Philippa Kaur

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Yak and Tibetan sheep thrive under a co-grazing system on the QTP and/or are fed with the same materials; this offers an excellent opportunity to compare the gut microbiota in different host species which share a similar diet. In addition, the grazing systems on the QTP undergo seasonal diets changes in terms of pasture location and forage composition, especially between winter and summer. This presents a good natural “treatment” which helps vary the diets of the yak and Tibetan sheep populations. In the current study, based on a more substantial sample size than the previous study1, we found that diet and environment (represented by seasons winter and summer) superseded host genetics to the family level. That is to say that the gut microbiota of the two animal species showed convergent adaptation to high altitude and harsh environment in QTP, but this convergence had seasonal diets characteristics. These findings may provide a cautionary note for ongoing efforts to link host genetics to gut microbiota composition and function and would provide some food for thought in the breeding of these two livestock groups.The mammalian gut microbiota is acquired from the environment starting at birth, and its assembly and composition is largely shaped by factors such as age, diet, lifestyle, hygiene, and disease state. Researchers subconsciously believe that host species play a greater role than environmental factors when it comes to shaping gut microbiota, especially when there is a large taxonomical difference between the host species. So far, the vast majority of research have focused on the ruminal ecosystem because the rumen is primary site of feed fermentation15,16,17. It is rare to find studies that directly compare the gut microbiota of different species. However, evidence showed that energetically-important microbial products, including VFA (10–13% of total GIT VFA) are produced in the ruminant distal gut3. Hence, it is important to study the composition of distal gut microbiota of ruminants.In this study, at the phylum level, the gut microbiota composition in both groups of livestock was dominated by Bacteroidetes and Firmicutes, which was in agreement with previous reports concerning the yak18. At the same time our result consistently with other study in dairy cows that two dominated phyla Bacteroidetes and Firmicutes found in fecal samples in different seasons were abundant19,20. Firmicutes and Bacteroidetes are responsible for digestion of carbohydrates and proteins, Members of Bacteroidetes having extremely stronger ability to degrade crystalline cellulose. The previous report showed that intestinal microbiome plays an important role in digestion and absorption of the food, and maintaining animals’ health21,22. Intestinal tracts of the ruminants are rich in symbiotic bacteria that helps the body digest plant fibers23,24. Glycans are processed by the distal gut microbiota, generating biologically significant short-chain fatty acids (SCFAs, predominantly acetate, butyrate, and propionate), which serve as the principal energy source for colonocytes25. Fibers may be involved in the regulation of food intake and energy balance via the SCFA-mediated modulation of the secretion of gut hormones26. The higher abundance of Firmicutes and Bacteroidetes in yak may be associated with high-energy consumption at high altitude18.It is worth noting that, at the family level, the dominant genera (Unclassified Ruminococcaceae, Bacteroidaceae, Unclassified BS11, Unclassified Prevotellaceae, Unclassified Christensenellaceae, CF231, Unclassified Mogibacteriaceae and Unclassified Paraprevotellaceae) in the intestines of yak and Tibetan sheep were more greatly influenced by season than genetics (Fig. 5). This has not previously been accurately identified, which may be because there have been few studies into the gut microbial communities of the yak and Tibetan sheep in QTP. So, to improve their husbandry, it is important in the future to study their microbiota profiles using more precise methods such as 16S full-length sequencing or metagenomic sequencing. Ruminococcaceae is a family of autochthonous and benignspecies that primarily inhabit in the caecum and the colon27. It is known that Ruminococcaceae are common in the rumen and hindgut of ruminants, capable of degrading cellulose and starch28. As a member of short chain fatty acid (SCFA) producers, Ruminococcaceae is considered to be the most important fiber and polysaccharides-degrading bacterium in the intestine of herbivores, and produces large amounts of cellulolytic enzymes, including exoglucanases, endoglucanase, glucosidases and hemicellulase29. The microbial community of Yak and Sheep is greatly influenced by alterations in dietary nutrition, Bacteroidaceae have the ability to degrade complex molecules (polysaccharides, proteins) in the intestine18, which can promote the Yak utilizes grasses as its major source