Prospects for systems biology and modeling of the gut microbiome

Abundant microorganisms that inhabit the human intestine are implicated in health and disease. The gut microbiome has been studied with metagenomic tools, and over 3 million genes have been discovered, constituting a 'parts list' of this ecosystem; further understanding requires studies of the interacting parts. Mouse models have provided a glimpse into the microbiota and host interactions at metabolic and immunologic levels; however, to provide more insight, there is a need to generate mathematical models that can reveal genotype-phenotype relationships and provide scaffolds for integrated analyses. To this end, we propose the use of genome-scale metabolic models that have successfully been used in studying interactions between human hosts and microbes, as well as microbes in isolation and in communities.     

Vertical distribution of wild Yakushima macaques (Macaca fuscata yakui) in the western area of Yakushima Island, Japan: Preliminary report

A census of wild Yakushima macaques (Macaca fuscata yakui) was carried out in a 23-km² area of the western coast of Yakushima Island, Japan. We analyzed the census data to investigate changes in monkey distribution associated with the vertical distribution of vegetation. In the lowland coastal zone of 0–300 m above sea level (a.s.l.), 4.8 troops and 62.4–99.8 monkeys are estimated to have existed per km². In the mountainside zones of 300–900 m a.s.l., the troop density decreased to 1.3–1.6 troops/km². Since there was no difference in size between the coastal and mountainside troops, population density should decrease with altitude to about 30–36 monkeys per km². On the other hand, 2.4 troops and about 36 monkeys were estimated to have inhabited per km² in the mountain summit zone of 900–1,323 m a.s.l. Nature Conservation College     

Environmental determinants of the altitudinal variations in relative group densities of Japanese macaques on Yakushima

Altitudinal variations in relative group densities of the Japanese macaques on Yakushima were studied. This is an ideal place for studying resource limitations because it avoids various complicating factors that are difficult to quantify but might affect animal densities, such as predation, interspecific competition, and past catastrophes. The relative group density was high in the coastal forest (0–400m), while it did not differ among the higher zones (400–800, 800–1200 and 1200–1886m). To examine this variation, three habitat variables were analyzed: total basal area of food trees per unit area, seasonal variations in fruit abundance, and total annual fleshy fruit production. All of these variables indicate that fruit and seeds are most available in the coastal forest. Thus, altitudinal variations in the density of Japanese macaques on Yakushima are determined by the total annual food abundance.     

Ranging patterns of Japanese macaques in the coniferous forest of Yakushima: Home range shift and travel rate

Ranging is one of the most important behavioral adaptations for coping with seasonally fluctuating food and thermal conditions. We studied the ranging patterns, in particular home range shift and travel rate of Japanese macaques (Macaca fuscata) in the coniferous forest of Yakushima by tracking a group for 17 months. We also supplemented our data with records collected every August over a 5-year annual census. The macaque group used the eastern part of their home range from May to September and the western part during the rest of the year. The eastern part of the home range was largely primary forest in the national park, and the altitude was higher than in the western part. When they used the western part, the macaques ate more herbs and fruits from small-sized trees, the availability of which was higher in the logged forest. This east–west home range shift occurred repeatedly over multiple years. A neighboring group occupied the western part of the focal group's home range in summer, which the focal group did not use in that season. Both temperature and diet affected seasonal changes in the monthly average travel rate. Animals need more energy for thermoregulation when the temperature is low, so the macaques decreased their ranging efforts to save energy at times of low temperature. They increased their ranging distance to eat fungi, since their encounters with this food would increase with the total distance walked. They also increased their travel rate when eating flowers, which had lower food patch (tree) density than other foods such as fruits. The data supported the hypothesis that the macaques capitalize on habitat heterogeneity in a seasonally fluctuating habitat by shifting their home range and modifying their travel rate.     

