Intestinal protozoan infections shape fecal bacterial microbiota in children from Guinea-Bissau

Intestinal parasitic infections, caused by helminths and protozoa, are globally distributed and major causes of worldwide morbidity. The gut microbiota may modulate parasite virulence and host response upon infection. The complex interplay between parasites and the gut microbiota is poorly understood, partly due to sampling difficulties in remote areas with high parasite burden. In a large study of children in Guinea-Bissau, we found high prevalence of intestinal parasites. By sequencing of the 16S rRNA genes of fecal samples stored on filter paper from a total of 1,204 children, we demonstrate that the bacterial microbiota is not significantly altered by helminth infections, whereas it is shaped by the presence of both pathogenic and nonpathogenic protozoa, including Entamoeba (E.) spp. and Giardia (G.) lamblia. Within-sample diversity remains largely unaffected, whereas overall community composition is significantly affected by infection with both nonpathogenic E. coli (R² = 0.0131, P = 0.0001) and Endolimax nana (R² = 0.00902, P = 0.0001), and by pathogenic E. histolytica (R² = 0.0164, P = 0.0001) and G. lamblia (R² = 0.00676, P = 0.0001). Infections with multiple parasite species induces more pronounced shifts in microbiota community than mild ones. A total of 31 bacterial genera across all four major bacterial phyla were differentially abundant in protozoan infection as compared to noninfected individuals, including increased abundance of Prevotella, Campylobacter and two Clostridium clades, and decreased abundance of Collinsella, Lactobacillus, Ruminococcus, Veillonella and one Clostridium clade. In the present study, we demonstrate that the fecal bacterial microbiota is shaped by intestinal parasitic infection, with most pronounced associations for protozoan species. Our results provide insights into the interplay between the microbiota and intestinal parasites, which are valuable to understand infection biology and design further studies aimed at optimizing treatment strategies.     

Dietary adjustability of grizzly bears and American black bears in Yellowstone National Park

Grizzly bears (Ursus arctos) and American black bears (U. americanus) are sympatric in much of Yellowstone National Park. Three primary bear foods, cutthroat trout (Oncorhynchus clarki), whitebark pine (Pinus albicaulis) nuts, and elk (Cervus elaphus), have declined in recent years. Because park managers and the public are concerned about the impact created by reductions in these foods, we quantified bear diets to determine how bears living near Yellowstone Lake are adjusting. We estimated diets using: 1) stable isotope and mercury analyses of hair samples collected from captured bears and from hair collection sites established along cutthroat trout spawning streams and 2) visits to recent locations occupied by bears wearing Global Positioning System collars to identify signs of feeding behavior and to collect scats for macroscopic identification of residues. Approximately 45 ± 22% ( ± SD) of the assimilated nitrogen consumed by male grizzly bears, 38 ± 20% by female grizzly bears, and 23 ± 7% by male and female black bears came from animal matter. These assimilated dietary proportions for female grizzly bears were the same as 10 years earlier in the Lake area and 30 years earlier in the Greater Yellowstone Ecosystem. However, the proportion of meat in the assimilated diet of male grizzly bears decreased over both time frames. The estimated biomass of cutthroat trout consumed by grizzly bears and black bears declined 70% and 95%, respectively, in the decade between 1997–2000 and 2007–2009. Grizzly bears killed an elk calf every 4.3 ± 2.7 days and black bears every 8.0 ± 4.0 days during June. Elk accounted for 84% of all ungulates consumed by both bear species. Whitebark pine nuts continue to be a primary food source for both grizzly bears and black bears when abundant, but are replaced by false-truffles (Rhizopogon spp.) in the diets of female grizzly bears and black bears when nut crops are minimal. Thus, both grizzly bears and black bears continue to adjust to changing resources, with larger grizzly bears continuing to occupy a more carnivorous niche than the smaller, more herbivorous black bear. © 2012 The Wildlife Society.     

Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears

The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C.?perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.     

