Microbiome-Metabolites Analysis Reveals Unhealthy Alterations in the Gut Microbiota but Improved Meat Quality with a High-Rice Diet Challenge in a Small Ruminant Model

Simple Summary

Effects of a high-rice dietary proportion on the meat quality, gut microbiota and metabolites in small ruminants are rarely reported. Thus, the objective of this study was to evaluate the slaughtering characteristic and meat quality, acute phase reaction proteins (APRPs) in plasma and colonic microbiota and metabolites of goats subjected to a high-rice diet. After a 35-day period, sixteen goats received a high-rice diet (HR, 90% concentrate) or a control diet (55% concentrate). In summary, the results showed that the slaughter performance and meat quality were improved in the growing goats after being fed the HR diet. However, the HR diet induced an acute phase reaction and disturbed the gut microbiota to some extent, which increases the health risk to growing goats.

Abstract

Effects of a high-rice dietary proportion on the meat quality, acute phase reaction proteins (APRPs) and colonic microbiota and metabolites in goats are rarely reported. This study was designed to investigate the meat quality and metabolism in goats. Sixteen goats were equally divided into two groups and fed a control diet (Con, 55% concentrate) or a high-rice diet (HR, 90% concentrate) for five weeks. We found that the HR diet improved the slaughtering characteristic and meat quality but induced an acute phase reaction and decreased bacterial richness and diversity when compared to the control group. Furthermore, the levels of acetate, propionate and total VFA concentrations were higher in the colonic contents of the HR-fed goats than in those of the control group (p < 0.05). Meanwhile, the HR diet decreased the pH value, lactic acid concentration and increased the activity of amylase and lipopolysaccharide concentration in the colonic contents of goats (p < 0.05). The proportion of Oscillibacter increased while Phocaeicola and Christensenellaceae_R-7_group significantly decreased with the HR diet (p < 0.05). Collectively, the HR diet induced an acute phase reaction and altered the colonic bacterial community, which increases the health risk to growing goats.

The Gut Microbiome in Patients With Chronic Pancreatitis Is Characterized by Significant Dysbiosis and Overgrowth by Opportunistic Pathogens

Exocrine pancreatic function is a critical host factor in determining the intestinal microbiota composition. Diseases affecting the exocrine pancreas could therefore influence the gut microbiome. We investigated the changes in gut microbiota of patients with chronic pancreatitis (CP).

Predicting the ecological impact of a recent range expansion in the structure of intertidal biofilms

Predicting the consequences of recent changes in species distributional ranges is paramount. The trochid Phorcus sauciatus has recently colonised the Azores and is the only intertidal trochid in these islands. In this study we used experimental mesocosms to examine whether its addition to the remainder of the intertidal assemblage of grazers composed of littorinids and patellids affects the structure of epilithic biofilms growing on experimental plates. We also examined if its presence can compensate the loss of patellid limpets to simulate areas where these are chronically harvested. Results showed that when the native assemblage of grazers (littorinids and patellids) are present, the addition of P. sauciatus had little influence on the overall structure of epilithic biofilms. However, when patellids were absent, and in contrast to expectations, biofilm standing stock on experimental plates decreased significantly. Results suggest that patellids may negatively affect the foraging activities of P. sauciatus via interference competition and are further discussed in face of ecological knowledge of these organisms.

Contrasting alien effects on native diversity along biotic and abiotic gradients in an arid protected area

Alien impact on native diversity could be a function of both the relatedness of alien species to native community and resources availability. Here, we investigated whether alien plants expand or decrease the functional and phylogenetic space of native plant communities, and how this is affected by alien relatedness to natives and by resources availability. We used a trait-environment dataset of 33 alien and 130 native plants in 83 pairs of invaded and non-invaded plots, covering a gradient of soil resources (organic matter-nitrogen) in Saint-Katherine-Protectorate, Egypt. First, we compared the changes in native composition and calculated alien relatedness to natives within each pair of plots. Second, we tested the effects of resources availability and relatedness on the magnitude of alien impact (defined as a change in native diversity). We found that native composition was phylogenetically less but functionally more diverse in invaded plots compared to non-invaded ones. Moreover, in resources-rich plots, dissimilar aliens to natives significantly increased native diversity, while in resource-limited ones, similar aliens to natives declined native diversity. These results suggest that the assessment of alien impacts in arid-regions is significantly linked to resources-availability and relatedness to natives. Hence, future studies should test the generality of our findings in different environments.

LDPE microplastics affect soil microbial communities and nitrogen cycling

Microplastics (MPs) are a contaminant of increasing concern in the environment. However, the impacts of MPs on soil ecosystems and biogeochemical processes like nitrogen cycle have not been well elucidated. In this study, we designed an indoor microcosm experiment to investigate the effects of exposure to low density polyethylene (LDPE) MPs on soil bacterial community and nitrogen cycling function over a 90-day incubation. Next-generation sequencing of the 16S rRNA genes revealed that both 2% and 7% LDPE MPs exposure slightly affected the soil bacterial diversity. Further analysis at the genus level showed differential tolerance to LDPE MPs, the genera Pedomicrobium, Steroidobacter, Pseudonocardia, Nitrospira and Turicibacter were enriched in the soil with 2% (w/w) LDPE MPs amendment, while the genera Pedomicrobium, Mycobacterium and Hyphomicrobium were significantly enriched in the soil with 7% (w/w) LDPE MPs amendment on days 15 and 30. Co-occurrence network analysis further suggested that LDPE MPs changed bacterial network complexity and modularity and Acidobacteria formed intimate associations with each other in responding to LDPE MPs exposure. Additionally, LDPE MPs in soil increased the abundance of nifH, AOBamoA and nirK genes involved in nitrogen cycling in different incubation phases compared to the control. The abundance of AOAamoA genes decreased on day 15 and then increased. Conversely, the abundance of nirS genes increased during the first 15 days and then decreased. These results suggested that both 2% and 7% LDPE MPs impact soil bacterial network structure and alters functional groups involved in soil nitrogen cycling processing.

A Grain-Based SARA Challenge Affects the Composition of Epimural and Mucosa-Associated Bacterial Communities throughout the Digestive Tract of Dairy Cows

The effects of a subacute ruminal acidosis (SARA) challenge on the composition of epimural and mucosa-associated bacterial communities throughout the digestive tract were determined in eight non-lactating Holstein cows. Treatments included feeding a control diet containing 19.6% dry matter (DM) starch and a SARA-challenge diet containing 33.3% DM starch for two days after a 4-day grain step-up. Subsequently, epithelial samples from the rumen and mucosa samples from the duodenum, proximal, middle and distal jejunum, ileum, cecum and colon were collected. Extracted DNA from these samples were analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Distinct clustering patterns for each diet existed for all sites. The SARA challenge decreased microbial diversity at all sites, with the exception of the middle jejunum. The SARA challenge also affected the relative abundances of several major phyla and genera at all sites but the magnitude of these effects differed among sites. In the rumen and colon, the largest effects were an increase in the relative abundance of Firmicutes and a reduction of Bacteroidetes. In the small intestine, the largest effect was an increase in the relative abundance of Actinobacteria. The grain-based SARA challenge conducted in this study did not only affect the composition and cause dysbiosis of epimural microbiota in the rumen, it also affected the mucosa-associated microbiota in the intestines. To assess the extent of this dysbiosis, its effects on the functionality of these microbiota must be determined in future.

