC, padj = 0.027), Bacteroides fragilis (6.73 L2FC, padj = 0.010), Alistipes onderdonkii (3.30 L2FC, padj = 0.049) and Parabacteroides distasonis (24.43 L2FC, padj < 0.001). Conclusions: Manipulation of the gut microbiota in these pts was feasible and safe. MET4-induced ecological changes are heterogenous and vary by taxa. MET4 taxa implicated in IO-response were increased by week 4 and week 8-10. This increase was higher in pts with stage III disease. These data suggest that specific subgroups may benefit from combination IO therapy and may guide pt selection for further interventional clinical trial design. Clinical trial information: NCT03838601.

Characterization of bacterial community and flavor differences of different types of Douchi.

According to the appearance and technology, traditional fermented Douchi can be divided into dried Douchi and wet Douchi. However, there are few reports on the difference of bacterial community structure between them or the influence of bacterial community on product flavor. In this study, high‐throughput sequencing technology and electronic nose were used to measure the bacterial diversity and flavor of 40 Douchi samples, and the correlation between them was explored by multivariate statistical means combined with COG database. Results showed that the cumulative average relative abundance of Firmicutes and Proteobacteria in the samples was as high as 95.93%, and the former was the core bacteria phylum. On the whole, the dominant bacteria in Douchi were Bacillus (50.67%), Staphylococcus (14.07%), Enterococcus (2.54%), Proteus (1.61%), Brevibacillus (1.46%), Providencia (1.26%), Weissella (1.24%), and Ureibacillus (1.19%). LEfSe analysis indicated that Bacillus can be used as a biomarker in dried fermented soybeans. Meanwhile, dried samples contained more intensive aromatic substances, but were significantly lower in W6S (selectivity to hydrogen) and W3S (methane‐aliph) compared with the wet samples. Aneurinibacillus and Brevibacillus were helpful to the formation of aromatic flavor in Douchi, but Vagococcus and Corynebacterium were the opposite. Gene and microbial phenotypic prediction showed that microorganisms in dried Douchi use protein more efficiently, while in wet Douchi, microbial energy metabolism was more vigorous. The pathogenic potential of microorganisms in dried samples was higher than that in wet. This study can sound the alarm for improving the safety of home‐brewed Douchi and provide guidance for the subsequent screening of strains that enhance the flavor of fermented soybeans.

Bacteroidetes Species Are Correlated with Disease Activity in Ulcerative Colitis.

Fecal microbiota transplantation following triple-antibiotic therapy (amoxicillin/fosfomycin/metronidazole) improves dysbiosis caused by reduced Bacteroidetes diversity in patients with ulcerative colitis (UC). We investigated the correlation between Bacteroidetes species abundance and UC activity. Fecal samples from 34 healthy controls and 52 patients with active UC (Lichtiger’s clinical activity index ≥5 or Mayo endoscopic subscore ≥1) were subjected to next-generation sequencing with HSP60 as a target in bacterial metagenome analysis. A multiplex gene expression assay using colonoscopy-harvested mucosal tissues determined the involvement of Bacteroidetes species in the mucosal immune response. In patients with UC, six Bacteroides species exhibited significantly lower relative abundance, and twelve Bacteroidetes species were found significantly correlated with at least one metric of disease activity. The abundance of five Bacteroidetes species (Alistipes putredinis, Bacteroides stercoris, Bacteroides uniformis, Bacteroides rodentium, and Parabacteroides merdae) was correlated with three metrics, and their cumulative relative abundance was strongly correlated with the sum of Mayo endoscopic subscore (R = −0.71, p = 2 × 10−9). Five genes (TARP, C10ORF54, ITGAE, TNFSF9, and LCN2) associated with UC pathogenesis were expressed by the 12 key species. The loss of key species may exacerbate UC activity, serving as potential biomarkers.

Seasonality of floral resources in relation to bee activity in agroecosystems.

