The relative contribution of acoustic signals versus movement cues in group coordination and collective decision-making.

To benefit from group living, individuals need to maintain cohesion and coordinate their activities. Effective communication thus becomes critical, facilitating rapid coordination of behaviours and reducing consensus costs when group members have differing needs and information. In many bird and mammal species, collective decisions rely on acoustic signals in some contexts but on movement cues in others. Yet, to date, there is no clear conceptual framework that predicts when decisions should evolve to be based on acoustic signals versus movement cues. Here, we first review how acoustic signals and movement cues are used for coordinating activities. We then outline how information masking, discrimination ability (Weber's Law) and encoding limitations, as well as trade-offs between these, can identify which types of collective behaviours likely rely on acoustic signals or movement cues. Specifically, our framework proposes that behaviours involving the timing of events or expression of specific actions should rely more on acoustic signals, whereas decisions involving complex choices with multiple options (e.g. direction and destination) should generally use movement cues because sounds are more vulnerable to information masking and Weber's Law effects. We then discuss potential future avenues of enquiry, including multimodal communication and collective decision-making by mixed-species animal groups. This article is part of the theme issue 'The power of sound: unravelling how acoustic communication shapes group dynamic'.

Mapping vocal interactions in space and time differentiates signal broadcast versus signal exchange in meerkat groups.

Animal vocal communication research traditionally focuses on acoustic and contextual features of calls, yet substantial information is also contained in response selectivity and timing during vocalization events. By examining the spatiotemporal structure of vocal interactions, we can distinguish between 'broadcast' and 'exchange' signalling modes, with the former potentially serving to transmit signallers' general state and the latter reflecting more interactive signalling behaviour. Here, we tracked the movements and vocalizations of wild meerkat (Suricata suricatta) groups simultaneously using collars to explore this distinction. We found evidence that close calls (used for maintaining group cohesion) are given as signal exchanges. They are typically given in temporally structured call-response sequences and are also strongly affected by the social environment, with individuals calling more when they have more neighbours and juveniles responding more to adults than the reverse. In contrast, short note calls appear mainly in sequences produced by single individuals and show little dependence on social surroundings, suggesting a broadcast signalling mode. Despite these differences, both call categories show similar clustering in space and time at a group level. Our results highlight how the fine-scale structure of vocal interactions can give important insights into the usage and function of signals in social groups. This article is part of the theme issue 'The power of sound: unravelling how acoustic communication shapes group dynamics.'

Dominance loss and tenure maintenance in Kalahari meerkats.

In many social species, both the acquisition of dominance and the duration that individuals maintain their status are important determinants of breeding tenure and lifetime reproductive success. However, few studies have yet examined the extent and causes of variation in dominance tenure and the duration of breeding lifespans. Here, we investigate the processes that terminate dominance tenures and examine how they differ between the sexes in wild Kalahari meerkats (Suricata suricatta), a cooperative breeder where a dominant breeding pair produces most of the young recruited into each group. Mortality and displacement by resident subordinate competitors were important forms of dominance loss for both sexes. However, dominant males (but rarely females) were also at risk of takeovers by extra-group invading males. Dominant males also differed from dominant females in that they abandoned their group after the death of their breeding partner, when no other breeding opportunities were present, whereas dominant females that lost their partner remained and continued to breed in the same group. We show that a larger number of processes can terminate dominance tenure in males with the result that the average male tenure of breeding positions was shorter than that of females, which contributes to the reduced variance in the lifetime reproductive success in males compared to females. Our analysis suggests that sex differences in emigration and immigration may often have downstream consequences for sex differences in reproductive variance and for the selection pressures operating on females and males.

Climate change drives loss of bacterial gut mutualists at the expense of host survival in wild meerkats.