Captive environment influences the composition and diversity of fecal microbiota in Indo-Pacific bottlenose dolphins,Tursiops aduncus

Captive environments impact the microbiota of captive animals; however, the comparison of microbiota between wild and captive dolphins has been poorly investigated. To explore the impact of a captive environment, we characterized the fecal microbiota of nine wild and four captive Indo-Pacific bottlenose dolphins, Tursiops aduncus, using a next-generation sequencing and revealed differences in the fecal microbiota between the analyzed groups. Statistical differences in abundances of the phyla Firmicutes and Proteobacteria were found between the wild and captive dolphins. Thirty-six genera (22.9% of the total genera detected in all dolphins) were shared between the groups, whereas 79 (50.3%) and 42 (26.8%) genera were found only in the wild or captive dolphins, respectively. Several pathogenic bacterial genera, including Morganella and Mycoplasma, were detected only in the captive dolphins, and the genus Lactobacillus was found only in the wild dolphins. LefSe and SIMPER analyses revealed that the genus Clostridium sensu stricto 1 was significantly more abundant in the captive dolphins than in the wild ones and contributed the most to the dissimilarity of fecal microbiota between the groups. Our results indicate that the captive environment impacts the fecal microbiota of dolphins and reinforces the importance of monitoring potentially pathogenic bacteria in captivity.     

Diet composition of polar bears in Svalbard and the western Barents Sea

We estimated both the numerical and biomass composition of the prey of polar bears (Ursus maritimus) from 135 opportunistic observations of kills in Svalbard and the western Barents Sea collected from March to October 1984-2001. By number, the prey composition was dominated by ringed seals (Phoca hispida) (63%), followed by bearded seals (Erignathus barbatus) (13%), harp seals (P. groenlandica) (8%) and unknown species (16%). However, when known prey were converted to biomass, the composition was dominated by bearded seals (55%), followed by ringed seals (30%) and harp seals (15%). Results indicated that bearded seals are an important dietary item for polar bears in the western Barents Sea. We believe that different patterns of space use by different bears may result in geographic variation of diet within the same population.     

Comparative study of bacterial groups within the human cecal and fecal microbiota

The composition of the human cecal microbiota is poorly known because of sampling difficulties. Samples of cecal fluid from eight subjects were collected via an intestinal tube. Feces were also collected. Total anaerobes, facultative anaerobes, bifidobacteria, and Bacteroides were enumerated by culture methods, and the predominant phylogenetic groups were quantified by molecular hybridization using a set of six rRNA-targeted probes. The numbers of strict anaerobes, bifidobacteria, Bacteroides, and members of the Clostridium coccoides group and Clostridium leptum subgroup were lower in the cecum. Facultative anaerobes represented 25% of total bacteria in the cecum versus 1% in the feces.     

Landscape partitioning and spatial inferences of competition between black and grizzly bears

Population effects of competition between large carnivore species may be evident by contrasting actual distributions of putative competitors against predictions of inherent landscape quality for each species. Such comparison can be insightful if covariation with external factors known to influence the occurrence, density, or persistence of each species over space and time can be controlled. We used systematically‐distributed DNA hair‐trap stations to sample the occurrence of black bears (Ursus americanus) and grizzly bears (U. arctos) across 5496 km² in southeastern British Columbia, Canada. We describe interspecific landscape partitioning according to terrain, vegetation and land‐cover variables at 2 spatial scales. We developed multivariate models to predict the potential distribution of each species. At sampling site‐session combinations that detected either species, we then investigated whether the expected or actual occurrence of each influenced the likelihood of detecting the other while controlling for human influence and inherent landscape quality. Black bears were more likely than grizzly bears to occur in gentle, valley bottom terrain with lower proportions of open habitats. Each species also was detected less frequently with the other species than predicted by their respective models; however, the strength of this relationship decreased as landscapes became more characteristic of black bear habitat. As landscapes showed higher inherent potential to support grizzly bears, black bears occurred more than model prediction in areas with higher human access and proximity to major highways but less in national parks. As potential to support black bears increased, grizzly bears occurred more than model prediction only in national parks and less with increasing human access and proximity to major highways. Results suggest that competition is occurring between the species, and that the differential response of each species to human disturbance or excessive mortality may influence the outcome and hence landscape partitioning. Moreover, black bears are more likely to benefit from human encroachment into landscapes of high inherent value for grizzly bears than vice versa. Conservation implications relate to potential mediating effects of habitat and human influence on competitive interactions between the species.     

Dietary protein content alters energy expenditure and composition of the mass gain in grizzly bears (Ursus arctos horribilis)

Many fruits contain high levels of available energy but very low levels of protein and other nutrients. The discrepancy between available energy and protein creates a physiological paradox for many animals consuming high-fruit diets, as they will be protein deficient if they eat to meet their minimum energy requirement. We fed young grizzly bears both high-energy pelleted and fruit diets containing from 1.6% to 15.4% protein to examine the role of diet-induced thermogenesis and fat synthesis in dealing with high-energy-low-protein diets. Digestible energy intake at mass maintenance increased 2.1 times, and composition of the gain changed from primarily lean mass to entirely fat when the protein content of the diet decreased from 15.4% to 1.6%. Daily fat gain was up to three times higher in bears fed low-protein diets ad lib., compared with bears consuming the higher-protein diet and gaining mass at the same rate. Thus, bears eating fruit can either consume other foods to increase dietary protein content and reduce energy expenditure, intake, and potentially foraging time or overeat high-fruit diets and use diet-induced thermogenesis and fat synthesis to deal with their skewed energy-to-protein ratio. These are not discrete options but a continuum that creates numerous solutions for balancing energy expenditure, intake, foraging time, fat accumulation, and ultimately fitness, depending on food availability, foraging efficiency, bear size, and body condition.     

