Google's "mobilegeddon" update last month, which was designed to favor mobile-friendly sites in search results, had no impact on HubPages. But a secretive algorithm tweak soon after was disastrous. HubPages, a collection of more than 870,000 miniblogs covering everything from the "History of advertising" to "How to identify venomous house spiders," saw its Google search traffic plunge 22 percent on May 3 from the prior week. Of the company's 100 top pages, 68 lost visitors over that stretch.

Unlike some previous updates that hurt HubPages' lower-performing sites, this one was indiscriminate, said Paul Edmondson, founder and CEO of the San Francisco-based company. Furthermore, Google refuses to provide any details.

Read MoreGoogle's secretive updates leave small sites scrambling "It was just a giant whack across the board," said Edmondson, whose 10-year-old company employs professional editors to work with its vast network of independent writers. "Imagine how hard it is to run a business when you see 22 percent of your traffic evaporate overnight." (Tweet This) Edmondson published a blog post on May 11, titled "The Google update that didn't happen." Glenn Gabe, a digital marketing expert and search engine optimization analyst, called it "Phantom 2" in a blog post, because it's the second significant unnamed update in two years.



According to Searchmetrics, which tracks search traffic, there was a clear pattern of a decline in visibility for certain how-to sites, mostly pertaining to those with "thin content," or lacking much value. HubPages and eHow, owned by Demand Media, are two sites that Searchmetrics identified. WikiHow and Answers.com also saw drops, although not as severe. Edmondson said the change hit HubPages sites broadly, not just the weaker ones. Representatives from Answers.com and wikiHow declined to comment, and a spokesperson for Demand Media couldn't be reached for comment. Read MoreWant to lift your Google ranking? Hire writers Google's algorithms, which take into account more than 200 signals that help the search engine predict what a user wants, have been the source of much consternation in recent years. Because Google controls two-thirds of the U.S. search market, its updates with names like Panda and Penguin have led numerous Web-based businesses to see plummeting traffic overnight, siphoning away critical ad dollars. Panda, which Google rolled out in 2011, ranks sites based on quality and relevance, while Penguin was launched the next year to weed out pages that abuse the use of links to artificially bolster traffic. Last month's mobilegeddon was the biggest algorithm update focused on mobile sites.

About a week after mobilegeddon, emails complaining of mysterious drops in traffic started to flood Gabe's inbox. He began digging into the data, and quickly concluded they weren't caused by the mobile update, because many of the sites were smartphone-friendly.

When you have a domain-level algorithm update or ranking change, it can impact the whole site. Glenn Gabe president of G-Squared Interactive

Instead, he found that, similar to Panda updates, low-quality sites were being punished. Clickbait articles, sites chock-full of supplementary information, pages of stacked videos and those that were hard to navigate all lost visibility, according to his May 11 blog post. But why did HubPages see declining visibility across the site, even for pages with informative, researched and edited content? According to Gabe, the algorithm is ruthless, punishing an entire domain when it recognizes a certain percentage of spammy pages. "When you have a domain-level algorithm update or ranking change, it can impact the whole site," said Gabe, whose firm, G-Squared Interactive, is based in Lawrenceville, New Jersey. "Pages that should be drawing well could also be pulled down in the results." Read MoreHas Google lost control of its anti-spam algorithm? A spokesperson for Google declined to comment for this story, but the Mountain View, California-based company is quietly acknowledging that a change took place. At the Search Marketing Expo in Sydney this week, Gary Illyes from Google's Webmaster Trends team, said it was part of a core algorithm update. That's all he would say. Google is notoriously secretive about the details of updates, primarily to avoid helping spammers game the system. "For the most part, Google is not very transparent about the updates because it's driven by engineers that try to improve the search quality," said Marcus Tober, founder and chief technology officer of Searchmetrics. "They don't think about the impact of their updates on other businesses." Read MoreHow this man is profiting from 'mobilegeddon' For how-to sites, life in the Google ecosystem has become an even greater challenge after the search engine altered how it displays results. Type "how to fry an egg" or "how to wax a surfboard" into a Google search box, and instructions pop up immediately so the user doesn't have to click away to another page. It's part of the Google Knowledge Graph, which the company introduced in 2012. Where Google used to drive traffic to other sites, it's now keeping people on its own properties, even though the information being displayed comes from other sources. The egg frying instructions, for example, are from foodnetwork.com. Read MoreHow Quora plans to sidestep Google's algorithm "This is a critical first step towards building the next generation of search, which taps into the collective intelligence of the Web and understands the world a bit more like people do," Google said in a May 2012 blog post.

The new format coupled with punitive algorithm changes is too much for many businesses to handle. "Any site that's providing factual information that can be found elsewhere and that Google will deem as public knowledge is susceptible," said Gabe. "If you mix a demotion with the Knowledge Graph, forget about it. You're dead in the water."