Fish: a new addition to the diet of Japanese macaques on Koshima Island

Recently, Japanese macaques on Koshima Island have begun to eat raw fish. This new habit was first observed in 1979, in adult males that live on the periphery of the group of macaques. The habit was first transmitted to the old dominant females in the group and then spread gradually to most other members of the group over the next 6 years. However, Koshima macaques do not appear to have a particular liking for fish. The eating of fish is discussed in relation to recent nutritional conditions in the macaques' habitat.     

粪便样本不同保存方式对肠道菌群测序结果的影响

[目的]本文探究了3种室温保存剂和-80℃C冷冻保存对粪便样本中菌群结构的影响,为大规模、标准化的采样提供参考.[方法]本研究采集了5名健康志愿者的新鲜粪便作为测试样本,采用4种不同的保存方式保存:DETs室温保存、GITC室温保存、RNAlater室温保存和-80℃冷冻保存,在保存0、1、3、7、14、28 d后,采...     

Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis

The microbiota of the mammalian intestine depend largely on dietary polysaccharides as energy sources. Most of these polymers are not degradable by the host, but herbivores can derive 70% of their energy intake from microbial breakdown--a classic example of mutualism. Moreover, dietary polysaccharides that reach the human large intestine have a major impact on gut microbial ecology and health. Insight into the molecular mechanisms by which different gut bacteria use polysaccharides is, therefore, of fundamental importance. Genomic analyses of the gut microbiota could revolutionize our understanding of these mechanisms and provide new biotechnological tools for the conversion of polysaccharides, including lignocellulosic biomass, into monosaccharides.     

Supra-annual variation in the influence of Myrica rubra fruit on the behavior of a troop of Japanese macaques in Yakushima

Observations were made on a well-habituated natural troop of Japanese macaques (Macaca fuscata yakui), living in warm-temperate, lowland forest in Yakushima. Between mid-May and the end of June the macaques feed on the fruit of the evergreen tree Myrica rubra (Myricaceae). The fruit of this species are abundant in some years and scarce in others. Data were compared for two heavy-fruiting years (1988 and 1990) and one poor-fruiting year (1991) to examine the influence of fruit availability on patterns of foraging, ranging, and the frequency of inter-troop encounters. In both heavy-fruiting years M. rubra fruit accounted for a maximum of over 70% of foraging time, compared with a maximum of <5% in the poor-fruiting year. Heavy fruiting was also associated with a marked decrease in the overall time spent foraging. In early May of all three years troop movements were largely confined to northern parts of the home range. By early June of both heavy-fruiting years ranging had shifted to the south-west, and included an area with a high concentration of M. rubra trees. This area was rarely visited at other times, and was not visited during the study period in the poor-fruiting year. The overlap in range-use between the two heavy-fruiting years was significantly greater than that between the heavy-fruiting years and the poor-fruiting year. Heavy fruiting was also associated with an increase in the frequency of inter-troop encounters. © 1995 Wiley-Liss, Inc.     

Laboratory rearing of huhu,Prionoplus reticularis (Cerambycidae): insights into the gut microbiome

We developed a laboratory rearing method for huhu grubs, Prionoplus reticularis White (Coleoptera: Cerambycidae), on defined cellulose (cotton) and lignocellulose (pine) diets. Huhu grubs were shown to both gain weight and eventually undergo metamorphosis on these diets, two indications of successful use of the substrates for healthy growth. Since insects typically rely on their gut microbiome to assist in nutrient assimilation this rearing method was used to study the gut microbiome of P. reticularis, using the frass produced as a proxy for the gut contents. In this preliminary study patterns of fungal community diversity in frass suggest that their composition is significantly influenced by diet; however, the influence of diet on bacterial community diversity was less clear. Results do demonstrate the potential of the experimental model for studying shifts in the gut microbiome induced by diet change. This approach could prove essential in identifying microorganisms, or consortia, involved in the breakdown of lignocellulose.     