Effects of the dietary grain content on rumen and fecal microbiota of dairy cows

Six non-lactating Holstein dairy cows received diets with forage to grain mixture ratios of 100:0 (G0), 75:25 (G25), and 50:50 (G50) that contained 0.5%, 10.0%, and 19.5% dry matter (DM) of starch, respectively. Rumen fluid and feces were sampled, and methane emissions were determined during the last week of 5 wk experimental periods. Taxonomic compositions of microbiota were determined using Illumina 16S rRNA sequencing. Increased grain feeding increased the acidity and volatile fatty acid concentrations of rumen fluid and feces, and decreased methane emissions expressed as L·kg−1 DM. Microbial diversities were highest for G25. The numbers of identified genera in rumen fluid were 185, 182, and 171 for G0, G25, and G50, respectively. In feces, these numbers were 197, 182, and 171 for these diets, respectively. In rumen digesta, seven genera were correlated positively to G0 and negatively to G50, and six genera were correlated negatively to G0 and positively to G50. In feces, 16 genera were correlated positively to G0 and negatively to G50, and 13 genera were correlated negatively to G0 and positively to G50. Increasing grain feeding affected a limited number of genera in rumen digesta and feces. This could not explain treatment effects on the functionalities of microbiota.

Does river channelization increase the abundance of invasive crayfish? Survey of Faxonius limosus in small Central European streams

The aim of this study was to assess whether regulated river reaches show higher numbers of the spiny cheek crayfish Faxonius limosus, a common freshwater invader in Europe. Man-made alterations of riverine habitats may increase their susceptibility to biological invasions. This phenomenon is commonly studied in the context of dam reservoirs; however, the impact of river channelization and the resulting riverine habitat homogenization on the success of invasive species are mostly lacking. Surveys were conducted in natural and channelised river stretches in five rivers of south-central Poland. General linear mixed model analysis showed that crayfish abundance is usually higher at sites located within regulated reaches. The likely reason for the detected differences in abundance of crayfish may be related to decreased food-web complexity and lack of predators in a homogenised habitat. The results suggest that the channelization of small watercourses may increase the abundance of invasive species F. limosus and its pressure on native European crayfish. However, due to limited data obtained in field, our study should be considered as a pilot one.

The impact of propagule pressure on whole community invasions in biomethane-producing communities

Microbes can invade as whole communities, but the ecology of whole community invasions is poorly understood. Here, we investigate how invader propagule pressure (the number of invading organisms) affects the composition and function of invaded laboratory methanogenic communities. An invading community was equally successful at establishing itself in a resident community regardless of propagule pressure, which varied between 0.01 and 10% of the size resident community. Invasion resulted in enhanced biogas production (to the level of the pure invading community) but only when propagule pressure was 1% or greater. This inconsistency between invasion success and changes in function can be explained by a lower richness of invading taxa at lower propagule pressures, and an important functional role of the taxa that were absent. Our results highlight that whole community invasion ecology cannot simply be extrapolated from our understanding of single species invasions. Moreover, we show that methane production can be enhanced by invading poorly performing reactors with a better performing community at levels that may be practical in industrial settings.

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Complex communities can successfully invade other communities

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Invasions change the community composition independently of propagule pressure

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Number of taxa invading increases with increased propagule pressure

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Larger propagule pressure impacts both the community structure and function

Clomazone improves the interactions between soil microbes and affects C and N cycling functions

Clomazone, a widely used herbicide, is mainly used in soybean fields. We previously found that clomazone alters Proteobacteria and Nitrospirae abundances and also alters urease activity, which result in changes in NH₄⁺ and NO₃^- contents in soil nitrogen cycling. It remains unknown, however, how the co-occurrence patterns of species and functions of soil ecosystems change in response to clomazone applications in soil. We designed a 3-month greenhouse experiment to investigate soil microorganism dynamics in response to clomazone. Clomazone was applied at three doses (e.g., T1, T10, T100), which significantly increased bacterial abundance at days 15 and 60. Fungal abundance was stimulated at day 30 in T10-treated soils, whereas fungal abundances decreased in T100-treated soils at day 15. Clomazone altered bacterial and fungal community structures. Network analyses showed more complex and highly connected microbial communities in clomazone-treated soils. Moreover, an Acidobacteria-dominated cluster was identified within each network of clomazone-treated soils. Clomazone applied at the recommended rate decreased the functional groups that were associated with denitrification and hydrogen oxidation at days 15 and 60, and enhanced photoheterotrophy from days 30 to 60. High clomazone inputs increased trophic types (e.g., chemoheterotrophy, phototrophy, photoautotrophy and cyanobacteria) and C cycling functional groups (e.g., fermentation and cellulolysis). The half-life of clomazone ranged from 40.1 to 93.5 days in three cases. Our results provide important information for use of this herbicide.

Only one can remain? Environmental and spatial factors influencing habitat partitioning among invasive and native crayfishes in the Pannonian Ecoregion (Hungary)

Biological invasions have increasingly threatened indigenous species, influence metacommunity organisation and consequently, global biodiversity. World-wide expansion of non-indigenous crayfish (NICS) is associated with dramatic changes in species poor indigenous crayfish (ICS) assemblages challenging conservation planning. We analysed long-term changes of crayfish occurrences from the pre-invasion state, through the first appearance of NICS, to their intensive spread in Hungarian waters. Further, we analysed present-day crayfish metacommunity patterns for co-occurrences and influence of spatial and environmental factors. Historic data revealed a marked pre-invasion decline in indigenous noble crayfish Astacus astacus and stone crayfish Austropotamobius torrentium populations, but not in the narrow-clawed crayfish Pontastacus leptodactylus. Historic data provided no direct evidence for the impact of NICS on ICS, rather it supported that NICS often entered areas where ICS had been extinct or were not present at all. Crayfish species extremely rarely co-occurred which could indicate their strong competition and be related to utilization of empty sites by NICS. Crayfish metacommunities were predominantly spatially structured indicating the primary influence of ongoing invasion. Crayfish species also exhibited different environmental preferences mainly along the altitude and temperature gradients. We conclude that the invasion is still in the expanding phase and without an effective conservational program the future of ICS is doubtful in Hungary. Conservation policy should focus on the preservation and reintroduction of the stone and noble crayfishes in highland refugees. Expansion of NICS should be prevented in refugee areas by utilizing possibilities provided by natural and artificial barriers, and education and strict ban should be simultaneously applied to prevent further illegal releases by aquarists.

Viewing Emerging Human Infectious Epidemics through the Lens of Invasion Biology

Invasion biology examines species originated elsewhere and moved with the help of humans, and those species’ impacts on biodiversity, ecosystem services, and human well-being. In a globalized world, the emergence and spread of many human infectious pathogens are quintessential biological invasion events. Some macroscopic invasive species themselves contribute to the emergence and transmission of human infectious agents. We review conceptual parallels and differences between human epidemics and biological invasions by animals and plants. Fundamental concepts in invasion biology regarding the interplay of propagule pressure, species traits, biotic interactions, eco-evolutionary experience, and ecosystem disturbances can help to explain transitions between stages of epidemic spread. As a result, many forecasting and management tools used to address epidemics could be applied to biological invasions and vice versa. Therefore, we advocate for increasing cross-fertilization between the two disciplines to improve prediction, prevention, treatment, and mitigation of invasive species and infectious disease outbreaks, including pandemics.