The contribution of wild insects to crop pollination is becoming increasingly important as global demand for crops dependent on animal pollination increases. If wild insect populations are to persist in agricultural landscapes, there must be sufficient resources over time and space. The temporal, within‐season component of floral resource availability has rarely been investigated, despite growing recognition of its likely importance for pollinator populations. Here, we examined the visitation rates of common bee genera and the spatiotemporal availability of floral resources in agroecosystems over one season to determine whether local wild bee activity was limited by landscape floral resource abundance, and if so, whether it was limited by the present or past abundance of landscape floral resources. Visitation rates and landscape floral resources were measured in 27 agricultural sites in Ontario and Québec, Canada, across four time periods and three spatial scales. Floral resources were determined based on species‐specific floral volume measurements, which we found to be highly correlated with published measurements of nectar sugar mass and pollen volume. Total floral volume at varying spatial scales predicted visits for commonly observed bee genera. We found Lasioglossum and Halictus visits were highest in landscapes that provided either a stable or increasing amount of floral resources over the season. Andrena visits were highest in landscapes with high floral resources at the start of the season, and Bombus visits appeared to be positively related to greater cumulative seasonal abundance of floral resources. These findings together suggest the importance of early‐season floral resources to bees. Megachile visits were negatively associated with the present abundance of floral resources, perhaps reflecting pollinator movement or dilution. Our research provides insight into how seasonal fluctuations in floral resources affect bee activity and how life history traits of bee genera influence their responses to food availability within agroecosystems.

The variety, terroir, and harvest types affect the yield and the phenolic and sterolic profiles of hemp seed oil

In this work, considering the rising interest towards the exploitation of hemp seed oil in human nutrition, 45 hemp seeds from mono-variety fields were analyzed for their yield, oil content, in vitro antioxidant activity, followed by a comprehensive assessment of phenolic and sterolic composition. The results demonstrated that seed dimension is inversely correlated to total oil content, thus being a potential reference for quality assessment of seeds and for further improvement of hemp varieties. The UHPLC-QTOF metabolomic analysis revealed a large abundance of phytosterols, lower-molecular-weight phenolic acids, and lignanamides. Differences across varieties could be described, with Diana hemp seed oil having the highest cumulative abundance of phytochemicals, recording 6.04 mg/g. Overall, the in vitro antioxidant activity results indicated that hemp seed oil antioxidants have a low potential for preventing oil rancidity, with phenolic acids being the most active radical scavengers. Besides, in the group of Futura 75 samples cultivated across Italy, the type of harvesting affected the acidity value significantly as a consequence of mechanical harvest and post-harvest handling. Finally, multivariate statistics following untargeted metabolomic analysis showed that variety, geographical origin, and harvest-type were able to affect the phytochemical profiles with different incidences, with some phytochemicals proposed for the first time as potential discriminant markers.

Nesting tree selection by scattered heronry birds of drought prone Northern Bankura, West Bengal, India: preference of Phoenix sylvestris near wetland-associated habitats

The present study was conducted in the Gangajalghati block of Northern Bankura, India, to investigate the habitat and nest tree preference of three colonial waterbirds viz. Nycticorax nycticorax, Egretta garzetta, and Ardeola grayii. The study sites were surveyed for 20 months between 2017 and 2020. A total of 817 nests with an average of 204 per year were recorded on 13 tree species. Nycticorax nycticorax showed the maximum nest count followed by Egretta garzetta and Ardeola grayii. Relative abundance data revealed Phoenix sylvestris as the most abundant species (45%) of the area and harbours the highest proportion (33%) of nests. Pooled nest count data showed significantly higher (p < 0.01) total nest counts in the wetland associated habitats than others. The study observed more nest density of all three species near a cluster of small ponds than in a large water body. Year-wise difference in cumulative nest number and mean nest abundance of all three species was statistically insignificant. The interspecific nearest neighbour on Phoenix sylvestris were Egretta garzetta (88.37%) for Nycticorax nycticorax and Nycticorax nycticorax (83.25%) for Egretta garzetta and Ardeola grayii. Further, the study evaluated the impact of two tropical cyclones (Amphan and Fani) on the total nest count and found that more than 75% nests (p < 0.05) were destroyed by the mighty Amphan in May 2020. The study provides a baseline data on nesting trees and habitat preference of three species of heronry birds from Northern Bankura.