Climate change and climate-driven increases in infectious disease threaten wildlife populations globally. Gut microbial responses are predicted to either buffer or exacerbate the negative impacts of these twin pressures on host populations. However, examples that document how gut microbial communities respond to long-term shifts in climate and associated disease risk, and the consequences for host survival, are rare. Over the past two decades, wild meerkats inhabiting the Kalahari have experienced rapidly rising temperatures, which is linked to the spread of tuberculosis (TB). We show that over the same period, the faecal microbiota of this population has become enriched in Bacteroidia and impoverished in lactic acid bacteria (LAB), a group of bacteria including Lactococcus and Lactobacillus that are considered gut mutualists. These shifts occurred within individuals yet were compounded over generations, and were better explained by mean maximum temperatures than mean rainfall over the previous year. Enriched Bacteroidia were additionally associated with TB exposure and disease, the dry season and poorer body condition, factors that were all directly linked to reduced future survival. Lastly, abundances of LAB taxa were independently and positively linked to future survival, while enriched taxa did not predict survival. Together, these results point towards extreme temperatures driving an expansion of a disease-associated pathobiome and loss of beneficial taxa. Our study provides the first evidence from a longitudinally sampled population that climate change is restructuring wildlife gut microbiota, and that these changes may amplify the negative impacts of climate change through the loss of gut mutualists. While the plastic response of host-associated microbiotas is key for host adaptation under normal environmental fluctuations, extreme temperature increases might lead to a breakdown of coevolved host-mutualist relationships.

Pregnancy reduces concurrent pup care behaviour in meerkats, generating differences between dominant and subordinate females.

In some mammals, and particularly in cooperative breeding ones, successive bouts of reproduction can overlap so that a female is often pregnant while still nurturing dependent young from her previous litter. Such an overlap requires females to divide their energetic budget between two reproductive activities, and pregnancy costs would consequently be expected to reduce investment in concurrent offspring care. However, explicit evidence for such reductions is scarce, and the potential effects they may have on work division in cooperative breeders have not been explored. Using 25 years of data on reproduction and cooperative behaviour in wild Kalahari meerkats, supplemented with field experiments, we investigated whether pregnancy reduces contributions to cooperative pup care behaviours, including babysitting, provisioning and raised guarding. We also explored whether pregnancy, which is more frequent in dominants than subordinates, could account for the reduced contributions of dominants to the cooperative pup care behaviours. We found that pregnancy, particularly at late stages of gestation, reduces contributions to cooperative pup care; that these reductions are eliminated when the food available to pregnant females is experimentally supplemented; and that pregnancy effects accounted for differences between dominants and subordinates in two of the three cooperative behaviours examined (pup provisioning and raised guarding but not babysitting). By linking pregnancy costs with reductions in concurrent pup care, our findings illuminate a trade-off between investment in successive, overlapping bouts of reproduction. They also suggest that some of the differences in cooperative behaviour between dominant and subordinate females in cooperative breeding mammals can be a direct consequence of differences in their breeding frequency.

Dispersal-induced social stress prolongs gestation in wild meerkats.

In the majority of mammals, gestation length is relatively consistent and seldom varies by more than 3%. In a few species, females can adjust gestation length by delaying the development of the embryo after implantation. Delays in embryonic development allow females to defer the rising energetic costs of gestation when conditions are unfavourable, reducing the risk of embryo loss. Dispersal in mammals that breed cooperatively is a period when food intake is likely to be suppressed and stress levels are likely to be high. Here, we show that pregnant dispersing meerkats (Suricata suricatta), which have been aggressively evicted from their natal group and experience weight loss and extended periods of social stress, prolong their gestation by means of delayed embryonic development. Repeated ultrasound scans of wild, unanaesthetized females throughout their pregnancies showed that pregnancies of dispersers were on average 6.3% longer and more variable in length (52-65 days) than those of residents (54-56 days). The variation in dispersers shows that, unlike most mammals, meerkats can adapt to stress by adjusting their pregnancy length by up to 25%. By doing so, they potentially rearrange the costs of gestation during adverse conditions of dispersal and enhance offspring survival.

Directional speakers as a tool for animal vocal communication studies.