of nutrition, due to shortage of grain and other nutrients. Prevotellaceae is responsible for hemicellulose, pectin and high carbohydrate food digestion30. The higher abundance of these microbes may contribute to gaining more energy, and play vital roles in the process of adaption of the hosts to the harsh natural environment15. Bacteroidales BS11 gut group are specialized to active hemicellulose monomeric sugars (e.g., xylose, fucose, mannose and rhamnose) fermentation and short-chain fatty acid (e.g., acetate and butyrate) production that are vital for ruminant energy31. The Bacteroidales BS11 was positively correlated with some metabolites that are involved in amino acid metabolism and biosynthesis, as well as the metabolism of energy sources, such as starch, sucrose, and galactose32.At the genus level, 5-7N15 was most abundant in winter in both animals, on the contrary, the Provotella was predominate. Here, our results indicated that seasonal diets change superseded variations derived from genetic differences between the host species, even though the yak and Tibetan sheep are very different, both taxonomically and in terms of body size. In summer, the forage grass on the Qinghai-Tibet Plateau is dominated by Agropyron cristatum, Elymus nutans, Festuca ovina, Kobresia humilis, Poa pratensis, Stipa aliena, Kobresia pygmaea, Oxytropis biflora, Saussurea hieracioides, Astragalus arnoldii Hemsl. In winter, the main forage was Brachypodium sylvaticum. Carex crebra, Trisetum spicatum and Bupleurum smithii. Stipa has both high palatability and nutritional value, with a high content of crude protein, crude fat, and nitrogen- free extract, and low levels of crude fiber33. The levels of crude protein, crude fat, and nitrogen-free extracts of Brachypodium sylvaticum. Carex crebra, Trisetum spicatum and Bupleurum smithii were lower than that of Stipa, whereas the content of crude fiber was higher than that of Stipa34. Crude protein is the main nutrient of herbage. Crude fat and nitrogen-free extracts provide heat and energy33.Lopes et al. reported that some OTUs known to be functionally relevant for fiber degradation and host development were shared across the entire gastrointestinal tract and present within the feces35. Microbial diversity increases in the distal segments of the gastrointestinal tract. Microbial fermentation appears to be reestablished in the large intestine, with the proportion of acetate, propionate and butyrate being similar to the rumen.Several explanations for this phenomenon are possible. Firstly, both the yak and Tibetan sheep are ruminants. In herbivores, the gut microbiota is dominated by Firmicutes and Bacteroides, the functions of which are related to cellulose digestion36. Therefore, ruminant microbes could possibly be more similar across species than gut microbes from elsewhere.Secondly, the yaks and Tibetan sheep in our study co-grazed from birth to death. As such, the initial gut microbiota source, responsible for populating the remainder of the gut in the months and years after the initial seeding at birth, would necessarily come from the same environment. It has been established that early life events are critical for gut microbiota development and for shaping the adult microbiota. Lifestyle and diet will further influence the composition and function of the gut microbiota. In our study, the investigated animals shared a very similar lifestyle and obtained their diets from the same source. The results revealed that sheep and yaks presented almost identical gut microbiota compositions in the winter, but by the date of collection of the summer samples they were quite different. The reason for this could be that during summer and summer there is pronounced pastoral grass growth, giving the animals more variety and choice in their diets; it is known, after all, that sheep have different diet preferences to yaks37. However, during the winter, the animals have no option but to eat the same food in order to survive until winter.Thirdly, there could be a convergent evolution of gut microbiomes in yaks and Tibetan sheep due to the extremely harsh environment in high-altitude regions1,38. When compared with their low-altitude relatives, cattle (Bos taurus) and ordinary sheep (Ovis aries), metagenomic analyses revealed significant enrichment in rumen microbial genes involving volatile fatty acid-yielding pathways in yaks and Tibetan sheep, whereas methanogenesis pathways were enriched in the cattle metagenome. Analyses of RNA transcriptomes revealed significant upregulation in 36 genes associated with volatile fatty acid transport and absorption in the ruminal epithelium of yaks and Tibetan sheep. This suggests that, aside from host genetics, long-term exposure to harsh environments has allowed the gut microbiome to adapt in order to boost health and survival. In other words, although yaks and Tibetan sheep are very different genetically, their gut microbiota could be similar due to the selection