Health-Associated Core Keystone (HACK)

💡 An intriguing paper just came out in Cell Reports by Cell Press by a team from Indraprastha Institute of Information Technology, Delhi. Their Health-Associated Core Keystone (HACK) index ranks 201 gut taxa derived using 141 global datasets: 45,424 gut microbiomes, subject age >18 years, representing 42 countries, 28 disease categories, and 10,021 longitudinal samples. From the abstract: HACK is "reproducible regardless of microbiome profiling strategies and cohort lifestyle. Specific consortia of high HACK index taxa respond positively to Mediterranean diet interventions and reflect immune checkpoint inhibitor responsiveness and associated with specific functional profiles at the genome level. The availability of HACK indices provides a rational basis for comparing microbiomes and facilitating selection and design of microbiome-based therapeutics."

⚡ The robustness of the index is interesting and exciting given the variability observed in many global studies. If confirmed, it has broad applicability.

💰 Of course, the punchline: which species are beneficial? Some of the usual suspects pop up (F. prausnitzii is the expected rock star), but other "well-known" beneficial species are middle of the pack.

TL;DR:

1️⃣ The top-ranking ones "included Faecalibacterium prausnitzii, Bacteroides uniformis, Bacteroides xylanisolvens, Odoribacter splanchnicus, Roseburia hominis, Roseburia inulinivorans, Coprococcus catus, Coprococcus comes, Agathobaculum butyriproducens, Fusicatenibacter saccharivoran,s and Eubacterium rectale. These taxa were referred to as the core keystones (core: because of high prevalence; keystone: because of high influence and stability association)."

2️⃣ And "many earlier-known “beneficial” taxa recently shown to have conflicting health associations, like Akkermansia and Prevotella copri (associated with high longitudinal variability),30 Eubacterium hallii, Anaerostipes hadrus, and Dorea longicatena,31,32 were identified with intermediate HACK indices."

3️⃣ "The taxa with low HACK indices were dominated by oral taxa (Actinomyces, Veillonella, Rothia, Streptococcus) and the known generally disease-associated lineages like Ruminococcus gnavus, the pathobiont Clostridia spp (C. ramosum/bolteae/clostridioforme/innocuum), Eggerthella lenta, Klebsiella, and Escherichia.