Alien plant invasions in Mediterranean habitats: an assessment for Sicily

Levels of plant invasions in different habitat types were assessed in several regional studies, but few of them were from the Mediterranean. Here we compare the levels of vascular plant invasion across habitats and plant communities of Sicily. We used a large dataset of plant species presences/absences in vegetation plots to analyze the invasion patterns across habitats considering biogeography, life form and phenology of alien plants. Vegetation plots were classified based on the EUNIS classification of European habitats. The invasiveness of each species was expressed in terms of its absolute and percentage frequency. Representation of different life forms and phenological patterns was compared between alien and native species. The fidelity of alien species to individual habitats was calculated using the phi coefficient. Our analysis shows that annual and woody species are the most represented life forms in the alien flora of Sicily and that alien species tend to have a longer flowering period than the native species. The investigated habitats differed strongly in their level of invasion by alien species, ranging from 0 to 15.6% of aliens of all species recorded. Most of the habitats were colonized by very few alien species or completely lacked them, except for sandy coasts, naturally-disturbed riverbeds, and synanthropic habitats. It must be noted, however, that the number of alien species occurring in a given habitat does not relate to the severity of the impact of invasion in that habitat. Some habitats are invaded by few (or single) species, which attain a high cover, transforming the whole ecosystem. The habitat-based approach proved to be suitable for evaluating the habitat specificity and frequency of alien species at a regional scale, improving the capacity for risk assessment in different ecological contexts.

Plant community and the influence of plant taxonomic diversity on community stability and invasibility: A case study based on Solidago canadensis L

Invasive alien plants (IAPs) can negatively affect plant taxonomic diversity, community stability, and invasibility in the invaded habitats. This study aimed to assess the degree of influence of the IAP Solidago canadensis L. under various levels of invasion (i.e., light, moderate, and heavy invasion based on its relative abundance in the invaded communities) on plant taxonomic diversity, community stability, and invasibility. In addition, we determined the contribution of plant taxonomic diversity to community stability and invasibility under various levels of S. canadensis invasion. The degree of influence of S. canadensis on plant taxonomic diversity and community stability increases as the level of S. canadensis invasion increases. Community invasibility increases as the level of S. canadensis invasion increases. The competitive advantage of S. canadensis is negatively associated with all indexes of plant taxonomic diversity and community stability but positively connected with community invasibility. Community stability is positively related to Shannon's diversity and Simpson's dominance indexes but negatively associated with community invasibility. Inversely, communities were more likely to be invaded when they had less plant taxonomic diversity. Thus, plant communities with lower values of plant taxonomic diversity and community stability are more vulnerable to S. canadensis invasion. Plant diversity causes a greater pressure on community stability than the other indexes of plant taxonomic diversity under various levels of S. canadensis invasion. However, the contribution intensity of the number of plant species to community invasibility is higher than the other indexes of plant taxonomic diversity under various levels of S. canadensis invasion.

Exocrine Pancreatic Function Modulates Plasma Metabolites Through Changes in Gut Microbiota Composition

PURPOSE

Exocrine pancreatic function is critically involved in regulating the gut microbiota composition. At the same time, its impairment acutely affects human metabolism. How these 2 roles are connected is unknown. We studied how the exocrine pancreas contributes to metabolism via modulation of gut microbiota.

DESIGN

Fecal samples were collected in 2226 participants of the population-based Study of Health in Pomerania (SHIP/SHIP-TREND) to determine exocrine pancreatic function (pancreatic elastase enzyme-linked immunosorbent assay) and intestinal microbiota profiles (16S ribosomal ribonucleic acid gene sequencing). Plasma metabolite levels were determined by mass spectrometry.

RESULTS

Exocrine pancreatic function was associated with changes in the abundance of 28 taxa and, simultaneously, with those of 16 plasma metabolites. Mediation pathway analysis revealed that a significant component of how exocrine pancreatic function affects the blood metabolome is mediated via gut microbiota abundance changes, most prominently, circulating serotonin and lysophosphatidylcholines.

CONCLUSION

These results imply that the effect of exocrine pancreatic function on intestinal microbiota composition alters the availability of microbial-derived metabolites in the blood and thus directly contributes to the host metabolic changes associated with exocrine pancreatic dysfunction.

Supplementation of tuna hydrolysate and insect larvae improves fishmeal replacement efficacy of poultry by-product in Lates calcarifer (Bloch, 1790) juveniles

The effects of feeding different levels of poultry by-product meal (PBM) replacing fishmeal (FM) protein, supplemented with tuna hydrolysate (TH) and Hermetia illucens (HI) larvae, on the growth, fillet quality, histological traits, immune status, oxidative biomarker levels and gut microbiota of juvenile barramundi, Lates calcarifer were investigated for six weeks. Barramundi were fed four isonitrogenous and isolipidic diets in which a FM based diet was used as the Control diet (Diet1) and compared with other non-FM diets containing 80%, 85% and 90% PBM along with the concurrent supplementation of 5% and/or 10% TH and HI larvae meal. These treatment diets were designated as 80PBM_10TH+10HI (Diet2), 85PBM_5TH+10HI (Diet3) and 90PBM_5TH+5HI (Diet4). The growth and condition factor of fish fed 80PBM_10TH+10HI and 85PBM_5TH+10HI were significantly higher than the Control. Total saturated, monounsaturated and polyunsaturated fatty acid retention in the fish muscle increased in fish fed PBM-based diets, supplemented with TH and HI larvae meal, with no adverse effect on post-harvest characteristics such as texture and colour of fish fillets. Improvement in serum total bilirubin and total protein content was found in all fish fed TH and HI larvae supplemented PBM. Similarly, immune response showed a significant increase in fish fed non-FM test diets than the Control. In the distal intestine, supplementation of any quantities of TH and HI larvae to PBM led to an increase in the microvilli density and neutral mucins while the number of goblet cells in the skin were unchanged. Liver, kidney, and spleen histology demonstrated a normal structure with no obvious changes in response to all test diets. Bacterial diversity increased in fish fed Diets 2 and 3 with a high abundance of Proteobacteria in Diets 1 and 4 and Firmicutes in Diets 2 and 3. The fish on test diets showed a lower abundance of genus Vibrio. Fish fed TH and HI larvae supplemented PBM diets showed lower infection rate to V. harveyi than the Control. Collectively, concurrent supplementation of TH and HI larvae could improve the quality of PBM diets with positive effects on growth, fillet quality, intestinal health, immunity, and disease resistance.

Long-term instability of the intestinal microbiome is associated with metabolic liver disease, low microbiota diversity, diabetes mellitus and impaired exocrine pancreatic function

OBJECTIVE

The intestinal microbiome affects the prevalence and pathophysiology of a variety of diseases ranging from inflammation to cancer. A reduced taxonomic or functional diversity of the microbiome was often observed in association with poorer health outcomes or disease in general. Conversely, factors or manifest diseases that determine the long-term stability or instability of the microbiome are largely unknown. We aimed to identify disease-relevant phenotypes associated with faecal microbiota (in-)stability.

DESIGN

A total of 2564 paired faecal samples from 1282 participants of the population-based Study of Health in Pomerania (SHIP) were collected at a 5-year (median) interval and microbiota profiles determined by 16S rRNA gene sequencing. The changes in faecal microbiota over time were associated with highly standardised and comprehensive phenotypic data to determine factors related to microbiota (in-)stability.

RESULTS

The overall microbiome landscape remained remarkably stable over time. The greatest microbiome instability was associated with factors contributing to metabolic syndrome such as fatty liver disease and diabetes mellitus. These, in turn, were associated with an increase in facultative pathogens such as Enterobacteriaceae or Escherichia/Shigella. Greatest stability of the microbiome was determined by higher initial alpha diversity, female sex, high household income and preserved exocrine pancreatic function. Participants who newly developed fatty liver disease or diabetes during the 5-year follow-up already displayed significant microbiota changes at study entry when the diseases were absent.