Cardiac Shock Wave Therapy Alleviates Hypoxia/Reoxygenation-Induced Myocardial Necroptosis by Modulating Autophagy.

Regulated necrosis (necroptosis) is crucially involved in cardiac ischaemia-reperfusion injury (MIRI). The aim of our study is to investigate whether shock wave therapy (SWT) is capable of exerting protective effects by inhibiting necroptosis during myocardial ischaemia-reperfusion (I/R) injury and the possible role of autophagy in this process. We established a hypoxia/reoxygenation (H/R) model in vitro using HL-1 cells to simulate MIRI. MTS assays and LDH cytotoxicity assay were performed to measure cell viability and cell damage. Annexin V/PI staining was used to determine apoptosis and necrosis. Western blotting was performed to assess the changes in cell signaling pathways associated with autophagy, necroptosis, and apoptosis. Reactive oxygen species (ROS) production was detected using DHE staining. Autophagosome generation and degradation (autophagic flux) were analysed using GFP and RFP tandemly tagged LC3 (tfLC3). HL-1 cells were then transfected with p62/SQSTM1 siRNA in order to analyse its role in cardioprotection. Our results revealed that SWT increased cell viability in the H/R model and decreased receptor-interacting serine/threonine-protein kinase 1 (RIPK1) and RIPK3 expression. ROS production was also inhibited by SWT. Moreover, SWT decreased Beclin1 expression and the ratio of LC3-II/LC3-I following H/R. Simultaneously, in the tfLC3 assay, the SWT provoked a decrease in the cumulative autophagosome abundance. siRNA-mediated knockdown of p62 attenuated H/R-induced necroptosis, and SWT did not exert additive effects. Taken together, SWT ameliorated H/R injury by inhibiting necroptosis. SWT also relieved the blockade of autophagic flux in response to H/R injury. The restoration of autophagic flux by SWT might contribute to its cardioprotective effect on necroptosis following H/R injury.

Summarizing abundance changes in waterbirds: some problems and a possible solution

After conducting replicated counts of migratory waterbirds at a given wetland, some authors choose to compute the mean abundance throughout the study period, whereas others report the peak value or the cumulative total. Here, we use fictitious and real examples to illustrate how some of these procedures can lead to distorted conclusions. For species with skewed abundance distributions, the mean does not summarize the central tendency in the data, and the median should be used; however, for many migratory waterbirds, median abundances at a given site can be null. Also, the probability of double-counting the same individuals increases when replicated surveys cover a long time. Moreover, since the cumulative abundance of a species/assemblage increases with the number of surveys, misleading results can be obtained if researchers apply different sampling efforts. Finally, the ranking and selection of wetlands for waterbird conservation can be misguided if cumulative totals are compared against standard criteria (i.e., Ramsar sites, IBAs). To avoid the above mentioned problems, we propose to use the maximum, peak abundance of a given waterbird species during the course of the study, or the sum of maxima, peak values across all the species in the same waterbird assemblage.

