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The gut microbiome contributes to host metabolism, protects against pathogens, educates the immune system, and, through these basic functions, affects directly or indirectly most physiologic functions of its host. Molecular techniques have allowed us to expand our knowledge by unveiling a wide range of unculturable bacteria that were previously unknown. Most bacterial sequences identified in the canine gastrointestinal (GI) tract fall into five phyla: Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria, and Actinobacteria. While there are variations in the microbiome composition along the GI tract, most clinical studies concentrate on fecal microbiota. Age, diet, and many other environmental factors may play a significant role in the maintenance of a healthy microbiome, however, the alterations they cause pale in comparison with the alterations found in diseased animals. GI dysfunctions are the most obvious association with gut dysbiosis. In dogs, intestinal inflammation, whether chronic or acute, is associated with significant differences in the composition of the intestinal microbiota. Gut dysbiosis happens when such alterations result in functional changes in the microbial transcriptome, proteome, or metabolome. Commonly affected metabolites include short-chain fatty acids, and amino acids, including tryptophan and its catabolites. A recently developed PCR-based algorithm termed \"Dysbiosis Index\" is a tool that allows veterinarians to quantify gut dysbiosis and can be used to monitor disease progression and response to treatment. Alterations or imbalances in the microbiota affect immune function, and strategies to manipulate the gut microbiome may be useful for GI related diseases. Antibiotic usage induces a rapid and significant drop in taxonomic richness, diversity, and evenness. For that reason, a renewed interest has been put on probiotics, prebiotics, and fecal microbiota transplantation (FMT). Although probiotics are typically unable to colonize the gut, the metabolites they produce during their transit through the GI tract can ameliorate clinical signs and modify microbiome composition. Another interesting development is FMT, which may be a promising tool to aid recovery from dysbiosis, but further studies are needed to evaluate its potential and limitations.

Primary production in freshwater ecosystems is largely a function of light and nutrient availability, both of which have been changing in many lakes and reservoirs in response to anthropogenic pressures. Recent studies focusing on natural lakes have found a hump-shaped response of primary production (sometimes measured as chlorophyll-a) to dissolved organic matter (DOM, measured as dissolved organic carbon, DOC), which has both light-absorbing chromophoric properties and DOM-bound nutrients. We used the United States National Lakes Assessment dataset to integrate reservoirs into this paradigm in comparison with natural lakes and assessed the relative differences in the predicted response’s model structure, regression parameter values, and drivers of the chlorophyll-a residuals. We found that chlorophyll-a in reservoirs exhibited a hump-shaped response to DOC, while natural lakes from this dataset were better fit with a linear response, differing from previous studies focused on boreal lakes. Despite this, reservoirs had a greater maximum chlorophyll-a response compared to natural lakes in this study (45.5 versus 33.8 μg L−1), which occurred at a lower DOC concentration threshold (18.3 versus 26.4 mg L−1) when compared using quadratic models. Reservoirs had lower median light:nutrient values compared to natural lakes, and greater median surface area and total phosphorus (TP), that can all influence the light environment and the peak chlorophyll-a responses. In both reservoirs and natural lakes, chlorophyll-a residuals were most strongly influenced by TP, where TP < 25–30 µg L−1 suppressed chlorophyll-a residuals and higher TP amplified them. Light:nutrient values were somewhat important predictors, and patterns with chlorophyll-a residuals supported previous work showing low light:nutrient values amplified chlorophyll-a responses and higher values suppressed them. Quantifying the shape of the response of primary production to DOM quantity and quality as well as the drivers of the residuals, namely TP for lakes and reservoirs in this dataset, will be important for understanding the effects that changes in water quality may have on primary production and freshwater ecosystem processes.

Increases in terrestrially-derived dissolved organic matter (DOM) have led to the browning of inland waters across regions of northeastern North America and Europe. Short-term experimental and comparative studies highlight the important ecological consequences of browning. These range from transparency-induced increases in thermal stratification and oxygen (O 2 ) depletion to changes in pelagic food web structure and alteration of the important role of inland waters in the global carbon cycle. However, multi-decadal studies that document the net ecological consequences of long-term browning are lacking. Here we show that browning over a 27 year period in two lakes of differing transparency resulted in fundamental changes in vertical habitat gradients and food web structure and that these responses were stronger in the more transparent lake. Surface water temperatures increased by 2–3 °C in both lakes in the absence of any changes in air temperature. Water transparency to ultraviolet (UV) radiation showed a fivefold decrease in the more transparent lake. The primary zooplankton grazers decreased and in the more transparent lake were largely replaced by a two trophic level zooplankton community. These findings provide new insights into the net effects of the complex and contrasting mechanisms that underlie the ecosystem consequences of browning.