pressures of the high altitude at which they live. Meanwhile, from our data based on functional gene composition (Fig. S3), it is also worth noting that there were no groups clearly distinguished from one another, although the PERMANOVA results indicated both a host and season effect, with the interaction between them being statistically significant. Though factors such as environment and diet (represented by seasons) can trump host genetics, we could not ignore the interplay of these factors as gut microbes are a very complex community.Winter is the harshest period for the survival of yak and Tibetan sheep. To maintain the survival, it’s best to feed the animals with a high protein content. Furthermore, to get more detailed data in different seasons and various dietary habits of yak and sheep, more study should be assessed about intestinal microbiota by collecting feces. More

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A model of diauxic community assemblyCommunity models studying diauxie should mimic serial dilution cultures instead of chemostats, in order to make their predictions both experimentally and ecologically relevant. Experimentally, microbial community assembly assays frequently utilize serial dilution cultures. Ecologically, diauxic growth is best suited to a “feast and famine” lifestyle, which a serial dilution culture mimics30,31,32. Therefore, throughout this manuscript, we model the assembly of a microbial community undergoing a sequence of growth-dilution cycles (see Fig. 1a). Community assembly occurs gradually through the addition of microbial species from a diverse species pool one at a time. Each species in the pool consumes resources diauxically, i.e., one at a time according to its resource preference.Fig. 1: Model of community assembly with diauxie and serial dilution.a Tables of growth rates and resource preferences of two species α (red) and β (yellow), each capable of consuming all four available resources, R1 to R4. The resource preference sets the sequence in which a microbial species utilizes resources, and the corresponding rates gXi indicate the growth rate while consuming each resource (see “Methods”). b Diauxic growth curve of species α during one serial dilution cycle, which has 4 phases of growth on each individual resource, with rates gα1, gα3, gα2, and gα4, respectively (with a brief lag period between two phases). At the end of each dilution cycle, we dilute the population by a factor D = 100, and supply fresh resources (see “Methods”). c Resource depletion curves corresponding to (b), where each resource is represented by a different color. R1 is exhausted at time T1; then species α consumes R3 which runs out at T3, which is followed by exhaustion of R2 at T2, and so on. d Schematic of serial dilution experiment. During community assembly, new species are added one by one from a species pool. After each successful invasion, the system undergoes several growth-dilution cycles until it reaches a steady state. e Population dynamics corresponding to the assembly process in (d). Panels (b) and (c) correspond to a small section of this process (highlighted in gray), where the community dynamics consist only of species α (red) reaching a steady state.Full size imageWe begin by illustrating the growth of a single species (labeled α) grown in an environment with four resources (Fig. 1a–c). The species first grows on its most preferred resource (R1) with a growth rate gα1 until time T1, when this resource gets exhausted. After a lag period τ, the species switches to growing on its next preferred resource (R3) with growth rate gα3 until time T3, when this resource also gets exhausted. This process of diauxic growth by sequential utilization of resources continues until either all resources are depleted, or the cycle ends at time T. At this point, a fraction 1/D of the medium containing the species is transferred to a fresh medium replete with resources. This corresponds to the dilution of species abundances by a factor D, mimicking serial dilution experiments in the laboratory.After several transfers, species dynamics converge to a steady state, where each species starts a cycle with the same initial abundance as the previous cycle. At this point, we add a small population of a new invader species, chosen randomly from the species pool, to the steady-state community (Fig. 1d, e). (Hence, we assume that species invasions are rare enough such that communities always reach a steady state before the next invasion.) The invader may differ from the resident species in both resource preference order and growth rates on each resource (Fig. 1a). Once introduced, the invader may grow and establish itself in the community in a new steady state (Fig. 1d, e), or it may fail, returning the community to its previous steady state.The growth rates and preference orders completely characterize a species, while the set of resource depletion times (T1, T2, etc.) characterize the current state of the