Audio playbacks are a common experimental tool in vocal communication research. However, low directionality of sound makes it hard to control the audience exposed to the stimuli. Parametric speakers offer a solution for transmitting directional audible signals by using ultrasonic carrier waves. The targeted transmission of vocal signals offers exciting opportunities for testing the diffusion of information in animal groups and mechanisms for resolving informational ambiguities. We have field tested the quality and directionality of a commercial parametric speaker, Soundlazer SL-01. Additionally, we assessed its usability for performing playback experiments by comparing behavioural responses of free-ranging meerkats (Suricata suricatta) with calls transmitted from conventional and parametric speakers. Our results show that the tested parametric speaker is highly directional. However, the acoustic structure of meerkat calls was strongly affected and low frequencies were not reliably reproduced by the parametric speaker. The playback trials elicited weakened behavioural responses probably due to the partial distortion of the signal but also indicating the potential importance of social facilitation for initiating mobbing events in meerkats. We conclude that parametric speakers can be useful tools for directed transmission of animals calls but after a careful assessment of signal fidelity.

Two decades of tuberculosis surveillance reveal disease spread, high levels of exposure and mortality and marked variation in disease progression in wild meerkats.

Infections with tuberculosis (TB)-causing agents of the Mycobacterium tuberculosis complex threaten human, livestock and wildlife health globally due to the high capacity to cross trans-species boundaries. Tuberculosis is a cryptic disease characterized by prolonged, sometimes lifelong subclinical infections, complicating disease monitoring. Consequently, our understanding of infection risk, disease progression, and mortality across species affected by TB remains limited. The TB agent Mycobacterium suricattae was first recorded in the late 1990s in a wild population of meerkats inhabiting the Kalahari in South Africa and has since spread considerably, becoming a common cause of meerkat mortality. This offers an opportunity to document the epidemiology of naturally spreading TB in a wild population. Here, we synthesize more than 25 years' worth of TB reporting and social interaction data across 3420 individuals to track disease spread, and quantify rates of TB social exposure, progression, and mortality. We found that most meerkats had been exposed to the pathogen within eight years of first detection in the study area, with exposure reaching up to 95% of the population. Approximately one quarter of exposed individuals progressed to clinical TB stages, followed by physical deterioration and death within a few months. Since emergence, 11.6% of deaths were attributed to TB, although the true toll of TB-related mortality is likely higher. Lastly, we observed marked variation in disease progression among individuals, suggesting inter-individual differences in both TB susceptibility and resistance. Our results highlight that TB prevalence and mortality could be higher than previously reported, particularly in species or populations with complex social group dynamics. Long-term studies, such as the present one, allow us to assess temporal variation in disease prevalence and progression and quantify exposure, which is rarely measured in wildlife. Long-term studies are highly valuable tools to explore disease emergence and ecology and study host-pathogen co-evolutionary dynamics in general, and its impact on social mammals.

Gut microbiota individuality is contingent on temporal scale and age in wild meerkats.

Inter-individual differences in gut microbiota composition are hypothesized to generate variation in host fitness-a premise for the evolution of host-gut microbe symbioses. However, recent evidence suggests that gut microbial communities are highly dynamic, challenging the notion that individuals harbour unique gut microbial phenotypes. Leveraging a long-term dataset of wild meerkats, we reconcile these concepts by demonstrating that the relative importance of identity for shaping gut microbiota phenotypes depends on the temporal scale. Across meerkat lifespan, year-to-year variation overshadowed the effects of identity and social group in predicting gut microbiota composition, with identity explaining on average less than 2% of variation. However, identity was the strongest predictor of microbial phenotypes over short sampling intervals (less than two months), predicting on average 20% of variation. The effect of identity was also dependent on meerkat age, with the gut microbiota becoming more individualized and stable as meerkats aged. Nevertheless, while the predictive power of identity was negligible after two months, gut microbiota composition remained weakly individualized compared to that of other meerkats for up to 1 year. These findings illuminate the degree to which individualized gut microbial signatures can be expected, with important implications for the time frames over which gut microbial phenotypes may mediate host physiology, behaviour and fitness in natural populations.

Disentangling influence over group speed and direction reveals multiple patterns of influence in moving meerkat groups.

Animals that travel together in groups must constantly come to consensus about both the direction and speed of movement, often simultaneously. Contributions to collective decisions may vary among group members, yet inferring who has influence over group decisions is challenging, largely due to the multifaceted nature of influence. Here we collected high-resolution GPS data from five habituated meerkat groups in their natural habitat during foraging and developed a method to quantify individual influence over both group direction and speed. We find that individual influence over direction and speed are correlated, but also exhibit substantial variation. Comparing patterns across social statuses reveals that dominant females have higher influence than other individuals over both group direction and speed. Individuals with high influence also tend to spend more time in the front of the group. We discuss our results in light of meerkat life-history and current literature on influence during group movement. Our method provides a general approach which can be applied to disentangle individual influence over group direction and speed in a wide range of species with cohesive movement, emphasizing the importance of integrating multiple lines of inquiry when inferring influence in moving animal groups.