Seasonal variations in the activity budget of Japanese macaques in the coniferous forest of Yakushima: effects of food and temperature

Seasonal variations in the activity budget of Japanese macaques in the coniferous forest of Yakushima were studied over the course of 1 year. On an annual basis, they spent 38% of the daytime feeding, 16% traveling, 14% in social interactions, and 32% engaged in resting. The effects of temperature and food-related factors (i.e., food distribution, feeding speed, and food abundance) on the seasonal variations of activity budget were examined by stepwise multiple regression analysis. When the temperature was low, the macaques decreased traveling and feeding time, in accordance with the prediction that endothermal animals save energy under severe thermoregulatory cost. When the feeding speed of available foods was slow, they spent more time feeding. When high-quality foods were abundant, they decreased feeding time. These macaques did not respond to fluctuations in food distribution. The present results indicate the importance of temperature, in addition to food-related factors, as a determinant of activity budgets.     

Food-snatching behavior of free-ranging Japanese macaques observed on Shodoshima Island: a preliminary report

We investigated the characteristics of a particular food-snatching behavior in which one individual forced another’s mouth open and grabbed the food, as performed by free-ranging Japanese macaques (Macaca fuscata) in Choshikei Monkey Park on Shodoshima Island, western Japan. We conducted a survey in late June 2012 and observed one of two monkey troops, comprising 214 monkeys. We recorded the age classes and sexes of the individuals who performed the snatching behavior and were snatched from, and examined the effects of provisioned food distribution and quantity on the frequency of snatching trials and success. During the survey, we recorded 747 snatching trials, of which 609 were successful, all of which were performed by seven individuals: one adult male and six adult females. The snatching behavior occurred only during provisioning. The target animals were primarily juveniles (650 trials, 578 successful), while cases in which food was snatched from adult females (93 trials, 30 successful) and subadult females (4 trials, 1 success) were less frequent. Among the juveniles, small juveniles had food snatched more frequently than large juveniles. The higher frequency of snatching trials against juveniles was likely due to their subordinate nature. Neither the distribution nor quantity of the provisioned foods had significant effects on the number of snatching trials and successes, while the time elapsed after provisioning had significant negative effects, attributed to a decrease in the number of wheat grains left within the mouth pouch of the potential target animals.     

A theoretical approach for zone-based management of the deer population on Yakushima Island

The biological balance of Yakushima Island is currently being compromised by overpopulation of sika deer (Cervus nippon yakushimae). We predicted that the island's deer population would continue to grow unless control efforts are raised threefold from their 2012 levels. To identify the best management practice for future implementation, we evaluated and compared the performances of three different zone-based management strategies. Under the current management scenario, the median population size of the sika deer on the island would temporarily decrease, but it would subsequently rebound. Under a scenario that allows management zones to be prioritized according to the occurrence of threatened plant species and deer population size, model simulations suggested that the scenario focusing on the central zone would show the best performance based on the probability of achievement of the management goal (assuming that there is no dispersal between zones). This course of action would lead to a decrease in the median deer population size and would further ensure a high probability of achieving the 2022 target population size across most zones (up to 85 %), even if catch levels were not increased. In a future study, we would need to conduct a more detailed analysis of plants and deer density distributions.     

The importance of scale in comparative microbiome research: New insights from the gut and glands of captive and wild lemurs

Research on animal microbiomes is increasingly aimed at determining the evolutionary and ecological factors that govern host–microbiome dynamics, which are invariably intertwined and potentially synergistic. We present three empirical studies related to this topic, each of which relies on the diversity of Malagasy lemurs (representing a total of 19 species) and the comparative approach applied across scales of analysis. In Study 1, we compare gut microbial membership across 14 species in the wild to test the relative importance of host phylogeny and feeding strategy in mediating microbiome structure. Whereas host phylogeny strongly predicted community composition, the same feeding strategies shared by distant relatives did not produce convergent microbial consortia, but rather shaped microbiomes in host lineage‐specific ways, particularly in folivores. In Study 2, we compare 14 species of wild and captive folivores, frugivores, and omnivores, to highlight the importance of captive populations for advancing gut microbiome research. We show that the perturbational effect of captivity is mediated by host feeding strategy and can be mitigated, in part, by modified animal management. In Study 3, we examine various scent‐gland microbiomes across three species in the wild or captivity and show them to vary by host species, sex, body site, and a proxy of social status. These rare data provide support for the bacterial fermentation hypothesis in olfactory signal production and implicate steroid hormones as mediators of microbial community structure. We conclude by discussing the role of scale in comparative microbial studies, the links between feeding strategy and host–microbiome coadaptation, the underappreciated benefits of captive populations for advancing conservation research, and the need to consider the entirety of an animal's microbiota. Ultimately, these studies will help move the field from exploratory to hypothesis‐driven research.     