CONCLUSION

This study identifies distinct components of metabolic liver disease to be associated with instability of the intestinal microbiome, increased abundance of facultative pathogens and thus greater susceptibility toward dysbiosis-associated diseases.

Long Term Interactions of Native and Invasive Species in a Marine Protected Area Suggest Complex Cascading Effects Challenging Conservation Outcomes

Understanding the interactions among invasive species, native species and marine protected areas (MPAs), and the long-term regime shifts in MPAs is receiving increased attention, since biological invasions can alter the structure and functioning of the protected ecosystems and challenge conservation efforts. Here we found evidence of marked modifications in the rocky reef associated biota in a Mediterranean MPA from 2009 to 2019 through visual census surveys, due to the presence of invasive species altering the structure of the ecosystem and triggering complex cascading effects on the long term. Low levels of the populations of native high-level predators were accompanied by the population increase and high performance of both native and invasive fish herbivores. Subsequently the overgrazing and habitat degradation resulted in cascading effects towards the diminishing of the native and invasive invertebrate grazers and omnivorous benthic species. Our study represents a good showcase of how invasive species can coexist or exclude native biota and at the same time regulate or out-compete other established invaders and native species.

Mechanistic reconciliation of community and invasion ecology

Community and invasion ecology have mostly grown independently. There is substantial overlap in the processes captured by different models in the two fields, and various frameworks have been developed to reduce this redundancy and synthesize information content. Despite broad recognition that community and invasion ecology are interconnected, a process-based framework synthesizing models across these two fields is lacking. Here we review 65 representative community and invasion models and propose a common framework articulated around six processes (dispersal, drift, abiotic interactions, within-guild interactions, cross-guild interactions, and genetic changes). The framework is designed to synthesize the content of the two fields, provide a general perspective on their development, and enable their comparison. The application of this framework and of a novel method based on network theory reveals some lack of coherence between the two fields, despite some historical similarities. Community ecology models are characterized by combinations of multiple processes, likely reflecting the search for an overarching theory to explain community assembly and structure, drawing predominantly on interaction processes, but also accounting largely for the other processes. In contrast, most models in invasion ecology invoke fewer processes and focus more on interactions between introduced species and their novel biotic and abiotic environment. The historical dominance of interaction processes and their independent developments in the two fields is also reflected in the lower level of coherence for models involving interactions, compared to models involving dispersal, drift, and genetic changes. It appears that community ecology, with a longer history than invasion ecology, has transitioned from the search for single explanations for patterns observed in nature to investigate how processes may interact mechanistically, thereby generating and testing hypotheses. Our framework paves the way for a similar transition in invasion ecology, to better capture the dynamics of multiple alien species introduced in complex communities. Reciprocally, applying insights from invasion to community ecology will help us understand and predict the future of ecological communities in the Anthropocene, in which human activities are weakening species' natural boundaries. Ultimately, the successful integration of the two fields could advance a predictive ecology that is urgently required in a rapidly changing world.

The Duration of Increased Grain Feeding Affects the Microbiota throughout the Digestive Tract of Yearling Holstein Steers

Effects of the duration of moderate grain feeding on the taxonomic composition of gastrointestinal microbiota were determined in 15 Holstein yearling steers. Treatments included feeding a diet of 92% dry matter (DM) hay (D0), and feeding a 41.5% barley grain diet for 7 (D7) or 21 d (D21) before slaughter. At slaughter, digesta samples were collected from six regions, i.e., the rumen, jejunum, ileum, cecum, colon, and rectum. Extracted DNA from these samples was analyzed using MiSeq Illumina sequencing of the V4 region of the 16S rRNA gene. Three distinct PCoA clusters existed, i.e., the rumen, the jejunum/ileum, and the cecum/colon/rectum. Feeding the grain diet for 7 d reduced microbial diversity in all regions, except the ileum. Extending the duration of grain feeding from 7 to 21 d did not affect this diversity further. Across regions, treatment changed the relative abundances of 89 genera. Most of the changes between D0 and D7 and between D7 and D21 were opposite, demonstrating the resilience of gastrointestinal microbiota to a moderate increase in grain feeding. Results show that the duration of a moderate increase in grain feeding affects how gastrointestinal microbiota respond to this increase.

Functional niche differences between native and invasive tree species from the southern Brazilian mixed forest

Biological invasion is a major threat to global biodiversity and ecosystem services. We examined the functional traits similarity between a set of native and non-native invasive tree species from the Southern Brazilian subtropical mixed forest, part of an important global hotspot for biodiversity conservation. We hypothesized that invasive species occupy marginal niche spaces. We ordered the species using the Principal Component Analysis based on their wood density, leaf area, and specific leaf area. These are all important traits that summarize essential ecological strategies associated with resource acquisition and conservation. Functional overlaps between non-native and native species were analyzed through kernel density estimation of continuous traits data. While native and non-native invasive species were distributed along the same functional gradients, the position of non-native species in the functional space is species and traits specific. We concluded that within Brazilian subtropical mixed forests, the functional dissimilarity as a key factor in invasion success could not be generalized for all species and traits.

The invasive Opuntia ficus-indica homogenizes native plant species compositions in the highlands of Eritrea

Invasion by exotic species is recognized as one of the major threats to biodiversity. The effects of invasion by Opuntia ficus-indica (Cactaceae) on the species diversity, richness and composition of invaded communities were studied at three sites in the highlands of Eritrea, East Africa. This paper investigates whether the presence of O. ficus-indica causes a negative effect on the native biodiversity in a region rarely studied so far. The vegetation in invaded and uninvaded plots with similar habitat conditions was sampled and differences in the species composition, diversity and richness were compared between the plots. The overall plant species composition differed significantly with invasion by O. ficus-indica. The invasion by O. ficus-indica also led to a significant homogenization of community compositions. The species richness and Shannon diversity index did not differ significantly between the invaded and uninvaded plots. Nevertheless, we still detected species with significantly lower occurrence in the invaded plots (Psiadia punctulata), but also species which preferred invaded plots (Plectranthus hadiensis). We conclude that O. ficus-indica exerts a negligible effect on the species diversity and richness but that it affects species composition and that there are species which suffer due to its presence. Due to the continuous pressure of the invasion by O. ficus-indica on the species composition and dry climates, further homogenization in the native species diversity is to be expected in the future for the highlands of Eritrea.

The Dynamics of Interacting Bacterial and Fungal Communities of the Mouse Colon Following Antibiotics

We tested two hypotheses concerning the dynamics of intestinal microbial communities of young mice following antibiotic-induced disturbance. The first is that disturbance of the bacterial community causes disturbance of the fungal community. Our results were consistent with that hypothesis. Antibiotics significantly altered bacterial community structure. Antibiotics also altered fungal community structure, significantly increasing the relative abundance of Candida lusitaniae, a known pathogen, while simultaneously significantly decreasing the relative abundances of several other common fungal species. The result was a temporary decrease in fungal diversity. Moreover, bacterial load was negatively correlated with the relative abundances of Candida lusitaniae and Candida parapsilosis, while it was positively correlated with the relative abundances of many other fungal species. Our second hypothesis is that control mice serve as a source of probiotics capable of invading intestines of mice with disturbed microbial communities and restoring pre-antibiotic bacterial and fungal communities. However, we found that control mice did not restore disturbed microbial communities. Instead, mice with disturbed microbial communities induced disturbance in control mice, consistent with the hypothesis that antibiotic-induced disturbance represents an alternate stable state that is easier to achieve than to correct. Our results indicate the occurrence of significant interactions among intestinal bacteria and fungi and suggest that the stimulation of certain bacterial groups may potentially be useful in countering the dominance of fungal pathogens such as Candida spp. However, the stability of disturbed microbial communities could complicate recovery.