Environmental stress and developmental stability in dentition of the Yellowstone grizzly bears

Asymmetry in bilateral traits is often used to assess an individual'squality and stress resistance, but stress-induced variationin developmental stability is largely undocumented for free-livingpopulations. Over many years, grizzly bears (Ursus arctos horribilis)extensively foraged around garbage dumps in Yellowstone NationalPark. Abrupt closure of these dumps 26 years ago was a severelystressful event and was followed by excessive mortality anda many-fold increase in grizzly home-range size. I examine howthis stress affected developmental stability by comparing dentitionof bears born before and after the dump closure. I predictedthat (1) asymmetry in dentition should be greater in bears bornafter dump closure compared to before closure, and asymmetryin sexually selected canines should change more than nonsexuallyselected premolars following dump closure and (2) the relationshipbetween tooth asymmetry and tooth size should change in thepopulations following the stressful events as compared withpopulations before stressful events. I found that developmentalstability of canines, which are under directional sexual selectionin males, was more responsive to stress compared to that ofmale premolars or female dentition (both under stabilizing selection),and, because of the increased cost of canine production, feweranimals were able to achieve both large size and symmetricaldevelopment of these teeth, and thus the slope of the relationshipbetween fluctuating asymmetry and canine size increased. I concludethat stress appears to act as an honesty-reinforcement mechanismin sexual selection for symmetrical dentition.     

A study of predominant aerobic microflora of black bears (Ursus americanus) and grizzly bears (Ursus arctos) in northwestern Alberta

Swab specimens were obtained from nasal, rectal, and preputial or vaginal areas of 37 grizzly and 17 black bears, captured during May to June of 1981 to 1983, to determine the types and frequency of predominant aerobic microflora. Bacterial genera most frequently isolated from bears were Escherichia, Citrobacter, Hafnia, Proteus, Staphylococcus, and Streptococcus species, comprising about 65% of the isolates. Erwinia, Xanthomonas, Agrobacterium, Rhizobium, and Gluconobacter/Acetobacter were also isolated but at lower frequencies (less than 5%). Comparison of bacterial generic composition using similarity quotient values showed no appreciable differences between grizzly and black bear flora. Also, no outstanding differences in bacterial generic composition were observed among grizzly bear samples; however, differences were noted among black bear samples. Fungal genera most commonly encountered included Cryptococcus, Rhodotorula, Cladosporium, Penicillium, Sporobolomyces, and Candida. In general, the microflora of both bear types were marked by generic diversity and random distribution. The majority of microorganisms isolated from the plant samples in the study area were also found in bear samples. This observation and the presence of certain water and soil bacteria in samples from bears suggest that the predominant microflora of both grizzly and black bears were transient and probably influenced by their foraging habits and surrounding environments.     

粪便菌群移植的研究与应用

粪便菌群移植早在半个世纪前就有报道应用于临床治疗,但一直没有受到人们的重视。过去的几年间,粪便菌群移植又在针对Clostridium difficile(艰难梭状芽胞杆菌)感染的治疗中逐渐兴起,并且有非常良好的治疗效果,对Clostridium difficile感染性肠炎的病症完全消失。因此,越来越多的患者开始尝试粪便菌群移植的治疗方法,以代替传统的药物治疗方法。肠道菌群的研究逐渐深入我们意识到,肠道菌群已经不仅仅是人体肠道共生微生物而已,而是可以视为人体一个独立且密不可分的人体器官,承担着免疫系统与代谢系统中重要的生理活动。这些关于肠道菌群的研究对粪便菌群移植有着强有力的推动。许多疾病的发病根源,尤其是与微生物紊乱有直接联系的代谢疾病,都可以从微生物与人体的互作模式中寻找答案。本课题综述了国内外近年来粪便菌群移植在人体疾病研究中的应用研究。     

Population fragmentation and inter-ecosystem movements of grizzly bears in western Canada and the northern United States