DIVERSITY AND ABUNDANCE OF LANDING APHIDS IN TWO AREAS OF SEED POTATO PRODUCTION IN TUNISIA; RELATIVE TO THE INCIDENCE OF POTATO VIRUSES

Aphid flight activities were monitored in 2015 in two areas of seed potato production in Tunisia. Yellow water traps were used to investigate the diversity of aphidofauna and the incidence of aphids involved in potato virus transmission. A total of 9966 specimens belonged to 73 taxa were captured. The cumulative abundance recorded in Douala (first site) was much higher than in El Ogla (second site) (8768 vs 1189 specimens). The most preponderant species in Douala were Aphis spiraecola Patch (66.1%) and Aphis spp. group (13.5%). In El Ogla Rhopalosiphum padi (L.) comprised 58.9% of total catches, followed by Acyrthosiphon pisum (Harris) (12%) and Aploneura lentisci (Passerini) (10.4%). The highest values of diversity indices were recorded on April 23 th [Shannon-Wiener index (H’)=2.58; Simpson index (1-D)=0.88] in Douala and on May 12th (H’=1.70; 1-D=0.75) in El Ogla. The detection of viral infections by DAS-ELISA determined the predominance of Potato virus Y amongst five main potato viruses tested. Overall Chi-square analysis determined significant differences crossing all areas of seed and ware potatoes and season crops. The highest incidence of viruses was recorded in Douala (18.5%) while El Ogla was under the threshold value (4%). This might be attributed to the occurrence of aphids in early season known previously to be efficient vectors of PVY and to the characteristics of area including climatic conditions, altitude and landscape structure. These results provide new evidence for El Ogla as ideal site to produce healthy tubers while conversely Douala is favourable for the propagation of vectors and viruses.

Isolation promotes abundance and species richness of fishes recruiting to coral reef patches

Habitat area and fragmentation are recognised as important factors that influence population size, community structure and extinction risk. Abundance and species richness universally increase with habitat area. However, the effects of different aspects of habitat fragmentation, including variation in patch size, number and isolation are often not distinguished from each other or the overall effects of habitat amount. Here we experimentally tested predictions concerning the effects of isolation on abundance, species richness and community structure of coral reef fishes colonising patch reefs by constructing clusters of patches of the same number and size, but manipulating reef spacing. Hexagonal clusters of 7 experimental patch reefs (6 edge and 1 central) with 3 levels of isolation (1 m, 5 m, and 15 m spacing) were established at Kavieng, Papua New Guinea and colonisation was recorded after 6 weeks in 2014. We also deployed video cameras to test whether isolation affected the activity of transient predatory fishes. As predicted, isolation had a positive effect on both mean abundance and species richness at both the cluster and patch scale. The cumulative abundance and species richness exhibited linear increases in relation to habitat area within clusters (from 1 to 7 patch reefs), but the slope increased with the degree of isolation. There was some evidence that transient predators remained longer and were more successful when patches were close together, which may explain the lower abundance and richness of juvenile fish assemblages on more aggregated patch reefs. This study demonstrates that while habitat amount is fundamentally important, isolation has significant effects that will need to be distinguished from other aspects of fragmentation when examining the processes structuring reef fish communities.

Comparison of the interest of four types of organic mulches to reclaim degraded areas: a field study based on their relative attractiveness for soil macrofauna