Optionality in animal communication: a novel framework for examining the evolution of arbitrariness.

A critical feature of language is that the form of words need not bear any perceptual similarity to their function - these relationships can be 'arbitrary'. The capacity to process these arbitrary form-function associations facilitates the enormous expressive power of language. However, the evolutionary roots of our capacity for arbitrariness, i.e. the extent to which related abilities may be shared with animals, is largely unexamined. We argue this is due to the challenges of applying such an intrinsically linguistic concept to animal communication, and address this by proposing a novel conceptual framework highlighting a key underpinning of linguistic arbitrariness, which is nevertheless applicable to non-human species. Specifically, we focus on the capacity to associate alternative functions with a signal, or alternative signals with a function, a feature we refer to as optionality. We apply this framework to a broad survey of findings from animal communication studies and identify five key dimensions of communicative optionality: signal production, signal adjustment, signal usage, signal combinatoriality and signal perception. We find that optionality is widespread in non-human animals across each of these dimensions, although only humans demonstrate it in all five. Finally, we discuss the relevance of optionality to behavioural and cognitive domains outside of communication. This investigation provides a powerful new conceptual framework for the cross-species investigation of the origins of arbitrariness, and promises to generate original insights into animal communication and language evolution more generally.

A practical guide for generating unsupervised, spectrogram-based latent space representations of animal vocalizations.

BACKGROUND: The manual detection, analysis and classification of animal vocalizations in acoustic recordings is laborious and requires expert knowledge. Hence, there is a need for objective, generalizable methods that detect underlying patterns in these data, categorize sounds into distinct groups and quantify similarities between them. Among all computational methods that have been proposed to accomplish this, neighbourhood-based dimensionality reduction of spectrograms to produce a latent space representation of calls stands out for its conceptual simplicity and effectiveness. Goal of the study/what was done: Using a dataset of manually annotated meerkat Suricata suricatta vocalizations, we demonstrate how this method can be used to obtain meaningful latent space representations that reflect the established taxonomy of call types. We analyse strengths and weaknesses of the proposed approach, give recommendations for its usage and show application examples, such as the classification of ambiguous calls and the detection of mislabelled calls. What this means: All analyses are accompanied by example code to help researchers realize the potential of this method for the study of animal vocalizations.

Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals.

The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.

Dispersal Decreases Survival but Increases Reproductive Opportunities for Subordinates in a Cooperative Breeder.

AbstractIn most socially structured populations, the formation of new groups depends on the survival and reproduction of dispersing individuals. Quantifying vital rates in dispersers, however, is difficult because of the logistic challenges of following wide-ranging animals. Here, using data from free-ranging meerkats (Suricata suricatta), we estimate survival and reproduction of dispersing females and compare these estimates to data for established residents. Meerkat groups consist of a dominant pair and several subordinate helpers. Female helpers are evicted from their resident groups by the dominant female, allowing her to monopolize reproduction, and evicted females may form small dispersing coalitions. We show that, as in established resident groups, one female is behaviorally dominant in parties of dispersing females. During dispersal and the first 4 months after new group formation, survival is lower for all females compared with established resident groups. At the same time, subordinates in disperser groups have higher birth rates than those in established groups, which rarely breed successfully. This may partly offset the survival costs of dispersal to subordinate females. Further studies of dispersal based on direct observation of dispersing animals are needed to explore the costs and benefits of dispersal in species with contrasting breeding systems.

CHARACTERIZING TUBERCULOSIS PROGRESSION IN WILD MEERKATS (SURICATA SURICATTA) FROM FECAL SAMPLES AND CLINICAL SIGNS.