Population fragmentation compromises population viability, reduces a species ability to respond to climate change, and ultimately may reduce biodiversity. We studied the current state and potential causes of fragmentation in grizzly bears over approximately 1,000,000 km² of western Canada, the northern United States (US), and southeast Alaska. We compiled much of our data from projects undertaken with a variety of research objectives including population estimation and trend, landscape fragmentation, habitat selection, vital rates, and response to human development. Our primary analytical techniques stemmed from genetic analysis of 3,134 bears, supplemented with radiotelemetry data from 792 bears. We used 15 locus microsatellite data coupled with measures of genetic distance, isolation-by-distance (IBD) analysis, analysis of covariance (ANCOVA), linear multiple regression, multi-factorial correspondence analysis (to identify population divisions or fractures with no a priori assumption of group membership), and population-assignment methods to detect individual migrants between immediately adjacent areas. These data corroborated observations of inter-area movements from our telemetry database. In northern areas, we found a spatial genetic pattern of IBD, although there was evidence of natural fragmentation from the rugged heavily glaciated coast mountains of British Columbia (BC) and the Yukon. These results contrasted with the spatial pattern of fragmentation in more southern parts of their distribution. Near the Canada–US border area, we found extensive fragmentation that corresponded to settled mountain valleys and major highways. Genetic distances across developed valleys were elevated relative to those across undeveloped valleys in central and northern BC. In disturbed areas, most inter-area movements detected were made by male bears, with few female migrants identified. North–south movements within mountain ranges (Mts) and across BC Highway 3 were more common than east–west movements across settled mountain valleys separating Mts. Our results suggest that relatively distinct subpopulations exist in this region, including the Cabinet, Selkirk South, and the decades-isolated Yellowstone populations. Current movement rates do not appear sufficient to consider the subpopulations we identify along the Canada–US border as 1 inter-breeding unit. Although we detected enough male movement to mediate gene flow, the current low rate of female movement detected among areas is insufficient to provide a demographic rescue effect between areas in the immediate future (0–15 yr). In Alberta, we found fragmentation corresponded to major east–west highways (Highways 3, 11, 16, and 43) and most inter-area movements were made by males. Gene flow and movement rates between Alberta and BC were highest across the Continental Divide south of Highway 1 and north of Highway 16. In the central region between Highways 1 and 11, we found evidence of natural fragmentation associated with the extensive glaciers and icefields along the Continental Divide. The discontinuities that we identified would form appropriate boundaries for management units. We related sex-specific movement rates between adjacent areas to several metrics of human use (highway traffic, settlement, and human-caused mortality) to understand the causes of fragmentation. This analysis used data from 1,508 bears sampled over a 161,500-km² area in southeastern BC, western Alberta, northern Idaho, and northern Montana during 1979–2007. This area was bisected by numerous human transportation and settlement corridors of varying intensity and complexity. We used multiple linear regression and ANCOVA to document the responses of female and male bears to disturbance. Males and females both demonstrated reduced movement rates with increasing settlement and traffic. However, females reduced their movement rates dramatically when settlement increased to >20% of the fracture zone. At this same threshold, male movement declined more gradually, in response to increased traffic and further settlement. In highly settled areas (>50%), both sexes had a similar reduction in movements in response to traffic, settlement, and mortality. We documented several small bear populations with male-only immigration, highlighting the importance of investigating sex-specific movements. Without female connectivity, small populations are not viable over the long term. The persistence of this regional female fragmented metapopulation likely will require strategic connectivity management. We therefore recommend enhancing female connectivity among fractured areas by securing linkage-zone habitat appropriate for female dispersal, and ensuring current large source subpopulations remain intact. The fragmentation we documented may also affect other species with similar ecological characteristics: sparse densities, slow reproduction, short male-biased dispersal, and a susceptibility to human-caused mortality and habitat degradation. Therefore, regional inter-jurisdictional efforts to manage broad landscapes for inter-area movement will likely benefit a broad spectrum of species and natural processes, particularly in light of climate change. © 2011 The Wildlife Society.     