abiotic environment. As we will later show, these resource depletion times are important observables in a community, since they determine the success or failure of an invader.A realistic example of a community captured by our model is the human gut microbiome, specifically the assembly of primary consumers (e.g., Bacteroides species) on the polysaccharides (e.g., starch, cellulose, and mucin) that they consume. Here, there is a significant overlap between the metabolic capabilities of the microbes, but they nevertheless coexist. These species often consume polysaccharides diauxically, and engage in resource competition. Moreover, several of these species have different resource preferences, which others have hypothesized help them coexist26,33.Throughout this paper, we neglect diauxic lag times (τ = 0) for simplicity. We will later show that adding lag times only quantitatively strengthens our main results (see “Discussion” and Fig. 5). We also assume that the supplied resource concentrations are sufficiently large, enabling species to always grow exponentially at their resource-specific growth rates. Further, we assume a balanced supply of resources, i.e., that resources are supplied in equal concentrations (see “Discussion” and Supplementary Text for results in an unbalanced resource supply).We simulated the assembly of 1000 communities, each being colonized from a pool of ~10,000 species (see “Methods”). Species could utilize all 4 supplied resources diauxically. Each species had a random resource preference order and different growth rates on each resource, which were picked randomly from a rectified normal distribution (with mean 0.25 and standard deviation 0.05). We assumed that the growth rate distributions for each of the 4 resources were the same, such that no resource was consistently better than the other. This is a simplifying assumption, but it nevertheless captures a variety of experimental observations showing remarkable growth rate variability of different microbial species on the same carbon sources34,35,36. Community assembly proceeded via introduction of species one at a time, in a random order, until each species had attempted to invade exactly once.Emergent properties of diauxic community assemblyTo study the emergent properties of communities of diauxic species, we followed the assembly process from a species pool via invasion of species one at a time. We used the number of invasion attempts to track time; communities matured over successive invasions. We found that the assembly process became slower over time—successful invasions became rarer as the community matured (Fig. 2a inset). Throughout the assembly process, we recorded four key properties of communities: total resource depletion time, species diversity, complementarity of the community, and prevalence of anomalous species (defined below).Fig. 2: Emergent properties of diauxic microbial communities.In all plots, solid bold lines represent the average over 958 individual community assembly simulations, while gray lines correspond to 100 randomly chosen community assembly simulations. a Total resource depletion time during community assembly (the time taken by the community to deplete all available resources). (Inset) Number of successful invasions during community assembly. b Total species diversity during community assembly (number of surviving species at steady state). c Resource utilization complementarity during community assembly. For each time point, the nth choice complementarity was calculated as a number of unique resources among the n-th preferred choices of all species in the community, divided by the number of unique resources in the environment. For a certain community, the null expectation (complementarity without selection) was defined by the complementarity of a random set of species from the pool that has the same diversity of that community. Colored lines show the average trend of complementarity on each preferred resource choice: top (light blue), second (cyan), third (deep green), and fourth (light green). The red dash-dotted line shows the average trend of null expectation. The gray dash-dotted line at the top corresponds to the perfect complementarity, which is 1. d Frequency of species with anomalous resource preferences during community assembly. The gray dash-dotted line is the expectation of fraction of anomalous species (75%) in the pools.Full size imageResource depletion timeIn each community, resources disappear at specific times and in a well-defined order (Fig. 1c). The total resource depletion time measures how quickly the community consumes all supplied resources. In this way, the total resource depletion time characterizes the overall speed at which a community consumes resources. The total resource depletion time decreased as communities assembled (Fig. 2a, solid line). The rate and degree of this decrease depend on the mean and variance of the growth rate distribution and the number of invasion attempts. In