The study focused on the attractiveness of mulches (consisting of the addition of a layer material to the soil surface) and their efficiency to promote recolonization by pedofauna of isolated and degraded areas. The experimental study was set up in the former coal mining area of Northern France. This area is particularly disturbed and fragmented by land-use change, urbanization, industry, intensive agriculture and metal pollution. To examine the movements of pedofauna, four kinds of mulches were applied: (i) Ramial Chipped Wood (RCW), (ii) chopped Miscanthus, (iii) dead leaves and (iv) wheat straw as well as plastic sheeting, a material often used in green spaces. A negative control consisted in soil without mulch addition. The experimental set-up consisted of a set of 18 bands of mulch (6 m long x 0.5 m width x 8 cm thick, i.e. a volume of 0.04 m3 per band) installed on three adjacent plots on a surface area which stretch on 4400 m2: (i) plot F1, a mixed plantation, (ii) plot M consisted of three rows of maples (both considered to be the reservoir of biodiversity) and (iii) plot BF, an ash plantation (with lower biodiversity). Faunistic communities of soil present within the mulches were monitoring using pitfall traps for four months (April to July), at a rate of eight surveys for each of the 90 traps installed, i.e. 720 samples. Different life traits and indices of diversity were studied, more specifically on carabid beetles. The main objective of the study was first to check whether mulches could or not reconnect different planted plots in a peri-urban landscape highly modified by human activities. The second aim was to find which type of mulch had the best efficiency in the recovery of the connectivity between plots. The last questions were which type of zoological groups could be favoured by the use of mulches and which benefits for ecosystem functioning. The main hypotheses of this study were: (i) Organic mulches would act as dispersal corridors and refuge zones to the soil organisms; (ii) organic mulches would be attractive to many organisms with various ecological needs.This study highlighted the potential benefits of using the mulching technique to support ecological connectivity in disturbed environment since this method highlighted the presence of individuals with different diets (saprophagous, predators, phytophagous and so forth), small and large size species which do not have the same dispersal capacities as well as species that are more dependent on forest environments and others that depend on more open environments. The study concluded that organic mulches are more favourable to pedofauna than soil without mulch or plastic sheeting. With regard to organic mulches, no difference was noted, either in terms of cumulative abundance or monthly monitoring. However, for carabids, it should be noted that dead leaves and wheat straw have higher specific richness than Miscanthus and RCW.

Gut Microbiota of Five Sympatrically Farmed Marine Fish Species in the Aegean Sea.

In this study, we hypothesized that sympatrically grown farmed fish, i.e. fish which experience similar environmental conditions and nutritionally similar diets, would have more convergent gut microbiota. Using a "common garden" approach, we identified the core microbiota and bacterial community structure differences between five fish species farmed in the same aquaculture site on the west coast of the Aegean Sea, Greece. The investigated individuals were at similar developmental stages and reared in adjacent (< 50 m) aquaculture cages; each cage had 15 kg fish m-3. The diets were nutritionally similar to support optimal growth for each fish species. DNA from the midgut of 3-6 individuals per fish species was extracted and sequenced for the V3-V4 region of the bacterial 16S rRNA. Only 3.9% of the total 181 operational taxonomic units (OTUs) were shared among all fish. Between 5 and 74 OTUs were unique to each fish species. Each of the investigated fish species had a distinct profile of dominant OTUs, i.e. cumulative relative abundance of ≥ 80%. Co-occurrence network analysis for each fish species showed that all networks were strongly dominated by positive correlations between the abundances of their OTUs. However, each fish species had different network characteristics suggesting the differential significance of the OTUs in each of the five fish species midgut. The results of the present study may provide evidence that adult fish farmed in the Mediterranean Sea have a rather divergent and species-specific gut microbiota profile, which are shaped independently of the similar environmental conditions under which they grow.