Intestinal microbiota composition in fishes is influenced by host ecology and environment

The digestive tracts of vertebrates are colonized by complex assemblages of micro-organisms, collectively called the gut microbiota. Recent studies have revealed important contributions of gut microbiota to vertebrate health and disease, stimulating intense interest in understanding how gut microbial communities are assembled and how they impact host fitness (Sekirov et al. 2010). Although all vertebrates harbour a gut microbiota, current information on microbiota composition and function has been derived primarily from mammals. Comparisons of different mammalian species have revealed intriguing associations between gut microbiota composition and host diet, anatomy and phylogeny (Ley et al. 2008b). However, mammals constitute <10% of all vertebrate species, and it remains unclear whether similar associations exist in more diverse and ancient vertebrate lineages such as fish. In this issue, Sullam et al. (2012) make an important contribution toward identifying factors determining gut microbiota composition in fishes. The authors conducted a detailed meta-analysis of 25 bacterial 16S rRNA gene sequence libraries derived from the intestines of different fish species. To provide a broader context for their analysis, they compared these data sets to a large collection of 16S rRNA gene sequence data sets from diverse free-living and host-associated bacterial communities. Their results suggest that variation in gut microbiota composition in fishes is strongly correlated with species habitat salinity, trophic level and possibly taxonomy. Comparison of data sets from fish intestines and other environments revealed that fish gut microbiota compositions are often similar to those of other animals and contain relatively few free-living environmental bacteria. These results suggest that the gut microbiota composition of fishes is not a simple reflection of the micro-organisms in their local habitat but may result from host-specific selective pressures within the gut (Bevins & Salzman 2011).     

粪菌移植的现状及未来

粪菌移植是一种直接改变受体肠道微生物群以使其正常化,从而获得治疗效益的方法。自2013年美国食品和药物管理局批准粪菌移植用于治疗复发性和难治性艰难梭菌感染以来,粪菌移植成为研究热点。从此,粪菌移植应用的范围迅速扩大,不仅用于胃肠道疾病,而且用于胃肠外疾病。虽然目前的证据认为粪菌移植是一种普遍安全、副作用少的治疗方法,但其扩大适应症及安全性问题尚未形成共识,需要更深入的研究。本文就目前粪菌移植与胃肠内外疾病的关系及临床安全性问题进行综述,为临床更好地开展粪菌移植提供参考。     

Diet composition and quality in indian bison (Bos gaurus) based on fecal analysis

Diet composition and quality of the Indian Bison (Bos gaurus) was estimated by fecal analysis. The results, together with studies in other parts of India, indicate that gaurs are primarily intermediate or adaptable mixed feeders. Fecal composition varied seasonally, with high proportion of grasses, forbs, and woody plant leaves, particularly Cynodon dactylon, Cyperus rotundus in monsoon and post monsoon, and Strobilanthes callosus, Strobilanthes ixiocephalus, Grewia tiliaefolia and Syzygium cumini in winter and summer. Gaur selected herbs, shrubs, and grasses, and avoided eating woody plants for most of the year. Seasonal changes in the chemical composition of the feces were related to changes in phenology. The levels of crude protein, within certain limitations, and lignin in the feces were probably the most reliable indicators of diet quality. The ratio of crude protein:lignin was highest in monsoon and winter, corresponding early growing and fruiting seasons respectively. The usefulness of feces in estimating the composition and quality of the diet of an intermediate feeder is assessed.     

Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals

The gut microbiota of mammals underpins the metabolic capacity and health of the host. Our understanding of what influences the composition of this community has been limited primarily to evidence from captive and terrestrial mammals. Therefore, the gut microbiota of southern elephant seals, Mirounga leonina, and leopard seals, Hydrurga leptonyx, inhabiting Antarctica were compared with captive leopard seals. Each seal exhibited a gut microbiota dominated by four phyla: Firmicutes (41.5 ± 4.0%), Fusobacteria (25.6 ± 3.9%), Proteobacteria (17.0 ± 3.2%) and Bacteroidetes (14.1 ± 1.7%). Species, age, sex and captivity were strong drivers of the composition of the gut microbiota, which can be attributed to differences in diet, gut length and physiology and social interactions. Differences in particular prey items consumed by seal species could contribute to the observed differences in the gut microbiota. The longer gut of the southern elephant seal provides a habitat reduced in available oxygen and more suitable to members of the phyla Bacteroidetes compared with other hosts. Among wild seals, 16 ‘core’ bacterial community members were present in the gut of at least 50% of individuals. As identified between southern elephant seal mother–pup pairs, ‘core’ members are passed on via vertical transmission from a young age and persist through to adulthood. Our study suggests that these hosts have co‐evolved with their gut microbiota and core members may provide some benefit to the host, such as developing the immune system. Further evidence of their strong evolutionary history is provided with the presence of 18 shared ‘core’ members in the gut microbiota of related seals living in the Arctic. The influence of diet and other factors, particularly in captivity, influences the composition of the community considerably. This study suggests that the gut microbiota has co‐evolved with wild mammals as is evident in the shared presence of ‘core’ members.