Eutrophication, biodiversity loss, and species invasions modify the relationship between host and parasite richness during host community assembly

Host and parasite richness are generally positively correlated, but the stability of this relationship in response to global change remains poorly understood. Rapidly changing biotic and abiotic conditions can alter host community assembly, which in turn, can alter parasite transmission. Consequently, if the relationship between host and parasite richness is sensitive to parasite transmission, then changes in host composition under various global change scenarios could strengthen or weaken the relationship between host and parasite richness. To test the hypothesis that host community assembly can alter the relationship between host and parasite richness in response to global change, we experimentally crossed host diversity (biodiversity loss) and resource supply to hosts (eutrophication), then allowed communities to assemble. As previously shown, initial host diversity and resource supply determined the trajectory of host community assembly, altering post-assembly host species richness, richness-independent host phylogenetic diversity, and colonization by exotic host species. Overall, host richness predicted parasite richness, and as predicted, this effect was moderated by exotic abundance-communities dominated by exotic species exhibited a stronger positive relationship between post-assembly host and parasite richness. Ultimately, these results suggest that, by modulating parasite transmission, community assembly can modify the relationship between host and parasite richness. These results thus provide a novel mechanism to explain how global environmental change can generate contingencies in a fundamental ecological relationship-the positive relationship between host and parasite richness.

The Relationship between Fungal Diversity and Invasibility of a Foliar Niche-The Case of Ash Dieback

European ash (Fraxinus excelsior) is threatened by the invasive ascomycete Hymenoscyphus fraxineus originating from Asia. Ash leaf tissues serve as a route for shoot infection but also as a sporulation substrate for this pathogen. Knowledge of the leaf niche partitioning by indigenous fungi and H. fraxineus is needed to understand the fungal community receptiveness to the invasion. We subjected DNA extracted from unwashed and washed leaflets of healthy and diseased European ash to PacBio sequencing of the fungal ITS1-5.8S-ITS2 rDNA region. Leaflets from co-inhabiting rowan trees (Sorbus aucuparia) served as a reference. The overlap in leaflet mycobiomes between ash and rowan was remarkably high, but unlike in rowan, in ash leaflets the sequence read proportion, and the qPCR-based DNA amount estimates of H. fraxineus increased vigorously towards autumn, concomitant with a significant decline in overall fungal richness. The niche of ash and rowan leaves was dominated by epiphytic propagules (Vishniacozyma yeasts, the dimorphic fungus Aureobasidion pullulans and the dematiaceous hyphomycete Cladosporium ramotenellum and H. fraxineus), and endophytic thalli of biotrophs (Phyllactinia and Taphrina species), the indigenous necrotroph Venturia fraxini and H. fraxineus. Mycobiome comparison between healthy and symptomatic European ash leaflets revealed no significant differences in relative abundance of H. fraxineus, but A. pullulans was more prevalent in symptomatic trees. The impacts of host specificity, spatiotemporal niche partitioning, species carbon utilization profiles and life cycle traits are discussed to understand the ecological success of H. fraxineus in Europe. Further, the inherent limitations of different experimental approaches in the profiling of foliicolous fungi are addressed.

Antimicrobial drug use in the first decade of life influences saliva microbiota diversity and composition

BACKGROUND

The human microbiota contributes to health and well-being. Antimicrobials (AM) have an immediate effect on microbial diversity and composition in the gut, but next to nothing is known about their long-term contribution to saliva microbiota. Our objectives were to investigate the long-term impact of AM use on saliva microbiota diversity and composition in preadolescents. We compared the lifetime effects by gender and AMs. We used data from 808 randomly selected children in the Finnish Health In Teens (Fin-HIT) cohort with register-based data on AM purchases from the Social Insurance Institution of Finland. Saliva microbiota was assessed with 16S rRNA (V3-V4) sequencing. The sequences were aligned to the SILVA ribosomal RNA database and classified and counted using the mothur pipeline. Associations between AM use and alpha-diversity (Shannon index) were identified with linear regression, while associations between beta-diversity (Bray-Curtis dissimilarity) and low, medium or high AM use were identified with PERMANOVA.

RESULTS

Of the children, 53.6% were girls and their mean age was 11.7 (0.4) years. On average, the children had 7.4 (ranging from 0 to 41) AM prescriptions during their lifespan. The four most commonly used AMs were amoxicillin (n = 2622, 43.7%), azithromycin (n = 1495, 24.9%), amoxicillin-clavulanate (n = 1123, 18.7%) and phenoxymethylpenicillin (n = 408, 6.8%). A linear inverse association was observed between the use of azithromycin and Shannon index (b - 0.015, p value = 0.002) in all children, the effect was driven by girls (b - 0.032, p value = 0.001), while not present in boys. Dissimilarities were marked between high, medium and low users of all AMs combined, in azithromycin users specifically, and in boys with amoxicillin use. Amoxicillin and amoxicillin-clavulanate use was associated with the largest decrease in abundance of Rikenellaceae. AM use in general and phenoxymethylpenicillin specifically were associated with a decrease of Paludibacter and pathways related to amino acid degradations differed in proportion between high and low AM users.

CONCLUSIONS

A systematic approach utilising reliable registry data on lifetime use of AMs demonstrated long-term effects on saliva microbiota diversity and composition. These effects are gender- and AM-dependent. We found that frequent lifelong use of AMs shifts bacterial profiles years later, which might have unforeseen health impacts in the future. Our findings emphasise a concern for high azithromycin use, which substantially decreases bacterial diversity and affects composition as well. Further studies are needed to determine the clinical implications of our findings. Video Abstract.

Fish Skin and Gut Microbiomes Show Contrasting Signatures of Host Species and Habitat

Teleost fish represent an invaluable repertoire of host species to study the factors shaping animal-associated microbiomes. Several studies have shown that the phylogenetic structure of the fish gut microbiome is driven by species-specific (e.g., host ancestry, genotype, or diet) and habitat-specific (e.g., hydrochemical parameters and bacterioplankton composition) factors. However, our understanding of other host-associated microbial niches, such as the skin mucus microbiome, remains limited. The goal of our study was to explore simultaneously the phylogenetic structure of the fish skin mucus and gut microbiome and compare the effect of species- and habitat-specific drivers on the structure of microbial communities in both tissues. We sampled 114 wild fish from 6 populations of 3 ecologically and phylogenetically contrasting Amazonian teleost species. Water samples were collected at each site, and 10 physicochemical parameters were characterized. The skin mucus, gut, and water microbial communities were characterized using a metabarcoding approach targeting the V3-V4 regions of the 16S rRNA. Our results showed a significant distinction between the phylogenetic profile and diversity of the microbiome from each microbial niche. Skin mucus and bacterioplankton communities were significantly closer in composition than gut and free-living communities. Species-specific factors mostly modulated gut bacterial communities, while the skin mucus microbiome was predominantly associated with environmental physicochemistry and bacterioplankton community structure. These results suggest that the variable skin mucus community is a relevant target for the development of microbial biomarkers of environmental status, while the more conserved gut microbiome is better suited to study long-term host-microbe interactions over evolutionary time scales.IMPORTANCE Whether host-associated microbiomes are mostly shaped by species-specific or environmental factors is still unresolved. In particular, it is unknown to what extent microbial communities from two different host tissues from the same host respond to these factors. Our study is one of the first to focus on the microbiome of teleost fish to shed a light on this topic as we investigate how the phylogenetic structure of microbial communities from two distinct fish tissues are shaped by species- and habitat-specific factors. Our study showed that in contrast to the teleost gut microbiome, skin mucus communities are highly environment dependent. This result has various implications: (i) the skin mucus microbiome should be used, rather than the gut, to investigate bacterial biomarkers of ecosystem perturbance in the wild, and (ii) the gut microbiome is better suited for studies of the drivers of phylosymbiosis, or the coevolution of fish and their symbionts.