addition, the variability in depletion times between communities reduced over community assembly (Fig. 2a, gray lines; coefficient of variation reduces by 47%, see Fig. S1). Thus the assembly process selects for communities that collectively consume resources quickly.Species diversityThe species diversity was quantified as the number of species coexisting in the steady-state community. In the model, like in other consumer-resource models, the number of coexisting species at steady state is limited by the number of resources, 4 (Fig. 2b, dashed line)10,37. This is a natural consequence of competition for resources in our model (see Supplementary Text, section F for a derivation). Notably, species with the same resource preferences can coexist in the model, as long as the number of species is less than the number of resources (e.g., pairs of E. coli strains can coexist in media with glucose and xylose, see below). We found that the average community diversity increased over time, but the rate slowed as the community matured (Fig. 2b; note the logarithmic x-axis scale). Communities displayed significant variability in the trajectories of increasing diversity (Fig. 2b, gray lines). We discuss the slow increase of diversity, and observed variability, in the next section.Top choice complementarityThe top choice complementarity of a community measured the overlap in the top choice resource of each of the species residing in the community. We defined the top choice complementarity of a community as the number of unique top choice resources among community residents, divided by the number of residents. Thus the top choice complementarity varied between 1, in a maximally complementary community where each resident species had a unique top choice resource (Fig. 2c, right), and 1 divided by the number of coexisting species in the community, where all residents chose the same resource as the top choice (Fig. 2c, left). During community assembly, top choice complementarity stayed close to the maximum value throughout the assembly process (Fig. 2c, blue). This observation was in sharp contrast to the prediction from a null model for the complementarity (Fig. 2c, red). We obtained the null prediction by measuring the complementarity of a group of randomly chosen species from the species pool (group size being the number of coexisting species in the community). This null prediction decreased during the assembly process, due to the increasing community diversity, unlike the top choice complementarity which remained close to the maximum value. We also recorded the complementarity in the second, third, and fourth choice resource of the assembled community (defined similarly to the top choice complementarity). The complementarity of all other choices agreed with the null prediction (Fig. 2c). Together, these observations suggest that communities of coexisting diauxic species exhibit high complementarity on the top-choice resources, in a manner reminiscent of niche partitioning in consumer-resource models.Prevalence of anomalous speciesIntuition gleaned from experiments with E. coli dictates that microbes often grow fastest on their top choice resource (glucose for E. coli)18,20. However, exceptions to this trend also exist, such as Bacteroides species in the human gut that often prefer polysaccharides that they grow slower on22,26,38. Based on this intuition, we defined anomalous microbes as microbes that do not grow fastest on their top choice resource. To investigate which resource preferences might give microbes a competitive advantage during community assembly, we tracked the fraction of anomalous resident species during community assembly. Despite the majority (75%) of species in the pool being anomalous (since growth rates and preferences were randomly picked; see “Methods”), anomalous species were absent in mature communities. The fraction of anomalous resident species decreased rapidly during assembly (Fig. 2d). Thus, anomalous resource preferences are strongly selected against during community assembly. Further investigation revealed a reduced selection pressure against anomalous species if either resource supply was severely imbalanced (i.e., the imbalance has to be comparable to the dilution factor, D = 100), or if the dilution factor was small (see Figs. S4 and S5; also see Supplementary Text, sections C and H). However, microbes with anomalous resource preferences were eventually outcompeted in all conditions.Top choice resources chiefly drive emergent assembly patternsTo understand what factors drove the maintenance of top choice complementarity—despite the steady increase in species diversity, expected to reduce complementarity—we focused on growth on top choice resources. We hypothesized that the reason for the much higher than expected top choice complementarity was the following: diauxic species derived most of their growth, and spent most of their time growing on their top choice resources. Co-utilizing microbes, instead, grow