Tuberculosis (TB) is an increasing threat to wildlife, yet tracking its spread is challenging because infections often appear to be asymptomatic, and diagnostic tools such as blood tests can be invasive and resource intensive. Our understanding of TB biology in wildlife is therefore limited to a small number of well-studied species. Testing of fecal samples using PCR is a noninvasive method that has been used to detect Mycobacterium bovis shedding amongst badgers, yet its utility more broadly for TB monitoring in wildlife is unclear. We combined observation data of clinical signs with PCR testing of 388 fecal samples to characterize longitudinal dynamics of TB progression in 66 wild meerkats (Suricata suricatta) socially exposed to Mycobacterium suricattae between 2000 and 2018. Our specific objectives were 1) to test whether meerkat fecal samples can be used to monitor TB; 2) to characterize TB progression between three infection states (PCR-negative exposed, PCR-positive asymptomatic, and PCR positive with clinical signs); and 3) estimate individual heterogeneity in TB susceptibility, defined here as the time between TB exposure and detection, and survival after TB detection. We found that the TB detection probability once meerkats developed clinical signs was 13% (95% confidence interval 3-46%). Nevertheless, with an adapted test protocol of 10 PCR replicates per sample we detected hidden TB infections in 59% of meerkats before the onset of clinical signs. Meerkats became PCR positive approximately 14 mo after initial exposure, developed clinical signs approximately 1 yr after becoming PCR positive, and died within 5 mo of developing clinical signs. Individual variation in disease progression was high, with meerkats developing clinical signs from immediately after exposure to 3.4 yr later. Overall, our study generates novel insights into wildlife TB progression, and may help guide adapted management strategies for TB-susceptible wildlife populations.

Vocalization-associated respiration patterns: thermography-based monitoring and detection of preparation for calling.

Vocal emission requires coordination with the respiratory system. Monitoring the increase in laryngeal pressure, which is needed for vocal production, allows detection of transitions from quiet respiration to vocalization-supporting respiration. Characterization of these transitions could be used to identify preparation for vocal emission and to examine the probability of it manifesting into an actual vocal production event. Specifically, overlaying the subject's respiration with conspecific calls can highlight events of call initiation and suppression, as a means of signalling coordination and avoiding jamming. Here, we present a thermal imaging-based methodology for synchronized respiration and vocalization monitoring of free-ranging meerkats. The sensitivity of this methodology is sufficient for detecting transient changes in the subject's respiration associated with the exertion of vocal production. The differences in respiration are apparent not only during the vocal output, but also prior to it, marking the potential time frame of the respiratory preparation for calling. A correlation between conspecific calls with elongation of the focal subject's respiration cycles could be related to fluctuations in attention levels or in the motivation to reply. This framework can be used for examining the capability for enhanced respiration control in animals during modulated and complex vocal sequences, detecting 'failed' vocalization attempts and investigating the role of respiration cues in the regulation of vocal interactions.

Decline and fall: The causes of group failure in cooperatively breeding meerkats.

In many social vertebrates, variation in group persistence exerts an important effect on individual fitness and population demography. However, few studies have been able to investigate the failure of groups or the causes of the variation in their longevity. We use data from a long-term study of cooperatively breeding meerkats, Suricata suricatta, to investigate the different causes of group failure and the factors that drive these processes. Many newly formed groups failed within a year of formation, and smaller groups were more likely to fail. Groups that bred successfully and increased their size could persist for several years, even decades. Long-lived groups principally failed in association with the development of clinical tuberculosis, Mycobacterium suricattae, a disease that can spread throughout the group and be fatal for group members. Clinical tuberculosis was more likely to occur in groups that had smaller group sizes and that had experienced immigration.

Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats.

Circadian rhythms in gut microbiota composition are crucial for metabolic function, yet the extent to which they govern microbial dynamics compared to seasonal and lifetime processes remains unknown. Here, we investigate gut bacterial dynamics in wild meerkats (Suricata suricatta) over a 20-year period to compare diurnal, seasonal, and lifetime processes in concert, applying ratios of absolute abundance. We found that diurnal oscillations in bacterial load and composition eclipsed seasonal and lifetime dynamics. Diurnal oscillations were characterised by a peak in Clostridium abundance at dawn, were associated with temperature-constrained foraging schedules, and did not decay with age. Some genera exhibited seasonal fluctuations, whilst others developed with age, although we found little support for microbial senescence in very old meerkats. Strong microbial circadian rhythms in this species may reflect the extreme daily temperature fluctuations typical of arid-zone climates. Our findings demonstrate that accounting for circadian rhythms is essential for future gut microbiome research.