Feeding behavior and diet of the Japanese monkey (Macaca fuscata yakui) on Yakushima Island,Japan

Feeding behavior in a troop of one subspecies of the Japanese monkey, the Yakuzaru (Macaca fuscata yakui), was observed for 407 hr on Yakushima Island between March and December 1976, after a three-month preliminary survey in 1975. The troop dwells in a mature warm temperate forest at a density of over 30 animals/km². The 5-min scanning technique was employed from August to December 1976, to detect the quantitative features of feeding behavior. The members of this troop fed on 76 plant species: on the leaves of 26, the fruits of 45, and other parts of 12 species. The Yakuzaru is essentially frugivorous. The pattern of food selection is discussed in relation to fruit production. The animals fed much more on the leaves of deciduous than of evergreen woody plants. “Selection ratio” the percentage of time spent feeding on each species to the percentage abundance of each species in the sample strip, was calculated in order to evaluate food selection from the plant community. In addition, the food habits of this subspecies were compared with that of six other populations in various habitats in Japan, by computing the similarity index for the woody plant community, all woody plant food species, and all major woody plant food species.     

The development and ecology of the Japanese macaque gut microbiome from weaning to early adolescence in association with diet

Previously we have shown that the Japanese macaque gut microbiome differs not by obesity per se, but rather in association with high‐fat diet (HFD) feeding. This held true for both pregnant dams, as well as their 1‐year‐old offspring, even when weaned onto a control diet. Here we aimed to examine the stability of the gut microbiome over time and in response to maternal and postweaning HFD feeding from 6 months of age, and at 1 and 3 years of age. In both cross‐sectional and longitudinal specimens, we performed analysis of the V4 hypervariable region of the 16S rRNA gene on anus swabs collected from pregnant dams and their juveniles at age 6 months to 3 years (n = 55). Extracted microbial DNA was subjected to 16S‐amplicon‐based metagenomic sequencing on the Illumina MiSeq platform. We initially identified 272 unique bacterial genera, and multidimensional scaling revealed samples to cluster by age and diet exposures. Dirichlet multinomial mixture modeling of microbiota abundances enabled identification of two predominant enterotypes to which samples sorted, characterized primarily by Treponema abundance, or lack thereof. Approximating the time of initial weaning (6 months), the Japanese macaque offspring microbiome underwent a significant state type transition which stabilized from 1 to 3 years of age. However, we also found the low abundance Treponema enterotype to be strongly associated with HFD exposure, be it during gestation/lactation or in the postweaning interval. Examination of taxonomic co‐occurrences revealed samples within the low Treponema cluster were relatively permissive (allowing for increased interactions between microbiota) whereas samples within the high Treponema cluster were relatively exclusionary (suggesting decreased interactions amongst microbiota). Taken together, these findings suggest that Treponemes are keystone species in the developing gut microbiome of the gut, and susceptible to HFD feeding in their relative abundance.     