Macrozoobenthos Diversities in Ciwulan River, Tasikmalaya Regency, West Java

Ciwulan River is one of the longest rivers in Tasikmalaya Regency with a diversity of macrozoobenthos as one of the biota contained therein. The purpose of this study was to describe the diversity of macrozoobenthos in The Ciwulan River, Tasikmalaya Regency. This research is important because macrozoobenthos is a component in determining river bioindicators. The method used in this study is exploratory with a purposive sampling technique. Sampling of macrozoobenthos is done using a surber net and measurement of environmental indicators is done in situ at the observation station. Samples of macrozoobenthos were taken from three different stations including upstream Station I (Salawu), middle part II (Sukaraja), and downstream Station III (Cikalong). Data collection was carried out in November 2019-April 2020 in the Ciwulan River, Tasikmalaya Regency. Analysis of the observed data was then calculated relative abundance, cumulative abundance, diversity index, uniformity index, and dominance index. The results showed that the macrozoobenthos were found to have 24 species with 476 individuals/m 2 belonging to the gastropod class as many as 21 species with 433 individual/m 2 , bivalve class two species with 37 individuals/m 2 and crustacean class one species with six individuals/m 2 . Macrozoobenthos that are commonly found are Tarebia granifera Lamarck, 1822 totaling 222 individuals/m 2 . The highest relative abundance was found in Station I with the Tarebia granifera Lamarck species, 1822 which was 0.65%. and the lowest relative abundance was found in Station II with the species Lymnaea (Radix) rubiginosa Michelin, 1831 and Gyraulus convexiusculus Hutton, 1849 by 0.006%. Cumulative abundance values range from 54-350 individuals/m 2 . Diversity index values range from 1.02-1.67 with the category of moderate diversity. Uniformity index values ranged from 0.58 to 0.73 with a high category. The dominance index value ranges from 0.33 to 0.47 with the low category. Overall based on environmental parameters and ecological index measurements, the Ciwulan River is classified as not yet polluted and the conditions are suitable for macrozoobenthos life and have a moderate diversity of categories with relatively stable environmental conditions

Fish assemblages and size-spectra variation among rivers of Lake Victoria Basin, Kenya

Riverine ecosystems are some of the most biologically diverse on earth, but are also among the most threatened by anthropogenic actions. Lack of local-scale studies monitoring changes in riverine populations makes it difficult to determine how communities respond to region-specific anthropogenic threats. In this study, we compared fish assemblage structure in six rivers in the Lake Victoria Basin (LVB), Kenya. Data collected during different periods between 2004 and 2018 were used to derive abundance size-spectra parameters and community diversity metrics as proxies for ecosystem condition and function. Species dominance in the rivers was high with only five species accounting for >72% of cumulative relative abundance while, 33 species contributed <10% of all individuals sampled. One-way analysis of similarity test (ANOSIM) indicated significant dissimilarity in fish composition between the rivers (Global R = 0.405, p = 0.0187) while, similarity percentage analysis (SIMPER) partitioned differences to variations in relative abundance of mainly two species (Labeobarbus altianalis, and Labeo victorianus). Eight species were restricted to single river basins suggesting presence of local endemism. Abundance size-spectra parameters (intercepts and slopes) used as proxies for food-web capacity and ecological efficiency fluctuated over time with periods of relative stability, indicating spatial (among rivers) and temporal (yearly) variations in ecological processes in the rivers. The food-web capacity and ecological efficiency indices showed basin-specific relationships with community metrics (dominance, richness, evenness, Shannon-Weiner and Simpson diversity indices) and catch per unit effort (CPUE), suggesting their potential use as indicators of ecosystem structure. The findings of this study show promise in the use of size-spectra parameters as proxies for riverine ecosystem structure and functioning under a gradient of perturbation.

Impact of Fiber-Based Enteral Nutrition on the Gut Microbiome of ICU Patients Receiving Broad-Spectrum Antibiotics: A Randomized Pilot Trial.