Urbanization can increase the invasive potential of alien species

Alien species often flourish and become invasive in urban ecosystems. How and why invaders succeed in urban systems is an important, yet poorly understood, question. We investigate whether the success of urban invaders is related to changes in species traits that enhance invasive potential. We also explore whether a trophic mechanism helps explain the success of invaders in urban systems. We use the guppy Poecilia reticulata, a globally distributed alien species that has invaded both urban and non-urban systems, as our model. We first characterize the effect of urbanization on streams where guppies are present. We measure guppy invasion success using their population density and size-frequency. Then we assess how traits that are related to the potential of guppies to invade (life history and condition) respond to urbanization. Next, we explore how urbanization affects the availability of food for guppies and their diets. We also test if the presence of other fish species grants biological resistance to invasion by dampening guppy invasive potential. We find that urban streams have high concentrations of ammonium and faecal coliforms, indicating contamination from sewage. On average, guppy populations from urban streams have 26× higher density and larger body sizes than non-urban populations. Urban guppies are in better condition and have on average five more offspring than non-urban guppies. Urbanization increases the availability and consumption of highly nutritious food (chironomid larvae) by guppies. We find a positive relationship between the consumption of chironomids and both fecundity and condition. The presence of other fish species in urban streams often has a negative but small effect on guppy traits and density. Our data suggest a relaxation of trade-offs that shape life-history traits which is related to increased food resources in urban streams. These indicate that urbanization enhances the invasive potential of guppies through a trophic mechanism that simultaneously increases reproduction and somatic investment. Such mechanism is likely widespread because chironomids are often highly abundant in urban systems. Thus, not only guppies but also other invasive species can take advantage of such a resource to invest in traits that enhance invasion success.

Enhanced biodiversity of gut flora and feed efficiency in pond cultured tilapia under reduced frequency feeding strategies

Feed constitutes 50-70% of total production costs of tilapia, one of the most widely cultured finfishes in the world. We evaluated reduced-feeding strategies for improving production efficiency of Nile tilapia (Oreochromis niloticus). In a 12-week pond trial, fish were fed daily, every other day, every third day, or not at all. Ponds were fertilized to enhance natural foods. In a fifth group fish were fed daily without pond fertilization. Fish fed daily with or without pond fertilization and fish fed every other day had higher specific growth rates, survivability, and net production than the other two treatments. Fish feed efficiency and benefit to cost ratio was highest for treatments fed in a pulsatile manner (i.e. fed every other day or every third day) with fish fed on alternate days providing the best net return among all groups. Fish fed on alternate days had more moderate gene expression levels of intestinal nutrient transporters which may allow for a more balanced and efficient nutrient uptake. Fecal microbe analyses identified 145 families of prokaryotic and 132 genera of eukaryotic organisms in tilapia. The highest diversity of prokaryotes was found in fish fed either every other day or daily in fertilized ponds and the highest diversity of eukaryotes was found in fish fed every other day. These studies indicate feeding Nile tilapia on alternate days along with weekly pond fertilization has no deleterious effects on growth, survivability, or production versus daily feeding regimes, but enhances feed efficiency by 76% and provides the greatest net return on investments. Our studies also suggest for the first time that combining alternate-day feeding with pond fertilization produces the greatest microbial biodiversity in the intestine that could contribute to enhanced feed efficiency and overall health of tilapia.

Impact of Probiotic Combination in InR[E19]/TM2 Drosophila melanogaster on Longevity, Related Gene Expression, and Intestinal Microbiota: A Preliminary Study

The insulin receptor (InR) pertains to the insulin receptor family, which plays a key role in the insulin/insulin-like growth factor (IGF)-like signaling (IIS) pathway. Insulin signaling defects may result in the development of metabolic diseases, such as type 2 diabetes, and the InR mutant has been suggested to bear insulin signaling deficiency. Numerous studies have reported that probiotics are beneficial for the treatment of diabetes; however, the effect of probiotics on patients with InR deficiency has seldom been reported. Therefore, we chose the InR[E19]/TM2 Drosophila melanogaster to investigate. The results indicated that probiotics significantly reduce the mean and median lifespan of InR[E19]/TM2 Drosophila (by 15.56% and 23.82%, respectively), but promote that of wild-type files (by 9.31% and 16.67%, respectively). Significant differences were obtained in the expression of lifespan- and metabolism-related genes, such as Imp-L2, Tor, and GstD2, between the standard diet groups and the probiotics groups. Furthermore, analysis of 16S rDNA via high throughput sequencing revealed that the gut bacterial diversity of Drosophila fed with a probiotic combination also differs from that of Drosophila fed with a standard diet. In summary, these findings indicate that a probiotic combination indeed affects InR[E19]/TM2 Drosophila, but not all of its impacts are positive.

Species richness both impedes and promotes alien plant invasions in the Brazilian Cerrado

Worldwide, alien plant invasions have been intensively studied in the past decades, but mechanisms controlling the invasibility of native communities are not fully understood yet. The stochastic niche hypothesis predicts that species-rich plant communities are less prone to alien plant invasions than species-poor communities, which is supported by some but not all field studies, with some very species-rich communities such as the Brazilian Cerrado becoming heavily invaded. However, species-rich communities potentially contain a greater variety of facilitative interactions in resource exploitation than species-poor communities, from which invasive plants might benefit. This alternative hypothetical mechanism might explain why nutrient-poor, species-rich ecosystems are prone to invasion. Here we show that a high species richness both impedes and promotes invasive plants in the Brazilian Cerrado, using structural equation modelling and data from 38 field sites. We found support for the stochastic niche hypothesis through an observed direct negative influence of species richness on abundance of alien invasive species, but an indirect positive effect of species richness on invasive alien plants through soil phosphatase activity that enhances P availability was also found. These field observations were supported with results from a mesocosm experiment. Root phosphatase activity of plants increased with species richness in the mesocosms, which was associated with greater community P and N uptake. The most prominent alien grass species of the region, Melinis minutiflora, benefited most from the higher N and P availability in the species mixtures. Hence, this study provides a novel explanation of why species-richness may sometimes promote rather than impede invasion, and highlights the need to perform facilitation experiments in multi-species communities.

Progression and survival of patients with motor neuron disease relative to their fecal microbiota

Gut microbiota studies have been well-investigated for neurodegenerative diseases such as Alzheimer's and Parkinson's disease, however, fewer studies have comprehensively examined the gut microbiome in Motor Neuron Disease (MND), with none examining its impact on disease prognosis. Here, we investigate MND prognosis and the fecal microbiota, using 16S rRNA case-control data from 100 individuals with extensive medical histories and metabolic measurements. We contrast the composition and diversity of fecal microbiome signatures from 49 MND and 51 healthy controls by combining current gold-standard 16S microbiome pipelines. Using stringent quality control thresholds, we conducted qualitative assessment approaches including; direct comparison of taxa, PICRUSt2 predicted metagenomics, Shannon and Chao1-index and Firmicutes/Bacteroidetes ratio. We show that the fecal microbiome of patients with MND is not significantly different from that of healthy controls that were matched by age, sex, and BMI, however there are distinct differences in Beta-diversity in some patients with MND. Weight, BMI, and metabolic and clinical features of disease in patients with MND were not related to the composition of their fecal microbiome, however, we observe a greater risk for earlier death in patients with MND with increased richness and diversity of the microbiome, and in those with greater Firmicutes to Bacteroidetes ratio. This was independent of anthropometric, metabolic, or clinical features of disease, and warrants support for further gut microbiota studies in MND. Given the disease heterogeneity in MND, and complexity of the gut microbiota, large studies are necessary to determine the detailed role of the gut microbiota and MND prognosis.