on multiple resources simultaneously, spending roughly equal time on each utilized resource.To test this hypothesis, we first simulated the growth of a single diauxic species in monoculture using our model. We found that indeed, the species derived the overwhelming majority of its growth (measured in generations of growth) and spent most of its time growing on its top choice resource (54%, Fig. 3a, b, left). For a simpler case, where a single species had the same growth rate g while growing on two resources (both supplied at the same concentration), and preferring resource R1 over R2, we derived the ratio of time spent growing on the top choice resource R1 (T1) versus the second choice R2 (T2 − T1). We obtained the following approximate expression for a large dilution factor D (see Supplementary Text, section A):$$frac{{T}_{1}}{{T}_{2}-{T}_{1}}=frac{,{{mbox{log}}}(D/2)}{{{mbox{log}}},(2)},$$
(1)
which explains that the fraction of time spent growing on the top choice resource increases with the dilution factor.Strikingly, the fraction of time spent growing on the top choice resource became even larger if the species grown in monoculture (Fig. 3b, top row) were instead part of a diverse community (i.e., in co-culture with 3 other species, top choice share 70% versus 54% in monoculture, Fig. 3b, bottom row and top row, respectively). This is because of the following reason. In our model, while a species consumes and grows on all available resources in monoculture, in co-culture, it may not have the opportunity to consume all the resources it can grow on because other species might deplete them first. This further skews growth in favor of the top choice resource. Such a phenomenon only occurs in diauxic species, not co-utilizing species (Supplementary Text, section I).Invader successInterestingly, once we understood that the top choice chiefly drove species growth, we could explain the other emergent patterns in diauxic communities. Importantly, the success of an invader depended on the growth rate on their top choice resource. As community assembly proceeded, the top choice growth rate of successful invaders increased consistently (Fig. 3c, blue line), while their growth rates on all other choices remained constant and close to the average growth rate (Fig. 3c, green lines). Selection on the top choice growth rate in diauxic communities is in striking contrast with co-utilizing communities, which we found select for the average growth rate across all resources instead (Supplementary Text, section I). Further, an invader whose top choice resource coincided with the last depleted resource in the community had the highest probability of invasion success (Fig. 3d). Invaders whose top choice resource was not depleted last had lesser time to grow on it, and thus a lower rate of invasion success. By depleting the last resource faster, invaders reduced the total resource depletion time in the community, thus explaining the trend observed in Fig. 2a. In addition, after a successful invasion, the community’s steady state could have a different resource depletion order.Complementarity and diversitySuccessful invasions could be classified into one of two types based on the “invaded resource”, i.e., the invader’s top choice. If the invaded resource was not the top choice of any other resident community member, we called it an invasion of an “unoccupied” resource (Fig. 3e; in our simulations, 33% of cases). If the invaded resource was instead already the top choice of at least one resident, we called it an invasion of an “occupied” resource (Fig. 3e; 67% of cases). Both types of successful invasions had different effects on species diversity, but interestingly, both maintained complementarity (on the top choice, as in Fig. 2c). invasions of unoccupied resources usually increased community diversity by 1 (62% of cases), and were less likely to result in the extinction of one or more other species (38% of cases). This is because, in that case, the invader did not have to compete with other residents for its top choice resource. For communities with a complementarity {T}_{2},$$
(2)
where gα1 and gα2 are the species α’s growth rates on R1 and R2, respectively. The two triangular regions separated by the diagonal define two complementary scenarios: when T1  T2, R1 is depleted second and the species grows on R1 after R2 is depleted.For a given set of initial resource and species concentrations, community dynamics must converge to a steady state lying on the ZNGI of the surviving species (e.g., the bold purple point in Fig. 4a). This point defines the resource depletion times by the resident species at steady state. Changing the resource supply or dilution factor moves this point along the ZNGI.The ZNGI of a species also separates the resource environment space into two regions: a region inside the ZNGI (towards the origin) where that species grows by a factor D. An invader is successful if it is able to grow by a factor ≥D in