Dietary fiber increases the abundance of bacteria that metabolize fiber into short-chain fatty acids and confers resistance against gut colonization with multidrug-resistant bacteria. This pilot trial estimated the effect of fiber on gut short-chain fatty acid-producing bacteria in the ICU. Randomized, controlled, open label trial. Medical ICU. Twenty ICU adults receiving broad-spectrum IV antibiotics for sepsis. 1:1 randomization to enteral nutrition with mixed soy- and oat-derived fiber (14.3 g fiber/L) versus calorie- and micronutrient-identical enteral nutrition with 0 g/L fiber. Rectal swabs and whole stools were collected at baseline and on study Days 3, 7, 14, and 30. The primary outcome was within-individual change in the cumulative relative abundance of short-chain fatty acid-producing taxa from baseline to Day 3 based on 16S sequencing of rectal swabs. The secondary outcome was Day 3 cumulative short-chain fatty acid levels based on mass spectrometry of whole stools. Analyses were all intent to treat. By Day 3, the fiber group received a median of 32.1 g fiber cumulatively (interquartile range, 17.6-54.6) versus 0 g fiber (interquartile range, 0-4.0) in the no fiber group. The median within-individual change in short-chain fatty acid producer relative abundance from baseline to Day 3 was +61% (interquartile range -51 to +1,688) in the fiber group versus -46% (interquartile range, -78 to +13) in the no fiber group (p = 0.28). Whole stool short-chain fatty acid levels on Day 3 were a median of 707 μg short-chain fatty acids/g stool (interquartile range, 190-7,265) in the fiber group versus 118 μg short-chain fatty acids/g stool (interquartile range, 22-1,195) in the no fiber group (p = 0.16). Enteral fiber was associated with nonsignificant trends toward increased relative abundance of short-chain fatty acid-producing bacteria and increased short-chain fatty acid levels among ICU patients receiving broad-spectrum IV antibiotics. Larger studies should be undertaken and our results can be used for effect size estimates.

Niche-based assembly of bacterial consortia on the diatom Thalassiosira rotula is stable and reproducible

With each cell division, phytoplankton create new space for primary colonization by marine bacteria. Although this surface microenvironment is available to all planktonic bacterial colonizers, we show the assembly of bacterial consortia on a cosmopolitan marine diatom to be highly specific and reproducible. While phytoplankton–bacteria interactions play fundamental roles in marine ecosystems, namely primary production and the carbon cycle, the ecological paradigm behind epiphytic microbiome assembly remains poorly understood. In a replicated and repeated primary colonization experiment, we exposed the axenic diatom Thalassiosira rotula to several complex and compositionally different bacterial inocula derived from phytoplankton species of varying degrees of relatedness to the axenic Thalassiosira host or natural seawater. This revealed a convergent assembly of diverse and compositionally different bacterial inocula, containing up to 2071 operational taxonomic units (OTUs), towards a stable and reproducible core community. Four of these OTUs already accounted for a cumulative abundance of 60%. This core community was dominated by Rhodobacteraceae (30.5%), Alteromonadaceae (27.7%), and Oceanospirillales (18.5%) which was qualitatively and quantitatively most similar to its conspecific original. These findings reject a lottery assembly model of bacterial colonization and suggest selective microhabitat filtering. This is likely due to diatom host traits such as surface properties and different levels of specialization resulting in reciprocal stable-state associations.

Interpretable and accurate prediction models for metagenomics data.

BackgroundMicrobiome biomarker discovery for patient diagnosis, prognosis, and risk evaluation is attracting broad interest. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as black boxes and seldom generalize well. Their interpretation is challenging for physicians and biologists, which makes them difficult to trust and use routinely in the physician–patient decision-making process. Novel methods that provide interpretability and biological insight are needed. Here, we introduce “predomics”, an original machine learning approach inspired by microbial ecosystem interactions that is tailored for metagenomics data. It discovers accurate predictive signatures and provides unprecedented interpretability. The decision provided by the predictive model is based on a simple, yet powerful score computed by adding, subtracting, or dividing cumulative abundance of microbiome measurements.ResultsTested on >100 datasets, we demonstrate that predomics models are simple and highly interpretable. Even with such simplicity, they are at least as accurate as state-of-the-art methods. The family of best models, discovered during the learning process, offers the ability to distil biological information and to decipher the predictability signatures of the studied condition. In a proof-of-concept experiment, we successfully predicted body corpulence and metabolic improvement after bariatric surgery using pre-surgery microbiome data.ConclusionsPredomics is a new algorithm that helps in providing reliable and trustworthy diagnostic decisions in the microbiome field. Predomics is in accord with societal and legal requirements that plead for an explainable artificial intelligence approach in the medical field.