Lesser leaf herbivore damage and structural defense and greater nutrient concentrations for invasive alien plants: Evidence from 47 pairs of invasive and non-invasive plants

Empirical evidence of enemy release is still inconsistent for invasive alien plant species, although enemy release is the key assumption for both the enemy release hypothesis (ERH) and the evolution of increased competitive ability hypothesis (EICA). In addition, little effort has been made to test this assumption in terms of defense investment using a multi-species comparative approach. Using a phylogenetically controlled within-study meta-analytical approach, we compared leaf herbivore damage, structural defenses and nutrients between 47 pairs of invasive versus native and/or non-invasive alien plants in China. The invasive relative to the co-occurring native or non-invasive (native and non-invasive alien) plants incurred lesser leaf herbivore damage, had lesser leaf concentrations of cellulose, hemicellulose, lignin and carbon, lesser leaf density and carbon or lignin to nitrogen ratio but greater nutrients, which may facilitate success of the invasive plants. The lesser structural investment did not result in lesser leaf construction costs for the invaders, which may be associated with their greater leaf nitrogen concentration. However, the invasive plants were not significantly different from the non-invasive alien plants in any trait. Our results provide strong evidence for ERH, also are consistent with EICA, and indicate that enemy release may be an important factor in alien plant invasions.

A conceptual map of invasion biology: Integrating hypotheses into a consensus network

BACKGROUND AND AIMS

Since its emergence in the mid-20th century, invasion biology has matured into a productive research field addressing questions of fundamental and applied importance. Not only has the number of empirical studies increased through time, but also has the number of competing, overlapping and, in some cases, contradictory hypotheses about biological invasions. To make these contradictions and redundancies explicit, and to gain insight into the field's current theoretical structure, we developed and applied a Delphi approach to create a consensus network of 39 existing invasion hypotheses.

RESULTS

The resulting network was analysed with a link-clustering algorithm that revealed five concept clusters (resource availability, biotic interaction, propagule, trait and Darwin's clusters) representing complementary areas in the theory of invasion biology. The network also displays hypotheses that link two or more clusters, called connecting hypotheses, which are important in determining network structure. The network indicates hypotheses that are logically linked either positively (77 connections of support) or negatively (that is, they contradict each other; 6 connections).

SIGNIFICANCE

The network visually synthesizes how invasion biology's predominant hypotheses are conceptually related to each other, and thus, reveals an emergent structure - a conceptual map - that can serve as a navigation tool for scholars, practitioners and students, both inside and outside of the field of invasion biology, and guide the development of a more coherent foundation of theory. Additionally, the outlined approach can be more widely applied to create a conceptual map for the larger fields of ecology and biogeography.

Meal Regularity Plays a Role in Shaping the Saliva Microbiota

BACKGROUND

Diet may influence health directly or indirectly via the human microbiota, emphasizing the need to unravel these complex relationships for future health benefits. Associations between eating habits and gut microbiota have been shown, but less is known about the association between eating habits and saliva microbiota.

OBJECTIVE

The aim of this study was to investigate if eating habits and meal patterns are associated with the saliva microbiota.

METHODS

In total, 842 adolescents, aged 11-14 years, from the Finnish Health in Teens (Fin-HIT) study cohort were included in this study. Eating habits and breakfast and dinner patterns were derived from a web-based questionnaire answered in school. Three major eating habit groups were identified: fruit and vegetable avoiders (FV avoiders), healthy and unhealthy. Microbiota profiles were produced from 16S rRNA gene (V3-V4) sequencing of DNA from the saliva samples. Statistical models were adjusted for gender, age, parental language, body mass index (BMI) categories, and sequencing depth.

RESULTS

Regular breakfast eaters had a higher alpha diversity (Shannon index with mean (standard error of means) 2.27 (0.03) vs. 2.22 (0.03), p = 0.06, inverse Simpson's index with 6.27 (0.17) vs. 5.80 (0.02), p = 0.01), and slight differences in bacterial composition (PERMANOVA: p = 0.001) compared with irregular breakfast eaters. A similar trend in alpha diversity was observed between regular and irregular dinner eaters (Shannon index with 2.27 (0.03) vs. 2.22 (0.03), p = 0.054, inverse Simpson's index with 6.23 (0.17) vs. 6.04 (0.22), p = 0.28), while no difference was found in composition (PERMANOVA: p = 0.08). No differences were identified between eating habit groups and saliva microbiota diversity (Shannon index p = 0.77, inverse Simpson's index p = 0.94) or composition (PERMANOVA: p = 0.13). FV avoiders, irregular breakfast eaters and irregular dinner eaters had high abundances of Prevotella.

CONCLUSION

Regularity of eating, especially breakfast eating, was associated with more diverse saliva microbiota and different composition compared with irregular eaters. However, the dissimilarities in composition were small between regular and irregular breakfast eaters. Our results suggest that Prevotella abundances in saliva were common in FV avoiders and meal skippers. However, the clinical implications of these findings need to be evaluated in future studies.

Composition and co-occurrence patterns of the microbiota of different niches of the bovine mammary gland: potential associations with mastitis susceptibility, udder inflammation, and teat-end hyperkeratosis

Background

Within complex microbial ecosystems, microbe-microbe interrelationships play crucial roles in determining functional properties such as metabolic potential, stability and colonization resistance. In dairy cows, microbes inhabiting different ecological niches of the udder may have the potential to interact with mastitis pathogens and therefore modulate susceptibility to intramammary infection. In the present study, we investigated the co-occurrence patterns of bacterial communities within and between different niches of the bovine mammary gland (teat canal vs. milk) in order to identify key bacterial taxa and evaluate their associations with udder health parameters and mastitis susceptibility.

Results

Overall, teat canal microbiota was more diverse, phylogenetically less dispersed, and compositionally distinct from milk microbiota. This, coupled with identification of a large number of bacterial taxa that were exclusive to the teat canal microbiota suggested that the intramammary ecosystem, represented by the milk microbiota, acts as a selective medium that disfavors the growth of certain environmental bacterial lineages. We further observed that the diversity of milk microbiota was negatively correlated with udder inflammation. By performing correlation network analysis, we identified two groups of phylogenetically distinct hub species that were either positively (unclassified Bacteroidaceae and Phascolarctobacterium) or negatively (Sphingobacterium) correlated with biodiversity metrics of the mammary gland (MG). The latter group of bacteria also showed positive associations with the future incidence of clinical mastitis.

Conclusions

Our results provide novel insights into the composition and structure of bacterial communities inhabiting different niches of the bovine MG. In particular, we identified hub species and candidate foundation taxa that were associated with the inflammatory status of the MG and/or future incidences of clinical mastitis. Further in vitro and in vivo interrogations of MG microbiota can shed light on different mechanisms by which commensal microbiota interact with mastitis pathogens and modulate udder homeostasis.