Low genetic diversity and biased distribution of mitochondrial DNA haplotypes in the Japanese macaque (Macaca fuscata yakui) on Yakushima Island

The Japanese macaques (Macaca fuscata yakui) on Yakushima Island are an endemic subspecies and are closely related to the population of Kyushu, one of the main islands of Japan. Using feces collected throughout Yakushima Island, we examined mitochondrial DNA (mtDNA) to investigate the phylogeography of Japanese macaques. Six haplotypes were observed for a 203-bp fragment of the mtDNA control region. The nucleotide diversity () was low (0.0021). The genetic divergence within the Yakushima population was lower (0.009) than that among four haplotypes of the Kyushu population (0.015), calculated using Kimuras two-parameter method. The mismatch distribution analysis of the six haplotypes of the Yakushima population suggested that the Yakushima population had experienced a sudden expansion in population size, which could be related to the bottleneck effect. The geographic distribution of the mtDNA haplotypes was not uniform. One haplotype was distributed widely, whereas the other five haplotypes were distributed only in the lowlands. The low genetic diversity and biased distribution are discussed in relation to an environmental crash caused by ancient volcanic activity near this island, which is postulated to have happened about 7,300 years ago, and the delayed recovery of highland vegetation.     

Long-term variation in fruiting and the food habits of wild Japanese macaques on Kinkazan Island, northern Japan

We studied the relationship between the food habits of Japanese macaques (Macaca fuscata) and the availability of nuts (Fagus crenata, Zelkova serrata, Carpinus spp., and Torreya nucifera) on Kinkazan Island, northern Japan, from 1997 to 2005 to examine the long-term variations in both food habits and availability. The food habits of the monkeys showed clear seasonal changes: the staple foods were woody leaves and flowers in spring (May and June), woody leaves and seeds or fruits other than nuts in summer (July and August), nuts and seeds or fruits other than nuts in fall (September-November), and herbaceous plants in winter (December-April). The availability of nuts, combinations of masting species, and energy production varied among years. Food habits varied among years, but the magnitude of variability of food habits differed among seasons, with large variability during summer and winter, and small variability in spring. Food availability was poor in summer and winter, but in several years the monkeys were able to consume nuts during those seasons. We emphasize the importance of conducting long-term studies on both food availability and the food habits of animals in the temperate zone.     

基于WOS和CNKI数据库分析肠道菌群与糖尿病的国内外研究趋势

目的 以文献计量学原理分析肠道菌群与糖尿病的研究现状和发展趋势。 方法 检索截至2019年12月31日的Web of Science外文数据库(WOS)和中国知网数据库(CNKI)内肠道菌群与糖尿病的所有研究文献,运用数据库提供的分析功能和Cite Space软件进行统计分析。 结果 WOS数据库内收录文献量以指数形式逐年上升。WOS数据库收录的文献被引95 466次,法国学者Cani为核心作者,学科类别以内分泌代谢学为主;中国作者文献被引10 061次,华大基因Wang Jun为国内领军人物,学科类别以食品科技学和内分泌腺及全身性疾病为主。WOS数据库中     

A multi-study analysis of gut microbiome data from the blue mussel (Mytilus edulis) emphasises the impact of depuration on biological interpretation

The blue mussel (Mytilus edulis) is a suspension feeder which has been used in gut-microbiome surveys. Although raw 16S sequence data are often publicly available, unifying secondary analyses are lacking. The present work analysed raw data from seven projects conducted by one group over 7 years. Although each project had different motivations, experimental designs and conclusions, all selected samples were from the guts of M. edulis collected from a single location in Long Island Sound. The goal of this analysis was to determine which independent factors (e.g., collection date, depuration status) were responsible for governing composition and diversity in the gut microbiomes. Results indicated that whether mussels had undergone depuration, defined here as voidance of faeces in a controlled, no-food period, was the primary factor that governed gut microbiome composition. Gut microbiomes from non-depurated mussels were mixtures of resident and transient communities and were influenced by temporal factors. Resident communities from depurated mussels were influenced by the final food source and length of time host mussels were held under laboratory conditions. These findings reinforce the paradigm that gut microbiota are divided into resident and transient components and suggest that depuration status should be taken into consideration when designing and interpreting future experiments.