Study of community assembly patterns and interspecific interactions involved in insect succession on rat carcasses

AbstractAlthough many forensic entomological studies have described patterns of carrion insect succession and theoretical studies have explained interspecific interactions that drive succession, empirical studies on the quantitative and ecological aspects of carrion insect succession, such as the degree of historical contingency in community assembly and interspecific interactions during succession, are limited. In this study, I investigated variability in the successional pathways of carrion insect communities in rat carcasses and their decomposition processes, and examined the interspecific interactions involved in succession, such as the effects of carcass utilization by early‐arriving species on late‐arriving species. Members of the families Calliphoridae and Formicidae and the species Eusilpha japonica (Motschulsky) and Nicrophorus concolor Kraatz were chiefly observed. In almost all carcasses, formicid species arrived first, and calliphorid species and E. japonica arrived simultaneously or immediately after. Nicrophorus concolor arrived last, with its time of colonization occurring earlier in carcasses with greater E. japonica abundance. Meanwhile, the early‐arriving species decreased when N. concolor arrived. Nicrophorus concolor tended to reproduce on carcasses with lower cumulative abundance of early‐arriving species and tended to feed on carcasses with greater cumulative abundance of early‐arriving species. These results show that the successional pathways of the chief carrion insect species are highly consistent among carcasses. In contrast, early‐arriving species seem to influence the utilization patterns of carcasses by late‐arriving species, and therefore produce variability in the decomposition process. These results also show that succession could be driven by facilitation and interspecific competition between early‐arriving and late‐arriving species.

Feasibility study of microbial ecosystem therapeutics (MET-4) to evaluate effects of fecal microbiome in patients on immunotherapy (MET4-IO).

TPS2664 Background: Differences in microbiome diversity and composition in immune checkpoint inhibitor (ICI)-responders vs non-responders have been demonstrated. Transplantation of responder feces in mouse models recapitulated the ICI-responsive phenotype. MET-4 is an oral alternative to fecal transplant consisting a well-defined mixture of intestinal bacteria isolated from healthy donor stool sample. We hypothesize that co-administration of MET-4 with ICI is safe and results in alterations of the gut microbiota. Methods: Three cohorts (n = 65) of subjects with any advanced solid tumor type treated with monotherapy anti- PD1/PD-L1 antibody outside of a therapeutic clinical trial will be enrolled. Group A: safety cohort of 5 subjects already on ICI will receive MET-4 in addition to standard of care (SOC) ICI. If &lt; 2 subjects report adverse events of CTCAE grade ≥3 within 4 weeks at least possibly related to MET-4, this dose will be declared safe and groups B/C may start enrolling. Group B (n = 40): subjects with advanced solid tumors starting on ICI, randomized 3:1 to MET-4 plus SOC vs. SOC. Group C (n = 20): subjects with advanced solid tumors already on ICI with first unconfirmed disease progression randomized 1:1 to MET-4 plus ICI continuation vs. continuing ICI. Serial stool samples will be collected for taxonomic composition, diversity, metagenomics content and MET-4 species abundance. We anticipate the following analyses: 16S rRNA sequencing, shotgun metagenomics sequencing, qPCR, Nanostring nucleic acid detection and metabolomics profiling. Serial blood sampling for flow cytometry/CyTOF. Immune microenvironment of tumor specimen will be examined using immunohistochemistry. Other major inclusion criteria: willingness to provide correlative samples, RECIST v1.1 measurable disease and ECOG 0-2. Subjects unable to swallow oral medications are excluded. For the primary objective of cumulative relative abundance and changes of ICI-responsiveness associated species between baseline and day 12 MET-4, assuming a change of 0.5 standard deviation (SD) of microbial alpha diversity, our study will have ≥84% power to identify a significant difference given a significance level at 0.05 in group B. Assuming a change of 0.9 SD of microbial alpha diversity, we will have ≥83% power to identify a significant difference in group C. Response rates and progression free survival will be assessed per RECIST v1.1 and compared with historical data. Clinical trial information: NCT03686202.