Gut Microbiome Toxicity: Connecting the Environment and Gut Microbiome-Associated Diseases

The human gut microbiome can be easily disturbed upon exposure to a range of toxic environmental agents. Environmentally induced perturbation in the gut microbiome is strongly associated with human disease risk. Functional gut microbiome alterations that may adversely influence human health is an increasingly appreciated mechanism by which environmental chemicals exert their toxic effects. In this review, we define the functional damage driven by environmental exposure in the gut microbiome as gut microbiome toxicity. The establishment of gut microbiome toxicity links the toxic effects of various environmental agents and microbiota-associated diseases, calling for more comprehensive toxicity evaluation with extended consideration of gut microbiome toxicity.

Disentangling the mechanisms underpinning disturbance-mediated invasion

Disturbances can play a major role in biological invasions: by destroying biomass, they alter habitat and resource abundances. Previous field studies suggest that disturbance-mediated invader success is a consequence of resource influxes, but the importance of other potential covarying causes, notably the opening up of habitats, have yet to be directly tested. Using experimental populations of the bacterium Pseudomonas fluorescens, we determined the relative importance of disturbance-mediated habitat opening and resource influxes, plus any interaction between them, for invader success of two ecologically distinct morphotypes. Resource addition increased invasibility, while habitat opening had little impact and did not interact with resource addition. Both invaders behaved similarly, despite occupying different ecological niches in the microcosms. Treatment also affected the composition of the resident population, which further affected invader success. Our results provide experimental support for the observation that resource input is a key mechanism through which disturbance increases invasibility.

Competition between the invasive Impatiens glandulifera and UK native species: the role of soil conditioning and pre-existing resident communities

Himalayan balsam (Impatiens glandulifera) is a highly invasive annual herb that has become extremely prevalent in riparian zones across the UK. The competitive ability of I. glandulifera, both in terms of resource exploitation and allelopathy (i.e., the release of biochemicals that may be toxic to neighbouring plants), is considered a key determinant of its success. Little is known, however, about the effects of the resident community on the establishment and growth of I. glandulifera. Here, we aim to increase our understanding of the competitive ability of this highly invasive plant by investigating the effects of soil conditioning on the performance of four co-occurring native species (Tanacetum vulgare, Urtica dioica, Chelidonium majus and Arabidopsis thaliana). In addition, we also aim to investigate the effect that the pre-existing species composition have on the performance of I. glandulifera seedlings by establishing artificial communities (monocultures and mixtures of four UK native species, including U. dioica). We found negative effects of soil conditioning by I. glandulifera in all four species, either by reducing above-ground biomass, chlorophyll content or both. Monocultures of U. dioica were the only artificial communities that reduced growth of I. glandulifera, and we did not find any support for the idea that a more diverse community may be more resistant to invasion. Our results confirm the high competitive ability of I. glandulifera and highlight how the identity of the natives in the resident community may be key to limit its success.

Plant Diversity and Agroecosystem Function in Riparian Agroforests: Providing Ecosystem Services and Land-Use Transition

Achieving biologically diverse agricultural systems requires a commitment to changes in land use. While in-field agrobiodiversity is a critical route to such a transition, riparian systems remain an important, yet understudied, pathway to achieve key diversity and ecosystem services and targets. Notably, at the interface of agricultural landscapes and aquatic systems, the diversification of riparian buffers with trees reduces the non-point source pollution in waterways. However, in riparian agroforestry systems, little is known about herbaceous community patterns and, importantly, the herbaceous community’s role in governing carbon (C) and nitrogen (N) cycling. Our study investigated herbaceous community taxonomic and phylogenetic diversity patterns in riparian (i) grasslands (GRASSLAND), (ii) rehabilitated agroforests (AGROFOREST-REHAB), and (iii) remnant forests (AGROFOREST-NATURAL). We then determined the biodiversity-ecosystem function relationships between community functional diversity metrics, C and N cycling, and greenhouse gas fluxes. We observed significant differences in taxonomic and phylogenetic diversity among riparian buffer types. We found that herbaceous plant communities in riparian agroforestry systems expressed plant trait syndromes associated with fast-growing, resource acquiring strategies, while grassland buffer plants exhibited slow-growing, resource conserving strategies. Herbaceous communities with high functional diversity and resource acquiring trait syndromes, such as those in the agroforestry riparian systems, were significantly correlated with lower rates of soil CO2 efflux and N mineralization, both of which are key fluxes related to ecosystem service delivery. Our findings provide further evidence that functionally diverse, and not necessarily taxonomically diverse, plant communities are strongly correlated to positive ecosystem processes in riparian agroforestry systems, and that these communities contribute to the transition of agricultural lands toward biologically and functionally diverse landscapes.

Regrowth of Microcosm Biofilms on Titanium Surfaces After Various Antimicrobial Treatments

Objectives: Our aim of this work was to investigate the regrowth of implant-related biofilms after various antimicrobial treatments in vitro. Methods: Saliva-derived microcosm biofilms were grown on titanium discs in an active attachment model. Treatments including hydrogen peroxide (HP), citric acid (CA), chlorhexidine (CHX), and distilled water (control), at different concentrations, were applied to 2-day biofilms for 1 or 5 min. The viability, lactic acid production, and composition of the biofilms were followed for 3 days. The biofilm composition was analyzed by 16S rDNA amplicon sequencing. Results: The short treatments of CA, CHX, and HP resulted in a 2-3 log reduction in biofilm viability and lactic acid production immediately. However, both parameters returned to the pre-treatment level within 2 days due to biofilm regrowth. The alpha diversity of the regrown biofilms in antimicrobial-treated groups tended to decrease, whereas the diversity of those in water-treated group increased. The composition of the regrown biofilms altered compared to those before treatments. Streptococcus and Enterobacteriaceae were enriched in the regrown biofilms. Conclusions: Although the antimicrobial treatments were efficient, the multi-species biofilms were indeed able to regrow within 2 days. The regrown biofilms display an altered microbial diversity and composition, which in the oral cavity may lead to an aggressive infection.

Measuring antibiotic levels and their relationship with the microbiome in chronic rhinosinusitis

Background

The evidence supporting the efficacy of antibiotic therapy in the treatment of chronic rhinosinusitis is not compelling. A limited number of studies show that the changes in the nasal microbiome in patients following drug therapy are unpredictable and variable. The evidence for the impact of oral antibiotics on the gut microbiota is stronger, possibly as a result of differences in drug distribution to various sites around the body. There are few studies on sinus mucosal and mucus levels of oral antibiotics used in the treatment of chronic rhinosinusitis. The distribution dependent effects of antibiotics on the sinonasal microbiome is unclear.

Conclusion

This review highlights that relative drug concentrations and their efficacy on microbiota at different sites is an important subject for future studies investigating chronic rhinosinusitis.

An Approach to Study Species Persistence in Unconstrained Random Networks

The connection between structure and stability of ecological networks has been widely studied in the last fifty years. A challenge that scientists continue to face is that in-depth mathematical model analysis is often difficult, unless the considered systems are specifically constrained. This makes it challenging to generalize results. Therefore, methods are needed that relax the required restrictions. Here, we introduce a novel heuristic approach that provides persistence estimates for random systems without limiting the admissible parameter range and system behaviour. We apply our approach to study persistence of species in random generalized Lotka-Volterra systems and present simulation results, which confirm the accuracy of our predictions. Our results suggest that persistence is mainly driven by the linkage density, whereby additional links can both favour and hinder persistence. In particular, we observed "persistence bistability", a rarely studied feature of random networks, leading to a dependency of persistence on initial species densities. Networks with this property exhibit tipping points, in which species loss can lead to a cascade of extinctions. The methods developed in this paper may facilitate the study of more general models and thereby provide a step forward towards a unifying framework of network architecture and stability.