Ebullitive methane (CH4) emissions in lentic ecosystems tend to concentrate at river‐lake interfaces and within shallow littoral zones. However, inconsistent definitions of the littoral zone and static representations of the lake or reservoir surface area contribute to major uncertainties in greenhouse gas (GHG) emissions estimates, particularly in reservoirs with large water‐level fluctuations. This study examines temporal variation in littoral and total surface areas of US reservoirs and demonstrates how different methods and data sources lead to discrepencies in reservoir GHG emissions at large scales and over time. We also explore variability in remotely sensed water occurrence according to maximum surface area, reservoir purposes, and hydrologic regions. Notably, the largest relative variability in surface area is exhibited by small reservoirs with a maximum surface area <1 km2 and non‐hydroelectric reservoirs. Additionally, we use a case study of measured CH4 emissions from the southeastern United States (Douglas Reservoir) to illustrate the effects of varying surface area on reservoir‐wide GHG estimates. Upscaled CH4 emissions in Douglas Reservoir differed by nearly two‐fold depending on the source of total surface area data and whether estimates accounted for seasonal fluctuations in surface area. During seasonal drawdown in Douglas Reservoir, relative littoral area varies non‐linearly; periods of lower pool elevation (and thus larger relative littoral area) likely contribute disproportionately high CH4 emission rates compared to the commonly sampled summer season when water levels are at full‐pool elevation. Improved GHG monitoring and upscaling techniques require accounting for temporal variability in reservoir surface extent and littoral area. Plain Language Summary Reservoirs can emit methane through several pathways, including bubbling from sediments which occurs most often in shallow zones. Different methods for estimating the area of this zone and disagreements in waterbody data sets results in uncertainty for large‐scale estimates of waterbody characteristics and methane emissions. Water detection algorithms applied to historical satellite imagery show that smaller reservoirs and those used for non‐hydroelectric purposes tend to have the highest variability in relative surface area. The high seasonal variability in both surface area and measured methane emissions, which contributes to uncertainty in the overall reservoir GHG footprint, is illustrated using data collected from Douglas Reservoir, in East Tennessee, USA. Key Points Estimates of total surface area and littoral area of US reservoirs vary three‐to four‐fold depending on the source of data and depth threshold used to delineate littoral area Relative to their maximum extent, the area of larger and hydroelectric reservoirs fluctuates less than small and nonhydroelectric reservoirs; interannual and seasonal recurrence of water is also more consistent in large reservoirs Estimates of reservoir GHG emissions based on field‐measured methane and carbon dioxide should account for fluctuations in lake levels and surface area

Background Metronidazole has a substantial impact on the gut microbiome. However, the recovery of the microbiome after discontinuation of administration, and the metabolic consequences of such alterations have not been investigated to date. Objectives To describe the impact of 14‐day metronidazole administration, alone or in combination with a hydrolyzed protein diet, on fecal microbiome, metabolome, bile acids (BAs), and lactate production, and on serum metabolome in healthy dogs. Animals Twenty‐four healthy pet dogs. Methods Prospective, nonrandomized controlled study. Dogs fed various commercial diets were divided in 3 groups: control group (no intervention, G1); group receiving hydrolyzed protein diet, followed by metronidazole administration (G2); and group receiving metronidazole only (G3). Microbiome composition was evaluated with sequencing of 16S rRNA genes and quantitative polymerase chain reaction (qPCR)‐based dysbiosis index. Untargeted metabolomics analysis of fecal and serum samples was performed, followed by targeted assays for fecal BAs and lactate. Results No changes were observed in G1, or G2 during diet change. Metronidazole significantly changed microbiome composition in G2 and G3, including decreases in richness (P < .001) and in key bacteria such as Fusobacteria (q < 0.001) that did not fully resolve 4 weeks after metronidazole discontinuation. Fecal dysbiosis index was significantly increased (P < .001). Those changes were accompanied by increased fecal total lactate (P < .001), and decreased secondary BAs deoxycholic acid and lithocholic acid (P < .001). Conclusion and Clinical Importance Our results indicate a minimum 4‐week effect of metronidazole on fecal microbiome and metabolome, supporting a cautious approach to prescription of metronidazole in dogs.

Lake surfaces are warming worldwide, raising concerns about lake organism responses to thermal habitat changes. Species may cope with temperature increases by shifting their seasonality or their depth to track suitable thermal habitats, but these responses may be constrained by ecological interactions, life histories or limiting resources. Here we use 32 million temperature measurements from 139 lakes to quantify thermal habitat change (percentage of non-overlap) and assess how this change is exacerbated by potential habitat constraints. Long-term temperature change resulted in an average 6.2% non-overlap between thermal habitats in baseline (1978–1995) and recent (1996–2013) time periods, with non-overlap increasing to 19.4% on average when habitats were restricted by season and depth. Tropical lakes exhibited substantially higher thermal non-overlap compared with lakes at other latitudes. Lakes with high thermal habitat change coincided with those having numerous endemic species, suggesting that conservation actions should consider thermal habitat change to preserve lake biodiversity.Using measurements from 139 global lakes, the authors demonstrate how long-term thermal habitat change in lakes is exacerbated by species’ seasonal and depth-related constraints. They further reveal higher change in tropical lakes, and those with high biodiversity and endemism.