Behavioural change during dispersal and its relationship to survival and reproduction in a cooperative breeder.

The ability of dispersing individuals to adjust their behaviour to changing conditions is instrumental in overcoming challenges and reducing dispersal costs, consequently increasing overall dispersal success. Understanding how dispersers' behaviour and physiology change during the dispersal process, and how they differ from resident individuals, can shed light on the mechanisms by which dispersers increase survival and maximise reproduction. By analysing individual behaviour and concentrations of faecal glucocorticoid metabolites (fGCM), a stress-associated biomarker, we sought to identify the proximate causes behind differences in survival and reproduction between dispersing and resident meerkats Suricata suricatta. We used data collected on 67 dispersing and 108 resident females to investigate (a) which individual, social and environmental factors are correlated to foraging and vigilance, and whether the role of such factors differs among dispersal phases, and between dispersers and residents; (b) how time allocated to either foraging or vigilance correlated to survival in dispersers and residents and (c) the link between aggression and change in fGCM concentration, and their relationship with reproductive rates in dispersing groups and resident groups with either long-established or newly established dominant females. Time allocated to foraging increased across dispersal phases, whereas time allocated to vigilance decreased. Time allocated to foraging and vigilance correlated positively and negatively, respectively, with dispersers' group size. We did not find a group size effect for residents. High proportions of time allocated to foraging correlated with high survival, and more so in dispersers, suggesting that maintaining good physical condition may reduce mortality during dispersal. Furthermore, while subordinate individuals rarely reproduced in resident groups, the conception rate of subordinates in newly formed dispersing groups was equal to that of their dominant individuals. Mirroring conception rates, in resident groups, fGCM concentrations were lower in subordinates than in dominants, whereas in disperser groups, fGCM concentrations did not differ between subordinates and dominants. Our results, which highlight the relationship between behavioural and physiological factors and demographic rates, provide insights into some of the mechanisms that individuals of a cooperative species can use to increase overall dispersal success.

Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species.

The filtering of gut microbial datasets to retain high prevalence taxa is often performed to identify a common core gut microbiome that may be important for host biological functions. However, prevalence thresholds used to identify a common core are highly variable, and it remains unclear how they affect diversity estimates and whether insights stemming from core microbiomes are comparable across studies. We hypothesized that if macroecological patterns in gut microbiome prevalence and abundance are similar across host species, then we would expect that increasing prevalence thresholds would yield similar changes to alpha diversity and beta dissimilarity scores across host species datasets. We analyzed eight gut microbiome datasets based on 16S rRNA gene amplicon sequencing and collected from different host species to (1) compare macroecological patterns across datasets, including amplicon sequence variant (ASV) detection rate with sequencing depth and sample size, occupancy-abundance curves, and rank-abundance curves; (2) test whether increasing prevalence thresholds generate universal or host-species specific effects on alpha and beta diversity scores; and (3) test whether diversity scores from prevalence-filtered core communities correlate with unfiltered data. We found that gut microbiomes collected from diverse hosts demonstrated similar ASV detection rates with sequencing depth, yet required different sample sizes to sufficiently capture rare ASVs across the host population. This suggests that sample size rather than sequencing depth tends to limit the ability of studies to detect rare ASVs across the host population. Despite differences in the distribution and detection of rare ASVs, microbiomes exhibited similar occupancy-abundance and rank-abundance curves. Consequently, increasing prevalence thresholds generated remarkably similar trends in standardized alpha diversity and beta dissimilarity across species datasets until high thresholds above 70%. At this point, diversity scores tended to become unpredictable for some diversity measures. Moreover, high prevalence thresholds tended to generate diversity scores that correlated poorly with the original unfiltered data. Overall, we recommend that high prevalence thresholds over 70% are avoided, and promote the use of diversity measures that account for phylogeny and abundance (Balance-weighted phylogenetic diversity and Weighted Unifrac for alpha and beta diversity, respectively), because we show that these measures are insensitive to prevalence filtering and therefore allow for the consistent comparison of core gut microbiomes across studies without the need for prevalence filtering.