the community it invades. Geometrically, the invader’s ZNGI must be closer to the origin than the resource environment corresponding to the invaded community (Fig. 4b). In this way, our geometric approach allows easy visualization of invasion criteria.We can also visualize invasion outcomes. A successful invasion of a single-species community leads to either displacement of the resident or coexistence between the invader and resident. For example, in Fig. 4b, because the ZNGI of the invader (blue) lies fully inside the ZNGI of the resident (purple), the invader displaces the resident. This is because the invader reduces the resource depletion times in the environment to a point where the resident can no longer survive, driving it extinct (bold blue point in Fig. 4b). In contrast, in Fig. 4c, the ZNGI of the invader (orange) intersects with the new resident (blue), in a manner that leads to coexistence between both species (albeit at a new set of resource depletion times, i.e., their intersection point in Fig. 4c). In general, whether two species will coexist depends on various factors, such as the supplied resource concentrations, but whenever two species coexist, they will do so at the intersection of their ZNGIs (Supplementary Text, section A). As a corollary, two species whose ZNGIs do not intersect cannot coexist. Notably, the orange and blue species in Fig. 4c coexist stably with each other; a short perturbation to the resource supply is quickly compensated by species growth, and the resource depletion times returned to the coexistence point (see Supplementary Text, section B for details).The geometric approach provides an alternative explanation to why species with complementary top choices are more likely to coexist than species with the same top choice (Fig. 2c). The ZNGIs of species sharing the same top choice are unlikely to intersect with each other (e.g., the blue and purple species in Fig. 4b). This is because of two reasons: (1) their segments in the yellow region are parallel to each other since both species prefer the same resource (R2), and (2) for the slanted segments in the green region to intersect, the blue species would need a higher growth rate on R1 than the purple species. This is as likely as the outcome of a coin toss, since both growth rates derive from the same distribution. Thus, an invasion of an occupied resource often leads to displacement of the resident, not coexistence (Fig. 4b, d) and no change in community diversity, while an invasion of an unoccupied resource often leads to coexistence (Fig. 4c) and an increase in community diversity (Fig. 3e).Fig. 3: Top choice resources chiefly drive community diversity and complementarity.a (top) Table showing the preferences of a diauxic microbial species (purple) for 4 resources, R1 to R4. (bottom) Plots showing the depletion of the 4 resources by the purple species during one serial dilution cycle, when grown alone in our model. b (top) Bar plots showing the time taken by the purple species in (a) to grow on each of the 4 resources. Percentages on each bar represent the fraction of time spent growing on each resource. (bottom) Bar plots showing the number of generations grown, or the number of doublings by the species when growing on each resource. In both cases, the plots on the left show the quantities when the purple species is in monoculture (growing alone), and those on the right show them when the purple species is in a community with 3 other species. c Mean growth rates of successful invaders during community assembly. The blue line corresponds to the invader’s top choice, while the other colors correspond to all other choices. The horizontal dashed line shows the mean growth rate of the species pool. Each quantity represents a moving average from 958 independent community assembly simulations. Error bars represent s.e.m. d Fraction of the successful invasions as a function of the order in which the invader’s top choice resource is depleted, 1 indicating cases where the invader prefers the earliest depleted resource, and 4 where it prefers the last depleted resource. Each bar represents the mean of such a fraction over 958 independent community assembly simulations, and error bars represent s.e.m. e, f Effect of invasions of community diversity and complementarity, based on whether the invader’s top choice was (e) unoccupied or (f) occupied. Cartoons show the typical effect of an invasion. Pie charts show the fraction of invasions that increase, decrease or maintain a community’s species diversity (middle) and complementarity (right). On unoccupied resources, diversity typically increases (62%), but sometimes stays constant (32%) or decreases (6%). On occupied resources, diversity typically stays the same (68%), but sometimes decreases (26%) and rarely increases (6%). In almost all cases complementarity either stays maintained or increases ( >95%), and very rarely decreases ( More

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