Lake surface water temperatures are warming worldwide, raising concerns about the future integrity of valuable lake ecosystem services. In contrast to surface water temperatures, we know far less about what is happening to water temperature beneath the surface, where most organisms live. Moreover, we know little about which characteristics make lakes more or less sensitive to climate change and other environmental stressors. We examined changes in lake thermal structure for 231 lakes across northeastern North America (NENA), a region with an exceptionally high density of lakes. We determined how lake thermal structure has changed in recent decades (1975–2012) and assessed which lake characteristics are related to changes in lake thermal structure. In general, NENA lakes had increasing near-surface temperatures and thermal stratification strength. On average, changes in deepwater temperatures for the 231 lakes were not significantly different than zero, but individually, half of the lakes experienced warming and half cooling deepwater temperature through time. More transparent lakes (Secchi transparency >5 m) tended to have higher near-surface warming and greater increases in strength of thermal stratification than less transparent lakes. Whole-lake warming was greatest in polymictic lakes, where frequent summer mixing distributed heat throughout the water column. Lakes often function as important sentinels of climate change, but lake characteristics within and across regions modify the magnitude of the signal with important implications for lake biology, ecology and chemistry.

Environmental drivers such as climate change are responsible for extreme events that are critically altering freshwater resources across the planet. In the continental US, these events range from increases in the frequency and duration of droughts and wildfires in the West, to increasing precipitation and floods that are turning lakes and reservoirs brown in the East. Such events transform and transport organic carbon in ways that affect the exposure of ecosystems to ultraviolet (UV) radiation and visible light, with important implications for ecosystem services. Organic matter dissolved in storm runoff or released as black carbon in smoke selectively reduces UV radiation exposure. In contrast, droughts generally increase water transparency, so that UV radiation and visible light penetrate to greater depths. These shifts in water transparency alter the potential for solar disinfection of waterborne parasites, the production of carcinogenic disinfection byproducts in drinking water, and the vertical distribution of zooplankton that are a critical link in aquatic food webs.

Antibiotic administration can be a cause of gastrointestinal disease in horses, creating a disruption in the normal population and function of bacteria found in the hindgut. The objective of this study was to describe the changes in the cecal and fecal microbiomes and metabolomes of clinically healthy horses before and after metronidazole administration. Metronidazole (15 mg/kg BID PO) was given to five horses with cecal cannulas. The study was suspended on Day 3 due to adverse gastrointestinal effects. Cecal and fecal samples were obtained before (Days minus52, m28, m14, and 0) and after (Days 7, 14, 28, and 52) metronidazole administration. DNA was extracted from the cecal and fecal samples, and 16S rRNA genes were sequenced. Richness and evenness indices were significantly decreased by metronidazole administration in both cecal and fecal samples, but the overall composition was only significantly changed in fecal samples on Day 3 (ANOSIM, p = 0.008). The most dominant phyla were Bacteroidetes and Firmicutes in all groups examined. In fecal samples, significant changes of the phyla Actinobacteria, Spirochaetes, Lentisphaerae, and Verrucomicrobia occurred on Day 3, which correlated with clinical signs of gastrointestinal disease. The metabolome was characterized by mass spectrometry-based methods and only named metabolites were included in the analysis. Fecal, but not cecal, metabolites were significantly affected by metronidazole. The fecal metabolites affected represent diverse metabolic pathways, such as the metabolism of amino acids, carbohydrates, lipids, nucleic acids and cofactors and vitamins. Metronidazole administration has potential to cause adverse effects in horses, alters the bacterial composition of the horse's cecal and fecal content, and the metabolome of fecal samples.

Antibiotic treatment in early life influences gastrointestinal (GI) microbial composition and function. In humans, the resultant intestinal dysbiosis is associated with an increased risk for certain diseases later in life. The objective of this study was to determine the temporal effects of antibiotic treatment on the GI microbiome of young cats. Fecal samples were collected from cats randomly allocated to receive either amoxicillin/clavulanic acid (20 mg/kg q12h) for 20 days (AMC group; 15 cats) or doxycycline (10 mg/kg q24h) for 28 days (DOX group;15 cats) as part of the standard treatment of upper respiratory tract infection. In addition, feces were collected from healthy control cats (CON group;15 cats). All cats were approximately two months of age at enrolment. Samples were collected on days 0 (baseline), 20 or 28 (AMC and DOX, respectively; last day of treatment), 60, 120, and 300. DNA was extracted and sequencing of the 16S rRNA gene and qPCR assays were performed. Fecal microbial composition was different on the last day of treatment for AMC cats, and 1 month after the end of antibiotic treatment for DOX cats, compared to CON cats. Species richness was significantly greater in DOX cats compared to CON cats on the last day of treatment. Abundance of Enterobacteriales was increased, and that of Erysipelotrichi was decreased in cats of the AMC group on the last day of treatment compared to CON cats. The abundance of the phylum Proteobacteria was increased in cats of the DOX group on days 60 and 120 compared to cats of the CON group. Only minor differences in abundances between the treatment groups and the control group were present on day 300. Both antibiotics appear to delay the developmental progression of the microbiome, and this effect is more profound during treatment with amoxicillin/clavulanic acid and one month after treatment with doxycycline. Future studies are required to determine if these changes influence microbiome function and whether they have possible effects on disease susceptibility in cats.